Innate Sensing of Influenza A Virus Hemagglutinin Glycoproteins by the Host Endoplasmic Reticulum (ER) Stress Pathway Triggers a Potent Antiviral Response via ER-Associated Protein Degradation.

PubMed

Frabutt, Dylan A; Wang, Bin; Riaz, Sana; Schwartz, Richard C; Zheng, Yong-Hui

2018-01-01

Innate immunity provides an immediate defense against infection after host cells sense danger signals from microbes. Endoplasmic reticulum (ER) stress arises from accumulation of misfolded/unfolded proteins when protein load overwhelms the ER folding capacity, which activates the unfolded protein response (UPR) to restore ER homeostasis. Here, we show that a mechanism for antiviral innate immunity is triggered after the ER stress pathway senses viral glycoproteins. When hemagglutinin (HA) glycoproteins from influenza A virus (IAV) are expressed in cells, ER stress is induced, resulting in rapid HA degradation via proteasomes. The ER-associated protein degradation (ERAD) pathway, an important UPR function for destruction of aberrant proteins, mediates HA degradation. Three class I α-mannosidases were identified to play a critical role in the degradation process, including EDEM1, EDEM2, and ERManI. HA degradation requires either ERManI enzymatic activity or EDEM1/EDEM2 enzymatic activity when ERManI is not expressed, indicating that demannosylation is a critical step for HA degradation. Silencing of EDEM1, EDEM2, and ERManI strongly increases HA expression and promotes IAV replication. Thus, the ER stress pathway senses influenza HA as "nonself" or misfolded protein and sorts HA to ERAD for degradation, resulting in inhibition of IAV replication. IMPORTANCE Viral nucleic acids are recognized as important inducers of innate antiviral immune responses that are sensed by multiple classes of sensors, but other inducers and sensors of viral innate immunity need to be identified and characterized. Here, we used IAV to investigate how host innate immunity is activated. We found that IAV HA glycoproteins induce ER stress, resulting in HA degradation via ERAD and consequent inhibition of IAV replication. In addition, we have identified three class I α-mannosidases, EDEM1, EDEM2, and ERManI, which play a critical role in initiating HA degradation. Knockdown of these proteins substantially increases HA expression and IAV replication. The enzymatic activities and joint actions of these mannosidases are required for this antiviral activity. Our results suggest that viral glycoproteins induce a strong innate antiviral response through activating the ER stress pathway during viral infection. Copyright © 2017 American Society for Microbiology.

Autophagy in lung disease pathogenesis and therapeutics

PubMed Central

Ryter, Stefan W.; Choi, Augustine M.K.

2015-01-01

Autophagy, a cellular pathway for the degradation of damaged organelles and proteins, has gained increasing importance in human pulmonary diseases, both as a modulator of pathogenesis and as a potential therapeutic target. In this pathway, cytosolic cargos are sequestered into autophagosomes, which are delivered to the lysosomes where they are enzymatically degraded and then recycled as metabolic precursors. Autophagy exerts an important effector function in the regulation of inflammation, and immune system functions. Selective pathways for autophagic degradation of cargoes may have variable significance in disease pathogenesis. Among these, the autophagic clearance of bacteria (xenophagy) may represent a crucial host defense mechanism in the pathogenesis of sepsis and inflammatory diseases. Our recent studies indicate that the autophagic clearance of mitochondria, a potentially protective program, may aggravate the pathogenesis of chronic obstructive pulmonary disease by activating cell death programs. We report similar findings with respect to the autophagic clearance of cilia components, which can contribute to airways dysfunction in chronic lung disease. In certain diseases such as pulmonary hypertension, autophagy may confer protection by modulating proliferation and cell death. In other disorders, such as idiopathic pulmonary fibrosis and cystic fibrosis, impaired autophagy may contribute to pathogenesis. In lung cancer, autophagy has multiple consequences by limiting carcinogenesis, modulating therapeutic effectiveness, and promoting tumor cell survival. In this review we highlight the multiple functions of autophagy and its selective autophagy subtypes that may be of significance to the pathogenesis of human disease, with an emphasis on lung disease and therapeutics. PMID:25617802

Calpain-mediated proteolysis of polycystin-1 C-terminus induces JAK2 and ERK signal alterations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Hyunho; Department of Medicine, University of Maryland, Baltimore, MD; Kang, Ah-Young

2014-01-01

Autosomal dominant polycystic kidney disease (ADPKD), a hereditary renal disease caused by mutations in PKD1 (85%) or PKD2 (15%), is characterized by the development of gradually enlarging multiple renal cysts and progressive renal failure. Polycystin-1 (PC1), PKD1 gene product, is an integral membrane glycoprotein which regulates a number of different biological processes including cell proliferation, apoptosis, cell polarity, and tubulogenesis. PC1 is a target of various proteolytic cleavages and proteosomal degradations, but its role in intracellular signaling pathways remains poorly understood. Herein, we demonstrated that PC1 is a novel substrate for μ- and m-calpains, which are calcium-dependent cysteine proteases. Overexpressionmore » of PC1 altered both Janus-activated kinase 2 (JAK2) and extracellular signal-regulated kinase (ERK) signals, which were independently regulated by calpain-mediated PC1 degradation. They suggest that the PC1 function on JAK2 and ERK signaling pathways might be regulated by calpains in response to the changes in intracellular calcium concentration. - Highlights: • Polycystin-1 is a target of ubiquitin-independent degradation by calpains. • The PEST domain is required for calpain-mediated degradation of polycystin-1. • Polycystin-1 may independently regulate JAK2 and ERK signaling pathways.« less

Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24.

PubMed

Lee, Sang-Yeop; Kim, Gun-Hwa; Yun, Sung Ho; Choi, Chi-Won; Yi, Yoon-Sun; Kim, Jonghyun; Chung, Young-Ho; Park, Edmond Changkyun; Kim, Seung Il

2016-01-01

Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs), including benzene, toluene, and xylene (BTX), as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX.

Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24

PubMed Central

Yun, Sung Ho; Choi, Chi-Won; Yi, Yoon-Sun; Kim, Jonghyun; Chung, Young-Ho; Park, Edmond Changkyun; Kim, Seung Il

2016-01-01

Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs), including benzene, toluene, and xylene (BTX), as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX. PMID:27124467

Ubiquitin-protein ligases in muscle wasting: multiple parallel pathways?

NASA Technical Reports Server (NTRS)

Lecker, Stewart H.; Goldberg, A. L. (Principal Investigator)

2003-01-01

PURPOSE OF REVIEW: Studies in a wide variety of animal models of muscle wasting have led to the concept that increased protein breakdown via the ubiquitin-proteasome pathway is responsible for the loss of muscle mass seen as muscle atrophy. The complexity of the ubiquitination apparatus has hampered our understanding of how this pathway is activated in atrophying muscles and which ubiquitin-conjugating enzymes in muscle are responsible. RECENT FINDINGS: Recent experiments have shown that two newly identified ubiquitin-protein ligases (E3s), atrogin-1/MAFbx and MURF-1, are critical in the development of muscle atrophy. Other in-vitro studies also implicated E2(14k) and E3alpha, of the N-end rule pathway, as playing an important role in the process. SUMMARY: It seems likely that multiple pathways of ubiquitin conjugation are activated in parallel in atrophying muscle, perhaps to target for degradation specific classes of muscle proteins. The emerging challenge will be to define the protein targets for, as well as inhibitors of, these E3s.

Biodegradation of alkaline lignin by Bacillus ligniniphilus L1

DOE PAGES

Zhu, Daochen; Zhang, Peipei; Xie, Changxiao; ...

2017-02-21

Lignin is the most abundant aromatic biopolymer in the biosphere and it comprises up to 30% of plant biomass. Although lignin is the most recalcitrant component of the plant cell wall, still there are microorganisms able to decompose it or degrade it. Fungi are recognized as the most widely used microbes for lignin degradation. However, bacteria have also been known to be able to utilize lignin as a carbon or energy source. Bacillus ligniniphilus L1 was selected in this study due to its capability to utilize alkaline lignin as a single carbon or energy source and its excellent ability tomore » survive in extreme environments. To investigate the aromatic metabolites of strain L1 decomposing alkaline lignin, GC–MS analysis was performed and fifteen single phenol ring aromatic compounds were identified. The dominant absorption peak included phenylacetic acid, 4-hydroxy-benzoicacid, and vanillic acid with the highest proportion of metabolites resulting in 42%. Comparison proteomic analysis was carried out for further study showed that approximately 1447 kinds of proteins were produced, 141 of which were at least twofold up-regulated with alkaline lignin as the single carbon source. The up-regulated proteins contents different categories in the biological functions of protein including lignin degradation, ABC transport system, environmental response factors, protein synthesis, assembly, etc. In conclusion, GC–MS analysis showed that alkaline lignin degradation of strain L1 produced 15 kinds of aromatic compounds. Comparison proteomic data and metabolic analysis showed that to ensure the degradation of lignin and growth of strain L1, multiple aspects of cells metabolism including transporter, environmental response factors, and protein synthesis were enhanced. Based on genome and proteomic analysis, at least four kinds of lignin degradation pathway might be present in strain L1, including a Gentisate pathway, the benzoic acid pathway and the β-ketoadipate pathway. The study provides an important basis for lignin degradation by bacteria.« less

Biodegradation of alkaline lignin by Bacillus ligniniphilus L1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Daochen; Zhang, Peipei; Xie, Changxiao

Background: Lignin is the most abundant aromatic biopolymer in the biosphere and it comprises up to 30% of plant biomass. Although lignin is the most recalcitrant component of the plant cell wall, still there are microorganisms able to decompose it or degrade it. Fungi are recognized as the most widely used microbes for lignin degradation. However, bacteria have also been known to be able to utilize lignin as a carbon or energy source. Bacillus ligniniphilus L1 was selected in this study due to its capability to utilize alkaline lignin as a single carbon or energy source and its excellent abilitymore » to survive in extreme environments. Results: To investigate the aromatic metabolites of strain L1 decomposing alkaline lignin, GC-MS analyze was performed and fifteen single phenol ring aromatic compounds were identified. The dominant absorption peak included phenylacetic acid, 4-hydroxy-benzoicacid, and vanillic acid with the highest proportion of metabolites resulting in 42%. Comparison proteomic analysis were carried out for further study showed that approximately 1447 kinds of proteins were produced, 141 of which were at least 2-fold up-regulated with alkaline lignin as the single carbon source. The up-regulated proteins contents different categories in the biological functions of protein including lignin degradation, ABC transport system, environmental response factors, protein synthesis and assembly, etc. Conclusions: GC-MS analysis showed that alkaline lignin degradation of strain L1 produced 15 kinds of aromatic compounds. Comparison proteomic data and metabolic analysis showed that to ensure the degradation of lignin and growth of strain L1, multiple aspects of cells metabolism including transporter, environmental response factors, and protein synthesis were enhanced. Based on genome and proteomic analysis, at least four kinds of lignin degradation pathway might be present in strain L1, including a Gentisate pathway, the benzoic acid pathway and the β-ketoadipate pathway. The study provides an important basis for lignin degradation by bacteria.« less

Biodegradation of alkaline lignin by Bacillus ligniniphilus L1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Daochen; Zhang, Peipei; Xie, Changxiao

Lignin is the most abundant aromatic biopolymer in the biosphere and it comprises up to 30% of plant biomass. Although lignin is the most recalcitrant component of the plant cell wall, still there are microorganisms able to decompose it or degrade it. Fungi are recognized as the most widely used microbes for lignin degradation. However, bacteria have also been known to be able to utilize lignin as a carbon or energy source. Bacillus ligniniphilus L1 was selected in this study due to its capability to utilize alkaline lignin as a single carbon or energy source and its excellent ability tomore » survive in extreme environments. To investigate the aromatic metabolites of strain L1 decomposing alkaline lignin, GC–MS analysis was performed and fifteen single phenol ring aromatic compounds were identified. The dominant absorption peak included phenylacetic acid, 4-hydroxy-benzoicacid, and vanillic acid with the highest proportion of metabolites resulting in 42%. Comparison proteomic analysis was carried out for further study showed that approximately 1447 kinds of proteins were produced, 141 of which were at least twofold up-regulated with alkaline lignin as the single carbon source. The up-regulated proteins contents different categories in the biological functions of protein including lignin degradation, ABC transport system, environmental response factors, protein synthesis, assembly, etc. In conclusion, GC–MS analysis showed that alkaline lignin degradation of strain L1 produced 15 kinds of aromatic compounds. Comparison proteomic data and metabolic analysis showed that to ensure the degradation of lignin and growth of strain L1, multiple aspects of cells metabolism including transporter, environmental response factors, and protein synthesis were enhanced. Based on genome and proteomic analysis, at least four kinds of lignin degradation pathway might be present in strain L1, including a Gentisate pathway, the benzoic acid pathway and the β-ketoadipate pathway. The study provides an important basis for lignin degradation by bacteria.« less

Hydrogen and carbon isotope fractionation during degradation of chloromethane by methylotrophic bacteria

PubMed Central

Nadalig, Thierry; Greule, Markus; Bringel, Françoise; Vuilleumier, Stéphane; Keppler, Frank

2013-01-01

Chloromethane (CH3Cl) is a widely studied volatile halocarbon involved in the destruction of ozone in the stratosphere. Nevertheless, its global budget still remains debated. Stable isotope analysis is a powerful tool to constrain fluxes of chloromethane between various environmental compartments which involve a multiplicity of sources and sinks, and both biotic and abiotic processes. In this study, we measured hydrogen and carbon isotope fractionation of the remaining untransformed chloromethane following its degradation by methylotrophic bacterial strains Methylobacterium extorquens CM4 and Hyphomicrobium sp. MC1, which belong to different genera but both use the cmu pathway, the only pathway for bacterial degradation of chloromethane characterized so far. Hydrogen isotope fractionation for degradation of chloromethane was determined for the first time, and yielded enrichment factors (ε) of −29‰ and −27‰ for strains CM4 and MC1, respectively. In agreement with previous studies, enrichment in 13C of untransformed CH3Cl was also observed, and similar isotope enrichment factors (ε) of −41‰ and −38‰ were obtained for degradation of chloromethane by strains CM4 and MC1, respectively. These combined hydrogen and carbon isotopic data for bacterial degradation of chloromethane will contribute to refine models of the global atmospheric budget of chloromethane. PMID:24019296

Ski regulates Hippo and TAZ signaling to suppress breast cancer progression

PubMed Central

Rashidian, Juliet; Le Scolan, Erwan; Ji, Xiaodan; Zhu, Qingwei; Mulvihill, Melinda M.; Nomura, Daniel; Luo, Kunxin

2015-01-01

Ski, the transforming protein of the avian Sloan-Kettering retrovirus, inhibits transforming growth factor–β (TGF-β)/Smad signaling and displays both pro-oncogenic and anti-oncogenic activities in human cancer. Inhibition of TGF-β signaling is likely responsible for the pro-oncogenic activity of Ski. We investigated the mechanism(s) underlying the tumor suppressor activity of Ski and found that Ski suppressed the activity of the Hippo signaling effectors TAZ and YAP to inhibit breast cancer progression. TAZ and YAP are transcriptional coactivators that can contribute to cancer by promoting proliferation, tumorigenesis, and cancer stem cell expansion. Hippo signaling activates the the Lats family of kinases, which phosphorylate TAZ and YAP, resulting in cytoplasmic retention and degradation and inhibition of their transcriptional activity. We showed that Ski interacted with multiple components of the Hippo pathway to facilitate activation of Lats2, resulting in increased phosphorylation and subsequent degradation of TAZ. Ski also promoted the degradation of a constitutively active TAZ mutant that is not phosphorylated by Lats, suggesting the existence of a Lats2-independent degradation pathway. Finally, we showed that Ski repressed the transcriptional activity of TAZ by binding to the TAZ partner TEAD and recruiting the transcriptional co-repressor NCoR1 to the TEAD-TAZ complex. Ski effectively reversed transformation and epithelial-to-mesenchyme transition in cultured breast cancer cells and metastasis in TAZ-expressing xenografted tumors. Thus, Ski inhibited the function of TAZ through multiple mechanisms in human cancer cells. PMID:25670202

Interconnections between mRNA degradation and RDR-dependent siRNA production in mRNA turnover in plants.

PubMed

Tsuzuki, Masayuki; Motomura, Kazuki; Kumakura, Naoyoshi; Takeda, Atsushi

2017-03-01

Accumulation of an mRNA species is determined by the balance between the synthesis and the degradation of the mRNA. Individual mRNA molecules are selectively and actively degraded through RNA degradation pathways, which include 5'-3' mRNA degradation pathway, 3'-5' mRNA degradation pathway, and RNA-dependent RNA polymerase-mediated mRNA degradation pathway. Recent studies have revealed that these RNA degradation pathways compete with each other in mRNA turnover in plants and that plants have a hidden layer of non-coding small-interfering RNA production from a set of mRNAs. In this review, we summarize the current information about plant mRNA degradation pathways in mRNA turnover and discuss the potential roles of a novel class of the endogenous siRNAs derived from plant mRNAs.

Ciliopathy proteins regulate paracrine signaling by modulating proteasomal degradation of mediators

PubMed Central

Liu, Yangfan P.; Tsai, I-Chun; Morleo, Manuela; Oh, Edwin C.; Leitch, Carmen C.; Massa, Filomena; Lee, Byung-Hoon; Parker, David S.; Finley, Daniel; Zaghloul, Norann A.; Franco, Brunella; Katsanis, Nicholas

2014-01-01

Cilia are critical mediators of paracrine signaling; however, it is unknown whether proteins that contribute to ciliopathies converge on multiple paracrine pathways through a common mechanism. Here, we show that loss of cilopathy-associated proteins Bardet-Biedl syndrome 4 (BBS4) or oral-facial-digital syndrome 1 (OFD1) results in the accumulation of signaling mediators normally targeted for proteasomal degradation. In WT cells, several BBS proteins and OFD1 interacted with proteasomal subunits, and loss of either BBS4 or OFD1 led to depletion of multiple subunits from the centrosomal proteasome. Furthermore, overexpression of proteasomal regulatory components or treatment with proteasomal activators sulforaphane (SFN) and mevalonolactone (MVA) ameliorated signaling defects in cells lacking BBS1, BBS4, and OFD1, in morphant zebrafish embryos, and in induced neurons from Ofd1-deficient mice. Finally, we tested the hypothesis that other proteasome-dependent pathways not known to be associated with ciliopathies are defective in the absence of ciliopathy proteins. We found that loss of BBS1, BBS4, or OFD1 led to decreased NF-κB activity and concomitant IκBβ accumulation and that these defects were ameliorated with SFN treatment. Taken together, our data indicate that basal body proteasomal regulation governs paracrine signaling pathways and suggest that augmenting proteasomal function might benefit ciliopathy patients. PMID:24691443

Mismatch repair proteins recruited to ultraviolet light-damaged sites lead to degradation of licensing factor Cdt1 in the G1 phase.

PubMed

Tanaka, Miyuki; Takahara, Michiyo; Nukina, Kohei; Hayashi, Akiyo; Sakai, Wataru; Sugasawa, Kaoru; Shiomi, Yasushi; Nishitani, Hideo

2017-04-03

Cdt1 is rapidly degraded by CRL4 Cdt2 E3 ubiquitin ligase after UV (UV) irradiation. Previous reports revealed that the nucleotide excision repair (NER) pathway is responsible for the rapid Cdt1-proteolysis. Here, we show that mismatch repair (MMR) proteins are also involved in the degradation of Cdt1 after UV irradiation in the G1 phase. First, compared with the rapid (within ∼15 min) degradation of Cdt1 in normal fibroblasts, Cdt1 remained stable for ∼30 min in NER-deficient XP-A cells, but was degraded within ∼60 min. The delayed degradation was also dependent on PCNA and CRL4 Cdt2 . The MMR proteins Msh2 and Msh6 were recruited to the UV-damaged sites of XP-A cells in the G1 phase. Depletion of these factors with small interfering RNAs prevented Cdt1 degradation in XP-A cells. Similar to the findings in XP-A cells, depletion of XPA delayed Cdt1 degradation in normal fibroblasts and U2OS cells, and co-depletion of Msh6 further prevented Cdt1 degradation. Furthermore, depletion of Msh6 alone delayed Cdt1 degradation in both cell types. When Cdt1 degradation was attenuated by high Cdt1 expression, repair synthesis at the damaged sites was inhibited. Our findings demonstrate that UV irradiation induces multiple repair pathways that activate CRL4 Cdt2 to degrade its target proteins in the G1 phase of the cell cycle, leading to efficient repair of DNA damage.

Manipulation of ubiquitin/SUMO pathways in human herpesviruses infection.

PubMed

Gan, Jin; Qiao, Niu; Strahan, Roxanne; Zhu, Caixia; Liu, Lei; Verma, Subhash C; Wei, Fang; Cai, Qiliang

2016-11-01

Post-translational modification of proteins with ubiquitin/small ubiquitin-like modifier (SUMO) molecules triggers multiple signaling pathways that are critical for many aspects of cellular physiology. Given that viruses hijack the biosynthetic and degradative systems of their host, it is not surprising that viruses encode proteins to manipulate the host's cellular machinery for ubiquitin/SUMO modification at multiple levels. Infection with a herpesvirus, among the most ubiquitous human DNA viruses, has been linked to many human diseases, including cancers. The interplay between human herpesviruses and the ubiquitylation/SUMOylation modification system has been extensively investigated in the past decade. In this review, we present an overview of recent advances to address how the ubiquitin/SUMO-modified system alters the latency and lytic replication of herpesvirus and how herpesviruses usurp the ubiquitin/SUMO pathways against the host's intrinsic and innate immune response to favor their pathogenesis. Copyright © 2016 John Wiley & Sons, Ltd.

Removal of 2,4-dichlorophenoxyacetic acid in aqueous solution by pulsed corona discharge treatment: Effect of different water constituents, degradation pathway and toxicity assay.

PubMed

Singh, Raj Kamal; Philip, Ligy; Ramanujam, Sarathi

2017-10-01

A multiple pin-plane corona discharge reactor was used to generate plasma for the degradation of 2,4 dichlorophenoxyacetic acid (2,4-D) from the aqueous solution. The 2,4-D of concentration 1 mg/L was completely removed within 6 min of plasma treatment. Almost complete mineralization was achieved after the treatment time of 14 min for a 2,4-D concentration of 10 mg/L. Effects of different water constituents such as carbonates, nitrate, sulphate, chloride ions, natural organic matter (humic acids) and pH on 2,4-D degradation was studied. A significant antagonistic effect of carbonate and humic acid was observed, whereas, the effects of other ions were insignificant. A higher first order rate constant of 1.73 min -1 was observed, which was significantly decreased in the presence of carbonate ions and humic acids. Also, a higher degradation of 2,4-D was observed in acidic pH conditions. Different 2,4-D intermediates were detected and the degradation pathway of 2,4-D in plasma treatment process was suggested. The toxicity of 10 mg/L 2,4-D was completely eradicated after 10 min of plasma treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mass Spectrometry: A Technique of Many Faces

PubMed Central

Olshina, Maya A.; Sharon, Michal

2016-01-01

Protein complexes form the critical foundation for a wide range of biological process, however understanding the intricate details of their activities is often challenging. In this review we describe how mass spectrometry plays a key role in the analysis of protein assemblies and the cellular pathways which they are involved in. Specifically, we discuss how the versatility of mass spectrometric approaches provides unprecedented information on multiple levels. We demonstrate this on the ubiquitin-proteasome proteolytic pathway, a process that is responsible for protein turnover. We follow the various steps of this degradation route and illustrate the different mass spectrometry workflows that were applied for elucidating molecular information. Overall, this review aims to stimulate the integrated use of multiple mass spectrometry approaches for analyzing complex biological systems. PMID:28100928

A Multi-omics Approach to Understand the Microbial Transformation of Lignocellulosic Materials in the Digestive System of the Wood-Feeding Beetle Odontotaenius disjunctus

NASA Astrophysics Data System (ADS)

Ceja Navarro, J. A.; Karaoz, U.; White, R. A., III; Lipton, M. S.; Adkins, J.; Mayali, X.; Blackwell, M.; Pett-Ridge, J.; Brodie, E.; Hao, Z.

2015-12-01

Odontotaenius disjuctus is a wood feeding beetle that processes large amounts of hardwoods and plays an important role in forest carbon cycling. In its gut, plant material is transformed into simple molecules by sequential processing during passage through the insect's digestive system. In this study, we used multiple 'omics approaches to analyze the distribution of microbial communities and their specific functions in lignocellulose deconstruction within the insect's gut. Fosmid clones were selected and sequenced from a pool of clones based on their expression of plant polymer degrading enzymes, allowing the identification of a wide range of carbohydrate degrading enzymes. Comparison of metagenomes of all gut regions demonstrated the distribution of genes across the beetle gut. Cellulose, starch, and xylan degradation genes were particularly abundant in the midgut and posterior hindgut. Genes involved in hydrogenotrophic production of methane and nitrogenases were more abundant in the anterior hindgut. Assembled contigs were binned into 127 putative genomes representing Bacteria, Archaea, Fungi and Nematodes. Eleven complete genomes were reconstructed allowing to identify linked functions/traits, including organisms with cellulosomes, and a combined potential for cellulose, xylan and starch hydrolysis and nitrogen fixation. A metaproteomic study was conducted to test the expression of the pathways identified in the metagenomic study. Preliminary analyses suggest enrichment of pathways related to hemicellulosic degradation. A complete xylan degradation pathway was reconstructed and GC-MS/MS based metabolomics identified xylobiose and xylose as major metabolite pools. To relate microbial identify to function in the beetle gut, Chip-SIP isotope tracing was conducted with RNA extracted from beetles fed 13C-cellulose. Multiple 13C enriched bacterial groups were detected, mainly in the midgut. Our multi-omics approach has allowed us to characterize the contribution of the gut microbiota to the transformation of woody biomass and the distribution of microbial-driven function in the beetle's gut. Through the study of such highly evolved polymer deconstruction and fermentation system we want to identify criteria for design of improved lignocellulosic fuel production processes.

Three degradation pathways of 1-octyl-3-methylimidazolium cation by activated sludge from wastewater treatment process.

PubMed

Cho, Chul-Woong; Pham, Thi Phuong Thuy; Kim, Sok; Song, Myung-Hee; Chung, Yun-Jo; Yun, Yeoung-Sang

2016-03-01

The biodegradability and degradation pathways of 1-octyl-3-methylimidazolium cation [OMIM](+) by microbial community of wastewater treatment plant in Jeonju city, Korea were investigated. It was found that [OMIM](+) could be easily degraded by the microbial community. New degradation products and pathways of [OMIM](+) were identified, which are partially different from previous results (Green Chem. 2008, 10, 214-224). For the analysis of the degradation pathways and intermediates, the mass peaks observed in the range m/z of 50-300 were screened by using a tandem mass spectrometer (MS), and their fragmentation patterns were investigated by MS/MS. Surprisingly, we found three different degradation pathways of [OMIM](+), which were separated according to the initially oxidized position i.e. middle of the long alkyl chain, end of the long alkyl chain, and end of the short alkyl chain. The degradation pathways showed that the long and short alkyl chains of [OMIM](+) gradually degraded by repeating oxidation and carbon release. The results presented here shows that [OMIM](+) can be easily biodegraded through three different degradation pathways in wastewater treatment plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Rab7: roles in membrane trafficking and disease.

PubMed

Zhang, Ming; Chen, Li; Wang, Shicong; Wang, Tuanlao

2009-06-01

The endocytosis pathway controls multiple cellular and physiological events. The lysosome is the destination of newly synthesized lysosomal hydrolytic enzymes. Internalized molecules or particles are delivered to the lysosome for degradation through sequential transport along the endocytic pathway. The endocytic pathway is also emerging as a signalling platform, in addition to the well-known role of the plasma membrane for signalling. Rab7 is a late endosome-/lysosome-associated small GTPase, perhaps the only lysosomal Rab protein identified to date. Rab7 plays critical roles in the endocytic processes. Through interaction with its partners (including upstream regulators and downstream effectors), Rab7 participates in multiple regulation mechanisms in endosomal sorting, biogenesis of lysosome [or LRO (lysosome-related organelle)] and phagocytosis. These processes are closely related to substrates degradation, antigen presentation, cell signalling, cell survival and microbial pathogen infection. Consistently, mutations or dysfunctions of Rab7 result in traffic disorders, which cause various diseases, such as neuropathy, cancer and lipid metabolism disease. Rab7 also plays important roles in microbial pathogen infection and survival, as well as in participating in the life cycle of viruses. Here, we give a brief review on the central role of Rab7 in endosomal traffic and summarize the studies focusing on the participation of Rab7 in disease pathogenesis. The underlying mechanism governed by Rab7 and its partners will also be discussed.

Microbial degradation and toxicity of hexahydro-1,3,5-trinitro-1,3,5-triazine.

PubMed

Khan, Muhammad Imran; Lee, Jaejin; Park, Joonhong

2012-10-01

In the present work, current knowledge on the potential fate, microbial degradation, and toxicity of hexahydro- 1,3,5-trinitro-1,3,5-triazine (RDX) was thoroughly reviewed, focusing on the toxicological assessment of a variety of potential RDX degradation pathways in bacteria and fungi. The present review on microbial degradation pathways and toxicities of degradation intermediates suggests that, among aerobic RDX degradation pathways, the one via denitration may be preferred in a toxicological perspective, and that among anaerobic pathways, those forming 4- nitro-2,4-diazabutanal (NDAB) via ring cleavage of 1-nitroso- 3,5-dinitro-1,3,5-triazinane (MNX) may be toxicologically advantageous owing to its potential mineralization under partial or complete anoxic conditions. These findings provide important information on RDX-degrading microbial pathways, toxicologically most suitable to be stimulated in contaminated fields.

Active Pin1 is a key target of all-trans retinoic acid in acute promyelocytic leukemia and breast cancer.

PubMed

Wei, Shuo; Kozono, Shingo; Kats, Lev; Nechama, Morris; Li, Wenzong; Guarnerio, Jlenia; Luo, Manli; You, Mi-Hyeon; Yao, Yandan; Kondo, Asami; Hu, Hai; Bozkurt, Gunes; Moerke, Nathan J; Cao, Shugeng; Reschke, Markus; Chen, Chun-Hau; Rego, Eduardo M; Lo-Coco, Francesco; Cantley, Lewis C; Lee, Tae Ho; Wu, Hao; Zhang, Yan; Pandolfi, Pier Paolo; Zhou, Xiao Zhen; Lu, Kun Ping

2015-05-01

A common key regulator of oncogenic signaling pathways in multiple tumor types is the unique isomerase Pin1. However, available Pin1 inhibitors lack the required specificity and potency for inhibiting Pin1 function in vivo. By using mechanism-based screening, here we find that all-trans retinoic acid (ATRA)--a therapy for acute promyelocytic leukemia (APL) that is considered the first example of targeted therapy in cancer, but whose drug target remains elusive--inhibits and degrades active Pin1 selectively in cancer cells by directly binding to the substrate phosphate- and proline-binding pockets in the Pin1 active site. ATRA-induced Pin1 ablation degrades the protein encoded by the fusion oncogene PML-RARA and treats APL in APL cell and animal models as well as in human patients. ATRA-induced Pin1 ablation also potently inhibits triple-negative breast cancer cell growth in human cells and in animal models by acting on many Pin1 substrate oncogenes and tumor suppressors. Thus, ATRA simultaneously blocks multiple Pin1-regulated cancer-driving pathways, an attractive property for treating aggressive and drug-resistant tumors.

Chromatographic analysis of tryptophan metabolites

PubMed Central

Sadok, Ilona; Gamian, Andrzej

2017-01-01

The kynurenine pathway generates multiple tryptophan metabolites called collectively kynurenines and leads to formation of the enzyme cofactor nicotinamide adenine dinucleotide. The first step in this pathway is tryptophan degradation, initiated by the rate‐limiting enzymes indoleamine 2,3‐dioxygenase, or tryptophan 2,3‐dioxygenase, depending on the tissue. The balanced kynurenine metabolism, which has been a subject of multiple studies in last decades, plays an important role in several physiological and pathological conditions such as infections, autoimmunity, neurological disorders, cancer, cataracts, as well as pregnancy. Understanding the regulation of tryptophan depletion provide novel diagnostic and treatment opportunities, however it requires reliable methods for quantification of kynurenines in biological samples with complex composition (body fluids, tissues, or cells). Trace concentrations, interference of sample components, and instability of some tryptophan metabolites need to be addressed using analytical methods. The novel separation approaches and optimized extraction protocols help to overcome difficulties in analyzing kynurenines within the complex tissue material. Recent developments in chromatography coupled with mass spectrometry provide new opportunity for quantification of tryptophan and its degradation products in various biological samples. In this review, we present current accomplishments in the chromatographic methodologies proposed for detection of tryptophan metabolites and provide a guide for choosing the optimal approach. PMID:28590049

The Arabidopsis endoplasmic reticulum associated degradation pathways are involved in the regulation of heat stress response

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Lin-Mao; University of Chinese Academy of Sciences, Beijing; Lü, Shi-You

Abstracts: The Cytosolic Protein Response (CPR) in the cytosol and the Unfolded Protein Response (UPR) and ER-associated degradation (ERAD) in the endoplasmic reticulum are major pathways of the cellular proteostasis network. However, despite years of effort, how these protein quality control systems coordinated in vivo remains largely unknown, particularly in plants. In this study, the roles of two evolutionarily conserved ERAD pathways (DOA10 and HRD1) in heat stress response were investigated through reverse genetic approaches in Arabidopsis. Phenotypic analysis of the mutants showed that the two ERAD pathways additively play negative roles in heat tolerance, which was demonstrated by higher survivalmore » rate and lower electrolyte leakage in the loss of function mutants compared to the wild type plants. Importantly, gene expression analysis revealed that the mutant plants showed elevated transcriptional regulation of several downstream genes, including those encoding CPR and UPR marker genes, under both basal and heat stress conditions. Finally, multiple components of ERAD genes exhibited rapid response to increasing temperature. Taken together, our data not only unravels key insights into the crosstalk between different protein quality control processes, but also provides candidate genes to genetically improve plant heat tolerance in the future. - Highlights: • ERAD pathways cooperatively regulate plant thermotolerance. • ERAD pathways cooperatively regulate UPR and CPR. • ERAD components gene expression are upregulated by heat stress.« less

Current Status on Biochemistry and Molecular Biology of Microbial Degradation of Nicotine

PubMed Central

Gurusamy, Raman; Natarajan, Sakthivel

2013-01-01

Bioremediation is one of the most promising methods to clean up polluted environments using highly efficient potent microbes. Microbes with specific enzymes and biochemical pathways are capable of degrading the tobacco alkaloids including highly toxic heterocyclic compound, nicotine. After the metabolic conversion, these nicotinophilic microbes use nicotine as the sole carbon, nitrogen, and energy source for their growth. Various nicotine degradation pathways such as demethylation pathway in fungi, pyridine pathway in Gram-positive bacteria, pyrrolidine pathway, and variant of pyridine and pyrrolidine pathways in Gram-negative bacteria have been reported. In this review, we discussed the nicotine-degrading pathways of microbes and their enzymes and biotechnological applications of nicotine intermediate metabolites. PMID:24470788

Tracing the evolution of degraders in activated sludge during the sludge’s acclimation to a xenobiotic organic

NASA Astrophysics Data System (ADS)

Chong, N. M.; Fan, C. H.; Yang, Y. C.

2017-01-01

The molecular biology method of high-throughput pyrosequencing was employed to examine the change of activated sludge community structures during the process in which activated sludge was acclimated to and degraded a target xenobiotic. The sample xenobiotic organic compound used as the activated sludge acclimation target was the herbicide 2,4-dichlorphenoxyacetic acid (2,4-D). Indigenous activated sludge microorganisms were acclimated to 2,4-D as the sole carbon source in both the batch and the continuous-flow reaction modes. Sludge masses at multiple time points during the course of acclimation were subjected to pyrosequencing targeting the microorganisms’ 16S rRNA genes. With the bacterial 16S rRNA sequencing results the genera that increased in abundance were checked with degradative pathway databases or literature to confirm that they are commonly seen as potent degraders of 2,4-D. From this systematic examination of degrader changes at time points during activated sludge acclimation and degradation of the target xenobiotic, the trend of degrader evolution in activated sludge over the sludge’s acclimation process to a xenobiotic was traced.

Multiple UBXN family members inhibit retrovirus and lentivirus production and canonical NFκΒ signaling by stabilizing IκBα.

PubMed

Hu, Yani; O'Boyle, Kaitlin; Auer, Jim; Raju, Sagar; You, Fuping; Wang, Penghua; Fikrig, Erol; Sutton, Richard E

2017-02-01

UBXN proteins likely participate in the global regulation of protein turnover, and we have shown that UBXN1 interferes with RIG-I-like receptor (RLR) signaling by interacting with MAVS and impeding its downstream effector functions. Here we demonstrate that over-expression of multiple UBXN family members decreased lentivirus and retrovirus production by several orders-of-magnitude in single cycle assays, at the level of long terminal repeat-driven transcription, and three family members, UBXN1, N9, and N11 blocked the canonical NFκB pathway by binding to Cullin1 (Cul1), inhibiting IκBα degradation. Multiple regions of UBXN1, including its UBA domain, were critical for its activity. Elimination of UBXN1 resulted in early murine embryonic lethality. shRNA-mediated knockdown of UBXN1 enhanced human immunodeficiency virus type 1 (HIV) production up to 10-fold in single cycle assays. In primary human fibroblasts, knockdown of UBXN1 caused prolonged degradation of IκBα and enhanced NFκB signaling, which was also observed after CRISPR-mediated knockout of UBXN1 in mouse embryo fibroblasts. Knockout of UBXN1 significantly up- and down-regulated hundreds of genes, notably those of several cell adhesion and immune signaling pathways. Reduction in UBXN1 gene expression in Jurkat T cells latently infected with HIV resulted in enhanced HIV gene expression, consistent with the role of UBXN1 in modulating the NFκB pathway. Based upon co-immunoprecipitation studies with host factors known to bind Cul1, models are presented as to how UBXN1 could be inhibiting Cul1 activity. The ability of UBXN1 and other family members to negatively regulate the NFκB pathway may be important for dampening the host immune response in disease processes and also re-activating quiescent HIV from latent viral reservoirs in chronically infected individuals.

Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis

PubMed Central

Bergstrand, Lee H.; Cardenas, Erick; Holert, Johannes; Van Hamme, Jonathan D.

2016-01-01

ABSTRACT Steroids are ubiquitous in natural environments and are a significant growth substrate for microorganisms. Microbial steroid metabolism is also important for some pathogens and for biotechnical applications. This study delineated the distribution of aerobic steroid catabolism pathways among over 8,000 microorganisms whose genomes are available in the NCBI RefSeq database. Combined analysis of bacterial, archaeal, and fungal genomes with both hidden Markov models and reciprocal BLAST identified 265 putative steroid degraders within only Actinobacteria and Proteobacteria, which mainly originated from soil, eukaryotic host, and aquatic environments. These bacteria include members of 17 genera not previously known to contain steroid degraders. A pathway for cholesterol degradation was conserved in many actinobacterial genera, particularly in members of the Corynebacterineae, and a pathway for cholate degradation was conserved in members of the genus Rhodococcus. A pathway for testosterone and, sometimes, cholate degradation had a patchy distribution among Proteobacteria. The steroid degradation genes tended to occur within large gene clusters. Growth experiments confirmed bioinformatic predictions of steroid metabolism capacity in nine bacterial strains. The results indicate there was a single ancestral 9,10-seco-steroid degradation pathway. Gene duplication, likely in a progenitor of Rhodococcus, later gave rise to a cholate degradation pathway. Proteobacteria and additional Actinobacteria subsequently obtained a cholate degradation pathway via horizontal gene transfer, in some cases facilitated by plasmids. Catabolism of steroids appears to be an important component of the ecological niches of broad groups of Actinobacteria and individual species of Proteobacteria. PMID:26956583

Distinct protein degradation profiles are induced by different disuse models of skeletal muscle atrophy

PubMed Central

Bialek, Peter; Morris, Carl; Parkington, Jascha; St. Andre, Michael; Owens, Jane; Yaworsky, Paul; Seeherman, Howard

2011-01-01

Skeletal muscle atrophy can be a consequence of many diseases, environmental insults, inactivity, age, and injury. Atrophy is characterized by active degradation, removal of contractile proteins, and a reduction in muscle fiber size. Animal models have been extensively used to identify pathways that lead to atrophic conditions. We used genome-wide expression profiling analyses and quantitative PCR to identify the molecular changes that occur in two clinically relevant mouse models of muscle atrophy: hindlimb casting and Achilles tendon laceration (tenotomy). Gastrocnemius muscle samples were collected 2, 7, and 14 days after casting or injury. The total amount of muscle loss, as measured by wet weight and muscle fiber size, was equivalent between models on day 14, although tenotomy resulted in a more rapid induction of muscle atrophy. Furthermore, tenotomy resulted in the regulation of significantly more mRNA transcripts then did casting. Analysis of the regulated genes and pathways suggest that the mechanisms of atrophy are distinct between these models. The degradation following casting was ubiquitin-proteasome mediated, while degradation following tenotomy was lysosomal and matrix-metalloproteinase mediated, suggesting a possible role for autophagy. These data suggest that there are multiple mechanisms leading to muscle atrophy and that specific therapeutic agents may be necessary to combat atrophy resulting from different conditions. PMID:21791639

Intracellular Trafficking Network of Protein Nanocapsules: Endocytosis, Exocytosis and Autophagy.

PubMed

Zhang, Jinxie; Zhang, Xudong; Liu, Gan; Chang, Danfeng; Liang, Xin; Zhu, Xianbing; Tao, Wei; Mei, Lin

2016-01-01

The inner membrane vesicle system is a complex transport system that includes endocytosis, exocytosis and autophagy. However, the details of the intracellular trafficking pathway of nanoparticles in cells have been poorly investigated. Here, we investigate in detail the intracellular trafficking pathway of protein nanocapsules using more than 30 Rab proteins as markers of multiple trafficking vesicles in endocytosis, exocytosis and autophagy. We observed that FITC-labeled protein nanoparticles were internalized by the cells mainly through Arf6-dependent endocytosis and Rab34-mediated micropinocytosis. In addition to this classic pathway: early endosome (EEs)/late endosome (LEs) to lysosome, we identified two novel transport pathways: micropinocytosis (Rab34 positive)-LEs (Rab7 positive)-lysosome pathway and EEs-liposome (Rab18 positive)-lysosome pathway. Moreover, the cells use slow endocytosis recycling pathway (Rab11 and Rab35 positive vesicles) and GLUT4 exocytosis vesicles (Rab8 and Rab10 positive) transport the protein nanocapsules out of the cells. In addition, protein nanoparticles are observed in autophagosomes, which receive protein nanocapsules through multiple endocytosis vesicles. Using autophagy inhibitor to block these transport pathways could prevent the degradation of nanoparticles through lysosomes. Using Rab proteins as vesicle markers to investigation the detail intracellular trafficking of the protein nanocapsules, will provide new targets to interfere the cellular behaver of the nanoparticles, and improve the therapeutic effect of nanomedicine.

Altered Micro-RNA Degradation Promotes Tumor Heterogeneity: A Result from Boolean Network Modeling.

PubMed

Wu, Yunyi; Krueger, Gerhard R F; Wang, Guanyu

2016-02-01

Cancer heterogeneity may reflect differential dynamical outcomes of the regulatory network encompassing biomolecules at both transcriptional and post-transcriptional levels. In other words, differential gene-expression profiles may correspond to different stable steady states of a mathematical model for simulation of biomolecular networks. To test this hypothesis, we simplified a regulatory network that is important for soft-tissue sarcoma metastasis and heterogeneity, comprising of transcription factors, micro-RNAs, and signaling components of the NOTCH pathway. We then used a Boolean network model to simulate the dynamics of this network, and particularly investigated the consequences of differential miRNA degradation modes. We found that efficient miRNA degradation is crucial for sustaining a homogenous and healthy phenotype, while defective miRNA degradation may lead to multiple stable steady states and ultimately to carcinogenesis and heterogeneity. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

The Vitamin Nicotinamide: Translating Nutrition into Clinical Care

PubMed Central

Maiese, Kenneth; Chong, Zhao Zhong; Hou, Jinling; Shang, Yan Chen

2009-01-01

Nicotinamide, the amide form of vitamin B3 (niacin), is changed to its mononucleotide compound with the enzyme nicotinic acide/nicotinamide adenylyl-transferase, and participates in the cellular energy metabolism that directly impacts normal physiology. However, nicotinamide also influences oxidative stress and modulates multiple pathways tied to both cellular survival and death. During disorders that include immune system dysfunction, diabetes, and aging-related diseases, nicotinamide is a robust cytoprotectant that blocks cellular inflammatory cell activation, early apoptotic phosphatidylserine exposure, and late nuclear DNA degradation. Nicotinamide relies upon unique cellular pathways that involve forkhead transcription factors, sirtuins, protein kinase B (Akt), Bad, caspases, and poly (ADP-ribose) polymerase that may offer a fine line with determining cellular longevity, cell survival, and unwanted cancer progression. If one is cognizant of the these considerations, it becomes evident that nicotinamide holds great potential for multiple disease entities, but the development of new therapeutic strategies rests heavily upon the elucidation of the novel cellular pathways that nicotinamide closely governs. PMID:19783937

Transcriptomic Assessment of Isozymes in the Biphenyl Pathway of Rhodococcus sp. Strain RHA1†

PubMed Central

Gonçalves, Edmilson R.; Hara, Hirofumi; Miyazawa, Daisuke; Davies, Julian E.; Eltis, Lindsay D.; Mohn, William W.

2006-01-01

Rhodococcus sp. RHA1 grows on a broad range of aromatic compounds and vigorously degrades polychlorinated biphenyls (PCBs). Previous work identified RHA1 genes encoding multiple isozymes for most of the seven steps of the biphenyl (BPH) pathway, provided evidence for coexpression of some of these isozymes, and indicated the involvement of some of these enzymes in the degradation of BPH, ethylbenzene (ETB), and PCBs. To investigate the expression of these isozymes and better understand how they contribute to the robust degradative capacity of RHA1, we comprehensively analyzed the 9.7-Mb genome of RHA1 for BPH pathway genes and characterized the transcriptome of RHA1 growing on benzoate (BEN), BPH, and ETB. Sequence analyses revealed 54 potential BPH pathway genes, including 28 not previously reported. Transcriptomic analysis with a DNA microarray containing 70-mer probes for 8,213 RHA1 genes revealed a suite of 320 genes of diverse functions that were upregulated during growth both on BPH and on ETB, relative to growth on the control substrate, pyruvate. By contrast, only 65 genes were upregulated during growth on BEN. Quantitative PCR assays confirmed microarray results for selected genes and indicated that some of the catabolic genes were upregulated over 10,000-fold. Our analysis suggests that up to 22 enzymes, including 8 newly identified ones, may function in the BPH pathway of RHA1. The relative expression levels of catabolic genes did not differ for BPH and ETB, suggesting a common regulatory mechanism. This study delineated a suite of catabolic enzymes for biphenyl and alkyl-benzenes in RHA1, which is larger than previously recognized and which may serve as a model for catabolism in other environmentally important bacteria having large genomes. PMID:16957245

Enzymes involved in a novel anaerobic cyclohexane carboxylic acid degradation pathway.

PubMed

Kung, Johannes W; Meier, Anne-Katrin; Mergelsberg, Mario; Boll, Matthias

2014-10-01

The anaerobic degradation of cyclohexane carboxylic acid (CHC) has so far been studied only in Rhodopseudomonas palustris, in which CHC is activated to cyclohexanoyl coenzyme A (cyclohexanoyl-CoA [CHCoA]) and then dehydrogenated to cyclohex-1-ene-1-carboxyl-CoA (CHeneCoA). This intermediate is further degraded by reactions of the R. palustris-specific benzoyl-CoA degradation pathway of aromatic compounds. However, CHeneCoA is not an intermediate in the degradation of aromatic compounds in all other known anaerobic bacteria; consequently, degradation of CHC was mostly unknown in anaerobic bacteria. We identified a previously unknown CHC degradation pathway in the Fe(III)-reducing Geobacter metallireducens by determining the following CHC-induced in vitro activities: (i) the activation of CHC to CHCoA by a succinyl-CoA:CHC CoA transferase, (ii) the 1,2-dehydrogenation of CHCoA to CHeneCoA by CHCoA dehydrogenase, and (iii) the unusual 1,4-dehydrogenation of CHeneCoA to cyclohex-1,5-diene-1-carboxyl-CoA. This last represents a previously unknown joint intermediate of the CHC and aromatic compound degradation pathway in bacteria other than R. palustris. The enzymes catalyzing the three reactions were purified and characterized as specific enzymes after heterologous expression of the encoding genes. Quantitative reverse transcription-PCR revealed that expression of these genes was highly induced during growth with CHC but not with benzoate. The newly identified CHC degradation pathway is suggested to be present in nearly all CHC-degrading anaerobic bacteria, including denitrifying, Fe(III)-reducing, sulfate-reducing, and fermenting bacteria. Remarkably, all three CHC degradation pathways always link CHC catabolism to the catabolic pathways of aromatic compounds. We propose that the capacity to use CHC as a carbon source evolved from already-existing aromatic compound degradation pathways. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Enzymes Involved in a Novel Anaerobic Cyclohexane Carboxylic Acid Degradation Pathway

PubMed Central

Kung, Johannes W.; Meier, Anne-Katrin; Mergelsberg, Mario

2014-01-01

The anaerobic degradation of cyclohexane carboxylic acid (CHC) has so far been studied only in Rhodopseudomonas palustris, in which CHC is activated to cyclohexanoyl coenzyme A (cyclohexanoyl-CoA [CHCoA]) and then dehydrogenated to cyclohex-1-ene-1-carboxyl-CoA (CHeneCoA). This intermediate is further degraded by reactions of the R. palustris-specific benzoyl-CoA degradation pathway of aromatic compounds. However, CHeneCoA is not an intermediate in the degradation of aromatic compounds in all other known anaerobic bacteria; consequently, degradation of CHC was mostly unknown in anaerobic bacteria. We identified a previously unknown CHC degradation pathway in the Fe(III)-reducing Geobacter metallireducens by determining the following CHC-induced in vitro activities: (i) the activation of CHC to CHCoA by a succinyl-CoA:CHC CoA transferase, (ii) the 1,2-dehydrogenation of CHCoA to CHeneCoA by CHCoA dehydrogenase, and (iii) the unusual 1,4-dehydrogenation of CHeneCoA to cyclohex-1,5-diene-1-carboxyl-CoA. This last represents a previously unknown joint intermediate of the CHC and aromatic compound degradation pathway in bacteria other than R. palustris. The enzymes catalyzing the three reactions were purified and characterized as specific enzymes after heterologous expression of the encoding genes. Quantitative reverse transcription-PCR revealed that expression of these genes was highly induced during growth with CHC but not with benzoate. The newly identified CHC degradation pathway is suggested to be present in nearly all CHC-degrading anaerobic bacteria, including denitrifying, Fe(III)-reducing, sulfate-reducing, and fermenting bacteria. Remarkably, all three CHC degradation pathways always link CHC catabolism to the catabolic pathways of aromatic compounds. We propose that the capacity to use CHC as a carbon source evolved from already-existing aromatic compound degradation pathways. PMID:25112478

Degradation of Akt using protein-catalyzed capture agents.

PubMed

Henning, Ryan K; Varghese, Joseph O; Das, Samir; Nag, Arundhati; Tang, Grace; Tang, Kevin; Sutherland, Alexander M; Heath, James R

2016-04-01

Abnormal signaling of the protein kinase Akt has been shown to contribute to human diseases such as diabetes and cancer, but Akt has proven to be a challenging target for drugging. Using iterative in situ click chemistry, we recently developed multiple protein-catalyzed capture (PCC) agents that allosterically modulate Akt enzymatic activity in a protein-based assay. Here, we utilize similar PCCs to exploit endogenous protein degradation pathways. We use the modularity of the anti-Akt PCCs to prepare proteolysis targeting chimeric molecules that are shown to promote the rapid degradation of Akt in live cancer cells. These novel proteolysis targeting chimeric molecules demonstrate that the epitope targeting selectivity of PCCs can be coupled with non-traditional drugging moieties to inhibit challenging targets. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Inhibition and Avoidance of mRNA Degradation by RNA Viruses

PubMed Central

Moon, Stephanie L.; Barnhart, Michael D.; Wilusz, Jeffrey

2012-01-01

The cellular mRNA decay machinery plays a major role in regulating the quality and quantity of gene expression in cells. This machinery involves multiple enzymes and pathways that converge to promote the exonucleolytic decay of mRNAs. The transcripts made by RNA viruses are susceptible to degradation by this machinery and, in fact, can be actively targeted. Thus, to maintain gene expression and replication, RNA viruses have evolved a number of strategies to avoid and/or inactivate aspects of the cellular mRNA decay machinery. Recent work uncovering the mechanisms used by RNA viruses to maintain the stability of their transcripts is described below. PMID:22626865

Direct interaction of menin leads to ubiquitin-proteasomal degradation of β-catenin.

PubMed

Kim, Byungho; Song, Tae-Yang; Jung, Kwan Young; Kim, Seul Gi; Cho, Eun-Jung

2017-10-07

Menin, encoded by the multiple endocrine neoplasia type 1 (MEN1) gene, is a tumor suppressor and transcription regulator. Menin interacts with various proteins as a scaffold protein and is proposed to play important roles in multiple physiological and pathological processes by controlling gene expression, proliferation, and apoptosis. The mechanisms underlying menin's suppression of tumorigenesis are largely elusive. In this study, we showed that menin was essential for the regulation of canonical Wnt/β-catenin signaling in cultured cells. The C-terminal domain of menin was able to directly interact with and promote ubiquitin-mediated degradation of β-catenin. We further revealed that overexpression of menin down-regulated the transcriptional activity of β-catenin and target gene expression. Moreover, menin efficiently inhibited β-catenin protein levels, transcriptional activity, and proliferation of human renal carcinoma cells with an activated β-catenin pathway. Taken together, our results provide novel molecular insights into the tumor suppressor activity of menin, which is partly mediated by proteasomal degradation of β-catenin and inhibition of Wnt/β-catenin signaling. Copyright © 2017 Elsevier Inc. All rights reserved.

Epigenomics and the concept of degeneracy in biological systems

PubMed Central

Mason, Paul H.; Barron, Andrew B.

2014-01-01

Researchers in the field of epigenomics are developing more nuanced understandings of biological complexity, and exploring the multiple pathways that lead to phenotypic expression. The concept of degeneracy—referring to the multiple pathways that a system recruits to achieve functional plasticity—is an important conceptual accompaniment to the growing body of knowledge in epigenomics. Distinct from degradation, redundancy and dilapidation; degeneracy refers to the plasticity of traits whose function overlaps in some environments, but diverges in others. While a redundant system is composed of repeated identical elements performing the same function, a degenerate system is composed of different elements performing similar or overlapping functions. Here, we describe the degenerate structure of gene regulatory systems from the basic genetic code to flexible epigenomic modifications, and discuss how these structural features have contributed to organism complexity, robustness, plasticity and evolvability. PMID:24335757

EIMS Fragmentation Pathways and MRM Quantification of 7α/β-Hydroxy-Dehydroabietic Acid TMS Derivatives

NASA Astrophysics Data System (ADS)

Rontani, Jean-François; Aubert, Claude; Belt, Simon T.

2015-09-01

EI mass fragmentation pathways of TMS derivatives οf 7α/β-hydroxy-dehydroabietic acids resulting from NaBH4-reduction of oxidation products of dehydroabietic acid (a component of conifers) were investigated and deduced by a combination of (1) low energy CID-GC-MS/MS, (2) deuterium labeling, (3) different derivatization methods, and (4) GC-QTOF accurate mass measurements. Having identified the main fragmentation pathways, the TMS-derivatized 7α/β-hydroxy-dehydroabietic acids could be quantified in multiple reaction monitoring (MRM) mode in sea ice and sediment samples collected from the Arctic. These newly characterized transformation products of dehydroabietic acid constitute potential tracers of biotic and abiotic degradation of terrestrial higher plants in the environment.

Removal of trimethylamine (fishy odor) by C₃ and CAM plants.

PubMed

Boraphech, Phattara; Thiravetyan, Paitip

2015-08-01

From screening 23 plant species, it was found that Pterocarpus indicus (C3) and Sansevieria trifasciata (crassulacean acid metabolism (CAM)) were the most effective in polar gaseous trimethylamine (TMA) uptake, reaching up to 90% uptake of initial TMA (100 ppm) within 8 h, and could remove TMA at cycles 1-4 without affecting photosystem II (PSII) photochemistry. Up to 55 and 45% of TMA was taken up by S. trifasciata stomata and leaf epicuticular wax, respectively. During cycles 1-4, interestingly, S. trifasciata changed its stomata apertures, which was directly induced by gaseous TMA and light treatments. In contrast, for P. indicus the leaf epicuticular wax and stem were the major pathways of TMA removal, followed by stomata; these pathways accounted for 46, 46, and 8%, respectively, of TMA removal percentages. Fatty acids, particularly tetradecanoic (C14) acid and octadecanoic (C18) acid, were found to be the main cuticular wax components in both plants, and were associated with TMA removal ability. Moreover, the plants could degrade TMA via multiple metabolic pathways associated with carbon/nitrogen interactions. In CAM plants, one of the crucial pathways enabled 78% of TMA to be transformed directly to dimethylamine (DMA) and methylamine (MA), which differed from C3 plant pathways. Various metabolites were also produced for further detoxification and mineralization so that TMA was completely degraded by plants.

Protection of therapeutic antibodies from visible light induced degradation: Use safe light in manufacturing and storage.

PubMed

Du, Cheng; Barnett, Gregory; Borwankar, Ameya; Lewandowski, Angela; Singh, Nripen; Ghose, Sanchayita; Borys, Michael; Li, Zheng Jian

2018-06-01

As macromolecules, biologics are susceptible to light exposure, which induces oxidation of multiple amino acid residues including tryptophan, tyrosine, phenylalanine, cysteine and methionine. Pertaining to safety, efficacy and potency, light-induced oxidation of biologics has been widely studied and necessary precautions need to be taken during biologics manufacturing process, drug substance and products handling and storage. Proteins will degrade to varying extents depending on the protein properties, degradation pathways, formulation compositions and type of light source. In addition to UV light, which has been widely known to degrade proteins, visible light from indoor fluorescent lighting also can mediate protein degradation. In this report, we examine and identify wavelengths in the visual spectrum (400-700 nm) that can cause monoclonal antibody and histidine buffer degradation. Installation of safe lights which exclude the identified damaging wavelengths from visible spectra in manufacturing and storage areas can provide a balance between lighting requirement for human operators and their safety and conservation of product quality. Copyright © 2018 Elsevier B.V. All rights reserved.

Ecosystem services capacity across heterogeneous forest types: understanding the interactions and suggesting pathways for sustaining multiple ecosystem services.

PubMed

Alamgir, Mohammed; Turton, Stephen M; Macgregor, Colin J; Pert, Petina L

2016-10-01

As ecosystem services supply from tropical forests is declining due to deforestation and forest degradation, much effort is essential to sustain ecosystem services supply from tropical forested landscapes, because tropical forests provide the largest flow of multiple ecosystem services among the terrestrial ecosystems. In order to sustain multiple ecosystem services, understanding ecosystem services capacity across heterogeneous forest types and identifying certain ecosystem services that could be managed to leverage positive effects across the wider bundle of ecosystem services are required. We sampled three forest types, tropical rainforests, sclerophyll forests, and rehabilitated plantation forests, over an area of 32,000m(2) from Wet Tropics bioregion, Australia, aiming to compare supply and evaluate interactions and patterns of eight ecosystem services (global climate regulation, air quality regulation, erosion regulation, nutrient regulation, cyclone protection, habitat provision, energy provision, and timber provision). On average, multiple ecosystem services were highest in the rainforests, lowest in sclerophyll forests, and intermediate in rehabilitated plantation forests. However, a wide variation was apparent among the plots across the three forest types. Global climate regulation service had a synergistic impact on the supply of multiple ecosystem services, while nutrient regulation service was found to have a trade-off impact. Considering multiple ecosystem services, most of the rehabilitated plantation forest plots shared the same ordination space with rainforest plots in the ordination analysis, indicating that rehabilitated plantation forests may supply certain ecosystem services nearly equivalent to rainforests. Two synergy groups and one trade-off group were identified. Apart from conserving rainforests and sclerophyll forests, our findings suggest two additional integrated pathways to sustain the supply of multiple ecosystem services from a heterogeneous tropical forest landscape: (i) rehabilitation of degraded forests aiming to provide global climate regulation and habitat provision ecosystem services and (ii) management intervention to sustain global climate regulation and habitat provision ecosystem services. Copyright © 2016 Elsevier B.V. All rights reserved.

Always cleave up your mess: targeting collagen degradation to treat tissue fibrosis.

PubMed

McKleroy, William; Lee, Ting-Hein; Atabai, Kamran

2013-06-01

Pulmonary fibrosis is a vexing clinical problem with no proven therapeutic options. In the normal lung there is continuous collagen synthesis and collagen degradation, and these two processes are precisely balanced to maintain normal tissue architecture. With lung injury there is an increase in the rate of both collagen production and collagen degradation. The increase in collagen degradation is critical in preventing the formation of permanent scar tissue each time the lung is exposed to injury. In pulmonary fibrosis, collagen degradation does not keep pace with collagen production, resulting in extracellular accumulation of fibrillar collagen. Collagen degradation occurs through both extracellular and intracellular pathways. The extracellular pathway involves cleavage of collagen fibrils by proteolytic enzyme including the metalloproteinases. The less-well-described intracellular pathway involves binding and uptake of collagen fragments by fibroblasts and macrophages for lysosomal degradation. The relationship between these two pathways and their relevance to the development of fibrosis is complex. Fibrosis in the lung, liver, and skin has been associated with an impaired degradative environment. Much of the current scientific effort in fibrosis is focused on understanding the pathways that regulate increased collagen production. However, recent reports suggest an important role for collagen turnover and degradation in regulating the severity of tissue fibrosis. The objective of this review is to evaluate the roles of the extracellular and intracellular collagen degradation pathways in the development of fibrosis and to examine whether pulmonary fibrosis can be viewed as a disease of impaired matrix degradation rather than a disease of increased matrix production.

Always cleave up your mess: targeting collagen degradation to treat tissue fibrosis

PubMed Central

McKleroy, William; Lee, Ting-Hein

2013-01-01

Pulmonary fibrosis is a vexing clinical problem with no proven therapeutic options. In the normal lung there is continuous collagen synthesis and collagen degradation, and these two processes are precisely balanced to maintain normal tissue architecture. With lung injury there is an increase in the rate of both collagen production and collagen degradation. The increase in collagen degradation is critical in preventing the formation of permanent scar tissue each time the lung is exposed to injury. In pulmonary fibrosis, collagen degradation does not keep pace with collagen production, resulting in extracellular accumulation of fibrillar collagen. Collagen degradation occurs through both extracellular and intracellular pathways. The extracellular pathway involves cleavage of collagen fibrils by proteolytic enzyme including the metalloproteinases. The less-well-described intracellular pathway involves binding and uptake of collagen fragments by fibroblasts and macrophages for lysosomal degradation. The relationship between these two pathways and their relevance to the development of fibrosis is complex. Fibrosis in the lung, liver, and skin has been associated with an impaired degradative environment. Much of the current scientific effort in fibrosis is focused on understanding the pathways that regulate increased collagen production. However, recent reports suggest an important role for collagen turnover and degradation in regulating the severity of tissue fibrosis. The objective of this review is to evaluate the roles of the extracellular and intracellular collagen degradation pathways in the development of fibrosis and to examine whether pulmonary fibrosis can be viewed as a disease of impaired matrix degradation rather than a disease of increased matrix production. PMID:23564511

Multiple functions of the E3 ubiquitin ligase CHIP in immunity.

PubMed

Zhan, Shaohua; Wang, Tianxiao; Ge, Wei

2017-09-03

The carboxyl terminal of Hsp70-interacting protein (CHIP) is an E3 ubiquitin ligase that plays a pivotal role in the protein quality control system by shifting the balance of the folding-refolding machinery toward the degradative pathway. However, the precise mechanisms by which nonnative proteins are selected for degradation by CHIP either directly or indirectly via chaperone Hsp70 or Hsp90 are still not clear. In this review, we aim to provide a comprehensive model of the mechanism by which CHIP degrades its substrate in a chaperone-dependent or direct manner. In addition, through tight regulation of the protein level of its substrates, CHIP plays important roles in many physiological and pathological conditions, including cancers, neurological disorders, cardiac diseases, bone metabolism, immunity, and so on. Nonetheless, the precise mechanisms underlying the regulation of the immune system by CHIP are still poorly understood despite accumulating developments in our understanding of the regulatory roles of CHIP in both innate and adaptive immune responses. In this review, we also aim to provide a view of CHIP-mediated regulation of immune responses and the signaling pathways involved in the model described. Finally, we discuss the roles of CHIP in immune-related diseases.

Elucidation of the Mechanisms and Environmental Relevance of cis-Dichloroethene and Vinyl Chloride Biodegradation

DTIC Science & Technology

2012-11-01

in iTRAQ study Table 3-12: Ratio of aldehyde and alcohol dehydrogenases from iTRAQ study Table 3-13: Proteins involved in proposed glyoxal...pathway for cDCE degradation proceeds through chloro-, or dichloroacetaldehyde. Multiple aldehyde dehydrogenases are annotated in the genome of...dichloroacetaldehyde is a fortuitous reaction. However, if the initial reaction is monooxygenation to an aldehyde then the true intermediate would be

Transcriptional profiling suggests that multiple metabolic adaptations are required for effective proliferation of Pseudomonas aeruginosa in jet fuel.

PubMed

Gunasekera, Thusitha S; Striebich, Richard C; Mueller, Susan S; Strobel, Ellen M; Ruiz, Oscar N

2013-01-01

Fuel is a harsh environment for microbial growth. However, some bacteria can grow well due to their adaptive mechanisms. Our goal was to characterize the adaptations required for Pseudomonas aeruginosa proliferation in fuel. We have used DNA-microarrays and RT-PCR to characterize the transcriptional response of P. aeruginosa to fuel. Transcriptomics revealed that genes essential for medium- and long-chain n-alkane degradation including alkB1 and alkB2 were transcriptionally induced. Gas chromatography confirmed that P. aeruginosa possesses pathways to degrade different length n-alkanes, favoring the use of n-C11-18. Furthermore, a gamut of synergistic metabolic pathways, including porins, efflux pumps, biofilm formation, and iron transport, were transcriptionally regulated. Bioassays confirmed that efflux pumps and biofilm formation were required for growth in jet fuel. Furthermore, cell homeostasis appeared to be carefully maintained by the regulation of porins and efflux pumps. The Mex RND efflux pumps were required for fuel tolerance; blockage of these pumps precluded growth in fuel. This study provides a global understanding of the multiple metabolic adaptations required by bacteria for survival and proliferation in fuel-containing environments. This information can be applied to improve the fuel bioremediation properties of bacteria.

Kinetics and mechanism for the sonochemical degradation of a nonionic surfactant.

PubMed

Singla, Ritu; Grieser, Franz; Ashokkumar, Muthupandian

2009-03-26

The sonolytic degradation of the nonionic surfactant, octaethylene glycol monododecyl ether (C(12)E(8)), has been studied at various initial concentrations below and above its critical micelle concentration (CMC). It has been observed that the degradation rate increases with an increase in the initial concentration of the surfactant until the CMC is reached. Above the CMC an almost constant degradation rate is observed, suggesting that the surfactant in its monomer form is involved in the degradation process. The degradation process of C(12)E(8) involves two distinct primary processes occurring at the bubble/solution interface: (a) hydroxylation/oxidation of the surfactant and (b) pyrolytic fragmentation of the surfactant. The oxidative cleavage of ethylene oxide units provides evidence for OH radical attack. Hydroxylation of the ethoxy chain gives rise to various short-chain carboxyalkyl-polyethylene glycol intermediates. The polyethylene glycol chain formed, due to the scission of the C(12)E(8) molecule, undergoes rapid hydroxylation/oxidation to yield simple compounds that have the potential to undergo further degradation. The detection of multiple intermediates indicates that several processes affect the complete degradation pathways of the surfactant molecule. TOC analysis, however, indicates that the sonolytic mineralization of the surfactant is difficult to achieve at reasonable rates due to the relatively low surface activity of the degradation products formed during sonolysis.

Pathway and rate-limiting step of glyphosate degradation by Aspergillus oryzae A-F02.

PubMed

Fu, Gui-Ming; Chen, Yan; Li, Ru-Yi; Yuan, Xiao-Qiang; Liu, Cheng-Mei; Li, Bin; Wan, Yin

2017-09-14

Aspergillus oryzae A-F02, a glyphosate-degrading fungus, was isolated from an aeration tank in a pesticide factory. The pathway and rate-limiting step of glyphosate (GP) degradation were investigated through metabolite analysis. GP, aminomethylphosphonic acid (AMPA), and methylamine were detected in the fermentation liquid of A. oryzae A-F02, whereas sarcosine and glycine were not. The pathway of GP degradation in A. oryzae A-F02 was revealed: GP was first degraded into AMPA, which was then degraded into methylamine. Finally, methylamine was further degraded into other products. Investigating the effects of the exogenous addition of substrates and metabolites showed that the degradation of GP to AMPA is the rate-limiting step of GP degradation by A. oryzae A-F02. In addition, the accumulation of AMPA and methylamine did not cause feedback inhibition in GP degradation. Results showed that degrading GP to AMPA was a crucial step in the degradation of GP, which determines the degradation rate of GP by A. oryzae A-F02.

Regulation of autophagy by cytoplasmic p53.

PubMed

Tasdemir, Ezgi; Maiuri, M Chiara; Galluzzi, Lorenzo; Vitale, Ilio; Djavaheri-Mergny, Mojgan; D'Amelio, Marcello; Criollo, Alfredo; Morselli, Eugenia; Zhu, Changlian; Harper, Francis; Nannmark, Ulf; Samara, Chrysanthi; Pinton, Paolo; Vicencio, José Miguel; Carnuccio, Rosa; Moll, Ute M; Madeo, Frank; Paterlini-Brechot, Patrizia; Rizzuto, Rosario; Szabadkai, Gyorgy; Pierron, Gérard; Blomgren, Klas; Tavernarakis, Nektarios; Codogno, Patrice; Cecconi, Francesco; Kroemer, Guido

2008-06-01

Multiple cellular stressors, including activation of the tumour suppressor p53, can stimulate autophagy. Here we show that deletion, depletion or inhibition of p53 can induce autophagy in human, mouse and nematode cells subjected to knockout, knockdown or pharmacological inhibition of p53. Enhanced autophagy improved the survival of p53-deficient cancer cells under conditions of hypoxia and nutrient depletion, allowing them to maintain high ATP levels. Inhibition of p53 led to autophagy in enucleated cells, and cytoplasmic, not nuclear, p53 was able to repress the enhanced autophagy of p53(-/-) cells. Many different inducers of autophagy (for example, starvation, rapamycin and toxins affecting the endoplasmic reticulum) stimulated proteasome-mediated degradation of p53 through a pathway relying on the E3 ubiquitin ligase HDM2. Inhibition of p53 degradation prevented the activation of autophagy in several cell lines, in response to several distinct stimuli. These results provide evidence of a key signalling pathway that links autophagy to the cancer-associated dysregulation of p53.

Regulation of autophagy by cytoplasmic p53

PubMed Central

Tasdemir, Ezgi; Maiuri, M. Chiara; Galluzzi, Lorenzo; Vitale, Ilio; Djavaheri-Mergny, Mojgan; D'Amelio, Marcello; Criollo, Alfredo; Morselli, Eugenia; Zhu, Changlian; Harper, Francis; Nannmark, Ulf; Samara, Chrysanthi; Pinton, Paolo; Vicencio, José Miguel; Carnuccio, Rosa; Moll, Ute M.; Madeo, Frank; Paterlini-Brechot, Patrizia; Rizzuto, Rosario; Szabadkai, Gyorgy; Pierron, Gérard; Blomgren, Klas; Tavernarakis, Nektarios; Codogno, Patrice; Cecconi, Francesco; Kroemer, Guido

2009-01-01

Multiple cellular stressors, including activation of the tumour suppressor p53, can stimulate autophagy. Here we show that knockout, knockdown or pharmacological inhibition of p53 can induce autophagy in human, mouse and nematode cells. Enhanced autophagy improved the survival of p53-deficient cancer cells under conditions of hypoxia and nutrient depletion, allowing them to maintain high ATP levels. Inhibition of p53 led to autophagy in enucleated cells, and cytoplasmic, not nuclear, p53 was able to repress the enhanced autophagy of p53-/- cells. Many different inducers of autophagy (for example, starvation, rapamycin and toxins affecting the endoplasmic reticulum) stimulated proteasome-mediated degradation of p53 through a pathway relying on the E3 ubiquitin ligase HDM2. Inhibition of p53 degradation prevented the activation of autophagy in several cell lines, in response to several distinct stimuli. These results provide evidence of a key signalling pathway that links autophagy to the cancer-associated dysregulation of p53. PMID:18454141

Biotransformation pathways of fluorotelomer-based polyfluoroalkyl substances: a review.

PubMed

Butt, Craig M; Muir, Derek C G; Mabury, Scott A

2014-02-01

The study reviews the current state of knowledge regarding the biotransformation of fluorotelomer-based compounds, with a focus on compounds that ultimately degrade to form perfluoroalkyl carboxylates (PFCAs). Most metabolism studies have been performed with either microbial systems or rats and mice, and comparatively few studies have used fish models. Furthermore, biotransformation studies thus far have predominately used the 8:2 fluorotelomer alcohol (FTOH) as the substrate. However, there have been an increasing number of studies investigating 6:2 FTOH biotransformation as a result of industry's transition to shorter-chain fluorotelomer chemistry. Studies with the 8:2 FTOH metabolism universally show the formation of perfluorooctanoate (PFOA) and, to a smaller fraction, perfluorononanoate (PFNA) and lower-chain-length PFCAs. In general, the overall yield of PFOA is low, presumably because of the multiple branches in the biotransformation pathways, including conjugation reactions in animal systems. There have been a few studies of non-FTOH biotransformation, which include polyfluoroalkyl phosphates (PAPs), 8:2 fluorotelomer acrylate (8:2 FTAC), and fluorotelomer carboxylates (FTCAs, FTUCAs). The PAPs compounds and 8:2 FTAC were shown to be direct precursors to FTOHs and thus follow similar degradation pathways. © 2013 SETAC.

Engineering of protein folding and secretion-strategies to overcome bottlenecks for efficient production of recombinant proteins.

PubMed

Delic, Marizela; Göngrich, Rebecca; Mattanovich, Diethard; Gasser, Brigitte

2014-07-20

Recombinant protein production has developed into a huge market with enormous positive implications for human health and for the future direction of a biobased economy. Limitations in the economic and technical feasibility of production processes are often related to bottlenecks of in vivo protein folding. Based on cell biological knowledge, some major bottlenecks have been overcome by the overexpression of molecular chaperones and other folding related proteins, or by the deletion of deleterious pathways that may lead to misfolding, mistargeting, or degradation. While important success could be achieved by this strategy, the list of reported unsuccessful cases is disappointingly long and obviously dependent on the recombinant protein to be produced. Singular engineering of protein folding steps may not lead to desired results if the pathway suffers from several limitations. In particular, the connection between folding quality control and proteolytic degradation needs further attention. Based on recent understanding that multiple steps in the folding and secretion pathways limit productivity, synergistic combinations of the cell engineering approaches mentioned earlier need to be explored. In addition, systems biology-based whole cell analysis that also takes energy and redox metabolism into consideration will broaden the knowledge base for future rational engineering strategies.

d-Xylose Degradation Pathway in the Halophilic Archaeon Haloferax volcanii

PubMed Central

Johnsen, Ulrike; Dambeck, Michael; Zaiss, Henning; Fuhrer, Tobias; Soppa, Jörg; Sauer, Uwe; Schönheit, Peter

2009-01-01

The pathway of d-xylose degradation in archaea is unknown. In a previous study we identified in Haloarcula marismortui the first enzyme of xylose degradation, an inducible xylose dehydrogenase (Johnsen, U., and Schönheit, P. (2004) J. Bacteriol. 186, 6198–6207). Here we report a comprehensive study of the complete d-xylose degradation pathway in the halophilic archaeon Haloferax volcanii. The analyses include the following: (i) identification of the degradation pathway in vivo following 13C-labeling patterns of proteinogenic amino acids after growth on [13C]xylose; (ii) identification of xylose-induced genes by DNA microarray experiments; (iii) characterization of enzymes; and (iv) construction of in-frame deletion mutants and their functional analyses in growth experiments. Together, the data indicate that d-xylose is oxidized exclusively to the tricarboxylic acid cycle intermediate α-ketoglutarate, involving d-xylose dehydrogenase (HVO_B0028), a novel xylonate dehydratase (HVO_B0038A), 2-keto-3-deoxyxylonate dehydratase (HVO_B0027), and α-ketoglutarate semialdehyde dehydrogenase (HVO_B0039). The functional involvement of these enzymes in xylose degradation was proven by growth studies of the corresponding in-frame deletion mutants, which all lost the ability to grow on d-xylose, but growth on glucose was not significantly affected. This is the first report of an archaeal d-xylose degradation pathway that differs from the classical d-xylose pathway in most bacteria involving the formation of xylulose 5-phosphate as an intermediate. However, the pathway shows similarities to proposed oxidative pentose degradation pathways to α-ketoglutarate in few bacteria, e.g. Azospirillum brasilense and Caulobacter crescentus, and in the archaeon Sulfolobus solfataricus. PMID:19584053

HUWE1 interacts with BRCA1 and promotes its degradation in the ubiquitin–proteasome pathway (Biochemical and Biophysical Research Communications, v. 444 issue 3)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xiaozhen; Institute of Systems Biology, Peking University, Beijing 100191; Lu, Guang

2014-02-14

Highlights: • The 2000–2634 aa region of HUWE1 mediates the interaction with BRCA1 degron. • HUWE1 promotes the degradation of BRCA1 through the ubiquitin–proteasome pathway. • HUWE1 expression is inversely correlated with BRCA1 in breast cancer cells. • RNAi inhibition of HUWE1 confers increased resistance of MCF-10F cells to IR and MMC. - Abstract: The cellular BRCA1 protein level is essential for its tumor suppression activity and is tightly regulated through multiple mechanisms including ubiquitn–proteasome system. E3 ligases are involved to promote BRCA1 for ubiquitination and degradation. Here, we identified HUWE1/Mule/ARF-BP1 as a novel BRCA1-interacting protein involved in the controlmore » of BRCA1 protein level. HUWE1binds BRCA1 through its N-terminus degron domain. Depletion of HUWE1 by siRNA-mediated interference significantly increases BRCA1 protein levels and prolongs the half-life of BRCA1. Moreover, exogenous expression of HUWE1 promotes BRCA1 degradation through the ubiquitin–proteasome pathway, which could explain an inverse correlation between HUWE1 and BRCA1 levels in MCF10F, MCF7 and MDA-MB-231 breast cancer cells. Consistent with a functional role for HUWE1 in regulating BRCA1-mediated cellular response to DNA damage, depletion of HUWE1 by siRNA confers increased resistance to ionizing radiation and mitomycin. These data indicate that HUWE1 is a critical negative regulator of BRCA1 and suggest a new molecular mechanism for breast cancer pathogenesis.« less

HUWE1 interacts with BRCA1 and promotes its degradation in the ubiquitin–proteasome pathway (Biochemical and Biophysical Research Communications, v. 444, isse 4)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xiaozhen; Institute of Systems Biology, Peking University, Beijing 100191; Lu, Guang

2014-02-21

Highlights: • The 2000–2634aa region of HUWE1 mediates the interaction with BRCA1 degron. • HUWE1 promotes the degradation of BRCA1 through the ubiquitin–proteasome pathway. • HUWE1 expression is inversely correlated with BRCA1 in breast cancer cells. • RNAi inhibition of HUWE1 confers increased resistance of MCF-10F cells to IR and MMC. - Abstract: The cellular BRCA1 protein level is essential for its tumor suppression activity and is tightly regulated through multiple mechanisms including ubiquitn–proteasome system. E3 ligases are involved to promote BRCA1 for ubiquitination and degradation. Here, we identified HUWE1/Mule/ARF-BP1 as a novel BRCA1-interacting protein involved in the control ofmore » BRCA1 protein level. HUWE1 binds BRCA1 through its N-terminus degron domain. Depletion of HUWE1 by siRNA-mediated interference significantly increases BRCA1 protein levels and prolongs the half-life of BRCA1. Moreover, exogenous expression of HUWE1 promotes BRCA1 degradation through the ubiquitin–proteasome pathway, which could explain an inverse correlation between HUWE1 and BRCA1 levels in MCF10F, MCF7 and MDA-MB-231 breast cancer cells. Consistent with a functional role for HUWE1 in regulating BRCA1-mediated cellular response to DNA damage, depletion of HUWE1 by siRNA confers increased resistance to ionizing radiation and mitomycin. These data indicate that HUWE1 is a critical negative regulator of BRCA1 and suggest a new molecular mechanism for breast cancer pathogenesis.« less

Transfer of the high-GC cyclohexane carboxylate degradation pathway from Rhodopseudomonas palustris to Escherichia coli for production of biotin.

PubMed

Bernstein, Jeffrey R; Bulter, Thomas; Liao, James C

2008-01-01

This work demonstrates the transfer of the five-gene cyclohexane carboxylate (CHC) degradation pathway from the high-GC alphaproteobacterium Rhodopseudomonas palustris to Escherichia coli, a gammaproteobacterium. The degradation product of this pathway is pimeloyl-CoA, a key metabolite in E. coli's biotin biosynthetic pathway. This pathway is useful for biotin overproduction in E. coli; however, the expression of GC-rich genes is troublesome in this host. When the native R. palustris CHC degradation pathway is transferred to a DeltabioH pimeloyl-CoA auxotroph of E. coli, it is unable to complement growth in the presence of CHC. To overcome this expression problem we redesigned the operon with decreased GC content and removed stretches of high-GC intergenic DNA which comprise the 5' untranslated region of each gene, replacing these features with shorter low-GC sequences. We show this synthetic construct enables growth of the DeltabioH strain in the presence of CHC. When the synthetic degradation pathway is overexpressed in conjunction with the downstream genes for biotin biosynthesis, we measured significant accumulation of biotin in the growth medium, showing that the pathway transfer is successfully integrated with the host metabolism.

CDK5-mediated tau accumulation triggers methamphetamine-induced neuronal apoptosis via endoplasmic reticulum-associated degradation pathway.

PubMed

Xiao, Ning; Zhang, Fu; Zhu, Bofeng; Liu, Chao; Lin, Zhoumeng; Wang, Huijun; Xie, Wei-Bing

2018-08-01

Overexposure to methamphetamine (METH) causes apoptosis in a number of cell types, particularly neuronal cells. However, the underlying mechanisms of METH-induced neuronal apoptosis remain to be elucidated. Accumulation of microtubule-associated protein Tau can lead to activation of multiple neurotoxic pathways, which is closely correlated with neuronal apoptosis. The aim of this study was to determine the role of Tau in METH-induced neuronal apoptosis. We determined the expression of two phosphorylated Tau proteins (serine 396 and threonine 231) in the human neuroblastoma SH-SY5Y cells and in the hippocampus of Sprague-Dawley rats treated with vehicle or METH using western blotting, immunohistochemical staining and immunofluorescence staining. We also measured the expression levels of the phosphorylated Tau protein, ubiquitination proteins, the intermediate products of proteasome degradation pathway, CD3-δ (a substrate of proteasome degradation pathway), endoplasmic reticulum stress signal molecule phosphorylated PERK (pPERK), and endoplasmic reticulum stress-specific apoptotic signal molecule caspase-12 in SH-SY5Y cells and in rats after inhibiting the expression of an upstream regulatory factor of phosphorylated Tau protein (CDK5) using siRNA or virus transfection. The results showed that exposure to METH significantly up-regulated the expression of phosphorylated Tau protein in vivo and in vitro and silencing the expression of CDK5 inhibited the up-regulation of phosphorylated Tau induced by METH exposure. METH exposure also significantly increased the expression of ubiquitination protein and CD3-δ and these effects were blocked by CDK5 silencing. In addition, METH exposure significantly elevated the levels of phosphorylated PERK and caspase-12 and these effects were suppressed after CDK5 silencing, which indicates that blockade of CDK5 expression can mitigate METH-induced neuronal apoptosis. These results suggest that METH can impair the endoplasmic reticulum-associated degradation (ERAD) pathway and induce neuronal apoptosis through endoplasmic reticulum stress, which is mainly mediated by abnormal CDK5-regulated Tau phosphorylation. Copyright © 2018 Elsevier B.V. All rights reserved.

Salinity effect on the metabolic pathway and microbial function in phenanthrene degradation by a halophilic consortium.

PubMed

Wang, Chongyang; Huang, Yong; Zhang, Zuotao; Wang, Hui

2018-04-25

With the close relationship between saline environments and industry, polycyclic aromatic hydrocarbons (PAHs) accumulate in saline/hypersaline environments. Therefore, PAHs degradation by halotolerant/halophilic bacteria has received increasing attention. In this study, the metabolic pathway of phenanthrene degradation by halophilic consortium CY-1 was first studied which showed a single upstream pathway initiated by dioxygenation at the C1 and C2 positions, and at several downstream pathways, including the catechol pathway, gentisic acid pathway and protocatechuic acid pathway. The effects of salinity on the community structure and expression of catabolic genes were further studied by a combination of high-throughput sequencing, catabolic gene clone library and real-time PCR. Pure cultures were also isolated from consortium CY-1 to investigate the contribution made by different microbes in the PAH-degrading process. Marinobacter is the dominant genus that contributed to the upstream degradation of phenanthrene especially in high salt content. Genus Halomonas made a great contribution in transforming intermediates in the subsequent degradation of catechol by using catechol 1,2-dioxygenase (C12O). Other microbes were predicted to be mediating bacteria that were able to utilize intermediates via different downstream pathways. Salinity was investigated to have negative effects on both microbial diversity and activity of consortium CY-1 and consortium CY-1 was found with a high degree of functional redundancy in saline environments.

Elucidation of the Mechanisms and Environmental Relevance of cis-Dichloroethene and Vinyl Chloride Biodegradation

DTIC Science & Technology

2012-11-01

iTRAQ study Table 3-12: Ratio of aldehyde and alcohol dehydrogenases from iTRAQ study Table 3-13: Proteins involved in proposed glyoxal transformation...pathway for cDCE degradation proceeds through chloro-, or dichloroacetaldehyde. Multiple aldehyde dehydrogenases are annotated in the genome of JS666...is a fortuitous reaction. However, if the initial reaction is monooxygenation to an aldehyde then the true intermediate would be

Simultaneous efficient removal of oxyfluorfen with electricity generation in a microbial fuel cell and its microbial community analysis.

PubMed

Zhang, Qinghua; Zhang, Lei; Wang, Han; Jiang, Qinrui; Zhu, Xiaoyu

2018-02-01

The performance of a microbial fuel cell (MFC) to degrade oxyfluorfen was investigated. Approximately 77% of 50 mg/L oxyfluorfen was degraded within 24 h by anodic biofilm. The temperature, pH, and initial oxyfluorfen concentration had a significant effect on oxyfluorfen degrading, and a maximum degradation rate of 94.95% could theoretically be achieved at 31.96 °C, a pH of 7.65, and an initial oxyfluorfen concentration of 120.05 mg/L. Oxyfluorfen was further catabolized through various microbial metabolism pathways. Moreover, the anodic biofilm exhibited multiple catabolic capacities to 4-nitrophenol, chloramphenicol, pyraclostrobin, and sulfamethoxazole. Microbial community analysis indicated that functional bacteria Arcobacter, Acinetobacter, Azospirillum, Azonexus, and Comamonas were the predominant genera in the anodic biofilm. In terms of the efficient removal of various organic compounds and energy recovery, the MFC seemed to be a promising approach for the treatment of environmental contaminants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Glucose deprivation reversibly down-regulates tissue plasminogen activator via proteasomal degradation in rat primary astrocytes.

PubMed

Cho, Kyu Suk; Joo, So Hyun; Choi, Chang Soon; Kim, Ki Chan; Ko, Hyun Myung; Park, Jin Hee; Kim, Pitna; Hur, Jun; Lee, Sung Hoon; Bahn, Geon Ho; Ryu, Jong Hoon; Lee, Jongmin; Han, Seol-Heui; Kwon, Kyoung Ja; Shin, Chan Young

2013-05-20

Tissue plasminogen activator (tPA) is an essential neuromodulator whose involvement in multiple functions such as synaptic plasticity, cytokine-like immune function and regulation of cell survival mandates rapid and tight tPA regulation in the brain. We investigated the possibility that a transient metabolic challenge induced by glucose deprivation may affect tPA activity in rat primary astrocytes, the main cell type responsible for metabolic regulation in the CNS. Rat primary astrocytes were incubated in serum-free DMEM without glucose. Casein zymography was used to determine tPA activity, and tPA mRNA was measured by RT-PCR. The signaling pathways regulating tPA activity were identified by Western blotting. Glucose deprivation rapidly down-regulated the activity of tPA without affecting its mRNA level in rat primary astrocytes; this effect was mimicked by translational inhibitors. The down-regulation of tPA was accompanied by increased tPA degradation, which may be modulated by a proteasome-dependent degradation pathway. Glucose deprivation induced activation of PI3K-Akt-GSK3β, p38 and AMPK, and inhibition of these pathways using LY294002, SB203580 and compound C significantly inhibited glucose deprivation-induced tPA down-regulation, demonstrating the essential role of these pathways in tPA regulation in glucose-deprived astrocytes. Rapid and reversible regulation of tPA activity in rat primary astrocytes during metabolic crisis may minimize energy-requiring neurologic processes in stressed situations. This effect may thereby increase the opportunity to invest cellular resources in cell survival and may allow rapid re-establishment of normal cellular function after the crisis. Copyright © 2013 Elsevier Inc. All rights reserved.

Cytochrome P450 Initiates Degradation of cis-Dichloroethene by Polaromonas sp. Strain JS666

PubMed Central

Nishino, Shirley F.; Shin, Kwanghee A.; Gossett, James M.

2013-01-01

Polaromonas sp. strain JS666 grows on cis-1,2-dichoroethene (cDCE) as the sole carbon and energy source under aerobic conditions, but the degradation mechanism and the enzymes involved are unknown. In this study, we established the complete pathway for cDCE degradation through heterologous gene expression, inhibition studies, enzyme assays, and analysis of intermediates. Several lines of evidence indicate that a cytochrome P450 monooxygenase catalyzes the initial step of cDCE degradation. Both the transient accumulation of dichloroacetaldehyde in cDCE-degrading cultures and dichloroacetaldehyde dehydrogenase activities in cell extracts of JS666 support a pathway for degradation of cDCE through dichloroacetaldehyde. The mechanism minimizes the formation of cDCE epoxide. The molecular phylogeny of the cytochrome P450 gene and the organization of neighboring genes suggest that the cDCE degradation pathway recently evolved in a progenitor capable of degrading 1,2-dichloroethane either by the recruitment of the cytochrome P450 monooxygenase gene from an alkane catabolic pathway or by selection for variants of the P450 in a preexisting 1,2-dichloroethane catabolic pathway. The results presented here add yet another role to the broad array of productive reactions catalyzed by cytochrome P450 enzymes. PMID:23354711

TMEM129 is a Derlin-1 associated ERAD E3 ligase essential for virus-induced degradation of MHC-I.

PubMed

van den Boomen, Dick J H; Timms, Richard T; Grice, Guinevere L; Stagg, Helen R; Skødt, Karsten; Dougan, Gordon; Nathan, James A; Lehner, Paul J

2014-08-05

The US11 gene product of human cytomegalovirus promotes viral immune evasion by hijacking the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway. US11 initiates dislocation of newly translocated MHC I from the ER to the cytosol for proteasome-mediated degradation. Despite the critical role for ubiquitin in this degradation pathway, the responsible E3 ligase is unknown. In a forward genetic screen for host ERAD components hijacked by US11 in near-haploid KBM7 cells, we identified TMEM129, an uncharacterized polytopic membrane protein. TMEM129 is essential and rate-limiting for US11-mediated MHC-I degradation and acts as a novel ER resident E3 ubiquitin ligase. TMEM129 contains an unusual cysteine-only RING with intrinsic E3 ligase activity and is recruited to US11 via Derlin-1. Together with its E2 conjugase Ube2J2, TMEM129 is responsible for the ubiquitination, dislocation, and subsequent degradation of US11-associated MHC-I. US11 engages two degradation pathways: a Derlin-1/TMEM129-dependent pathway required for MHC-I degradation and a SEL1L/HRD1-dependent pathway required for "free" US11 degradation. Our data show that TMEM129 is a novel ERAD E3 ligase and the central component of a novel mammalian ERAD complex.

Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salinero, Kennan Kellaris; Keller, Keith; Feil, William S.

2008-11-17

Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for this microbe. It is considered to be a free-living organism. The a priori prediction that the D. aromatica genome would contain previously characterized 'central' enzymes involved in anaerobic aromatic degradation proved to be false, suggesting the presence of novel anaerobic aromatic degradation pathways in this species. These missing pathways include the benzyl succinyl synthase (bssABC) genes (responsiblemore » for formate addition to toluene) and the central benzoylCoA pathway for monoaromatics. In depth analyses using existing TIGRfam, COG, and InterPro models, and the creation of de novo HMM models, indicate a highly complex lifestyle with a large number of environmental sensors and signaling pathways, including a relatively large number of GGDEF domain signal receptors and multiple quorum sensors. A number of proteins indicate interactions with an as yet unknown host, as indicated by the presence of predicted cell host remodeling enzymes, effector enzymes, hemolysin-like proteins, adhesins, NO reductase, and both type III and type VI secretory complexes. Evidence of biofilm formation including a proposed exopolysaccharide complex with the somewhat rare exosortase (epsH), is also present. Annotation described in this paper also reveals evidence for several metabolic pathways that have yet to be observed experimentally, including a sulphur oxidation (soxFCDYZAXB) gene cluster, Calvin cycle enzymes, and nitrogen fixation (including RubisCo, ribulose-phosphate 3-epimerase, and nif gene families, respectively). Analysis of the D. aromatica genome indicates there is much to be learned regarding the metabolic capabilities, and life-style, for this microbial species. Examples of recent gene duplication events in signaling as well as dioxygenase clusters are present, indicating selective gene family expansion as a relatively recent event in D. aromatica's evolutionary history. Gene families that constitute metabolic cycles presumed to create D. aromatica's environmental 'foot-print' indicate a high level of diversification between its predicted capabilities and those of its close relatives, A. aromaticum str EbN1 and Azoarcus BH72.« less

Enhanced endocannabinoid tone as a potential target of pharmacotherapy.

PubMed

Toczek, Marek; Malinowska, Barbara

2018-07-01

The endocannabinoid system is up-regulated in numerous pathophysiological states such as inflammatory, neurodegenerative, gastrointestinal, metabolic and cardiovascular diseases, pain, and cancer. It has been suggested that this phenomenon primarily serves an autoprotective role in inhibiting disease progression and/or diminishing signs and symptoms. Accordingly, enhancement of endogenous endocannabinoid tone by inhibition of endocannabinoid degradation represents a promising therapeutic approach for the treatment of many diseases. Importantly, this allows for the avoidance of unwanted psychotropic side effects that accompany exogenously administered cannabinoids. The effects of endocannabinoid metabolic pathway modulation are complex, as endocannabinoids can exert their actions directly or via numerous metabolites. The two main strategies for blocking endocannabinoid degradation are inhibition of endocannabinoid-degrading enzymes and inhibition of endocannabinoid cellular uptake. To date, the most investigated compounds are inhibitors of fatty acid amide hydrolase (FAAH), an enzyme that degrades the endocannabinoid anandamide. However, application of FAAH inhibitors (and consequently other endocannabinoid degradation inhibitors) in medicine became questionable due to a lack of therapeutic efficacy in clinical trials and serious adverse effects evoked by one specific compound. In this paper, we discuss multiple pathways of endocannabinoid metabolism, changes in endocannabinoid levels across numerous human diseases and corresponding experimental models, pharmacological strategies for enhancing endocannabinoid tone and potential therapeutic applications including multi-target drugs with additional targets outside of the endocannabinoid system (cyclooxygenase-2, cholinesterase, TRPV1, and PGF 2α -EA receptors), and currently used medicines or medicinal herbs that additionally enhance endocannabinoid levels. Ultimately, further clinical and preclinical studies are warranted to develop medicines for enhancing endocannabinoid tone. Copyright © 2018 Elsevier Inc. All rights reserved.

Assessment of photocatalytic potentiality and determination of ecotoxicity (using plant model for better environmental applicability) of synthesized copper, copper oxide and copper-doped zinc oxide nanoparticles

PubMed Central

Das, Debadrito; Kumbhakar, Divya Vishambhar; Ghosh, Bapi; Pramanik, Ankita; Gupta, Sudha; Mandal, Aninda

2017-01-01

NPs synthesis, characterization and azo-dye degradation A facile cost effective wet chemical method of synthesis is proposed for Cu-NPs, CuO-NPs and Cu-doped ZnO-NPs. The nanomaterials are opto-physically characterized for nano standard quality. Cu-doped ZnO-NPs based catalytic system is found to possess most efficient photocatalytic activity in degradation of two organic azo-dyes namely methyl red (MR) and malachite green (MG) that are released as industrial effluents in eco-environment intercollegium. Two possible photocatalytic degradation pathways are proposed to understand the mechanism of interaction prevailing during the mineralization of MR and MG dyes. Such study provides insight for waste water management. The uniqueness of the present work is 1) possible routes of MG dye degradation by Cu-doped ZnO-NPs and subsequent intermediate by-products are novel and pioneered of its kind. 2) two new intermediate byproducts are identified suggesting prevalence of multiple MR degradation pathways by Cu-doped ZnO-NPs. Assessment of ecotoxicity For assessment of residual NPs impact on environment, eco-toxicological assay is performed using plant system (Sesamum indicum L.) as model. The study encompasses seed germination, seedling morphology, quantification of endogenous H2O2 and MDA generation, estimation of DNA double strand break and analysis of cell cycle inhibition. Results highlight reduced ecotoxicity of Cu-doped ZnO-NPs compared to the other synthesized nanomaterials thereby suggesting better environmental applicability in waste water purification. PMID:28796823

Strigolactone regulates shoot development through a core signalling pathway

PubMed Central

Müller, Dörte

2016-01-01

ABSTRACT Strigolactones are a recently identified class of hormone that regulate multiple aspects of plant development. The DWARF14 (D14) α/β fold protein has been identified as a strigolactone receptor, which can act through the SCFMAX2 ubiquitin ligase, but the universality of this mechanism is not clear. Multiple proteins have been suggested as targets for strigolactone signalling, including both direct proteolytic targets of SCFMAX2, and downstream targets. However, the relevance and importance of these proteins to strigolactone signalling in many cases has not been fully established. Here we assess the contribution of these targets to strigolactone signalling in adult shoot developmental responses. We find that all examined strigolactone responses are regulated by SCFMAX2 and D14, and not by other D14-like proteins. We further show that all examined strigolactone responses likely depend on degradation of SMXL proteins in the SMXL6 clade, and not on the other proposed proteolytic targets BES1 or DELLAs. Taken together, our results suggest that in the adult shoot, the dominant mode of strigolactone signalling is D14-initiated, MAX2-mediated degradation of SMXL6-related proteins. We confirm that the BRANCHED1 transcription factor and the PIN-FORMED1 auxin efflux carrier are plausible downstream targets of this pathway in the regulation of shoot branching, and show that BRC1 likely acts in parallel to PIN1. PMID:27793831

Degradation of connexins and gap junctions

PubMed Central

Falk, Matthias M.; Kells, Rachael M.; Berthoud, Viviana M.

2014-01-01

Connexin proteins are short-lived within the cell, whether present in the secretory pathway or in gap junction plaques. Their levels can be modulated by their rate of degradation. Connexins, at different stages of assembly, are degraded through the proteasomal, endo-/lysosomal, and phago-/lysosomal pathways. In this review, we summarize the current knowledge about connexin and gap junction degradation including the signals and protein-protein interactions that participate in their targeting for degradation. PMID:24486527

The C-Terminal Sequence of RhoB Directs Protein Degradation through an Endo-Lysosomal Pathway

PubMed Central

Ramos, Irene; Herrera, Mónica; Stamatakis, Konstantinos

2009-01-01

Background Protein degradation is essential for cell homeostasis. Targeting of proteins for degradation is often achieved by specific protein sequences or posttranslational modifications such as ubiquitination. Methodology/Principal Findings By using biochemical and genetic tools we have monitored the localization and degradation of endogenous and chimeric proteins in live primary cells by confocal microscopy and ultra-structural analysis. Here we identify an eight amino acid sequence from the C-terminus of the short-lived GTPase RhoB that directs the rapid degradation of both RhoB and chimeric proteins bearing this sequence through a lysosomal pathway. Elucidation of the RhoB degradation pathway unveils a mechanism dependent on protein isoprenylation and palmitoylation that involves sorting of the protein into multivesicular bodies, mediated by the ESCRT machinery. Moreover, RhoB sorting is regulated by late endosome specific lipid dynamics and is altered in human genetic lipid traffic disease. Conclusions/Significance Our findings characterize a short-lived cytosolic protein that is degraded through a lysosomal pathway. In addition, we define a novel motif for protein sorting and rapid degradation, which allows controlling protein levels by means of clinically used drugs. PMID:19956591

FoxO Transcription Factors and Regenerative Pathways in Diabetes Mellitus

PubMed Central

Maiese, Kenneth

2015-01-01

Mammalian forkhead transcription factors of the O class (FoxO) are exciting targets under consideration for the development of new clinical entities to treat metabolic disorders and diabetes mellitus (DM). DM, a disorder that currently affects greater than 350 million individuals globally, can become a devastating disease that leads to cellular injury through oxidative stress pathways and affects multiple systems of the body. FoxO proteins can regulate insulin signaling, gluconeogenesis, insulin resistance, immune cell migration, and cell senescence. FoxO proteins also control cell fate through oxidative stress and pathways of autophagy and apoptosis that either lead to tissue regeneration or cell demise. Furthermore, FoxO signaling can be dependent upon signal transduction pathways that include silent mating type information regulation 2 homolog 1 (S. cerevisiae) (SIRT1), Wnt, and Wnt1 inducible signaling pathway protein 1 (WISP1). Cellular metabolic pathways driven by FoxO proteins are complex, can lead to variable clinical outcomes, and require in-depth analysis of the epigenetic and post-translation protein modifications that drive FoxO protein activation and degradation. PMID:26256004

Pathway and kinetics of cyhalothrin biodegradation by Bacillus thuringiensis strain ZS-19

PubMed Central

Chen, Shaohua; Deng, Yinyue; Chang, Changqing; Lee, Jasmine; Cheng, Yingying; Cui, Zining; Zhou, Jianuan; He, Fei; Hu, Meiying; Zhang, Lian-Hui

2015-01-01

Cyhalothrin is a common environmental pollutant which poses increased risks to non-target organisms including human beings. This study reported for the first time a newly isolated strain, Bacillus thuringiensis ZS-19 completely degraded cyhalothrin in minimal medium within 72 h. The bacterium transformed cyhalothrin by cleavage of both the ester linkage and diaryl bond to yield six intermediate products. Moreover, a novel degradation pathway of cyhalothrin in strain ZS-19 was proposed on the basis of the identified metabolites. In addition to degradation of cyhalothrin, this strain was found to be capable of degrading 3-phenoxybenzoic acid, a common metabolite of pyrethroids. Furthermore, strain ZS-19 participated in efficient degradation of a wide range of pyrethroids including cyhalothrin, fenpropathrinn, deltamethrin, beta-cypermethrin, cyfluthrin and bifenthrin. Taken together, our results provide insights into the mechanism of cyhalothrin degradation and also highlight the promising potentials of B.thuringiensis ZS-19 in bioremediation of pyrethroid-contaminated environment. This is the first report of (i) degradation of cyhalothrin and other pyrethroids by B.thuringiensis, (ii) identification of 3-phenoxyphenyl acetonitrile and N-(2-isoproxy-phenyl)-4-phenoxy-benzamide as the metabolites in the degradation pathway of pyrethroids, and (iii) a pathway of degradation of cyhalothrin by cleavage of both the ester linkage and diaryl bond in a microorganism. PMID:25740758

Working your SOCS off: The role of ASB10 and protein degradation pathways in glaucoma.

PubMed

Keller, Kate E; Wirtz, Mary K

2017-05-01

Evidence is accumulating to suggest that mutations in the Ankyrin and SOCS Box-containing protein-10 (ASB10) gene are associated with glaucoma. Since its identification in a large Oregon family with primary open-angle glaucoma (POAG), ASB10 variants have been associated with disease in US, German and Pakistani cohorts. ASB10 is a member of the ASB family of proteins, which have a common structure including a unique N-terminus, a variable number of central ankyrin (ANK) repeat domains and a suppressor of cytokine signaling (SOCS) box at the C-terminus. Mutations in ASB10 are distributed throughout the entire length of the gene including the two alternatively spliced variants of exon 1. A homozygous mutation in a Pakistani individual with POAG, which lies in the center of the SOCS box, is associated with a particularly severe form of the disease. Like other SOCS box-containing proteins, ASB10 functions in ubiquitin-mediated degradation pathways. The ANK repeats bind to proteins destined for degradation. The SOCS box recruits ubiquitin ligase proteins to form a complex to transfer ubiquitin to a substrate bound to the ANK repeats. The ubiquitin-tagged protein then enters either the proteasomal degradation pathway or the autophagic-lysosomal pathway. The choice of pathway appears to be dependent on which lysine residues are used to build polyubiquitin chains. However, these reciprocal pathways work in tandem to degrade proteins because inhibition of one pathway increases degradation via the other pathway. In this publication, we will review the literature that supports identification of ASB10 as a glaucoma-associated gene and the current knowledge of the function of the ASB10 protein. In addition, we present new data that indicates ASB10 expression is up-regulated by the inflammatory cytokines tumor necrosis factor-α and interleukin-1α. Finally, we will describe the emerging role of other SOCS box-containing proteins in protein degradation pathways in ocular cells. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chemical-agnostic hazard prediction: statistical inference of in ...

EPA Pesticide Factsheets

Toxicity pathways have been defined as normal cellular pathways that, when sufficiently perturbed as a consequence of chemical exposure, lead to an adverse outcome. If an exposure alters one or more normal biological pathways to an extent that leads to an adverse toxicity outcome, a significant correlation must exist between the exposure, the extent of pathway alteration, and the degree of adverse outcome. Biological pathways are regulated at multiple levels, including transcriptional, post-transcriptional, post-translational, and targeted degradation, each of which can affect the levels and extents of modification of proteins involved in the pathways. Significant alterations of toxicity pathways resulting from changes in regulation at any of these levels therefore are likely to be detectable as alterations in the proteome. We hypothesize that significant correlations between exposures, adverse outcomes, and changes in the proteome have the potential to identify putative toxicity pathways, facilitating selection of candidate targets for high throughput screening, even in the absence of a priori knowledge of either the specific pathways involved or the specific agents inducing the pathway alterations. We explored this hypothesis in vitro in BEAS-2B human airway epithelial cells exposed to different concentrations of Ni2+, Cd2+, and Cr6+, alone and in defined mixtures. Levels and phosphorylation status of a variety of signaling pathway proteins and cytokines were

Genome Sequencing Reveals the Potential of Achromobacter sp. HZ01 for Bioremediation

PubMed Central

Hong, Yue-Hui; Ye, Cong-Cong; Zhou, Qian-Zhi; Wu, Xiao-Ying; Yuan, Jian-Ping; Peng, Juan; Deng, Hailin; Wang, Jiang-Hai

2017-01-01

Petroleum pollution is a severe environmental issue. Comprehensively revealing the genetic backgrounds of hydrocarbon-degrading microorganisms contributes to developing effective methods for bioremediation of crude oil-polluted environments. Marine bacterium Achromobacter sp. HZ01 is capable of degrading hydrocarbons and producing biosurfactants. In this study, the draft genome (5.5 Mbp) of strain HZ01 has been obtained by Illumina sequencing, containing 5,162 predicted genes. Genome annotation shows that “amino acid metabolism” is the most abundant metabolic pathway. Strain HZ01 is not capable of using some common carbohydrates as the sole carbon sources, which is due to that it contains few genes associated with carbohydrate transport and lacks some important enzymes related to glycometabolism. It contains abundant proteins directly related to petroleum hydrocarbon degradation. AlkB hydroxylase and its homologs were not identified. It harbors a complete enzyme system of terminal oxidation pathway for n-alkane degradation, which may be initiated by cytochrome P450. The enzymes involved in the catechol pathway are relatively complete for the degradation of aromatic compounds. This bacterium lacks several essential enzymes for methane oxidation, and Baeyer-Villiger monooxygenase involved in the subterminal oxidation pathway and cycloalkane degradation was not identified. These results suggest that strain HZ01 degrades n-alkanes via the terminal oxidation pathway, degrades aromatic compounds primarily via the catechol pathway and cannot perform methane oxidation or cycloalkane degradation. Additionally, strain HZ01 possesses abundant genes related to the metabolism of secondary metabolites, including some genes involved in biosurfactant (such as glycolipids and lipopeptides) synthesis. The genome analysis also reveals its genetic basis for nitrogen metabolism, antibiotic resistance, regulatory responses to environmental changes, cell motility, and material transport. The obtained genome data provide us with a better understanding of hydrocarbon-degrading bacteria, which may contribute to the future design of rational strategies for bioremediation of petroleum-polluted marine environments. PMID:28848520

An Integrated Clinico-transcriptomic Approach Identifies a Central Role of the Heme Degradation Pathway for Septic Complications after Trauma.

PubMed

Rittirsch, Daniel; Schoenborn, Veit; Lindig, Sandro; Wanner, Elisabeth; Sprengel, Kai; Günkel, Sebastian; Blaess, Markus; Schaarschmidt, Barbara; Sailer, Patricia; Märsmann, Sonja; Simmen, Hans-Peter; Cinelli, Paolo; Bauer, Michael; Claus, Ralf A; Wanner, Guido A

2016-12-01

The present study was aimed to identify mechanisms linked to complicated courses and adverse events after severe trauma by a systems biology approach. In severe trauma, overwhelming systemic inflammation can result in additional damage and the development of complications, including sepsis. In a prospective, longitudinal single-center study, RNA samples from circulating leukocytes from patients with multiple injury (injury severity score ≥17 points; n = 81) were analyzed for dynamic changes in gene expression over a period of 21 days by whole-genome screening (discovery set; n = 10 patients; 90 samples) and quantitative RT-PCR (validation set; n = 71 patients, 517 samples). Multivariate correlational analysis of transcripts and clinical parameters was used to identify mechanisms related to sepsis. Transcriptome profiling of the discovery set revealed the strongest changes between patients with either systemic inflammation or sepsis in gene expression of the heme degradation pathway. Using quantitative RT-PCR analyses (validation set), the key components haptoglobin (HP), cluster of differentiation (CD) 163, heme oxygenase-1 (HMOX1), and biliverdin reductase A (BLVRA) showed robust changes following trauma. Upregulation of HP was associated with the severity of systemic inflammation and the development of sepsis. Patients who received allogeneic blood transfusions had a higher incidence of nosocomial infections and sepsis, and the amount of blood transfusion as source of free heme correlated with the expression pattern of HP. These findings indicate that the heme degradation pathway is associated with increased susceptibility to septic complications after trauma, which is indicated by HP expression in particular.

Estrogen Degraders and Estrogen Degradation Pathway Identified in an Activated Sludge.

PubMed

Chen, Yi-Lung; Fu, Han-Yi; Lee, Tzong-Huei; Shih, Chao-Jen; Huang, Lina; Wang, Yu-Sheng; Ismail, Wael; Chiang, Yin-Ru

2018-05-15

The environmental release and fate of estrogens are becoming an increasing public concern. Bacterial degradation has been considered the main process for eliminating estrogens from wastewater treatment plants. Various bacterial isolates are reportedly capable of aerobic estrogen degradation, and several estrogen degradation pathways have been proposed in proteobacteria and actinobacteria. However, the ecophysiological relevance of estrogen-degrading bacteria in the environment is unclear. In this study, we investigated the estrogen degradation pathway and corresponding degraders in activated sludge collected from the Dihua Sewage Treatment Plant, Taipei, Taiwan. Cultivation-dependent and cultivation-independent methods were used to assess estrogen biodegradation in the collected activated sludge. Estrogen metabolite profile analysis revealed the production of pyridinestrone acid and two A/B-ring cleavage products in activated sludge incubated with estrone (1 mM), which are characteristic of the 4,5- seco pathway. PCR-based functional assays detected sequences closely related to alphaproteobacterial oecC , a key gene of the 4,5- seco pathway. Metagenomic analysis suggested that Novosphingobium spp. are major estrogen degraders in estrone-amended activated sludge. Novosphingobium sp. strain SLCC, an estrone-degrading alphaproteobacterium, was isolated from the examined activated sludge. The general physiology and metabolism of this strain were characterized. Pyridinestrone acid and the A/B-ring cleavage products were detected in estrone-grown strain SLCC cultures. The production of pyridinestrone acid was also observed during the aerobic incubation of strain SLCC with 3.7 nM (1 μg/liter) estrone. This concentration is close to that detected in many natural and engineered aquatic ecosystems. The presented data suggest the ecophysiological relevance of Novosphingobium spp. in activated sludge. IMPORTANCE Estrogens, which persistently contaminate surface water worldwide, have been classified as endocrine disruptors and human carcinogens. We contribute new knowledge on the major estrogen biodegradation pathway and estrogen degraders in wastewater treatment plants. This study considerably advances the understanding of environmental estrogen biodegradation, which is instrumental for the efficient elimination of these hazardous pollutants. Moreover, this study substantially improves the understanding of microbial estrogen degradation in the environment. Copyright © 2018 American Society for Microbiology.

Reactions Involved in the Lower Pathway for Degradation of 4-Nitrotoluene by Mycobacterium Strain HL 4-NT-1

PubMed Central

He, Zhongqi; Spain, Jim C.

2000-01-01

In spite of the variety of initial reactions, the aerobic biodegradation of aromatic compounds generally yields dihydroxy intermediates for ring cleavage. Recent investigation of the degradation of nitroaromatic compounds revealed that some nitroaromatic compounds are initially converted to 2-aminophenol rather than dihydroxy intermediates by a number of microorganisms. The complete pathway for the metabolism of 2-aminophenol during the degradation of nitrobenzene by Pseudomonas pseudoalcaligenes JS45 has been elucidated previously. The pathway is parallel to the catechol extradiol ring cleavage pathway, except that 2-aminophenol is the ring cleavage substrate. Here we report the elucidation of the pathway of 2-amino-4-methylphenol (6-amino-m-cresol) metabolism during the degradation of 4-nitrotoluene by Mycobacterium strain HL 4-NT-1 and the comparison of the substrate specificities of the relevant enzymes in strains JS45 and HL 4-NT-1. The results indicate that the 2-aminophenol ring cleavage pathway in strain JS45 is not unique but is representative of the pathways of metabolism of other o-aminophenolic compounds. PMID:10877799

Excitable toxin-antitoxin modules coordinated through intracellular bottlenecks

NASA Astrophysics Data System (ADS)

Mather, William

Chronic infections and pathogenic biofilms present a serious threat to the health of humans by decreasing life expectancy and quality. The resilience of these microbial communities has been attributed to the spontaneous formation of persister cells, which constitute a small fraction of the population capable of surviving a wide range of environmental stressors. Gating of bacterial persistence has recently been linked to toxin-antitoxin (TA) modules, which are operons with an evolutionarily conserved motif that includes a toxin that halts cell growth and a corresponding antitoxin that neutralizes the toxin. While many such modules have been identified and studied in a wide range of organisms, little consideration of the interactions between multiple modules within a single host has been made. Moreover, the multitude of different antitoxin species are degraded by a relatively small number of proteolytic pathways, strongly suggesting competition between antitoxins for degradation machinery, i.e. queueing coupling. Here we present a theoretical understanding of the dynamics of multiple TA modules that are coupled through either proteolytic queueing, a toxic effect on cell growth rate, or both. We conclude that indirect queueing coordination between multiple TA modules may be central to controlling bacterial persistence. NSF Award Number MCB-1330180.

Establishment of an Arabidopsis callus system to study the interrelations of biosynthesis, degradation and accumulation of carotenoids

PubMed Central

Schaub, Patrick; Rodriguez-Franco, Marta; Cazzonelli, Christopher Ian; Álvarez, Daniel; Wüst, Florian

2018-01-01

The net amounts of carotenoids accumulating in plant tissues are determined by the rates of biosynthesis and degradation. While biosynthesis is rate-limited by the activity of PHYTOENE SYNTHASE (PSY), carotenoid losses are caused by catabolic enzymatic and non-enzymatic degradation. We established a system based on non-green Arabidopsis callus which allowed investigating major determinants for high steady-state levels of β-carotene. Wild-type callus development was characterized by strong carotenoid degradation which was only marginally caused by the activity of carotenoid cleavage oxygenases. In contrast, carotenoid degradation occurred mostly non-enzymatically and selectively affected carotenoids in a molecule-dependent manner. Using carotenogenic pathway mutants, we found that linear carotenes such as phytoene, phytofluene and pro-lycopene resisted degradation and accumulated while β-carotene was highly susceptible towards degradation. Moderately increased pathway activity through PSY overexpression was compensated by degradation revealing no net increase in β-carotene. However, higher pathway activities outcompeted carotenoid degradation and efficiently increased steady-state β-carotene amounts to up to 500 μg g-1 dry mass. Furthermore, we identified oxidative β-carotene degradation products which correlated with pathway activities, yielding β-apocarotenals of different chain length and various apocarotene-dialdehydes. The latter included methylglyoxal and glyoxal as putative oxidative end products suggesting a potential recovery of carotenoid-derived carbon for primary metabolic pathways. Moreover, we investigated the site of β-carotene sequestration by co-localization experiments which revealed that β-carotene accumulated as intra-plastid crystals which was confirmed by electron microscopy with carotenoid-accumulating roots. The results are discussed in the context of using the non-green calli carotenoid assay system for approaches targeting high steady-state β-carotene levels prior to their application in crops. PMID:29394270

Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters.

PubMed

de Lima-Morales, Daiana; Chaves-Moreno, Diego; Wos-Oxley, Melissa L; Jáuregui, Ruy; Vilchez-Vargas, Ramiro; Pieper, Dietmar H

2016-01-01

Pseudomonas veronii 1YdBTEX2, a benzene and toluene degrader, and Pseudomonas veronii 1YB2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. These strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. Extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydroxymuconic semialdehyde dehydrogenase necessary for benzene degradation but typically absent from isopropylbenzene dioxygenase-encoding gene clusters. The benzene dihydrodiol dehydrogenase-encoding gene was not clustered with any other aromatic degradation genes, and the encoded protein was only distantly related to dehydrogenases of aromatic degradation pathways. The involvement of the different gene clusters in the degradation pathways was suggested by real-time quantitative reverse transcription PCR. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Drug Targets from Genetics: Alpha-Synuclein

PubMed Central

Danzer, Karin M.; McLean, Pamela J.

2012-01-01

One of the critical issues in Parkinson disease (PD) research is the identity of the specific toxic, pathogenic moiety. In PD, mutations in alpha-synuclein (αsyn) or multiplication of the SNCA gene encoding αsyn, result in a phenotype of cellular inclusions, cell death, and brain dysfunction. While the historical point of view has been that the macroscopic aggregates containing αsyn are the toxic species, in the last several years evidence has emerged that suggests instead that smaller soluble species - likely oligomers containing misfolded αsyn - are actually the toxic moiety and that the fibrillar inclusions may even be a cellular detoxification pathway and less harmful. If soluble misfolded species of αsyn are the toxic moieties, then cellular mechanisms that degrade misfolded αsyn would be neuroprotective and a rational target for drug development. In this review we will discuss the fundamental mechanisms underlying αsyn toxicity including oligomer formation, oxidative stress, and degradation pathways and consider rational therapeutic strategies that may have the potential to prevent or halt αsyn induced pathogenesis in PD. PMID:21838671

Pollen S-locus F-box proteins of Petunia involved in S-RNase-based self-incompatibility are themselves subject to ubiquitin-mediated degradation.

PubMed

Sun, Penglin; Li, Shu; Lu, Dihong; Williams, Justin S; Kao, Teh-Hui

2015-07-01

Many flowering plants show self-incompatibility, an intra-specific reproductive barrier by which pistils reject self-pollen to prevent inbreeding and accept non-self pollen to promote out-crossing. In Petunia, the polymorphic S-locus determines self/non-self recognition. The locus contains a gene encoding an S-RNase, which controls pistil specificity, and multiple S-locus F-box (SLF) genes that collectively control pollen specificity. Each SLF is a component of an SCF (Skp1/Cullin/F-box) complex that is responsible for mediating degradation of non-self S-RNase(s), with which the SLF interacts, via the ubiquitin-26S proteasome pathway. A complete set of SLFs is required to detoxify all non-self S-RNases to allow cross-compatible pollination. Here, we show that SLF1 of Petunia inflata is itself subject to degradation via the ubiquitin-26S proteasome pathway, and identify an 18 amino acid sequence in the C-terminal region of S2 -SLF1 (SLF1 of S2 haplotype) that contains a degradation motif. Seven of the 18 amino acids are conserved among all 17 SLF proteins of S2 haplotype and S3 haplotype involved in pollen specificity, suggesting that all SLF proteins are probably subject to similar degradation. Deleting the 18 amino acid sequence from S2 -SLF1 stabilized the protein but abolished its function in self-incompatibility, suggesting that dynamic cycling of SLF proteins is an integral part of their function in self-incompatibility. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Multiple models guide strategies for agricultural nutrient reductions

USGS Publications Warehouse

Scavia, Donald; Kalcic, Margaret; Muenich, Rebecca Logsdon; Read, Jennifer; Aloysius, Noel; Bertani, Isabella; Boles, Chelsie; Confesor, Remegio; DePinto, Joseph; Gildow, Marie; Martin, Jay; Redder, Todd; Robertson, Dale M.; Sowa, Scott P.; Wang, Yu-Chen; Yen, Haw

2017-01-01

In response to degraded water quality, federal policy makers in the US and Canada called for a 40% reduction in phosphorus (P) loads to Lake Erie, and state and provincial policy makers in the Great Lakes region set a load-reduction target for the year 2025. Here, we configured five separate SWAT (US Department of Agriculture's Soil and Water Assessment Tool) models to assess load reduction strategies for the agriculturally dominated Maumee River watershed, the largest P source contributing to toxic algal blooms in Lake Erie. Although several potential pathways may achieve the target loads, our results show that any successful pathway will require large-scale implementation of multiple practices. For example, one successful pathway involved targeting 50% of row cropland that has the highest P loss in the watershed with a combination of three practices: subsurface application of P fertilizers, planting cereal rye as a winter cover crop, and installing buffer strips. Achieving these levels of implementation will require local, state/provincial, and federal agencies to collaborate with the private sector to set shared implementation goals and to demand innovation and honest assessments of water quality-related programs, policies, and partnerships.

Natural Attenuation of Fuel Hydrocarbon Contaminants: Correlation of Biodegradation with Hydraulic Conductivity in a Field Case Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Guoping; Zheng, Chunmiao

Two biodegradation models are developed to represent natural attenuation of fuel-hydrocarbon contaminants as observed in a comprehensive natural-gradient tracer test in a heterogeneous aquifer on the Columbus Air Force Base in Mississippi, USA. The first, a first-order mass loss model, describes the irreversible losses of BTEX and its individual components, i.e., benzene (B), toluene (T), ethyl benzene (E), and xylene (X). The second, a reactive pathway model, describes sequential degradation pathways for BTEX utilizing multiple electron acceptors, including oxygen, nitrate, iron and sulfate, and via methanogenesis. The heterogeneous aquifer is represented by multiple hydraulic conductivity (K) zones delineated on themore » basis of numerous flowmeter K measurements. A direct propagation artificial neural network (DPN) is used as an inverse modeling tool to estimate the biodegradation rate constants associated with each of the K zones. In both the mass loss model and the reactive pathway model, the biodegradation rate constants show an increasing trend with the hydraulic conductivity. The finding of correlation between biodegradation kinetics and hydraulic conductivity distributions is of general interest and relevance to characterization and modeling of natural attenuation of hydrocarbons in other petroleum-product contaminated sites.« less

Natural attenuation of fuel hydrocarbon contaminants: Hydraulic conductivity dependency of biodegradation rates in a field case study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Guoping; Zheng, Chunmiao

Two biodegradation models are developed to represent natural attenuation of fuel-hydrocarbon contaminants as observed in a comprehensive natural-gradient tracer test in a heterogeneous aquifer on the Columbus Air Force Base in Mississippi. The first, a first-order mass loss model, describes the irreversible losses of BTEX and its individual components, i.e., benzene (B), toluene (T), ethyl benzene (E), and xylene (X). The second, a reactive pathway model, describes sequential degradation pathways for BTEX utilizing multiple electron acceptors, including oxygen, nitrate, iron and sulfate, and via methanogenesis. The heterogeneous aquifer is represented by multiple hydraulic conductivity (K) zones delineated on the basismore » of numerous flowmeter K measurements. A direct propagation artificial neural network (DPN) is used as an inverse modeling tool to estimate the biodegradation rate constants associated with each of the K zones. In both the mass loss model and the reactive pathway model, the biodegradation rate constants show an increasing trend with the hydraulic conductivity. The finding of correlation between biodegradation kinetics and hydraulic conductivity distributions is of general interest and relevance to characterization and modeling of natural attenuation of hydrocarbons in other petroleum-product contaminated sites.« less

Involvement of Two Latex-Clearing Proteins during Rubber Degradation and Insights into the Subsequent Degradation Pathway Revealed by the Genome Sequence of Gordonia polyisoprenivorans Strain VH2

PubMed Central

Hiessl, Sebastian; Schuldes, Jörg; Thürmer, Andrea; Halbsguth, Tobias; Bröker, Daniel; Angelov, Angel; Liebl, Wolfgang; Daniel, Rolf

2012-01-01

The increasing production of synthetic and natural poly(cis-1,4-isoprene) rubber leads to huge challenges in waste management. Only a few bacteria are known to degrade rubber, and little is known about the mechanism of microbial rubber degradation. The genome of Gordonia polyisoprenivorans strain VH2, which is one of the most effective rubber-degrading bacteria, was sequenced and annotated to elucidate the degradation pathway and other features of this actinomycete. The genome consists of a circular chromosome of 5,669,805 bp and a circular plasmid of 174,494 bp with average GC contents of 67.0% and 65.7%, respectively. It contains 5,110 putative protein-coding sequences, including many candidate genes responsible for rubber degradation and other biotechnically relevant pathways. Furthermore, we detected two homologues of a latex-clearing protein, which is supposed to be a key enzyme in rubber degradation. The deletion of these two genes for the first time revealed clear evidence that latex-clearing protein is essential for the microbial utilization of rubber. Based on the genome sequence, we predict a pathway for the microbial degradation of rubber which is supported by previous and current data on transposon mutagenesis, deletion mutants, applied comparative genomics, and literature search. PMID:22327575

Toll-Like Receptor Signaling Induces Nrf2 Pathway Activation through p62-Triggered Keap1 Degradation.

PubMed

Yin, Shasha; Cao, Wangsen

2015-08-01

Toll-like receptors (TLRs) induce inflammation and tissue repair through multiple signaling pathways. The Nrf2 pathway plays a key role in defending against the tissue damage incurred by microbial infection or inflammation-associated diseases. The critical event that mediates TLR-induced Nrf2 activation is still poorly understood. In this study, we found that lipopolysaccharide (LPS) and other Toll-like receptor (TLR) agonists activate Nrf2 signaling and the activation is due to the reduction of Keap1, the key Nrf2 inhibitor. TLR signaling-induced Keap1 reduction promoted Nrf2 translocation from the cytoplasm to the nucleus, where it activated transcription of its target genes. TLR agonists modulated Keap1 at the protein posttranslation level through autophagy. TLR signaling increased the expression of autophagy protein p62 and LC3-II and induced their association with Keap1 in the autophagosome-like structures. We also characterized the interaction between p62 and Keap1 and found that p62 is indispensable for TLR-mediated Keap1 reduction: TLR signaling had no effect on Keap1 if cells lacked p62 or if cells expressed a mutant Keap1 that could not interact with p62. Our study indicates that p62-mediated Keap1 degradation through autophagy represents a critical linkage for TLR signaling regulation of the major defense network, the Nrf2 signaling pathway. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Protein degradation pathways in Parkinson's disease: curse or blessing.

PubMed

Ebrahimi-Fakhari, Darius; Wahlster, Lara; McLean, Pamela J

2012-08-01

Protein misfolding, aggregation and deposition are common disease mechanisms in many neurodegenerative diseases including Parkinson's disease (PD). Accumulation of damaged or abnormally modified proteins may lead to perturbed cellular function and eventually to cell death. Thus, neurons rely on elaborated pathways of protein quality control and removal to maintain intracellular protein homeostasis. Molecular chaperones, the ubiquitin-proteasome system (UPS) and the autophagy-lysosomal pathway (ALP) are critical pathways that mediate the refolding or removal of abnormal proteins. The successive failure of these protein degradation pathways, as a cause or consequence of early pathological alterations in vulnerable neurons at risk, may present a key step in the pathological cascade that leads to spreading neurodegeneration. A growing number of studies in disease models and patients have implicated dysfunction of the UPS and ALP in the pathogenesis of Parkinson's disease and related disorders. Deciphering the exact mechanism by which the different proteolytic systems contribute to the elimination of pathogenic proteins, like α-synuclein, is therefore of paramount importance. We herein review the role of protein degradation pathways in Parkinson's disease and elaborate on the different contributions of the UPS and the ALP to the clearance of altered proteins. We examine the interplay between different degradation pathways and provide a model for the role of the UPS and ALP in the evolution and progression of α-synuclein pathology. With regards to exciting recent studies we also discuss the putative potential of using protein degradation pathways as novel therapeutic targets in Parkinson's disease.

Mineralization of pyrrole, a recalcitrant heterocyclic compound, by electrochemical method: Multi-response optimization and degradation mechanism.

PubMed

Hiwarkar, Ajay Devidas; Singh, Seema; Srivastava, Vimal Chandra; Mall, Indra Deo

2017-08-01

In this study, the electrochemical (EC) oxidation of a recalcitrant heterocyclic compound namely pyrrole has been reported using platinum coated titanium (Pt/Ti) electrodes. Response surface methodology (RSM) comprising of full factorial central composite design (CCD) with four factors and five levels has been used to examine the effects of different operating parameters such as current density (j), aqueous solution pH, conductivity (k) and treatment time (t) in an EC batch reactor. Pyrrole mineralization in aqueous solution was examined with multiple responses such as chemical oxygen demand (COD) (response, Y 1 ) and specific energy consumption (SEC) in kWh/kg of COD removed (response, Y 2 ). During multiple response optimization, the desirability function approach was employed to concurrently maximize Y 1 and minimize Y 2 . At the optimum condition, 82.9% COD removal and 7.7 kWh/kg of COD removed were observed. Degradation mechanism of pyrrole in wastewater was elucidated at the optimum condition of treatment by using UV-visible spectroscopy, Fourier transformed infra-red spectroscopy (FTIR), cyclic voltammetry (CV), ion chromatography (IC), higher performance liquid chromatography (HPLC) and gas chromatography-mass spectroscopy (GC-MS). The degradation pathway of pyrrole was proposed on the basis of the various analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Hypothalamic digoxin, hemispheric chemical dominance, and oncogenesis: evidence from multiple myeloma.

PubMed

Kurup, Ravi Kumar; Kurup, Paramesware Achutha

2003-12-01

This study assessed the changes in the isoprenoid pathway and its metabolites digoxin, dolichol, and ubiquinone in multiple myeloma. The isoprenoid pathway and digoxin status were also studied for comparison in individuals of differing hemispheric dominance to find out the rote of cerebral dominance in the genesis of multiple myeloma and neoplasms. The following parameters were assessed: isoprenoid pathway metabolites, tyrosine and tryptophan catabolites, glycoconjugate metabolism, RBC membrane composition, and free radical metabolism--in multiple myeloma, as well as in individuals of differing hemispheric dominance. There was elevation in plasma HMG CoA reductase activity, serum digoxin, and dolichol, and a reduction in RBC membrane Na(+)-K+ ATPase activity, serum ubiquinone, and magnesium levels. Serum tryptophan, serotonin, nicotine, strychnine, and quinolinic acid were elevated, while tyrosine, dopamine, noradrenaline, and morphine were decreased. The total serum glycosaminoglycans and glycosaminoglycan fractions, the activity of GAG degrading enzymes and glycohydrolases, carbohydrate residues of glycoproteins, and serum glycolipids were elevated. The RBC membrane glycosaminoglycans, hexose, and fucose residues of glycoproteins, cholesterol, and phospholipids were reduced. The activity of all free-radical scavenging enzymes, concentration of glutathione, iron binding capacity, and ceruloplasmin decreased significantly, while the concentration of lipid peroxidation products and nitric oxide increased. Hyperdigoxinemia-related altered intracellular Ca++/Mg++ ratios mediated oncogene activation, dolichol-induced altered glycoconjugate metabolism, and ubiquinone deficiency-related mitochondrial dysfunction can contribute to the pathogenesis of multiple myeloma. The biochemical patterns obtained in multiple myeloma are similar to those obtained in left-handed/right hemispheric chemically dominant individuals by the dichotic listening test. But all the patients with multiple myeloma were right-handed/left hemispheric dominant by the dichotic listening test. Hemispheric chemical dominance has no correlation with handedness or the dichotic listening test. Multiple myeloma occurs in right hemispheric chemically dominant individuals and is a reflection of altered brain function.

Reading impairment in schizophrenia: dysconnectivity within the visual system.

PubMed

Vinckier, Fabien; Cohen, Laurent; Oppenheim, Catherine; Salvador, Alexandre; Picard, Hernan; Amado, Isabelle; Krebs, Marie-Odile; Gaillard, Raphaël

2014-01-01

Patients with schizophrenia suffer from perceptual visual deficits. It remains unclear whether those deficits result from an isolated impairment of a localized brain process or from a more diffuse long-range dysconnectivity within the visual system. We aimed to explore, with a reading paradigm, the functioning of both ventral and dorsal visual pathways and their interaction in schizophrenia. Patients with schizophrenia and control subjects were studied using event-related functional MRI (fMRI) while reading words that were progressively degraded through word rotation or letter spacing. Reading intact or minimally degraded single words involves mainly the ventral visual pathway. Conversely, reading in non-optimal conditions involves both the ventral and the dorsal pathway. The reading paradigm thus allowed us to study the functioning of both pathways and their interaction. Behaviourally, patients with schizophrenia were selectively impaired at reading highly degraded words. While fMRI activation level was not different between patients and controls, functional connectivity between the ventral and dorsal visual pathways increased with word degradation in control subjects, but not in patients. Moreover, there was a negative correlation between the patients' behavioural sensitivity to stimulus degradation and dorso-ventral connectivity. This study suggests that perceptual visual deficits in schizophrenia could be related to dysconnectivity between dorsal and ventral visual pathways. © 2013 Published by Elsevier Ltd.

Characterization of phenol and cresol biodegradation by compound-specific stable isotope analysis.

PubMed

Wei, Xi; Gilevska, Tetyana; Wetzig, Felix; Dorer, Conrad; Richnow, Hans-Hermann; Vogt, Carsten

2016-03-01

Microbial degradation of phenol and cresols can occur under oxic and anoxic conditions by different degradation pathways. One recent technique to take insight into reaction mechanisms is compound-specific isotope analysis (CSIA). While enzymes and reaction mechanisms of several degradation pathways have been characterized in (bio)chemical studies, associated isotope fractionation patterns have been rarely reported, possibly due to constraints in current analytical methods. In this study, carbon enrichment factors and apparent kinetic isotope effects (AKIEc) of the initial steps of different aerobic and anaerobic phenol and cresols degradation pathways were analyzed by isotope ratio mass spectrometry connected with liquid chromatography (LC-IRMS). Significant isotope fractionation was detected for aerobic ring hydroxylation, anoxic side chain hydroxylation, and anoxic fumarate addition, while anoxic carboxylation reactions produced small and inconsistent fractionation. The results suggest that several microbial degradation pathways of phenol and cresols are detectable in the environment by CSIA. Copyright © 2015 Elsevier Ltd. All rights reserved.

Efficient elimination of caffeine from water using Oxone activated by a magnetic and recyclable cobalt/carbon nanocomposite derived from ZIF-67.

PubMed

Lin, Kun-Yi Andrew; Chen, Bo-Chau

2016-02-28

To eliminate caffeine, one of the most common pharmaceuticals and personal care products, from water, Oxone (peroxymonosulfate salt) was proposed to degrade it. To accelerate the generation of sulfate radicals from Oxone, a magnetic cobalt/carbon nanocomposite (CCN) was prepared from a one-step carbonization of a cobalt-based Zeolitic Imidazolate Framework (ZIF-67). The resultant CCN exhibits immobilized cobalt and increased porosity, and can be magnetically manipulated. These characteristics make CCN a promising heterogeneous catalyst to activate Oxone for caffeine degradation. Factors affecting the caffeine degradation were investigated, including CCN loading, Oxone dosage, temperature, pH, surfactants, salts and inhibitors. A higher CCN loading, Oxone dosage and temperature greatly improved the caffeine degradation by CCN-activated Oxone. Acidic conditions were also preferable over basic conditions for caffeine degradation. The addition of cetyltrimethylammonium bromide (CTAB) and NaCl both significantly hindered caffeine degradation because bromide from CTAB and chloride from NaCl scavenged sulfate radicals. Based on the effects of inhibitors (i.e., methanol and tert-butyl alcohol), the caffeine degradation by CCN-activated Oxone was considered to primarily involve sulfate radicals and, less commonly, hydroxyl radicals. The intermediates generated during the caffeine degradation were analyzed using GC-MS and a possible degradation pathway was proposed. CCN was also able to activate Oxone for caffeine degradation for multiple cycles without changing its catalytic activity. These features reveal that CCN is an effective and promising catalyst for the activation of Oxone for the degradation of caffeine.

New Hydrocarbon Degradation Pathways in the Microbial Metagenome from Brazilian Petroleum Reservoirs

PubMed Central

Sierra-García, Isabel Natalia; Correa Alvarez, Javier; Pantaroto de Vasconcellos, Suzan; Pereira de Souza, Anete; dos Santos Neto, Eugenio Vaz; de Oliveira, Valéria Maia

2014-01-01

Current knowledge of the microbial diversity and metabolic pathways involved in hydrocarbon degradation in petroleum reservoirs is still limited, mostly due to the difficulty in recovering the complex community from such an extreme environment. Metagenomics is a valuable tool to investigate the genetic and functional diversity of previously uncultured microorganisms in natural environments. Using a function-driven metagenomic approach, we investigated the metabolic abilities of microbial communities in oil reservoirs. Here, we describe novel functional metabolic pathways involved in the biodegradation of aromatic compounds in a metagenomic library obtained from an oil reservoir. Although many of the deduced proteins shared homology with known enzymes of different well-described aerobic and anaerobic catabolic pathways, the metagenomic fragments did not contain the complete clusters known to be involved in hydrocarbon degradation. Instead, the metagenomic fragments comprised genes belonging to different pathways, showing novel gene arrangements. These results reinforce the potential of the metagenomic approach for the identification and elucidation of new genes and pathways in poorly studied environments and contribute to a broader perspective on the hydrocarbon degradation processes in petroleum reservoirs. PMID:24587220

Lithium Down-regulates Histone Deacetylase 1 (HDAC1) and Induces Degradation of Mutant Huntingtin*

PubMed Central

Wu, Shuai; Zheng, Shui-Di; Huang, Hong-Ling; Yan, Li-Chong; Yin, Xiao-Fei; Xu, Hai-Neng; Zhang, Kang-Jian; Gui, Jing-Hua; Chu, Liang; Liu, Xin-Yuan

2013-01-01

Lithium is an effective mood stabilizer that has been clinically used to treat bipolar disorder for several decades. Recent studies have suggested that lithium possesses robust neuroprotective and anti-tumor properties. Thus far, a large number of lithium targets have been discovered. Here, we report for the first time that HDAC1 is a target of lithium. Lithium significantly down-regulated HDAC1 at the translational level by targeting HDAC1 mRNA. We also showed that depletion of HDAC1 is essential for the neuroprotective effects of lithium and for the lithium-mediated degradation of mutant huntingtin through the autophagic pathway. Our studies explain the multiple functions of lithium and reveal a novel mechanism for the function of lithium in neurodegeneration. PMID:24165128

THE DELICATE BALANCE BETWEEN SECRETED PROTEIN FOLDING AND ENDOPLASMIC RETICULUM-ASSOCIATED DEGRADATION IN HUMAN PHYSIOLOGY

PubMed Central

Guerriero, Christopher J.; Brodsky, Jeffrey L.

2014-01-01

Protein folding is a complex, error-prone process that often results in an irreparable protein by-product. These by-products can be recognized by cellular quality control machineries and targeted for proteasome-dependent degradation. The folding of proteins in the secretory pathway adds another layer to the protein folding “problem,” as the endoplasmic reticulum maintains a unique chemical environment within the cell. In fact, a growing number of diseases are attributed to defects in secretory protein folding, and many of these by-products are targeted for a process known as endoplasmic reticulum-associated degradation (ERAD). Since its discovery, research on the mechanisms underlying the ERAD pathway has provided new insights into how ERAD contributes to human health during both normal and diseases states. Links between ERAD and disease are evidenced from the loss of protein function as a result of degradation, chronic cellular stress when ERAD fails to keep up with misfolded protein production, and the ability of some pathogens to coopt the ERAD pathway. The growing number of ERAD substrates has also illuminated the differences in the machineries used to recognize and degrade a vast array of potential clients for this pathway. Despite all that is known about ERAD, many questions remain, and new paradigms will likely emerge. Clearly, the key to successful disease treatment lies within defining the molecular details of the ERAD pathway and in understanding how this conserved pathway selects and degrades an innumerable cast of substrates. PMID:22535891

Pathways for degradation of plastic polymers floating in the marine environment.

PubMed

Gewert, Berit; Plassmann, Merle M; MacLeod, Matthew

2015-09-01

Each year vast amounts of plastic are produced worldwide. When released to the environment, plastics accumulate, and plastic debris in the world's oceans is of particular environmental concern. More than 60% of all floating debris in the oceans is plastic and amounts are increasing each year. Plastic polymers in the marine environment are exposed to sunlight, oxidants and physical stress, and over time they weather and degrade. The degradation processes and products must be understood to detect and evaluate potential environmental hazards. Some attention has been drawn to additives and persistent organic pollutants that sorb to the plastic surface, but so far the chemicals generated by degradation of the plastic polymers themselves have not been well studied from an environmental perspective. In this paper we review available information about the degradation pathways and chemicals that are formed by degradation of the six plastic types that are most widely used in Europe. We extrapolate that information to likely pathways and possible degradation products under environmental conditions found on the oceans' surface. The potential degradation pathways and products depend on the polymer type. UV-radiation and oxygen are the most important factors that initiate degradation of polymers with a carbon-carbon backbone, leading to chain scission. Smaller polymer fragments formed by chain scission are more susceptible to biodegradation and therefore abiotic degradation is expected to precede biodegradation. When heteroatoms are present in the main chain of a polymer, degradation proceeds by photo-oxidation, hydrolysis, and biodegradation. Degradation of plastic polymers can lead to low molecular weight polymer fragments, like monomers and oligomers, and formation of new end groups, especially carboxylic acids.

IL-1-induced ERK1/2 activation up-regulates p21{sup Waf1/Cip1} protein by inhibition of degradation via ubiquitin-independent pathway in human melanoma cells A375

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arakawa, Tomohiro; Hayashi, Hidetoshi; Itoh, Saotomo

2010-02-12

IL-1 inhibits the proliferation of human melanoma cells A375 by arresting the cell cycle at G0/G1 phase, which accompanies the increase of p21{sup Waf1/Cip1} (p21) protein. Here, we demonstrate that IL-1 induces the stabilization of p21 protein via ERK1/2 pathway. The degradation of p21 was inhibited by IL-1, however the ubiquitination level of p21 was not affected. In addition, the degradation of non-ubiquitinated form of lysine less mutant p21-K6R was also inhibited by IL-1, suggesting that IL-1 stabilized p21 protein via ubiquitin-independent pathway. Furthermore, the inhibition of p21 protein degradation was prevented by a selective inhibitor of ERK1/2 pathway, PD98059.more » These results suggest that IL-1-induced ERK1/2 activation leads to the up-regulation of p21 by inhibiting degradation via ubiquitin-independent pathway in human melanoma cells A375.« less

A Novel Aerobic Degradation Pathway for Thiobencarb Is Initiated by the TmoAB Two-Component Flavin Mononucleotide-Dependent Monooxygenase System in Acidovorax sp. Strain T1

PubMed Central

Chu, Cui-Wei; Liu, Bin; Li, Na; Yao, Shi-Gang; Cheng, Dan; Zhao, Jia-Dong; Qiu, Ji-Guo; Yan, Xin; He, Jian

2017-01-01

ABSTRACT Thiobencarb is a thiocarbamate herbicide used in rice paddies worldwide. Microbial degradation plays a crucial role in the dissipation of thiobencarb in the environment. However, the physiological and genetic mechanisms underlying thiobencarb degradation remain unknown. In this study, a novel thiobencarb degradation pathway was proposed in Acidovorax sp. strain T1. Thiobencarb was oxidized and cleaved at the C—S bond, generating diethylcarbamothioic S-acid and 4-chlorobenzaldehyde (4CDA). 4CDA was then oxidized to 4-chlorobenzoic acid (4CBA) and hydrolytically dechlorinated to 4-hydroxybenzoic acid (4HBA). The identification of catabolic genes suggested further hydroxylation to protocatechuic acid (PCA) and finally degradation through the protocatechuate 4,5-dioxygenase pathway. A novel two-component monooxygenase system identified in the strain, TmoAB, was responsible for the initial catabolic reaction. TmoA shared 28 to 32% identity with the oxygenase components of pyrimidine monooxygenase from Agrobacterium fabrum, alkanesulfonate monooxygenase from Pseudomonas savastanoi, and dibenzothiophene monooxygenase from Rhodococcus sp. TmoB shared 25 to 37% identity with reported flavin reductases and oxidized NADH but not NADPH. TmoAB is a flavin mononucleotide (FMN)-dependent monooxygenase and catalyzed the C—S bond cleavage of thiobencarb. Introduction of tmoAB into cells of the thiobencarb degradation-deficient mutant T1m restored its ability to degrade and utilize thiobencarb. A dehydrogenase gene, tmoC, was located 7,129 bp downstream of tmoAB, and its transcription was clearly induced by thiobencarb. The purified TmoC catalyzed the dehydrogenation of 4CDA to 4CBA using NAD+ as a cofactor. A gene cluster responsible for the complete 4CBA metabolic pathway was also cloned, and its involvement in thiobencarb degradation was preliminarily verified by transcriptional analysis. IMPORTANCE Microbial degradation is the main factor in thiobencarb dissipation in soil. In previous studies, thiobencarb was degraded initially via N-deethylation, sulfoxidation, hydroxylation, and dechlorination. However, enzymes and genes involved in the microbial degradation of thiobencarb have not been studied. This study revealed a new thiobencarb degradation pathway in Acidovorax sp. strain T1 and identified a novel two-component FMN-dependent monooxygenase system, TmoAB. Under TmoAB-mediated catalysis, thiobencarb was cleaved at the C—S bond, producing diethylcarbamothioic S-acid and 4CDA. Furthermore, the downstream degradation pathway of thiobencarb was proposed. Our study provides the physiological, biochemical, and genetic foundation of thiobencarb degradation in this microorganism. PMID:28939603

A Novel Aerobic Degradation Pathway for Thiobencarb Is Initiated by the TmoAB Two-Component Flavin Mononucleotide-Dependent Monooxygenase System in Acidovorax sp. Strain T1.

PubMed

Chu, Cui-Wei; Liu, Bin; Li, Na; Yao, Shi-Gang; Cheng, Dan; Zhao, Jia-Dong; Qiu, Ji-Guo; Yan, Xin; He, Qin; He, Jian

2017-12-01

Thiobencarb is a thiocarbamate herbicide used in rice paddies worldwide. Microbial degradation plays a crucial role in the dissipation of thiobencarb in the environment. However, the physiological and genetic mechanisms underlying thiobencarb degradation remain unknown. In this study, a novel thiobencarb degradation pathway was proposed in Acidovorax sp. strain T1. Thiobencarb was oxidized and cleaved at the C-S bond, generating diethylcarbamothioic S -acid and 4-chlorobenzaldehyde (4CDA). 4CDA was then oxidized to 4-chlorobenzoic acid (4CBA) and hydrolytically dechlorinated to 4-hydroxybenzoic acid (4HBA). The identification of catabolic genes suggested further hydroxylation to protocatechuic acid (PCA) and finally degradation through the protocatechuate 4,5-dioxygenase pathway. A novel two-component monooxygenase system identified in the strain, TmoAB, was responsible for the initial catabolic reaction. TmoA shared 28 to 32% identity with the oxygenase components of pyrimidine monooxygenase from Agrobacterium fabrum , alkanesulfonate monooxygenase from Pseudomonas savastanoi , and dibenzothiophene monooxygenase from Rhodococcus sp. TmoB shared 25 to 37% identity with reported flavin reductases and oxidized NADH but not NADPH. TmoAB is a flavin mononucleotide (FMN)-dependent monooxygenase and catalyzed the C-S bond cleavage of thiobencarb. Introduction of tmoAB into cells of the thiobencarb degradation-deficient mutant T1m restored its ability to degrade and utilize thiobencarb. A dehydrogenase gene, tmoC , was located 7,129 bp downstream of tmoAB , and its transcription was clearly induced by thiobencarb. The purified TmoC catalyzed the dehydrogenation of 4CDA to 4CBA using NAD + as a cofactor. A gene cluster responsible for the complete 4CBA metabolic pathway was also cloned, and its involvement in thiobencarb degradation was preliminarily verified by transcriptional analysis. IMPORTANCE Microbial degradation is the main factor in thiobencarb dissipation in soil. In previous studies, thiobencarb was degraded initially via N -deethylation, sulfoxidation, hydroxylation, and dechlorination. However, enzymes and genes involved in the microbial degradation of thiobencarb have not been studied. This study revealed a new thiobencarb degradation pathway in Acidovorax sp. strain T1 and identified a novel two-component FMN-dependent monooxygenase system, TmoAB. Under TmoAB-mediated catalysis, thiobencarb was cleaved at the C-S bond, producing diethylcarbamothioic S -acid and 4CDA. Furthermore, the downstream degradation pathway of thiobencarb was proposed. Our study provides the physiological, biochemical, and genetic foundation of thiobencarb degradation in this microorganism. Copyright © 2017 American Society for Microbiology.

Proteasome storage granules protect proteasomes from autophagic degradation upon carbon starvation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marshall, Richard S.; Vierstra, Richard D.

26S proteasome abundance is tightly regulated at multiple levels, including the elimination of excess or inactive particles by autophagy. In yeast, this proteaphagy occurs upon nitrogen starvation but not carbon starvation, which instead stimulates the rapid sequestration of proteasomes into cytoplasmic puncta termed proteasome storage granules (PSGs). Here, we show that PSGs help protect proteasomes from autophagic degradation. Both the core protease and regulatory particle sub-complexes are sequestered separately into PSGs via pathways dependent on the accessory proteins Blm10 and Spg5, respectively. Modulating PSG formation, either by perturbing cellular energy status or pH, or by genetically eliminating factors required formore » granule assembly, not only influences the rate of proteasome degradation, but also impacts cell viability upon recovery from carbon starvation. PSG formation and concomitant protection against proteaphagy also occurs in Arabidopsis, suggesting that PSGs represent an evolutionarily conserved cache of proteasomes that can be rapidly re-mobilized based on energy availability.« less

Methods to Measure Lipophagy in Yeast.

PubMed

Cristobal-Sarramian, A; Radulovic, M; Kohlwein, S D

2017-01-01

Maintenance of cellular and organismal lipid homeostasis is critical for life, and any deviation from a balanced equilibrium between fat uptake and degradation may have deleterious consequences, resulting in severe lipid-associated disorders. Excess fat is typically stored in cytoplasmic organelles termed "lipid droplets" (LDs); to adjust for a constantly fluctuating supply of and demand for cellular fat, these organelles are metabolically highly dynamic and subject to multiple levels of regulation. In addition to a well-described cytosolic lipid degradation pathway, recent evidence underscores the importance of "lipophagy" in cellular lipid homeostasis, i.e., the degradation of LD by autophagy in the lysosome/vacuole. Pioneering work in yeast mutant models has unveiled the requirement of key components of the autophagy machinery, providing evidence for a highly conserved process of lipophagy from yeast to man. However, further work is required to unveil the intricate metabolic interaction between LD metabolism and autophagy to sustain membrane homeostasis and cellular survival. © 2017 Elsevier Inc. All rights reserved.

Proteasome storage granules protect proteasomes from autophagic degradation upon carbon starvation

DOE PAGES

Marshall, Richard S.; Vierstra, Richard D.

2018-04-06

26S proteasome abundance is tightly regulated at multiple levels, including the elimination of excess or inactive particles by autophagy. In yeast, this proteaphagy occurs upon nitrogen starvation but not carbon starvation, which instead stimulates the rapid sequestration of proteasomes into cytoplasmic puncta termed proteasome storage granules (PSGs). Here, we show that PSGs help protect proteasomes from autophagic degradation. Both the core protease and regulatory particle sub-complexes are sequestered separately into PSGs via pathways dependent on the accessory proteins Blm10 and Spg5, respectively. Modulating PSG formation, either by perturbing cellular energy status or pH, or by genetically eliminating factors required formore » granule assembly, not only influences the rate of proteasome degradation, but also impacts cell viability upon recovery from carbon starvation. PSG formation and concomitant protection against proteaphagy also occurs in Arabidopsis, suggesting that PSGs represent an evolutionarily conserved cache of proteasomes that can be rapidly re-mobilized based on energy availability.« less

Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis.

PubMed

Sass, Andrea; Marchbank, Angela; Tullis, Elizabeth; Lipuma, John J; Mahenthiralingam, Eshwar

2011-07-22

Burkholderia cenocepacia is a member of the Burkholderia cepacia complex group of bacteria that cause infections in individuals with cystic fibrosis. B. cenocepacia isolate J2315 has been genome sequenced and is representative of a virulent, epidemic CF strain (ET12). Its genome encodes multiple antimicrobial resistance pathways and it is not known which of these is important for intrinsic or spontaneous resistance. To map these pathways, transcriptomic analysis was performed on: (i) strain J2315 exposed to sub-inhibitory concentrations of antibiotics and the antibiotic potentiator chlorpromazine, and (ii) on spontaneous mutants derived from J2315 and with increased resistance to the antibiotics amikacin, meropenem and trimethoprim-sulfamethoxazole. Two pan-resistant ET12 outbreak isolates recovered two decades after J2315 were also compared to identify naturally evolved gene expression changes. Spontaneous resistance in B. cenocepacia involved more gene expression changes and different subsets of genes than those provoked by exposure to sub inhibitory concentrations of each antibiotic. The phenotype and altered gene expression in the resistant mutants was also stable irrespective of the presence of the priming antibiotic. Both known and novel genes involved in efflux, antibiotic degradation/modification, membrane function, regulation and unknown functions were mapped. A novel role for the phenylacetic acid (PA) degradation pathway genes was identified in relation to spontaneous resistance to meropenem and glucose was found to repress their expression. Subsequently, 20 mM glucose was found to produce greater that 2-fold reductions in the MIC of multiple antibiotics against B. cenocepacia J2315. Mutation of an RND multidrug efflux pump locus (BCAM0925-27) and squalene-hopene cyclase gene (BCAS0167), both upregulated after chlorpromazine exposure, confirmed their role in resistance. The recently isolated outbreak isolates had altered the expression of multiple genes which mirrored changes seen in the antibiotic resistant mutants, corroborating the strategy used to model resistance. Mutation of an ABC transporter gene (BCAS0081) upregulated in both outbreak strains, confirmed its role in B. cenocepacia resistance. Global mapping of the genetic pathways which mediate antibiotic resistance in B. cenocepacia has revealed that they are multifactorial, identified potential therapeutic targets and also demonstrated that putative catabolite repression of genes by glucose can improve antibiotic efficacy.

Effect of Fe(III) on 1,1,2,2-tetrachloroethane degradation and vinyl chloride accumulation in wetland sediments of the Aberdeen proving ground

USGS Publications Warehouse

Jones, E.J.P.; Voytek, M.A.; Lorah, M.M.

2004-01-01

1,1,2,2-Tetrachloroethane (TeCA) contaminated groundwater at the Aberdeen Proving Ground discharges through an anaerobic wetland in West Branch Canal Creek, MD, where dechlorination occurred. Two microbially mediated pathways, dichloroelimination and hydrogenolysis, account for most of the TeCA degradation at this site. The dichloroelimination pathways led to the formation of vinyl chloride (VC), a recalcitrant carcinogen of great concern. The effect of adding Fe(III) to TeCA-amended microcosms of wetland sediment was studied. Differences were identified in the TeCA degradation pathway between microcosms treated with amorphous ferric oxyhydroxide (AFO-treated) and untreated (no AFO) microcosms. TeCA degradation was accompanied by a lower accumulation of VC in AFO-treated microcosms than no AFO microcosms. The microcosm incubations and subsequent experiments with the microcosm materials showed that AFO treatment resulted in lower production of VC by shifting TeCA degradation from dichloroelimination pathways to production of a greater proportion of chlorinated ethane products, and decreasing the microbial capability to produce VC from 1,2-dichloroethylene. VC degradation was not stimulated in the presence of Fe(III). Rather, VC degradation occurred readily under methanogenic conditions and was inhibited under Fe(III)-reducing conditions.

Vitamin C degradation products and pathways in the human lens.

PubMed

Nemet, Ina; Monnier, Vincent M

2011-10-28

Vitamin C and its degradation products participate in chemical modifications of proteins in vivo through non-enzymatic glycation (Maillard reaction) and formation of different products called advanced glycation end products. Vitamin C levels are particularly high in selected tissues, such as lens, brain and adrenal gland, and its degradation products can inflict substantial protein damage via formation of advanced glycation end products. However, the pathways of in vivo vitamin C degradation are poorly understood. Here we have determined the levels of vitamin C oxidation and degradation products dehydroascorbic acid, 2,3-diketogulonic acid, 3-deoxythreosone, xylosone, and threosone in the human lens using o-phenylenediamine to trap both free and protein-bound adducts. In the protein-free fraction and water-soluble proteins (WSP), all five listed degradation products were identified. Dehydroascorbic acid, 2,3-diketogulonic acid, and 3-deoxythreosone were the major products in the protein-free fraction, whereas in the WSP, 3-deoxythreosone was the most abundant measured dicarbonyl. In addition, 3-deoxythreosone in WSP showed positive linear correlation with age (p < 0.05). In water-insoluble proteins, only 3-deoxythreosone and threosone were detected, whereby the level of 3-deoxythreosone was ∼20 times higher than the level of threosone. The identification of 3-deoxythreosone as the major degradation product bound to human lens proteins provides in vivo evidence for the non-oxidative pathway of dehydroascorbate degradation into erythrulose as a major pathway for vitamin C degradation in vivo.

Neuronal-Targeted TFEB Accelerates Lysosomal Degradation of APP, Reducing Aβ Generation and Amyloid Plaque Pathogenesis

PubMed Central

Xiao, Qingli; Yan, Ping; Ma, Xiucui; Liu, Haiyan; Perez, Ronaldo; Zhu, Alec; Gonzales, Ernesto; Tripoli, Danielle L.; Czerniewski, Leah; Ballabio, Andrea; Cirrito, John R.

2015-01-01

In AD, an imbalance between Aβ production and removal drives elevated brain Aβ levels and eventual amyloid plaque deposition. APP undergoes nonamyloidogenic processing via α-cleavage at the plasma membrane, amyloidogenic β- and γ-cleavage within endosomes to generate Aβ, or lysosomal degradation in neurons. Considering multiple reports implicating impaired lysosome function as a driver of increased amyloidogenic processing of APP, we explored the efficacy of targeting transcription factor EB (TFEB), a master regulator of lysosomal pathways, to reduce Aβ levels. CMV promoter-driven TFEB, transduced via stereotactic hippocampal injections of adeno-associated virus particles in APP/PS1 mice, localized primarily to neuronal nuclei and upregulated lysosome biogenesis. This resulted in reduction of APP protein, the α and β C-terminal APP fragments (CTFs), and in the steady-state Aβ levels in the brain interstitial fluid. In aged mice, total Aβ levels and amyloid plaque load were selectively reduced in the TFEB-transduced hippocampi. TFEB transfection in N2a cells stably expressing APP695, stimulated lysosome biogenesis, reduced steady-state levels of APP and α- and β-CTFs, and attenuated Aβ generation by accelerating flux through the endosome-lysosome pathway. Cycloheximide chase assays revealed a shortening of APP half-life with exogenous TFEB expression, which was prevented by concomitant inhibition of lysosomal acidification. These data indicate that TFEB enhances flux through lysosomal degradative pathways to induce APP degradation and reduce Aβ generation. Activation of TFEB in neurons is an effective strategy to attenuate Aβ generation and attenuate amyloid plaque deposition in AD. SIGNIFICANCE STATEMENT A key driver for AD pathogenesis is the net balance between production and clearance of Aβ, the major component of amyloid plaques. Here we demonstrate that lysosomal degradation of holo-APP influences Aβ production by limiting the availability of APP for amyloidogenic processing. Using viral gene transfer of transcription factor EB (TFEB), a master regulator of lysosome biogenesis in neurons of APP/PS1 mice, steady-state levels of APP were reduced, resulting in decreased interstitial fluid Aβ levels and attenuated amyloid deposits. These effects were caused by accelerated lysosomal degradation of endocytosed APP, reflected by reduced APP half-life and steady-state levels in TFEB-expressing cells, with resultant decrease in Aβ production and release. Additional studies are needed to explore the therapeutic potential of this approach. PMID:26338325

Microbial Gutta-Percha Degradation Shares Common Steps with Rubber Degradation by Nocardia nova SH22a

PubMed Central

Luo, Quan; Hiessl, Sebastian; Poehlein, Anja

2013-01-01

Nocardia nova SH22a, a bacterium capable of degrading gutta-percha (GP) and natural rubber (NR), was used to investigate the GP degradation mechanism and the relations between the GP and NR degradation pathways. For this strain, a protocol of electroporation was systematically optimized, and an efficiency of up to 4.3 × 107 CFU per μg of plasmid DNA was achieved. By applying this optimized protocol to N. nova SH22a, a Tn5096-based transposon mutagenesis library of this bacterium was constructed. Among about 12,000 apramycin-resistant transformants, we identified 76 stable mutants defective in GP or NR utilization. Whereas 10 mutants were specifically defective in GP utilization, the growth of the other 66 mutants was affected on both GP and NR. This indicated that the two degradation pathways are quite similar and share many common steps. The larger number of GP-degrading defective mutants could be explained in one of two ways: either (i) the GP pathway is more complex and harbors more specific steps or (ii) the steps for both pathways are almost identical, but in the case of GP degradation there are fewer enzymes involved in each step. The analysis of transposition loci and genetic studies on interesting genes confirmed the crucial role of an α-methylacyl-coenzyme A racemase in the degradation of both GP and NR. We also demonstrated the probable involvement of enzymes participating in oxidoreduction reactions, β-oxidation, and the synthesis of complex cell envelope lipids in the degradation of GP. PMID:23220954

Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons.

PubMed

Meckenstock, Rainer U; Boll, Matthias; Mouttaki, Housna; Koelschbach, Janina S; Cunha Tarouco, Paola; Weyrauch, Philip; Dong, Xiyang; Himmelberg, Anne M

2016-01-01

Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers. © 2016 S. Karger AG, Basel.

Gene discovery for enzymes involved in limonene modification or utilization by the mountain pine beetle-associated pathogen Grosmannia clavigera.

PubMed

Wang, Ye; Lim, Lynette; Madilao, Lina; Lah, Ljerka; Bohlmann, Joerg; Breuil, Colette

2014-08-01

To successfully colonize and eventually kill pine trees, Grosmannia clavigera (Gs cryptic species), the main fungal pathogen associated with the mountain pine beetle (Dendroctonus ponderosae), has developed multiple mechanisms to overcome host tree chemical defenses, of which terpenoids are a major component. In addition to a monoterpene efflux system mediated by a recently discovered ABC transporter, Gs has genes that are highly induced by monoterpenes and that encode enzymes that modify or utilize monoterpenes [especially (+)-limonene]. We showed that pine-inhabiting Ophiostomale fungi are tolerant to monoterpenes, but only a few, including Gs, are known to utilize monoterpenes as a carbon source. Gas chromatography-mass spectrometry (GC-MS) revealed that Gs can modify (+)-limonene through various oxygenation pathways, producing carvone, p-mentha-2,8-dienol, perillyl alcohol, and isopiperitenol. It can also degrade (+)-limonene through the C-1-oxygenated pathway, producing limonene-1,2-diol as the most abundant intermediate. Transcriptome sequencing (RNA-seq) data indicated that Gs may utilize limonene 1,2-diol through beta-oxidation and then valine and tricarboxylic acid (TCA) metabolic pathways. The data also suggested that at least two gene clusters, located in genome contigs 108 and 161, were highly induced by monoterpenes and may be involved in monoterpene degradation processes. Further, gene knockouts indicated that limonene degradation required two distinct Baeyer-Villiger monooxygenases (BVMOs), an epoxide hydrolase and an enoyl coenzyme A (enoyl-CoA) hydratase. Our work provides information on enzyme-mediated limonene utilization or modification and a more comprehensive understanding of the interaction between an economically important fungal pathogen and its host's defense chemicals.

Gene Discovery for Enzymes Involved in Limonene Modification or Utilization by the Mountain Pine Beetle-Associated Pathogen Grosmannia clavigera

PubMed Central

Wang, Ye; Lim, Lynette; Madilao, Lina; Lah, Ljerka; Bohlmann, Joerg

2014-01-01

To successfully colonize and eventually kill pine trees, Grosmannia clavigera (Gs cryptic species), the main fungal pathogen associated with the mountain pine beetle (Dendroctonus ponderosae), has developed multiple mechanisms to overcome host tree chemical defenses, of which terpenoids are a major component. In addition to a monoterpene efflux system mediated by a recently discovered ABC transporter, Gs has genes that are highly induced by monoterpenes and that encode enzymes that modify or utilize monoterpenes [especially (+)-limonene]. We showed that pine-inhabiting Ophiostomale fungi are tolerant to monoterpenes, but only a few, including Gs, are known to utilize monoterpenes as a carbon source. Gas chromatography-mass spectrometry (GC-MS) revealed that Gs can modify (+)-limonene through various oxygenation pathways, producing carvone, p-mentha-2,8-dienol, perillyl alcohol, and isopiperitenol. It can also degrade (+)-limonene through the C-1-oxygenated pathway, producing limonene-1,2-diol as the most abundant intermediate. Transcriptome sequencing (RNA-seq) data indicated that Gs may utilize limonene 1,2-diol through beta-oxidation and then valine and tricarboxylic acid (TCA) metabolic pathways. The data also suggested that at least two gene clusters, located in genome contigs 108 and 161, were highly induced by monoterpenes and may be involved in monoterpene degradation processes. Further, gene knockouts indicated that limonene degradation required two distinct Baeyer-Villiger monooxygenases (BVMOs), an epoxide hydrolase and an enoyl coenzyme A (enoyl-CoA) hydratase. Our work provides information on enzyme-mediated limonene utilization or modification and a more comprehensive understanding of the interaction between an economically important fungal pathogen and its host's defense chemicals. PMID:24837377

mir-30d Regulates multiple genes in the autophagy pathway and impairs autophagy process in human cancer cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaojun; Department of General Surgery, Gansu Provincial Hospital, Lanzhou, Gansu 710000; Zhong, Xiaomin

2013-02-15

Highlights: ► Gene set enrichment analysis indicated mir-30d might regulate the autophagy pathway. ► mir-30d represses the expression of BECN1, BNIP3L, ATG12, ATG5 and ATG2. ► BECN1, BNIP3L, ATG12, ATG5 and ATG2 are direct targets of mir-30d. ► mir-30d inhibits autophagosome formation and LC3B-I conversion to LC3B-II. ► mir-30d regulates the autophagy process. -- Abstract: In human epithelial cancers, the microRNA (miRNA) mir-30d is amplified with high frequency and serves as a critical oncomir by regulating metastasis, apoptosis, proliferation, and differentiation. Autophagy, a degradation pathway for long-lived protein and organelles, regulates the survival and death of many cell types. Increasingmore » evidence suggests that autophagy plays an important function in epithelial tumor initiation and progression. Using a combined bioinformatics approach, gene set enrichment analysis, and miRNA target prediction, we found that mir-30d might regulate multiple genes in the autophagy pathway including BECN1, BNIP3L, ATG12, ATG5, and ATG2. Our further functional experiments demonstrated that the expression of these core proteins in the autophagy pathway was directly suppressed by mir-30d in cancer cells. Finally, we showed that mir-30d regulated the autophagy process by inhibiting autophagosome formation and LC3B-I conversion to LC3B-II. Taken together, our results provide evidence that the oncomir mir-30d impairs the autophagy process by targeting multiple genes in the autophagy pathway. This result will contribute to understanding the molecular mechanism of mir-30d in tumorigenesis and developing novel cancer therapy strategy.« less

Degradation pathway of malachite green in a novel dual-tank photoelectrochemical catalytic reactor.

PubMed

Diao, Zenghui; Li, Mingyu; Zeng, Fanyin; Song, Lin; Qiu, Rongliang

2013-09-15

A novel dual-tank photoelectrochemical catalytic reactor was designed to investigate the degradation pathway of malachite green. A thermally formed TiO₂/Ti thin film electrode was used as photoanode, graphite was used as cathode, and a saturated calomel electrode was employed as the reference electrode in the reactor. In the reactor, the anode and cathode tanks were connected by a cation exchange membrane. Results showed that the decolorization ratio of malachite green in the anode and cathode was 98.5 and 96.5% after 120 min, respectively. Malachite green in the two anode and cathode tanks was oxidized, achieving the bipolar double effect. Malachite green in both the anode and cathode tanks exhibited similar catalytic degradation pathways. The double bond of the malachite green molecule was attacked by strong oxidative hydroxyl radicals, after which the organic compound was degraded by the two pathways into 4,4-bis(dimethylamino) benzophenone, 4-(dimethylamino) benzophenone, 4-(dimethylamino) phenol, and other intermediate products. Eventually, malachite green was degraded into oxalic acid as a small molecular organic acid, which was degraded by processes such as demethylation, deamination, nitration, substitution, addition, and other reactions. Copyright © 2013 Elsevier B.V. All rights reserved.

Degradation Kinetics of VX

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gary S. Groenewold

2010-12-01

O-ethyl S-(2-diisopropylaminoethyl)phosphonothiolate (VX) is the most toxic of the conventional chemical warfare agents. It is a persistent compound, an attribute derived from its relative involatility and slow rates of hydrolysis. These properties suggest that VX can linger in an exposed environment for extended periods of time long after the air has cleared. Concern over prolonged risk from VX exposure is exacerbated by the fact that it poses a dermal contact hazard. Hence a detailed understanding of volatilization rates, and degradation pathways and rates occurring in various environments is needed. Historically, volatilization has not been considered to be an important mechanismmore » for VX depletion, but recent studies have shown that a significant fraction of VX may volatilize, depending on the matrix. A significant body of research has been conducted over the years to unravel VX degradation reaction pathways and to quantify the rates at which they proceed. Rigorous measurement of degradation rates is frequently difficult, and thus in many cases the degradation of VX has been described in terms of half lives, while in fewer instances rate constants have been measured. This variable approach to describing degradation kinetics reflects uncertainty regarding the exact nature of the degradation mechanisms. In this review, rates of VX degradation are compared on the basis of pseudo-first order rate constants, in order to provide a basis for assessing likelihood of VX persistence in a given environment. An issue of specific concern is that one VX degradation pathway produces S-2-(diisopropylaminoethyl) methylphosphonothioic acid (known as EA2192), which is a degradation product that retains much of the original toxicity of VX. Consequently degradation pathways and rates for EA2192 are also discussed.« less

Structures of Degradation Products and Degradation Pathways of Aflatoxin B1 by High-Voltage Atmospheric Cold Plasma (HVACP) Treatment.

PubMed

Shi, Hu; Cooper, Bruce; Stroshine, Richard L; Ileleji, Klein E; Keener, Kevin M

2017-08-02

High-voltage atmospheric cold plasma (HVACP) is a novel nonthermal decontamination technology that has potential for use in the food industry. In this study, HVACP was applied to treat pure aflatoxin B 1 (AFB 1 ) powder on a glass slide. AFB 1 was degraded by 76% using a 5 min HVACP treatment in air having 40% relative humidity. The degradation products of AFB 1 were separated, and their molecular formulas were elucidated using liquid-chromatography time-of-flight mass spectrometry (HPLC-TOF-MS). Six main degradation products were observed. The structures of the degradation products were further clarified via orbitrap mass spectrometry by means of fragmentation of the parental ions. Two degradation pathways were proposed on the basis of the structure of the degradation products. Among the six degradation products, two were ozonolysis products of AFB 1 . The appearance of the other four degradation products indicates that AFB 1 was degraded by other reactive species besides ozone that were generated during HVACP treatment. Reactive oxygen gas species are suggested as the major agents for aflatoxin degradation during HVACP treatment. Two degradation pathways of AFB 1 by HVACP treatment were proposed. One pathway involves reactions in which H • , OH • , CHO • radicals are added. The other involves epoxidation by HO 2 • radicals and oxidation of AFB 1 by the combined effects of the oxidative species OH • , H 2 O 2 , and O 3 . According to the structure-bioactivity relationship of AFB 1 , the bioactivity of the AFB 1 samples subjected to HVACP treatment is significantly reduced because of the disappearance of the C8═C9 double bond in the furofuran ring in all of the major degradation products as well as the modification of the lactone ring, cyclopentanone, and the methoxyl group.

Genetic and Genomic Insights into the Role of Benzoate-Catabolic Pathway Redundancy in Burkholderia xenovorans LB400†

PubMed Central

Denef, V. J.; Klappenbach, J. A.; Patrauchan, M. A.; Florizone, C.; Rodrigues, J. L. M.; Tsoi, T. V.; Verstraete, W.; Eltis, L. D.; Tiedje, J. M.

2006-01-01

Transcriptomic and proteomic analyses of Burkholderia xenovorans LB400, a potent polychlorinated biphenyl (PCB) degrader, have implicated growth substrate- and phase-dependent expression of three benzoate-catabolizing pathways: a catechol ortho cleavage (ben-cat) pathway and two benzoyl-coenzyme A pathways, encoded by gene clusters on the large chromosome (boxC) and the megaplasmid (boxM). To elucidate the significance of this apparent redundancy, we constructed mutants with deletions of the ben-cat pathway (the ΔbenABCD::kan mutant), the boxC pathway (the ΔboxABC::kan mutant), and both pathways (the ΔbenABCDΔ boxABC::kan mutant). All three mutants oxidized benzoate in resting-cell assays. However, the ΔbenABCD::kan and ΔbenABCD ΔboxABC::kan mutants grew at reduced rates on benzoate and displayed increased lag phases. By contrast, growth on succinate, on 4-hydroxybenzoate, and on biphenyl was unaffected. Microarray and proteomic analyses revealed that cells of the ΔbenABCD::kan mutant growing on benzoate expressed both box pathways. Overall, these results indicate that all three pathways catabolize benzoate. Deletion of benABCD abolished the ability of LB400 to grow using 3-chlorobenzoate. None of the benzoate pathways could degrade 2- or 4-chlorobenzoate, indicating that the pathway redundancy does not directly contribute to LB400's PCB-degrading capacities. Finally, an extensive sigmaE-regulated oxidative stress response not present in wild-type LB400 grown on benzoate was detected in these deletion mutants, supporting our earlier suggestion that the box pathways are preferentially active under reduced oxygen tension. Our data further substantiate the expansive network of tightly interconnected and complexly regulated aromatic degradation pathways in LB400. PMID:16391095

Modulation of apoptosis sensitivity through the interplay with autophagic and proteasomal degradation pathways

PubMed Central

Delgado, M E; Dyck, L; Laussmann, M A; Rehm, M

2014-01-01

Autophagic and proteasomal degradation constitute the major cellular proteolysis pathways. Their physiological and pathophysiological adaptation and perturbation modulates the relative abundance of apoptosis-transducing proteins and thereby can positively or negatively adjust cell death susceptibility. In addition to balancing protein expression amounts, components of the autophagic and proteasomal degradation machineries directly interact with and co-regulate apoptosis signal transduction. The influence of autophagic and proteasomal activity on apoptosis susceptibility is now rapidly gaining more attention as a significant modulator of cell death signalling in the context of human health and disease. Here we present a concise and critical overview of the latest knowledge on the molecular interplay between apoptosis signalling, autophagy and proteasomal protein degradation. We highlight that these three pathways constitute an intricate signalling triangle that can govern and modulate cell fate decisions between death and survival. Owing to rapid research progress in recent years, it is now possible to provide detailed insight into the mechanisms of pathway crosstalk, common signalling nodes and the role of multi-functional proteins in co-regulating both protein degradation and cell death. PMID:24457955

"Dark" Singlet Oxygen and Electron Paramagnetic Resonance Spin Trapping as Convenient Tools to Assess Photolytic Drug Degradation.

PubMed

Persich, Peter; Hostyn, Steven; Joie, Céline; Winderickx, Guy; Pikkemaat, Jeroen; Romijn, Edwin P; Maes, Bert U W

2017-05-01

Forced degradation studies are an important tool for a systematic assessment of decomposition pathways and identification of reactive sites in active pharmaceutical ingredients (APIs). Two methodologies have been combined in order to provide a deeper understanding of singlet oxygen-related degradation pathways of APIs under light irradiation. First, we report that a "dark" singlet oxygen test enables the investigation of drug reactivity toward singlet oxygen independently of photolytic irradiation processes. Second, the photosensitizing properties of the API producing the singlet oxygen was proven and quantified by spin trapping and electron paramagnetic resonance analysis. A combination of these techniques is an interesting addition to the forced degradation portfolio as it can be used for (1) revealing unexpected degradation pathways of APIs due to singlet oxygen, (2) clarifying photolytic drug-drug interactions in fixed-dose combinations, and (3) synthesizing larger quantities of hardly accessible oxidative drug degradants. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Selective Targeting of Proteins within Secretory Pathway for Endoplasmic Reticulum-associated Degradation

PubMed Central

Vecchi, Lara; Petris, Gianluca; Bestagno, Marco; Burrone, Oscar R.

2012-01-01

The endoplasmic reticulum-associated degradation (ERAD) is a cellular quality control mechanism to dispose of misfolded proteins of the secretory pathway via proteasomal degradation. SEL1L is an ER-resident protein that participates in identification of misfolded molecules as ERAD substrates, therefore inducing their ER-to-cytosol retrotranslocation and degradation. We have developed a novel class of fusion proteins, termed degradins, composed of a fragment of SEL1L fused to a target-specific binding moiety located on the luminal side of the ER. The target-binding moiety can be a ligand of the target or derived from specific mAbs. Here, we describe the ability of degradins with two different recognition moieties to promote degradation of a model target. Degradins recognize the target protein within the ER both in secretory and membrane-bound forms, inducing their degradation following retrotranslocation to the cytosol. Thus, degradins represent an effective technique to knock-out proteins within the secretory pathway with high specificity. PMID:22523070

Engineering posttranslational proofreading to discriminate nonstandard amino acids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kunjapur, Aditya M.; Stork, Devon A.; Kuru, Erkin

Accurate incorporation of nonstandard amino acids (nsAAs) is central for genetic code expansion to increase the chemical diversity of proteins. However, aminoacyl-tRNA synthetases are polyspecific and facilitate incorporation of multiple nsAAs. We investigated and repurposed a natural protein degradation pathway, the N-end rule pathway, to devise an innovative system for rapid assessment of the accuracy of nsAA incorporation. Using this tool to monitor incorporation of the nsAA biphenylalanine allowed the identification of tyrosyl-tRNA synthetase (TyrRS) variants with improved amino acid specificity. The evolved TyrRS variants enhanced our ability to contain unwanted proliferation of genetically modified organisms. In conclusion, this posttranslationalmore » proofreading system will aid the evolution of orthogonal translation systems for specific incorporation of diverse nsAAs.« less

Engineering posttranslational proofreading to discriminate nonstandard amino acids

DOE PAGES

Kunjapur, Aditya M.; Stork, Devon A.; Kuru, Erkin; ...

2018-01-04

Accurate incorporation of nonstandard amino acids (nsAAs) is central for genetic code expansion to increase the chemical diversity of proteins. However, aminoacyl-tRNA synthetases are polyspecific and facilitate incorporation of multiple nsAAs. We investigated and repurposed a natural protein degradation pathway, the N-end rule pathway, to devise an innovative system for rapid assessment of the accuracy of nsAA incorporation. Using this tool to monitor incorporation of the nsAA biphenylalanine allowed the identification of tyrosyl-tRNA synthetase (TyrRS) variants with improved amino acid specificity. The evolved TyrRS variants enhanced our ability to contain unwanted proliferation of genetically modified organisms. In conclusion, this posttranslationalmore » proofreading system will aid the evolution of orthogonal translation systems for specific incorporation of diverse nsAAs.« less

Analyses of soft tissue from Tyrannosaurus rex suggest the presence of protein.

PubMed

Schweitzer, Mary Higby; Suo, Zhiyong; Avci, Recep; Asara, John M; Allen, Mark A; Arce, Fernando Teran; Horner, John R

2007-04-13

We performed multiple analyses of Tyrannosaurus rex (specimen MOR 1125) fibrous cortical and medullary tissues remaining after demineralization. The results indicate that collagen I, the main organic component of bone, has been preserved in low concentrations in these tissues. The findings were independently confirmed by mass spectrometry. We propose a possible chemical pathway that may contribute to this preservation. The presence of endogenous protein in dinosaur bone may validate hypotheses about evolutionary relationships, rates, and patterns of molecular change and degradation, as well as the chemical stability of molecules over time.

Biochemical pathways and enhanced degradation of di-n-octyl phthalate (DOP) in sequencing batch reactor (SBR) by Arthrobacter sp. SLG-4 and Rhodococcus sp. SLG-6 isolated from activated sludge.

PubMed

Zhang, Ke; Liu, Yihao; Chen, Qiang; Luo, Hongbing; Zhu, Zhanyuan; Chen, Wei; Chen, Jia; Mo, You

2018-04-01

Two bacterial strains designated as Arthrobacter sp. SLG-4 and Rhodococcus sp. SLG-6, capable of utilizing di-n-octyl phthalate (DOP) as sole source of carbon and energy, were isolated from activated sludge. The analysis of DOP degradation intermediates indicated Arthrobacter sp. SLG-4 could completely degrade DOP. Whereas DOP could not be mineralized by Rhodococcus sp. SLG-6 and the final metabolic product was phthalic acid (PA). The proposed DOP degradation pathway by Arthrobacter sp. SLG-4 was that strain SLG-4 initially transformed DOP to PA via de-esterification pathway, and then PA was metabolized to protocatechuate acid and eventually converted to tricarboxylic acid (TCA) cycle through meta-cleavage pathway. Accordingly, Phthalate 3,4-dioxygenase genes (phtA) responsible for PA degradation were successfully detected in Arthrobacter sp. SLG-4 by real-time quantitative PCR (q-PCR). q-PCR analysis demonstrated that the quantity of phthalate 3,4-dioxygenase was positively correlated to DOP degradation in SBRs. Bioaugmentation by inoculating DOP-degrading bacteria effectively shortened the start-up of SBRs and significantly enhanced DOP degradation in bioreactors. More than 91% of DOP (500 mg L -1 ) was removed in SBR bioaugmented with bacterial consortium, which was double of the control SBR. This study suggests bioaugmentation is an effective and feasible technique for DOP bioremediation in practical engineering.

Kinetics of biotransformation of chlorpyrifos in aqueous and soil slurry environments.

PubMed

Tiwari, Manoj K; Guha, Saumyen

2014-03-15

The attenuation of chlorpyrifos (CPF) by the enriched indigenous soil microorganism was studied in 15 d aerobic and 60 d anaerobic batch experiments in aqueous and soil slurry (1:3 w/w) media. At the end of the batch experiments, 2.78 ± 0.11 μM of CPF was degraded by 82% in aerobic and 66% in anaerobic aqueous environments, while 12.4 ± 0.5 μM of CPF was degraded by 48% in aerobic and 31% in anaerobic soil slurries. The reduced degradation in the soil slurries was due to the significantly (2-10 times) slower rate of degradation of soil phase CPF compared with its degradation rate in water. The pathways of degradation of CPF were identified, including a partial anaerobic degradation pathway that is constructed for the first time. The simulation of the various conversions in the degradation pathways using first order kinetics was used to analyze relative persistence of metabolites. The common metabolite 3,5,6-trichloro-2-pyridinol (TCP) accumulated (increased monotonically during the period of experiments) in aerobic soil slurry and in anaerobic aqueous as well as soil slurry systems but did not accumulate in aerobic aqueous system. The most toxic compound in the pathway, chlorpyrifos oxon (CPFO) was not detected in anaerobic environment. In aerobic environment, CPFO was short lived in aqueous medium, but accumulated slowly in the soils. Copyright © 2013 Elsevier Ltd. All rights reserved.

Biominerlization and possible endosulfan degradation pathway adapted by Aspergillus niger.

PubMed

Bhalerao, Tejomyee S

2013-11-28

Endosulfan is a chlorinated pesticide; its persistence in the environment and toxic effects on biota are demanding its removal. This study aims at improving the tolerance of the previously isolated fungus Aspergillus niger (A. niger) ARIFCC 1053 to endosulfan. Released chloride, dehalogenase activity, and released proteins were estimated along with analysis of endosulfan degradation and pathway identification. The culture could tolerate 1,000 mg/ml of technical grade endosulfan. Complete disappearance of endosulfan was seen after 168 h of incubation. The degradation study could easily be correlated with increase in released chlorides, dehalogenase activity and protein released. Comparative infrared spectral analysis suggested that the molecule of endosulfan was degraded efficiently by A. niger ARIFCC 1053. Obtained mass ion values by GC-MS suggested a hypothetical pathway during endosulfan degradation by A. niger ARIFCC 1053. All these results provide a basis for the development of bioremediation strategies to remediate the pollutant under study in the environment.

Selective autophagy: ubiquitin-mediated recognition and beyond.

PubMed

Kraft, Claudine; Peter, Matthias; Hofmann, Kay

2010-09-01

Eukaryotic cells use autophagy and the ubiquitin-proteasome system as their major protein degradation pathways. Whereas the ubiquitin-proteasome system is involved in the rapid degradation of proteins, autophagy pathways can selectively remove protein aggregates and damaged or excess organelles. Proteasome-mediated degradation requires previous ubiquitylation of the cargo, which is then recognized by ubiquitin receptors directing it to 26S proteasomes. Although autophagy has long been viewed as a random cytoplasmic degradation system, the involvement of ubiquitin as a specificity factor for selective autophagy is rapidly emerging. Recent evidence also suggests active crosstalk between proteasome-mediated degradation and selective autophagy. Here, we discuss the molecular mechanisms that link autophagy and the proteasome system, as well as the emerging roles of ubiquitin and ubiquitin-binding proteins in selective autophagy. On the basis of the evolutionary history of autophagic ubiquitin receptors, we propose a common origin for metazoan ubiquitin-dependent autophagy and the cytoplasm-to-vacuole targeting pathway of yeast.

Biodegradation of trichloroethylene and involvement of an aromatic biodegradative pathway.

PubMed Central

Nelson, M J; Montgomery, S O; Mahaffey, W R; Pritchard, P H

1987-01-01

Biodegradation of trichloroethylene (TCE) by bacterial strain G4 resulted in complete dechlorination of the compound, as indicated by the production of inorganic chloride. A component of the water from which strain G4 was isolated that was required for TCE degradation was identified as phenol. Strain G4 degraded TCE in the presence of chloramphenicol only when preinduced with phenol. Toluene, o-cresol. and m-cresol could replace the phenol requirement. Two of the inducers of TCE metabolism, phenol and toluene, apparently induced the same aromatic degradative pathway that cleaved the aromatic ring by meta fission. Cells induced with either phenol or toluene had similar oxidation rates for several aromatic compounds and had similar levels of catechol-2,3-dioxygenase. The results indicate that one or more enzymes of an inducible pathway for aromatic degradation in strain G4 are responsible for the degradation of TCE. PMID:3606099

Autophagy modulation as a potential therapeutic target for diverse diseases

PubMed Central

Rubinsztein, David C.; Codogno, Patrice; Levine, Beth

2012-01-01

Autophagy is an essential, conserved lysosomal degradation pathway that controls the quality of the cytoplasm by eliminating protein aggregates and damaged organelles. It begins when double-membraned autophagosomes engulf portions of the cytoplasm, which is followed by fusion of these vesicles with lysosomes and degradation of the autophagic contents. In addition to its vital homeostatic role, this degradation pathway is involved in various human disorders, including metabolic conditions, neurodegenerative diseases, cancers and infectious diseases. This article provides an overview of the mechanisms and regulation of autophagy, the role of this pathway in disease and strategies for therapeutic modulation. PMID:22935804

Nanoscale zerovalent iron-mediated degradation of DDT in soil.

PubMed

Han, Yuling; Shi, Nan; Wang, Huifang; Pan, Xiong; Fang, Hua; Yu, Yunlong

2016-04-01

Nanoscale zerovalent iron (nZVI)-mediated degradation of 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) was investigated in a spiked soil under different conditions (iron sources, iron dosage, soil moisture, temperature, and soil types) and DDT-contaminated field. The degradation efficiency of p,p'-DDT by nZVI and nZVI coated with sodium oleate (SO-nZVI) was much higher than that by nZVI coated with polyimide (PI-nZVI). The rapid degradation of p,p'-DDT by nZVI only occurred in flooded soil. The degradation half-life of p,p'-DDT decreased significantly from 58.3 to 27.6 h with nZVI dosage from 0.5 to 2.0% and from 46.5 to 32.0 h with temperature from 15 to 35 °C. The degradation efficiency of p,p'-DDT by nZVI differed in Jinhua (JH), Jiaxing (JX), Xiaoshan (XS), Huajiachi (HJC), and Heilongjiang (HLJ) soils. A good correlation was found between the degradation half-life of p,p'-DDT and multiple soil properties. The probable nZVI-mediated degradation pathway of p,p'-DDT in soil was proposed as DDT → DDD/DDE → DDNS → DDOH based on the metabolites identified by GC-MS. The in situ degradation efficiency of residual DDTs in a contaminated field was profoundly enhanced by the addition of nZVI as compared to the control. It is concluded that nZVI might be an efficient agent for the remediation of DDT-contaminated soil under anaerobic environment.

Combination of degradation pathways for naphthalene utilization in Rhodococcus sp. strain TFB

PubMed Central

Tomás-Gallardo, Laura; Gómez-Álvarez, Helena; Santero, Eduardo; Floriano, Belén

2014-01-01

Rhodococcus sp. strain TFB is a metabolic versatile bacterium able to grow on naphthalene as the only carbon and energy source. Applying proteomic, genetic and biochemical approaches, we propose in this paper that, at least, three coordinated but independently regulated set of genes are combined to degrade naphthalene in TFB. First, proteins involved in tetralin degradation are also induced by naphthalene and may carry out its conversion to salicylaldehyde. This is the only part of the naphthalene degradation pathway showing glucose catabolite repression. Second, a salicylaldehyde dehydrogenase activity that converts salicylaldehyde to salicylate is detected in naphthalene-grown cells but not in tetralin-or salicylate-grown cells. Finally, we describe the chromosomally located nag genes, encoding the gentisate pathway for salicylate conversion into fumarate and pyruvate, which are only induced by salicylate and not by naphthalene. This work shows how biodegradation pathways in Rhodococcus sp. strain TFB could be assembled using elements from different pathways mainly because of the laxity of the regulatory systems and the broad specificity of the catabolic enzymes. PMID:24325207

Effect of Fe(III) on 1,1,2,2-Tetrachloroethane degradation and vinyl chloride accumulation in wetland sediments of the Aberdeen Proving Ground

USGS Publications Warehouse

Jones, Elizabeth; Voytek, Mary; Lorah, Michelle

2004-01-01

1,1,2,2-Tetrachloroethane (TeCA) contaminated groundwater at the Aberdeen Proving Ground discharges through an anaerobic wetland in West Branch Canal Creek (MD), where dechlorination occurs. Two microbially mediated pathways, dichloroelimination and hydrogenolysis, account for most of the TeCA degradation at this site. The dichloroelimination pathways lead to the formation of vinyl chloride (VC), a recalcitrant carcinogen of great concern. The goal of this investigation was to determine whether microbially-available Fe(III) in the wetland surface sediment influenced the fate of TeCA and its daughter products. Differences were identified in the TeCA degradation pathway between microcosms treated with amorphous ferric oxyhydroxide (AFO-treated) and untreated (no AFO) microcosms. TeCA degradation was accompanied by a lower accumulation of VC in AFO-treated microcosms than untreated microcosms. The microcosm incubations and subsequent experiments with the microcosm materials showed that AFO treatment resulted in lower production of VC by (1) shifting TeCA degradation from dichloroelimination pathways to production of a greater proportion of chlorinated ethane products, and (2) decreasing the microbial capability to produce VC from 1,2-dichloroethene (DCE). VC degradation was not stimulated in the presence of Fe(III). Rather, VC degradation occurred readily under methanogenic conditions and was inhibited under Fe(III)-reducing conditions.

Mechanisms of protein-folding diseases at a glance.

PubMed

Valastyan, Julie S; Lindquist, Susan

2014-01-01

For a protein to function appropriately, it must first achieve its proper conformation and location within the crowded environment inside the cell. Multiple chaperone systems are required to fold proteins correctly. In addition, degradation pathways participate by destroying improperly folded proteins. The intricacy of this multisystem process provides many opportunities for error. Furthermore, mutations cause misfolded, nonfunctional forms of proteins to accumulate. As a result, many pathological conditions are fundamentally rooted in the protein-folding problem that all cells must solve to maintain their function and integrity. Here, to illustrate the breadth of this phenomenon, we describe five examples of protein-misfolding events that can lead to disease: improper degradation, mislocalization, dominant-negative mutations, structural alterations that establish novel toxic functions, and amyloid accumulation. In each case, we will highlight current therapeutic options for battling such diseases.

Methods for the Detection of Autophagy in Mammalian Cells

PubMed Central

Zhang, Ziyan; Singh, Rajat; Aschner, Michael

2016-01-01

Macroautophagy (hereafter referred to as autophagy) is a degradation pathway that delivers cytoplasmic materials to lysosomes via double-membraned vesicles designated autophagosomes. Cytoplasmic constituents are sequestered into autophagosomes, which subsequently fuse with lysosomes, where the cargo is degraded. Autophagy is a crucial mechanism involved in many aspects of cell function, including cellular metabolism and energy balance; and alterations in autophagy have been linked to various human pathological processes. Thus, methods that accurately measure autophagic activity are necessary. In this unit, we introduce several approaches to analyze autophagy in mammalian cells, including immunoblotting analysis of LC3 and p62, detection of autophagosome formation by fluorescence microscopy, and monitoring autophagosome maturation by tandem mRFP-GFP fluorescence microscopy. Overall, we recommend a combined use of multiple methods to accurately assess the autophagic activity in any given biological setting. PMID:27479363

MUC4-induced nuclear translocation of β-catenin: a novel mechanism for growth, metastasis and angiogenesis in pancreatic cancer.

PubMed

Zhi, Xiaofei; Tao, Jinqiu; Xie, Kunling; Zhu, Yi; Li, Zheng; Tang, Jie; Wang, Weizhi; Xu, Hao; Zhang, Jingjing; Xu, Zekuan

2014-04-28

The membrane mucin MUC4 is aberrantly expressed in multiple cancers and is of clinical significance to diagnosis and prognosis in pancreatic cancer. However, the role of MUC4 in angiogenesis and the potential association among these malignant capabilities have not been explored. In this study, we investigated the collective signaling mechanisms associated with MUC4-induced growth, metastasis and angiogenesis in pancreatic cancer. Knockdown of MUC4 in two pancreatic cancer cell lines led to downregulation of lysosomal degradation of E-cadherin by Src kinase through downregulation of pFAK and pSrc pathway. The downregulation of lysosomal degradation of E-cadherin in turn induced the formation of E-cadherin/β-catenin complex and membrane translocation of β-catenin, resulting in the downregulation of Wnt/β-catenin signaling pathway. Thus, the Wnt/β-catenin target genes c-Myc, Cyclin D1, CD44 and VEGF were down-regulated and their malignant functions proliferation, metastasis and angiogenesis were reduced. Taken together, MUC4-induced nuclear translocation of β-catenin is a novel mechanism for growth, metastasis and angiogenesis of pancreatic cancer. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Photocatalytic degradation of 17α-ethinylestradiol (EE2) in the presence of TiO2-doped zeolite.

PubMed

Pan, Zhong; Stemmler, Elizabeth A; Cho, Hong Je; Fan, Wei; LeBlanc, Lawrence A; Patterson, Howard H; Amirbahman, Aria

2014-08-30

Current design limitations and ineffective remediation techniques in wastewater treatment plants have led to concerns about the prevalence of pharmaceutical and personal care products (PPCPs) in receiving waters. A novel photocatalyst, TiO2-doped low-silica X zeolite (TiO2-LSX), was used to study the degradation of the pharmaceutical compound, 17α-ethinylestradiol (EE2). The catalyst was synthesized and characterized using XRD, BET surface analysis, SEM-EDAX, and ICP-OES. The effects of different UV light intensities, initial EE2 concentrations, and catalyst dosages on the EE2 removal efficiency were studied. A higher EE2 removal efficiency was attained with UV-TiO2-LSX when compared with UV-TiO2 or UV alone. The EE2 degradation process followed pseudo-first-order kinetics. A comprehensive empirical model was developed to describe the EE2 degradation kinetics under different conditions using multiple linear regression analysis. The EE2 degradation mechanism was proposed based on molecular calculations, identification of photoproducts using HPLC-MS/MS, and reactive species quenching experiments; the results showed that oxidative degradation pathways initiated by hydroxyl radicals were predominant. This novel TiO2-doped zeolite system provides a promising application for the UV disinfection process in wastewater treatment plants. Copyright © 2014 Elsevier B.V. All rights reserved.

Modeling the Interaction of H2 on Root Exudate Degradation and Methanogenesis in Wetland Sediments

NASA Astrophysics Data System (ADS)

Pal, D. S.; Jaffe, P. R.

2014-12-01

CH4 is produced in wetland sediments from the microbial degradation of organic carbon through multiple fermentation steps and methanogenesis pathways. There are many potential sources of carbon for methananogenesis; in vegetated wetland sediments, microbial communities consume root exudates as a major source of organic carbon. In many methane models propionate is used as a model carbon molecule. This simple sugar is fermented into acetate and H2, acetate is transformed to methane and CO2 while the H2 and CO2 is synthesized to form an additional CH4 molecule. The hydrogenotrophic pathway involves the equilibrium of two dissolved gases, CH4 and H2. In an effort to limit CH4 emissions from wetlands, there has been growing interest in finding ways to limit plant transport of soil gases through root systems. While this may decrease the direct emissions of methane, there is little understanding about how H2 dynamics may feedback into overall methane production. Since H2 is used in methane production and produced in propionate fermentation, increased subsurface H2 concentrations can simultaneously inhibit propionate fermentation and acetate production and enhance hydrogenotrophic methanogenesis. For this study, we incubated soil samples from vegetated wetland sediments with propionate or acetate and four different hydrogen concentrations. The headspaces from these incubations were simultaneously analyzed for H2 and CH4 at multiple time points over two months. The comparison of methane production between different hydrogen concentrations and different carbon sources can indicate which process is most affected by increased hydrogen concentrations. The results from this study were combined with a newly formulated steady-state model of propionate degradation and formation of methane, that also accounts for the venting off both gases via plants. The resulting model indicates how methane production and emissions would be affected by plant volatilization.

Biodegradation of phthalate esters by newly isolated Rhizobium sp. LMB-1 and its biochemical pathway of di-n-butyl phthalate.

PubMed

Tang, W-J; Zhang, L-S; Fang, Y; Zhou, Y; Ye, B-C

2016-07-01

To isolate a novel strain that could degrade many kinds PAEs efficiently and investigate the DBP-degrading pathway in this strain. Based on its 16S rRNA gene sequence, the strain was identified as Rhizobium sp. This strain, named LMB-1, can also utilize phthalates, such as DEHP, DMP, DBP and DEP. During the degradation of DBP, six possible metabolites, diethyl phthalate, mono-ethyl phthalate, di-methyl phthalate, mono-methyl phthalate, phthalic acid and tartaric acid, were identified by gas chromatography-mass spectrometry (GC-MS) analysis, and the degradation pathway of DBP was also identified in this study. In summary, strain LMB-1, identified as Rhizobium sp., was found to be capable of efficiently degrading PAEs, and it was determined that the strain degraded DMP completely within 45 h. DEP, DMP, MEP, MMP, PA and tartaric acid were detected during the course of DBP degradation by LMB-1. We propose that this strain could completely degrade DBP or other PAEs. Our results offer a novel and potential candidate, Rhizobium sp. LMB-1, for use in the bioremediation of cultivated soil contaminated by PAEs. This is the first report concerning the complete degradation of phthalate esters by Rhizobium sp. © 2016 The Society for Applied Microbiology.

Fibrin(ogen) is internalized and degraded by activated human monocytoid cells via Mac-1 (CD11b/CD18): a nonplasmin fibrinolytic pathway.

PubMed

Simon, D I; Ezratty, A M; Francis, S A; Rennke, H; Loscalzo, J

1993-10-15

Fibrin(ogen) (FGN) is important for hemostasis and wound healing and is cleared from sites of injury primarily by the plasminogen activator system. However, there is emerging evidence in plasminogen activator-deficient transgenic mice that nonplasmin pathways may be important in fibrin(ogen)olysis, as well. Given the proximity of FGN and monocytes within the occlusive thrombus at sites of vascular injury, we considered the possibility that monocytes may play an ancillary role in the degradation and clearance of fibrin. We found that monocytes possess an alternative fibrinolytic pathway that uses the integrin Mac-1, which directly binds and internalizes FGN, resulting in its lysosomal degradation. At 4 degrees C, FGN binds to U937 monocytoid cells in a specific and saturable manner with a kd of 1.8 mumol/L. Binding requires adenosine diphosphate stimulation and is calcium-dependent. At 37 degrees C, FGN and fibrin monomer (FM) are internalized and degraded at rates of 0.37 +/- 0.13 and 0.55 +/- 0.03 microgram/10(6) cells/h by U937 cells, 1.38 +/- 0.02 and 1.20 +/- 0.30 microgram/10(6) cells/h by THP-1 cells, and 2.10 +/- 0.20 and 2.52 +/- 0.18 micrograms/10(6) cells/h by human peripheral blood mononuclear cells, respectively. The serine protease inhibitors, PPACK and aprotinin, and the specific elastase inhibitor, AAPVCK, do not significantly inhibit degradation. However, degradation is inhibited by chloroquine, suggesting that a lysosomal pathway is involved. Factor X, a competitive ligand with FGN for the Mac-1 receptor, also blocks degradation, as does a monoclonal antibody to the alpha-subunit of Mac-1. Autoradiography of radioiodinated, internalized FGN shows that FGN proteolysis by the pathway produces a unique degradation pattern distinct from that observed with plasmin. In a fibrin clot lysis assay, Mac-1-mediated fibrinolysis contributed significantly to total fibrinolysis. In summary, FGN is internalized and degraded by activated human monocytoid cells via Mac-1 in the absence of plasmin, thereby providing an alternative fibrinolytic pathway. Thus, in addition to the function of cell adhesion, integrins may also act as receptors that mediate the internalization and degradation of bound ligands.

ORGANOPHOSPHATE PESTICIDE DEGRADATION PATHWAYS DURING DRINKING WATER TREATMENT

EPA Science Inventory

Free chlorine has been found to react with organophosphate (OP) pesticides resulting in the more toxic oxon products. We will discuss OP pesticide degradation pathways and modeling in the presence of chlorine and chloramines, as well as present a relationship between structure a...

Insights into RNA processing pathways and associated-RNA degrading enzymes in Archaea.

PubMed

Clouet-d'Orval, Béatrice; Batista, Manon; Bouvier, Marie; Quentin, Yves; Fichant, Gwennaele; Marchfelder, Anita; Maier, Lisa-Katharina

2018-04-19

RNA processing pathways are at the center of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes is still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya. In this context, this review provides a state of the art overview of archaeal endoribonucleases and exoribonucleases that cleave and trim RNA species and also of the key small archaeal proteins that bind RNAs. Furthermore, synthetic up-to-date views of processing and biogenesis pathways of archaeal transfer and ribosomal RNAs as well as of maturation of stable small non-coding RNAs such as CRISPR RNAs, small C/D and H/ACA box guide RNAs, and other emerging classes of small RNAs are described. Finally prospective post-transcriptional mechanisms to control archaeal messenger RNA quality and quantity are discussed.

Global transcriptomic profiling of aspen trees under elevated [CO2] to identify potential molecular mechanisms responsible for enhanced radial growth.

PubMed

Wei, Hairong; Gou, Jiqing; Yordanov, Yordan; Zhang, Huaxin; Thakur, Ramesh; Jones, Wendy; Burton, Andrew

2013-03-01

Aspen (Populus tremuloides) trees growing under elevated [CO(2)] at a free-air CO(2) enrichment (FACE) site produced significantly more biomass than control trees. We investigated the molecular mechanisms underlying the observed increase in biomass by producing transcriptomic profiles of the vascular cambium zone (VCZ) and leaves, and then performed a comparative study to identify significantly changed genes and pathways after 12 years exposure to elevated [CO(2)]. In leaves, elevated [CO(2)] enhanced expression of genes related to Calvin cycle activity and linked pathways. In the VCZ, the pathways involved in cell growth, cell division, hormone metabolism, and secondary cell wall formation were altered while auxin conjugation, ABA synthesis, and cytokinin glucosylation and degradation were inhibited. Similarly, the genes involved in hemicellulose and pectin biosynthesis were enhanced, but some genes that catalyze important steps in lignin biosynthesis pathway were inhibited. Evidence from systemic analysis supported the functioning of multiple molecular mechanisms that underpin the enhanced radial growth in response to elevated [CO(2)].

Cellular proteostasis: degradation of misfolded proteins by lysosomes

PubMed Central

Jackson, Matthew P.

2016-01-01

Proteostasis refers to the regulation of the cellular concentration, folding, interactions and localization of each of the proteins that comprise the proteome. One essential element of proteostasis is the disposal of misfolded proteins by the cellular pathways of protein degradation. Lysosomes are an important site for the degradation of misfolded proteins, which are trafficked to this organelle by the pathways of macroautophagy, chaperone-mediated autophagy and endocytosis. Conversely, amyloid diseases represent a failure in proteostasis, in which proteins misfold, forming amyloid deposits that are not degraded effectively by cells. Amyloid may then exacerbate this failure by disrupting autophagy and lysosomal proteolysis. However, targeting the pathways that regulate autophagy and the biogenesis of lysosomes may present approaches that can rescue cells from the deleterious effects of amyloidogenic proteins. PMID:27744333

Complement Evasion by Pathogenic Leptospira.

PubMed

Fraga, Tatiana Rodrigues; Isaac, Lourdes; Barbosa, Angela Silva

2016-01-01

Leptospirosis is a neglected infectious disease caused by spirochetes from the genus Leptospira . Pathogenic microorganisms, notably those which reach the blood circulation such as Leptospira , have evolved multiple strategies to escape the host complement system, which is important for innate and acquired immunity. Leptospira avoid complement-mediated killing through: (i) recruitment of host complement regulators; (ii) acquisition of host proteases that cleave complement proteins on the bacterial surface; and, (iii) secretion of proteases that inactivate complement proteins in the Leptospira surroundings. The recruitment of host soluble complement regulatory proteins includes the acquisition of Factor H (FH) and FH-like-1 (alternative pathway), C4b-binding protein (C4BP) (classical and lectin pathways), and vitronectin (Vn) (terminal pathway). Once bound to the leptospiral surface, FH and C4BP retain cofactor activity of Factor I in the cleavage of C3b and C4b, respectively. Vn acquisition by leptospires may result in terminal pathway inhibition by blocking C9 polymerization. The second evasion mechanism lies in plasminogen (PLG) binding to the leptospiral surface. In the presence of host activators, PLG is converted to enzymatically active plasmin, which is able to degrade C3b, C4b, and C5 at the surface of the pathogen. A third strategy used by leptospires to escape from complement system is the active secretion of proteases. Pathogenic, but not saprophytic leptospires, are able to secrete metalloproteases that cleave C3 (central complement molecule), Factor B (alternative pathway), and C4 and C2 (classical and lectin pathways). The purpose of this review is to fully explore these complement evasion mechanisms, which act together to favor Leptospira survival and multiplication in the host.

Complement Evasion by Pathogenic Leptospira

PubMed Central

Fraga, Tatiana Rodrigues; Isaac, Lourdes; Barbosa, Angela Silva

2016-01-01

Leptospirosis is a neglected infectious disease caused by spirochetes from the genus Leptospira. Pathogenic microorganisms, notably those which reach the blood circulation such as Leptospira, have evolved multiple strategies to escape the host complement system, which is important for innate and acquired immunity. Leptospira avoid complement-mediated killing through: (i) recruitment of host complement regulators; (ii) acquisition of host proteases that cleave complement proteins on the bacterial surface; and, (iii) secretion of proteases that inactivate complement proteins in the Leptospira surroundings. The recruitment of host soluble complement regulatory proteins includes the acquisition of Factor H (FH) and FH-like-1 (alternative pathway), C4b-binding protein (C4BP) (classical and lectin pathways), and vitronectin (Vn) (terminal pathway). Once bound to the leptospiral surface, FH and C4BP retain cofactor activity of Factor I in the cleavage of C3b and C4b, respectively. Vn acquisition by leptospires may result in terminal pathway inhibition by blocking C9 polymerization. The second evasion mechanism lies in plasminogen (PLG) binding to the leptospiral surface. In the presence of host activators, PLG is converted to enzymatically active plasmin, which is able to degrade C3b, C4b, and C5 at the surface of the pathogen. A third strategy used by leptospires to escape from complement system is the active secretion of proteases. Pathogenic, but not saprophytic leptospires, are able to secrete metalloproteases that cleave C3 (central complement molecule), Factor B (alternative pathway), and C4 and C2 (classical and lectin pathways). The purpose of this review is to fully explore these complement evasion mechanisms, which act together to favor Leptospira survival and multiplication in the host. PMID:28066433

SCFSlmb E3 ligase-mediated degradation of Expanded is inhibited by the Hippo pathway in Drosophila

PubMed Central

Zhang, Hongtao; Li, Changqing; Chen, Hanqing; Wei, Chuanxian; Dai, Fei; Wu, Honggang; Dui, Wen; Deng, Wu-Min; Jiao, Renjie

2015-01-01

Deregulation of the evolutionarily conserved Hippo pathway has been implicated in abnormal development of animals and in several types of cancer. One mechanism of Hippo pathway regulation is achieved by controlling the stability of its regulatory components. However, the executive E3 ligases that are involved in this process, and how the process is regulated, remain poorly defined. In this study, we identify, through a genetic candidate screen, the SCFSlmb E3 ligase as a novel negative regulator of the Hippo pathway in Drosophila imaginal tissues via mediation of the degradation of Expanded (Ex). Mechanistic study shows that Slmb-mediated degradation of Ex is inhibited by the Hippo signaling. Considering the fact that Hippo signaling suppresses the transcription of ex, we propose that the Hippo pathway employs a double security mechanism to ensure fine-tuned homeostasis during development. PMID:25522691

Degradation of sulfadimethoxine catalyzed by laccase with soybean meal extract as natural mediator: Mechanism and reaction pathway.

PubMed

Liang, Shangtao; Luo, Qi; Huang, Qingguo

2017-08-01

Natural laccase-mediator systems have been well recognized as an eco-friendly and energy-saving approach in environmental remediation, whose further application is however limited by the high cost of natural mediators and relatively long treatment time span. This study evaluated the water extract of soybean meal, a low-cost compound system, in mediating the laccase catalyzed degradation of a model contaminant of emerging concern, sulfadimethoxine (SDM), and demonstrated it as a promising alternative mediator for soil and water remediation. Removal of 73.3% and 65.6% was achieved in 9 h using soybean meal extract (SBE) as the mediating system for laccase-catalyzed degradation of sulfadimethoxine at the concentration of 1 ppm and 10 ppm, respectively. Further degradation of sulfadimethoxine was observed with multiple SBE additions. Using SBE as mediator increased the 9-h removal of SDM at 1 ppm initial concentration by 52.9%, 49.4%, and 36.3% in comparison to the system mediated by 1-Hydroxybenzotriazole (HBT), p-Coumaric acid (COU) and 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonate) (ABTS), respectively. With the detection of stable coupling products formed with radical scavenger (5,5-Dimethyl-1-pyrroline N-oxide, DMPO), three phenolic compounds (vanillin, apocynin, and daidzein) in SBE were confirmed to serve as mediators for Trametes versicolor laccase. Reaction pathways were proposed based on the results of High Resolution Mass Spectrometry. SO 2 excursion happened during SDM transformation, leading to elimination of antimicrobial activity. Therefore, as a natural, phenol rich, and affordable compound system, the future application of SBE in wastewater and soil remediation is worth exploring. Copyright © 2017 Elsevier Ltd. All rights reserved.

Isotopic study of mercury sources and transfer between a freshwater lake and adjacent forest food web.

PubMed

Kwon, Sae Yun; Blum, Joel D; Nadelhoffer, Knute J; Timothy Dvonch, J; Tsui, Martin Tsz-Ki

2015-11-01

Studies of monomethylmercury (MMHg) sources and biogeochemical pathways have been extensive in aquatic ecosystems, but limited in forest ecosystems. Increasing evidence suggests that there is significant mercury (Hg) exchange between aquatic and forest ecosystems. We use Hg stable isotope ratios (δ(202)Hg and Δ(199)Hg) to investigate the relative importance of MMHg sources and assess Hg transfer pathways between Douglas Lake and adjacent forests located at the University of Michigan Biological Station, USA. We characterize Hg isotopic compositions of basal resources and use linear regression of % MMHg versus δ(202)Hg and Δ(199)Hg to estimate Hg isotope values for inorganic mercury (IHg) and MMHg in the aquatic and adjacent forest food webs. In the aquatic ecosystem, we found that lake sediment represents a mixture of IHg pools deposited via watershed runoff and precipitation. The δ(202)Hg and Δ(199)Hg values estimated for IHg are consistent with other studies that measured forest floor in temperate forests. The Δ(199)Hg value estimated for MMHg in the aquatic food web indicates that MMHg is subjected to ~20% photochemical degradation prior to bioaccumulation. In the forest ecosystem, we found a significant negative relationship between total Hg and δ(202)Hg and Δ(199)Hg of soil collected at multiple distances from the lakeshore and lake sediment. This suggests that IHg input from watershed runoff provides an important Hg transfer pathway between the forest and aquatic ecosystems. We measured Δ(199)Hg values for high trophic level insects and compared these insects at multiple distances perpendicular to the lake shoreline. The Δ(199)Hg values correspond to the % canopy cover suggesting that forest MMHg is subjected to varying extents of photochemical degradation and the extent may be controlled by sunlight. Our study demonstrates that the use of Hg isotopes adds important new insight into the relative importance of MMHg sources and complex Hg transfer pathways across ecosystem boundaries. Copyright © 2015 Elsevier B.V. All rights reserved.

An unexplored pathway for degradation of cholate requires a 7α-hydroxysteroid dehydratase and contributes to a broad metabolic repertoire for the utilization of bile salts in Novosphingobium sp. strain Chol11.

PubMed

Yücel, Onur; Drees, Steffen; Jagmann, Nina; Patschkowski, Thomas; Philipp, Bodo

2016-12-01

Bile salts such as cholate are surface-active steroid compounds with functions for digestion and signaling in vertebrates. Upon excretion into soil and water bile salts are an electron- and carbon-rich growth substrate for environmental bacteria. Degradation of bile salts proceeds via intermediates with a 3-keto-Δ 1,4 -diene structure of the steroid skeleton as shown for e.g. Pseudomonas spp. Recently, we isolated bacteria degrading cholate via intermediates with a 3-keto-7-deoxy-Δ 4,6 -structure of the steroid skeleton suggesting the existence of a second pathway for cholate degradation. This potential new pathway was investigated with Novosphingobium sp. strain Chol11. A 7α-hydroxysteroid dehydratase encoded by hsh2 was identified, which was required for the formation of 3-keto-7-deoxy-Δ 4,6 -metabolites. A hsh2 deletion mutant could still grow with cholate but showed impaired growth. Cholate degradation of this mutant proceeded via 3-keto-Δ 1,4 -diene metabolites. Heterologous expression of Hsh2 in the bile salt-degrading Pseudomonas sp. strain Chol1 led to the formation of a dead-end steroid with a 3-keto-7-deoxy-Δ 4,6 -diene structure. Hsh2 is the first steroid dehydratase with an important function in a metabolic pathway of bacteria that use bile salts as growth substrates. This pathway contributes to a broad metabolic repertoire of Novosphingobium strain Chol11 that may be advantageous in competition with other bile salt-degrading bacteria. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Phytosphingosine degradation pathway includes fatty acid α-oxidation reactions in the endoplasmic reticulum.

PubMed

Kitamura, Takuya; Seki, Naoya; Kihara, Akio

2017-03-28

Although normal fatty acids (FAs) are degraded via β-oxidation, unusual FAs such as 2-hydroxy (2-OH) FAs and 3-methyl-branched FAs are degraded via α-oxidation. Phytosphingosine (PHS) is one of the long-chain bases (the sphingolipid components) and exists in specific tissues, including the epidermis and small intestine in mammals. In the degradation pathway, PHS is converted to 2-OH palmitic acid and then to pentadecanoic acid (C15:0-COOH) via FA α-oxidation. However, the detailed reactions and genes involved in the α-oxidation reactions of the PHS degradation pathway have yet to be determined. In the present study, we reveal the entire PHS degradation pathway: PHS is converted to C15:0-COOH via six reactions [phosphorylation, cleavage, oxidation, CoA addition, cleavage (C1 removal), and oxidation], in which the last three reactions correspond to the α-oxidation. The aldehyde dehydrogenase ALDH3A2 catalyzes both the first and second oxidation reactions (fatty aldehydes to FAs). In Aldh3a2 -deficient cells, the unmetabolized fatty aldehydes are reduced to fatty alcohols and are incorporated into ether-linked glycerolipids. We also identify HACL2 (2-hydroxyacyl-CoA lyase 2) [previous name, ILVBL; ilvB (bacterial acetolactate synthase)-like] as the major 2-OH acyl-CoA lyase involved in the cleavage (C1 removal) reaction in the FA α-oxidation of the PHS degradation pathway. HACL2 is localized in the endoplasmic reticulum. Thus, in addition to the already-known FA α-oxidation in the peroxisomes, we have revealed the existence of FA α-oxidation in the endoplasmic reticulum in mammals.

Putative pathway of sex pheromone biosynthesis and degradation by expression patterns of genes identified from female pheromone gland and adult antenna of Sesamia inferens (Walker).

PubMed

Zhang, Ya-Nan; Xia, Yi-Han; Zhu, Jia-Yao; Li, Sheng-Yun; Dong, Shuang-Lin

2014-05-01

The general pathway of biosynthesis and degradation for Type-I sex pheromones in moths is well established, but some genes involved in this pathway remain to be characterized. The purple stem borer, Sesamia inferens, employs a pheromone blend containing components with three different terminal functional groups (Z11-16:OAc, Z11-16:OH, and Z11-16:Ald) of Type-I sex pheromones. Thus, it provides a good model to study the diversity of genes involved in pheromone biosynthesis and degradation pathways. By analyzing previously obtained transcriptomic data of the sex pheromone glands and antennae, we identified 73 novel genes that are possibly related to pheromone biosynthesis (46 genes) or degradation (27 genes). Gene expression patterns and phylogenetic analysis revealed that one desaturase (SinfDes4), one fatty acid reductase (SinfFAR2), and one fatty acid xtransport protein (SinfFATP1) genes were predominantly expressed in pheromone glands, and clustered with genes involved in pheromone synthesis in other moth species. Ten genes including five carboxylesterases (SinfCXE10, 13, 14, 18, and 20), three aldehyde oxidases (SinfAOX1, 2 and 3), and two alcohol dehydrogenases (SinfAD1 and 3) were expressed specifically or predominantly in antennae, and could be candidate genes involved in pheromone degradation. SinfAD1 and 3 are the first reported alcohol dehydrogenase genes with antennae-biased expression. Based on these results we propose a pathway involving these potential enzyme-encoding gene candidates in sex pheromone biosynthesis and degradation in S. inferens. This study provides robust background information for further elucidation of the genetic basis of sex pheromone biosynthesis and degradation, and ultimately provides potential targets to disrupt sexual communication in S. inferens for control purposes.

Evidence for the involvement of the anthranilate degradation pathway in Pseudomonas aeruginosa biofilm formation

PubMed Central

Costaglioli, Patricia; Barthe, Christophe; Claverol, Stephane; Brözel, Volker S; Perrot, Michel; Crouzet, Marc; Bonneu, Marc; Garbay, Bertrand; Vilain, Sebastien

2012-01-01

Bacterial biofilms are complex cell communities found attached to surfaces and surrounded by an extracellular matrix composed of exopolysaccharides, DNA, and proteins. We investigated the whole-genome expression profile of Pseudomonas aeruginosa sessile cells (SCs) present in biofilms developed on a glass wool substratum. The transcriptome and proteome of SCs were compared with those of planktonic cell cultures. Principal component analysis revealed a biofilm-specific gene expression profile. Our study highlighted the overexpression of genes controlling the anthranilate degradation pathway in the SCs grown on glass wool for 24 h. In this condition, the metabolic pathway that uses anthranilate for Pseudomonas quinolone signal production was not activated, which suggested that anthranilate was primarily being consumed for energy metabolism. Transposon mutants defective for anthranilate degradation were analyzed in a simple assay of biofilm formation. The phenotypic analyses confirmed that P. aeruginosa biofilm formation partially depended on the activity of the anthranilate degradation pathway. This work points to a new feature concerning anthranilate metabolism in P. aeruginosa SCs. PMID:23170231

Metagenomic analysis of the pinewood nematode microbiome reveals a symbiotic relationship critical for xenobiotics degradation

PubMed Central

Cheng, Xin-Yue; Tian, Xue-Liang; Wang, Yun-Sheng; Lin, Ren-Miao; Mao, Zhen-Chuan; Chen, Nansheng; Xie, Bing-Yan

2013-01-01

Our recent research revealed that pinewood nematode (PWN) possesses few genes encoding enzymes for degrading α-pinene, which is the main compound in pine resin. In this study, we examined the role of PWN microbiome in xenobiotics detoxification by metagenomic and bacteria culture analyses. Functional annotation of metagenomes illustrated that benzoate degradation and its related metabolisms may provide the main metabolic pathways for xenobiotics detoxification in the microbiome, which is obviously different from that in PWN that uses cytochrome P450 metabolism as the main pathway for detoxification. The metabolic pathway of degrading α-pinene is complete in microbiome, but incomplete in PWN genome. Experimental analysis demonstrated that most of tested cultivable bacteria can not only survive the stress of 0.4% α-pinene, but also utilize α-pinene as carbon source for their growth. Our results indicate that PWN and its microbiome have established a potentially mutualistic symbiotic relationship with complementary pathways in detoxification metabolism. PMID:23694939

E3 ubiquitin ligase Mule targets β-catenin under conditions of hyperactive Wnt signaling

PubMed Central

Dominguez-Brauer, Carmen; Khatun, Rahima; Elia, Andrew J.; Thu, Kelsie L.; Ramachandran, Parameswaran; Baniasadi, Shakiba P.; Hao, Zhenyue; Jones, Lisa D.; Haight, Jillian; Sheng, Yi; Mak, Tak W.

2017-01-01

Wnt signaling, named after the secreted proteins that bind to cell surface receptors to activate the pathway, plays critical roles both in embryonic development and the maintenance of homeostasis in many adult tissues. Two particularly important cellular programs orchestrated by Wnt signaling are proliferation and stem cell self-renewal. Constitutive activation of the Wnt pathway resulting from mutation or improper modulation of pathway components contributes to cancer development in various tissues. Colon cancers frequently bear inactivating mutations of the adenomatous polyposis coli (APC) gene, whose product is an important component of the destruction complex that regulates β-catenin levels. Stabilization and nuclear localization of β-catenin result in the expression of a panel of Wnt target genes. We previously showed that Mule/Huwe1/Arf-BP1 (Mule) controls murine intestinal stem and progenitor cell proliferation by modulating the Wnt pathway via c-Myc. Here we extend our investigation of Mule’s influence on oncogenesis by showing that Mule interacts directly with β-catenin and targets it for degradation under conditions of hyperactive Wnt signaling. Our findings suggest that Mule uses various mechanisms to fine-tune the Wnt pathway and provides multiple safeguards against tumorigenesis. PMID:28137882

E3 ubiquitin ligase Mule targets β-catenin under conditions of hyperactive Wnt signaling.

PubMed

Dominguez-Brauer, Carmen; Khatun, Rahima; Elia, Andrew J; Thu, Kelsie L; Ramachandran, Parameswaran; Baniasadi, Shakiba P; Hao, Zhenyue; Jones, Lisa D; Haight, Jillian; Sheng, Yi; Mak, Tak W

2017-02-14

Wnt signaling, named after the secreted proteins that bind to cell surface receptors to activate the pathway, plays critical roles both in embryonic development and the maintenance of homeostasis in many adult tissues. Two particularly important cellular programs orchestrated by Wnt signaling are proliferation and stem cell self-renewal. Constitutive activation of the Wnt pathway resulting from mutation or improper modulation of pathway components contributes to cancer development in various tissues. Colon cancers frequently bear inactivating mutations of the adenomatous polyposis coli ( APC ) gene, whose product is an important component of the destruction complex that regulates β-catenin levels. Stabilization and nuclear localization of β-catenin result in the expression of a panel of Wnt target genes. We previously showed that Mule/Huwe1/Arf-BP1 (Mule) controls murine intestinal stem and progenitor cell proliferation by modulating the Wnt pathway via c-Myc. Here we extend our investigation of Mule's influence on oncogenesis by showing that Mule interacts directly with β-catenin and targets it for degradation under conditions of hyperactive Wnt signaling. Our findings suggest that Mule uses various mechanisms to fine-tune the Wnt pathway and provides multiple safeguards against tumorigenesis.

Jab1 Mediates Protein Degradation of Rad9/Rad1/Hus1 Checkpoint Complex

PubMed Central

Huang, Jin; Yuan, Honglin; Lu, Chongyuan; Liu, Ximeng; Cao, Xu; Wan, Mei

2009-01-01

Summary The Rad1-Rad9-Hus1 (9-1-1) complex serves a dual role as a DNA-damage sensor in checkpoint signaling and as a mediator in DNA repair pathway. However, the intercellular mechanisms that regulate 9-1-1 complex are poorly understood. Jab1, the fifth component of the COP9 signalosome complex, plays a central role in the degradation of multiple proteins and is emerging as an important regulator in cancer development. Here, we tested the hypothesis that Jab1 controls the protein stability of the 9-1-1 complex via the proteosome pathway. We provide evidence that Jab1 physically associates with the 9-1-1 complex. This association is mediated through direct interaction between Jab1 and Rad1, one of the subunits of 9-1-1 complex. Importantly, Jab1 causes the translocation of the 9-1-1 complex from the nucleus to the cytoplasm, mediating rapid degradation of the 9-1-1 complex via 26S proteasome. Furthermore, Jab1 significantly suppresses checkpoint signaling activation, DNA synthesis recovery from blockage and cell viability after replication stresses such as UV exposure, γ radiation and hydroxyurea treatment. These results suggest that Jab1 is an important regulator for 9-1-1 protein stability control in cells, which may provide novel information on the involvement of Jab1 in checkpoint and DNA repair signaling in response to DNA damage. PMID:17583730

Characterization of endoplasmic reticulum-associated degradation of a protein S mutant identified in a family of quantitative protein S deficiency.

PubMed

Tsuda, Hiroko; Tokunaga, Fuminori; Nagamitsu, Hiroshi; Koide, Takehiko

2006-01-01

Misfolded and unassembled glycoproteins are eliminated from the endoplasmic reticulum (ER) lumen by the ER-associated degradation (ERAD). We previously identified a Tyr595Cys (Y595C) mutation of protein S (PS) in a family of a quantitative PS deficiency. The mutation causes intracellular degradation and decreased secretion of the Y595C mutant PS. The aim of the present study was to further characterize the molecular basis of the intracellular degradation of the mutant. We stably expressed the mutant in mammalian cells, and analyzed the intracellular localization of the protein. The intracellular degradation pathway was determined by pulse-chase analyses in the presence of various inhibitors of ERAD. Endoglycosidase H digestion and immunofluorescence staining revealed the mutant being retained in the ER. Epoxomicin, a potent and specific proteasome inhibitor, and Ala-Ala-Phe-CH(2)Cl (AAF), an inhibitor of tripeptidyl peptidase II (TPPII), suppressed the intracellular degradation of the mutant by about 65% and 50%, respectively. When epoxomicin was combined with AAF, the inhibitory effect was substantially enhanced. Although castanospermine, an inhibitor of glucosidases I and II, did not affect the degradation, kifunensine, an inhibitor of ER mannosidase I, suppressed it. Thus, it appears that the Y595C mutant is degraded through more than one pathway of ERAD, including the proteasome-dependent pathway and an alternate proteasome-independent pathway where proteases such as TPPII may be involved. Production of the critical B isoform of Man(8)GlcNAc(2) targets the mutant for ERAD, however, the interaction with calnexin/calreticulin through monoglucosylated oligosaccharides may not be required for the degradation of the mutant.

Comparative Proteomics Analysis Reveals L-Arginine Activates Ethanol Degradation Pathways in HepG2 Cells.

PubMed

Yan, Guokai; Lestari, Retno; Long, Baisheng; Fan, Qiwen; Wang, Zhichang; Guo, Xiaozhen; Yu, Jie; Hu, Jun; Yang, Xingya; Chen, Changqing; Liu, Lu; Li, Xiuzhi; Purnomoadi, Agung; Achmadi, Joelal; Yan, Xianghua

2016-03-17

L-Arginine (Arg) is a versatile amino acid that plays crucial roles in a wide range of physiological and pathological processes. In this study, to investigate the alteration induced by Arg supplementation in proteome scale, isobaric tags for relative and absolute quantification (iTRAQ) based proteomic approach was employed to comparatively characterize the differentially expressed proteins between Arg deprivation (Ctrl) and Arg supplementation (+Arg) treated human liver hepatocellular carcinoma (HepG2) cells. A total of 21 proteins were identified as differentially expressed proteins and these 21 proteins were all up-regulated by Arg supplementation. Six amino acid metabolism-related proteins, mostly metabolic enzymes, showed differential expressions. Intriguingly, Ingenuity Pathway Analysis (IPA) based pathway analysis suggested that the three ethanol degradation pathways were significantly altered between Ctrl and +Arg. Western blotting and enzymatic activity assays validated that the key enzymes ADH1C, ALDH1A1, and ALDH2, which are mainly involved in ethanol degradation pathways, were highly differentially expressed, and activated between Ctrl and +Arg in HepG2 cells. Furthermore, 10 mM Arg significantly attenuated the cytotoxicity induced by 100 mM ethanol treatment (P < 0.0001). This study is the first time to reveal that Arg activates ethanol degradation pathways in HepG2 cells.

BadR and BadM Proteins Transcriptionally Regulate Two Operons Needed for Anaerobic Benzoate Degradation by Rhodopseudomonas palustris

PubMed Central

Hirakawa, Hidetada; Hirakawa, Yuko; Greenberg, E. Peter

2015-01-01

The bacterium Rhodopseudomonas palustris grows with the aromatic acid benzoate and the alicyclic acid cyclohexanecarboxylate (CHC) as sole carbon sources. The enzymatic steps in an oxygen-independent pathway for CHC degradation have been elucidated, but it was unknown how the CHC operon (badHI aliAB badK) encoding the enzymes for CHC degradation was regulated. aliA and aliB encode enzymes for the conversion of CHC to cyclohex-1-enecarboxyl–coenzyme A (CHene-CoA). At this point, the pathway for CHC degradation merges with the pathway for anaerobic benzoate degradation, as CHene-CoA is an intermediate in both degradation pathways. Three enzymes, encoded by badK, badH, and badI, prepare and cleave the alicyclic ring of CHene-CoA to yield pimelyl-CoA. Here, we show that the MarR transcription factor family member, BadR, represses transcription of the CHC operon by binding near the transcription start site of badH. 2-Ketocyclohexane-1-carboxyl–CoA, an intermediate of CHC and benzoate degradation, interacts with BadR to abrogate repression. We also present evidence that the transcription factor BadM binds to the promoter of the badDEFGAB (Bad) operon for the anaerobic conversion of benzoate to CHene-CoA to repress its expression. Contrary to previous reports, BadR does not appear to control expression of the Bad operon. These data enhance our view of the transcriptional regulation of anaerobic benzoate degradation by R. palustris. PMID:25888170

A novel pathway for nicotine degradation by Aspergillus oryzae 112822 isolated from tobacco leaves.

PubMed

Meng, Xiang Jing; Lu, Li Li; Gu, Guo Feng; Xiao, Min

2010-09-01

An efficient nicotine-degrading fungus was isolated from tobacco leaves and identified as Aspergillus oryzae 112822 based on morphological characteristics and sequence analysis of 18S rDNA, 5.8S rDNA and the internal transcribed spacer (5.8S-ITS region). When the strain was cultured in a medium with tobacco leaf extract for 40 h, the maximum amount of cell growth was 3.6 g l(-1) and nicotine degradation was 2.19 g l(-1). The intermediates of nicotine degradation by resting cells were isolated by preparative TLC or semi-preparative HPLC, and identified by TLC, MS, NMR, Fourier-transform (FT)-IR and GC-MS analysis. The pathway for nicotine degradation in A. oryzae 112822 was proposed to be from nicotine to 2,3-dihydroxypyridine through the intermediates nornicotine, myosmine, N-methylnicotinamide and 2-hydroxy-N-methylnicotinamide. The ring of 2,3-dihydroxypyridine was opened between the 2- and 3-hydroxy positions to yield succinic acid. N-methylnicotinamide and 2,3-dihydroxypyridine were satisfactorily verified as metabolites of nicotine degradation. This is the first elucidation of a pathway for nicotine degradation in fungi. Copyright 2010 Elsevier Masson SAS. All rights reserved.

Arsenic degrades PML or PML-RARalpha through a SUMO-triggered RNF4/ubiquitin-mediated pathway.

PubMed

Lallemand-Breitenbach, Valérie; Jeanne, Marion; Benhenda, Shirine; Nasr, Rihab; Lei, Ming; Peres, Laurent; Zhou, Jun; Zhu, Jun; Raught, Brian; de Thé, Hugues

2008-05-01

In acute promyelocytic leukaemia (APL), arsenic trioxide induces degradation of the fusion protein encoded by the PML-RARA oncogene, differentiation of leukaemic cells and produces clinical remissions. SUMOylation of its PML moiety was previously implicated, but the nature of the degradation pathway involved and the role of PML-RARalpha catabolism in the response to therapy have both remained elusive. Here, we demonstrate that arsenic-induced PML SUMOylation triggers its Lys 48-linked polyubiquitination and proteasome-dependent degradation. When exposed to arsenic, SUMOylated PML recruits RNF4, the human orthologue of the yeast SUMO-dependent E3 ubiquitin-ligase, as well as ubiquitin and proteasomes onto PML nuclear bodies. Arsenic-induced differentiation is impaired in cells transformed by a non-degradable PML-RARalpha SUMOylation mutant or in APL cells transduced with a dominant-negative RNF4, directly implicating PML-RARalpha catabolism in the therapeutic response. We thus identify PML as the first protein degraded by SUMO-dependent polyubiquitination. As PML SUMOylation recruits not only RNF4, ubiquitin and proteasomes, but also many SUMOylated proteins onto PML nuclear bodies, these domains could physically integrate the SUMOylation, ubiquitination and degradation pathways.

Mutants of Pseudomonas cepacia G4 defective in catabolism of aromatic compounds and trichloroethylene.

PubMed Central

Shields, M S; Montgomery, S O; Cuskey, S M; Chapman, P J; Pritchard, P H

1991-01-01

Pseudomonas cepacia G4 possesses a novel pathway of toluene catabolism that is shown to be responsible for the degradation of trichloroethylene (TCE). This pathway involves conversion of toluene via o-cresol to 3-methylcatechol. In order to determine the enzyme of toluene degradation that is responsible for TCE degradation, chemically induced mutants, blocked in the toluene ortho-monooxygenase (TOM) pathway of G4, were examined. Mutants of the phenotypic class designated TOM A- were all defective in their ability to oxidize toluene, o-cresol, m-cresol, and phenol, suggesting that a single enzyme is responsible for conversion of these compounds to their hydroxylated products (3-methylcatechol from toluene, o-cresol, and m-cresol and catechol from phenol) in the wild type. Mutants of this class did not degrade TCE. Two other mutant classes which were blocked in toluene catabolism, TOM B-, which lacked catechol-2,3-dioxygenase, and TOM C-, which lacked 2-hydroxy-6-oxoheptadienoic acid hydrolase activity, were fully capable of TCE degradation. Therefore, TCE degradation is directly associated with the monooxygenation capability responsible for toluene, cresol, and phenol hydroxylation. PMID:1892384

Anaerobic benzene degradation by bacteria

PubMed Central

Vogt, Carsten; Kleinsteuber, Sabine; Richnow, Hans‐Hermann

2011-01-01

Summary Benzene is a widespread and toxic contaminant. The fate of benzene in contaminated aquifers seems to be primarily controlled by the abundance of oxygen: benzene is aerobically degraded at high rates by ubiquitous microorganisms, and the oxygen‐dependent pathways for its breakdown were elucidated more than 50 years ago. In contrast, benzene was thought to be persistent under anoxic conditions until 25 years ago. Nevertheless, within the last 15 years, several benzene‐degrading cultures have been enriched under varying electron acceptor conditions in laboratories around the world, and organisms involved in anaerobic benzene degradation have been identified, indicating that anaerobic benzene degradation is a relevant environmental process. However, only a few benzene degraders have been isolated in pure culture so far, and they all use nitrate as an electron acceptor. In some highly enriched strictly anaerobic cultures, benzene has been described to be mineralized cooperatively by two or more different organisms. Despite great efforts, the biochemical mechanism by which the aromatic ring of benzene is activated in the absence of oxygen is still not fully elucidated; methylation, hydroxylation and carboxylation are discussed as likely reactions. This review summarizes the current knowledge about the ‘key players’ of anaerobic benzene degradation under different electron acceptor conditions and the possible pathway(s) of anaerobic benzene degradation. PMID:21450012

Reductive and oxidative degradation of iopamidol, iodinated X-ray contrast media, by Fe(III)-oxalate under UV and visible light treatment.

PubMed

Zhao, Cen; Arroyo-Mora, Luis E; DeCaprio, Anthony P; Sharma, Virender K; Dionysiou, Dionysios D; O'Shea, Kevin E

2014-12-15

Iopamidol, widely employed as iodinated X-ray contrast media (ICM), is readily degraded in a Fe(III)-oxalate photochemical system under UV (350 nm) and visible light (450 nm) irradiation. The degradation is nicely modeled by pseudo first order kinetics. The rates of hydroxyl radical (OH) production for Fe(III)-oxalate/H2O2/UV (350 nm) and Fe(III)-oxalate/H2O2/visible (450 nm) systems were 1.19 ± 0.12 and 0.30 ± 0.01 μM/min, respectively. The steady-state concentration of hydroxyl radical (OH) for the Fe(III)-oxalate/H2O2/UV (350 nm) conditions was 10.88 ± 1.13 × 10(-14) M and 2.7 ± 0.1 × 10(-14) M for the Fe(III)-oxalate/H2O2/visible (450 nm). The rate of superoxide anion radical (O2(-)) production under Fe(III)-oxalate/H2O2/UV (350 nm) was 0.19 ± 0.02 μM/min with a steady-state concentration of 5.43 ± 0.473 × 10(-10) M. Detailed product studies using liquid chromatography coupled to Q-TOF/MS demonstrate both reduction (multiple dehalogenations) and oxidation (aromatic ring and side chains) contribute to the degradation pathways. The reduction processes appear to be initiated by the carbon dioxide anion radical (CO2(-)) while oxidation processes are consistent with OH initiated reaction pathways. Unlike most advanced oxidation processes the Fe(III)-oxalate/H2O2/photochemical system can initiate to both reductive and oxidative degradation processes. The observed reductive dehalogenation is an attractive remediation strategy for halogenated organic compounds as the process can dramatically reduce the formation of the problematic disinfection by-products often associated with oxidative treatment processes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Degradation of Serotonin N-Acetyltransferase, a Circadian Regulator, by the N-end Rule Pathway.

PubMed

Wadas, Brandon; Borjigin, Jimo; Huang, Zheping; Oh, Jang-Hyun; Hwang, Cheol-Sang; Varshavsky, Alexander

2016-08-12

Serotonin N-acetyltransferase (AANAT) converts serotonin to N-acetylserotonin (NAS), a distinct biological regulator and the immediate precursor of melatonin, a circulating hormone that influences circadian processes, including sleep. N-terminal sequences of AANAT enzymes vary among vertebrates. Mechanisms that regulate the levels of AANAT are incompletely understood. Previous findings were consistent with the possibility that AANAT may be controlled through its degradation by the N-end rule pathway. By expressing the rat and human AANATs and their mutants not only in mammalian cells but also in the yeast Saccharomyces cerevisiae, and by taking advantage of yeast genetics, we show here that two "complementary" forms of rat AANAT are targeted for degradation by two "complementary" branches of the N-end rule pathway. Specifically, the N(α)-terminally acetylated (Nt-acetylated) Ac-AANAT is destroyed through the recognition of its Nt-acetylated N-terminal Met residue by the Ac/N-end rule pathway, whereas the non-Nt-acetylated AANAT is targeted by the Arg/N-end rule pathway, which recognizes the unacetylated N-terminal Met-Leu sequence of rat AANAT. We also show, by constructing lysine-to-arginine mutants of rat AANAT, that its degradation is mediated by polyubiquitylation of its Lys residue(s). Human AANAT, whose N-terminal sequence differs from that of rodent AANATs, is longer-lived than its rat counterpart and appears to be refractory to degradation by the N-end rule pathway. Together, these and related results indicate both a major involvement of the N-end rule pathway in the control of rodent AANATs and substantial differences in the regulation of rodent and human AANATs that stem from differences in their N-terminal sequences. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Dysfunction of different cellular degradation pathways contributes to specific β-amyloid42-induced pathologies.

PubMed

Ji, Xuan-Ru; Cheng, Kuan-Chung; Chen, Yu-Ru; Lin, Tzu-Yu; Cheung, Chun Hei Antonio; Wu, Chia-Lin; Chiang, Hsueh-Cheng

2018-03-01

The endosomal-lysosomal system (ELS), autophagy, and ubiquitin-proteasome system (UPS) are cellular degradation pathways that each play a critical role in the removal of misfolded proteins and the prevention of the accumulation of abnormal proteins. Recent studies on Alzheimer's disease (AD) pathogenesis have suggested that accumulation of aggregated β-amyloid (Aβ) peptides in the AD brain results from a dysfunction in these cellular clearance systems. However, the specific roles of these pathways in the removal of Aβ peptides and the pathogenesis underlying AD are unclear. Our in vitro and in vivo genetic approaches revealed that ELS mainly removed monomeric β-amyloid42 (Aβ42), while autophagy and UPS clear oligomeric Aβ42. Although overproduction of phosphatidylinositol 4-phosphate-5 increased Aβ42 clearance, it reduced the life span of Aβ42 transgenic flies. Our behavioral studies further demonstrated impaired autophagy and UPS-enhanced Aβ42-induced learning and memory deficits, but there was no effect on Aβ42-induced reduction in life span. Results from genetic fluorescence imaging showed that these pathways were damaged in the following order: UPS, autophagy, and finally ELS. The results of our study demonstrate that different degradation pathways play distinct roles in the removal of Aβ42 aggregates and in disease progression. These findings also suggest that pharmacologic treatments that are designed to stimulate cellular degradation pathways in patients with AD should be used with caution.-Ji, X.-R., Cheng, K.-C., Chen, Y.-R., Lin, T.-Y., Cheung, C. H. A., Wu, C.-L., Chiang, H.-C. Dysfunction of different cellular degradation pathways contributes to specific β-amyloid42-induced pathologies.

Simultaneous knockdown of six non-family genes using a single synthetic RNAi fragment in Arabidopsis thaliana

DOE Office of Scientific and Technical Information (OSTI.GOV)

Czarnecki, Olaf; Bryan, Anthony C.; Jawdy, Sara S.

Genetic engineering of plants that results in successful establishment of new biochemical or regulatory pathways requires stable introduction of one or more genes into the plant genome. It might also be necessary to down-regulate or turn off expression of endogenous genes in order to reduce activity of competing pathways. An established way to knockdown gene expression in plants is expressing a hairpin-RNAi construct, eventually leading to degradation of a specifically targeted mRNA. Knockdown of multiple genes that do not share homologous sequences is still challenging and involves either sophisticated cloning strategies to create vectors with different serial expression constructs ormore » multiple transformation events that is often restricted by a lack of available transformation markers. Synthetic RNAi fragments were assembled in yeast carrying homologous sequences to six or seven non-family genes and introduced into pAGRIKOLA. Transformation of Arabidopsis thaliana and subsequent expression analysis of targeted genes proved efficient knockdown of all target genes. In conclusion, we present a simple and cost-effective method to create constructs to simultaneously knockdown multiple non-family genes or genes that do not share sequence homology. The presented method can be applied in plant and animal synthetic biology as well as traditional plant and animal genetic engineering.« less

Simultaneous knockdown of six non-family genes using a single synthetic RNAi fragment in Arabidopsis thaliana

DOE PAGES

Czarnecki, Olaf; Bryan, Anthony C.; Jawdy, Sara S.; ...

2016-02-17

Genetic engineering of plants that results in successful establishment of new biochemical or regulatory pathways requires stable introduction of one or more genes into the plant genome. It might also be necessary to down-regulate or turn off expression of endogenous genes in order to reduce activity of competing pathways. An established way to knockdown gene expression in plants is expressing a hairpin-RNAi construct, eventually leading to degradation of a specifically targeted mRNA. Knockdown of multiple genes that do not share homologous sequences is still challenging and involves either sophisticated cloning strategies to create vectors with different serial expression constructs ormore » multiple transformation events that is often restricted by a lack of available transformation markers. Synthetic RNAi fragments were assembled in yeast carrying homologous sequences to six or seven non-family genes and introduced into pAGRIKOLA. Transformation of Arabidopsis thaliana and subsequent expression analysis of targeted genes proved efficient knockdown of all target genes. In conclusion, we present a simple and cost-effective method to create constructs to simultaneously knockdown multiple non-family genes or genes that do not share sequence homology. The presented method can be applied in plant and animal synthetic biology as well as traditional plant and animal genetic engineering.« less

Noncoding Subgenomic Flavivirus RNA: Multiple Functions in West Nile Virus Pathogenesis and Modulation of Host Responses

PubMed Central

Roby, Justin A.; Pijlman, Gorben P.; Wilusz, Jeffrey; Khromykh, Alexander A.

2014-01-01

Flaviviruses are a large group of positive strand RNA viruses transmitted by arthropods that include many human pathogens such as West Nile virus (WNV), Japanese encephalitis virus (JEV), yellow fever virus, dengue virus, and tick-borne encephalitis virus. All members in this genus tested so far are shown to produce a unique subgenomic flavivirus RNA (sfRNA) derived from the 3' untranslated region (UTR). sfRNA is a product of incomplete degradation of genomic RNA by the cell 5'–3' exoribonuclease XRN1 which stalls at highly ordered secondary RNA structures at the beginning of the 3'UTR. Generation of sfRNA results in inhibition of XRN1 activity leading to an increase in stability of many cellular mRNAs. Mutant WNV deficient in sfRNA generation was highly attenuated displaying a marked decrease in cytopathicity in cells and pathogenicity in mice. sfRNA has also been shown to inhibit the antiviral activity of IFN-α/β by yet unknown mechanism and of the RNAi pathway by likely serving as a decoy substrate for Dicer. Thus, sfRNA is involved in modulating multiple cellular pathways to facilitate viral pathogenicity; however the overlying mechanism linking all these multiple functions of sfRNA remains to be elucidated. PMID:24473339

A non-canonical RNA degradation pathway suppresses RNAi-dependent epimutations in the human fungal pathogen Mucor circinelloides.

PubMed

Calo, Silvia; Nicolás, Francisco E; Lee, Soo Chan; Vila, Ana; Cervantes, Maria; Torres-Martinez, Santiago; Ruiz-Vazquez, Rosa M; Cardenas, Maria E; Heitman, Joseph

2017-03-01

Mucorales are a group of basal fungi that includes the casual agents of the human emerging disease mucormycosis. Recent studies revealed that these pathogens activate an RNAi-based pathway to rapidly generate drug-resistant epimutant strains when exposed to stressful compounds such as the antifungal drug FK506. To elucidate the molecular mechanism of this epimutation pathway, we performed a genetic analysis in Mucor circinelloides that revealed an inhibitory role for the non-canonical RdRP-dependent Dicer-independent silencing pathway, which is an RNAi-based mechanism involved in mRNA degradation that was recently identified. Thus, mutations that specifically block the mRNA degradation pathway, such as those in the genes r3b2 and rdrp3, enhance the production of drug resistant epimutants, similar to the phenotype previously described for mutation of the gene rdrp1. Our genetic analysis also revealed two new specific components of the epimutation pathway related to the quelling induced protein (qip) and a Sad-3-like helicase (rnhA), as mutations in these genes prevented formation of drug-resistant epimutants. Remarkably, drug-resistant epimutant production was notably increased in M. circinelloides f. circinelloides isolates from humans or other animal hosts. The host-pathogen interaction could be a stressful environment in which the phenotypic plasticity provided by the epimutant pathway might provide an advantage for these strains. These results evoke a model whereby balanced regulation of two different RNAi pathways is determined by the activation of the RNAi-dependent epimutant pathway under stress conditions, or its repression when the regular maintenance of the mRNA degradation pathway operates under non-stress conditions.

Genes Involved in Degradation of para-Nitrophenol Are Differentially Arranged in Form of Non-Contiguous Gene Clusters in Burkholderia sp. strain SJ98

PubMed Central

Vikram, Surendra; Pandey, Janmejay; Kumar, Shailesh; Raghava, Gajendra Pal Singh

2013-01-01

Biodegradation of para-Nitrophenol (PNP) proceeds via two distinct pathways, having 1,2,3-benzenetriol (BT) and hydroquinone (HQ) as their respective terminal aromatic intermediates. Genes involved in these pathways have already been studied in different PNP degrading bacteria. Burkholderia sp. strain SJ98 degrades PNP via both the pathways. Earlier, we have sequenced and analyzed a ~41 kb fragment from the genomic library of strain SJ98. This DNA fragment was found to harbor all the lower pathway genes; however, genes responsible for the initial transformation of PNP could not be identified within this fragment. Now, we have sequenced and annotated the whole genome of strain SJ98 and found two ORFs (viz., pnpA and pnpB) showing maximum identity at amino acid level with p-nitrophenol 4-monooxygenase (PnpM) and p-benzoquinone reductase (BqR). Unlike the other PNP gene clusters reported earlier in different bacteria, these two ORFs in SJ98 genome are physically separated from the other genes of PNP degradation pathway. In order to ascertain the identity of ORFs pnpA and pnpB, we have performed in-vitro assays using recombinant proteins heterologously expressed and purified to homogeneity. Purified PnpA was found to be a functional PnpM and transformed PNP into benzoquinone (BQ), while PnpB was found to be a functional BqR which catalyzed the transformation of BQ into hydroquinone (HQ). Noticeably, PnpM from strain SJ98 could also transform a number of PNP analogues. Based on the above observations, we propose that the genes for PNP degradation in strain SJ98 are arranged differentially in form of non-contiguous gene clusters. This is the first report for such arrangement for gene clusters involved in PNP degradation. Therefore, we propose that PNP degradation in strain SJ98 could be an important model system for further studies on differential evolution of PNP degradation functions. PMID:24376843

Molecular chaperone Hsp27 regulates the Hippo tumor suppressor pathway in cancer

PubMed Central

Vahid, Sepideh; Thaper, Daksh; Gibson, Kate F.; Bishop, Jennifer L.; Zoubeidi, Amina

2016-01-01

Heat shock protein 27 (Hsp27) is a molecular chaperone highly expressed in aggressive cancers, where it is involved in numerous pro-tumorigenic signaling pathways. Using functional genomics we identified for the first time that Hsp27 regulates the gene signature of transcriptional co-activators YAP and TAZ, which are negatively regulated by the Hippo Tumor Suppressor pathway. The Hippo pathway inactivates YAP by phosphorylating and increasing its cytoplasmic retention with the 14.3.3 proteins. Gain and loss of function experiments in prostate, breast and lung cancer cells showed that Hsp27 knockdown induced YAP phosphorylation and cytoplasmic localization while overexpression of Hsp27 displayed opposite results. Mechanistically, Hsp27 regulates the Hippo pathway by accelerating the proteasomal degradation of ubiquitinated MST1, the core Hippo kinase, resulting in reduced phosphorylation/activity of LATS1 and MOB1, its downstream effectors. Importantly, our in vitro results were supported by data from human tumors; clinically, high expression of Hsp27 in prostate tumors is correlated with increased expression of YAP gene signature and reduced phosphorylation of YAP in lung and invasive breast cancer clinical samples. This study reveals for the first time a link between Hsp27 and the Hippo cascade, providing a novel mechanism of deregulation of this tumor suppressor pathway across multiple cancers. PMID:27555231

Molecular chaperone Hsp27 regulates the Hippo tumor suppressor pathway in cancer.

PubMed

Vahid, Sepideh; Thaper, Daksh; Gibson, Kate F; Bishop, Jennifer L; Zoubeidi, Amina

2016-08-24

Heat shock protein 27 (Hsp27) is a molecular chaperone highly expressed in aggressive cancers, where it is involved in numerous pro-tumorigenic signaling pathways. Using functional genomics we identified for the first time that Hsp27 regulates the gene signature of transcriptional co-activators YAP and TAZ, which are negatively regulated by the Hippo Tumor Suppressor pathway. The Hippo pathway inactivates YAP by phosphorylating and increasing its cytoplasmic retention with the 14.3.3 proteins. Gain and loss of function experiments in prostate, breast and lung cancer cells showed that Hsp27 knockdown induced YAP phosphorylation and cytoplasmic localization while overexpression of Hsp27 displayed opposite results. Mechanistically, Hsp27 regulates the Hippo pathway by accelerating the proteasomal degradation of ubiquitinated MST1, the core Hippo kinase, resulting in reduced phosphorylation/activity of LATS1 and MOB1, its downstream effectors. Importantly, our in vitro results were supported by data from human tumors; clinically, high expression of Hsp27 in prostate tumors is correlated with increased expression of YAP gene signature and reduced phosphorylation of YAP in lung and invasive breast cancer clinical samples. This study reveals for the first time a link between Hsp27 and the Hippo cascade, providing a novel mechanism of deregulation of this tumor suppressor pathway across multiple cancers.

Isolation of an isocarbophos-degrading strain of Arthrobacter sp. scl-2 and identification of the degradation pathway.

PubMed

Rong, Li; Guo, Xinqiang; Chen, Kai; Zhu, Jianchun; Li, Shunpeng; Jiang, Jiandong

2009-11-01

Isocarbophos is a widely used organophosphorus insecticide that has caused environmental pollution in many areas. However, degradation of isocarbophos by pure cultures has not been extensively studied, and the degradation pathway has not been determined. In this paper, a highly effective isocarbophos-degrading strain, scl-2, was isolated from isocarbophos-polluted soil. Strain scl-2 was preliminarily identified as Arthrobacter sp. based on its morphological, physiological, and biochemical properties, as well as 16S rDNA analysis. Strain scl-2 could utilize isocarbophos as its sole source of carbon and phosphorus for growth. One hundred mg/l isocarbophos could be degraded to a nondetectable level in 18 h by scl-2 in cell culture, and isofenphos-methyl, profenofos, and phosmet could also be degraded. During the degradation of isocarbophos, the metabolites isopropyl salicylate, salicylate, and gentisate were detected and identified based on MS/MS analysis and their retention times in HPLC. Transformation of gentisate to pyruvate and fumarate via maleylpyruvate and fumarylpyruvate was detected by assaying for the activities of gentisate 1,2- dioxygenase (GDO) and maleylpyruvate isomerase. Therefore, we have identified the degradation pathway of isocarbophos in Arthrobacter sp. scl-2 for the first time. This study highlights an important potential use of the strain scl-2 for the cleanup of environmental contamination by isocarbophos and presents a mechanism of isocarbophos metabolism.

Solar photocatalytic degradation of naphthenic acids in oil sands process-affected water.

PubMed

Leshuk, Tim; Wong, Timothy; Linley, Stuart; Peru, Kerry M; Headley, John V; Gu, Frank

2016-02-01

Bitumen mining in the Canadian oil sands creates large volumes of oil sands process-affected water (OSPW), the toxicity of which is due in part to naphthenic acids (NAs) and other acid extractable organics (AEO). The objective of this work was to evaluate the potential of solar photocatalysis over TiO2 to remove AEO from OSPW. One day of photocatalytic treatment under natural sunlight (25 MJ/m(2) over ∼14 h daylight) eradicated AEO from raw OSPW, and acute toxicity of the OSPW toward Vibrio fischeri was eliminated. Nearly complete mineralization of organic carbon was achieved within 1-7 day equivalents of sunlight exposure, and degradation was shown to proceed through a superoxide-mediated oxidation pathway. High resolution mass spectrometry (HRMS) analysis of oxidized intermediate compounds indicated preferential degradation of the heavier and more cyclic NAs (higher number of double bond equivalents), which are the most environmentally persistent fractions. The photocatalyst was shown to be recyclable for multiple uses, and thus solar photocatalysis may be a promising "green" advanced oxidation process (AOP) for OSPW treatment. Copyright © 2015 Elsevier Ltd. All rights reserved.

Synthetic Gene Network with Positive Feedback Loop Amplifies Cellulase Gene Expression in Neurospora crassa.

PubMed

Matsu-Ura, Toru; Dovzhenok, Andrey A; Coradetti, Samuel T; Subramanian, Krithika R; Meyer, Daniel R; Kwon, Jaesang J; Kim, Caleb; Salomonis, Nathan; Glass, N Louise; Lim, Sookkyung; Hong, Christian I

2018-05-18

Second-generation or lignocellulosic biofuels are a tangible source of renewable energy, which is critical to combat climate change by reducing the carbon footprint. Filamentous fungi secrete cellulose-degrading enzymes called cellulases, which are used for production of lignocellulosic biofuels. However, inefficient production of cellulases is a major obstacle for industrial-scale production of second-generation biofuels. We used computational simulations to design and implement synthetic positive feedback loops to increase gene expression of a key transcription factor, CLR-2, that activates a large number of cellulases in a filamentous fungus, Neurospora crassa. Overexpression of CLR-2 reveals previously unappreciated roles of CLR-2 in lignocellulosic gene network, which enabled simultaneous induction of approximately 50% of 78 lignocellulosic degradation-related genes in our engineered Neurospora strains. This engineering results in dramatically increased cellulase activity due to cooperative orchestration of multiple enzymes involved in the cellulose degradation pathway. Our work provides a proof of principle in utilizing mathematical modeling and synthetic biology to improve the efficiency of cellulase synthesis for second-generation biofuel production.

[Application of synthetic biology in environmental remediation].

PubMed

Tang, Hongzhi; Wang, Weiwei; Zhang, Lige; Huang, Ling; Lu, Xinyu; Xu, Ping

2017-03-25

Environmental problems are the most serious challenges in the 21st century. With the rapid development of modern industry and agriculture, ecological and environmental deterioration have become the most important factors to restrict the sustainable development of social economy. Microbial cells have strong ability for environmental remediation, but their evolution speed is slower than the speed of emerging pollutants. Therefore, the treatment using the synthetic biology is in urgent need. Full understanding of the microbial degradation characteristics (pathways) of refractory organic pollutants with the help of abundant microbial and gene resources in China is important. Using synthetic biology to redesign and transform the existing degrading strain will be used to degrade particular organic pollutants or multiple organic pollutants. For the complex pollutants, such as wastewater, based on the establishment of metabolic or regulation or resistance related gene modules of typical organic pollutants, artificial flora could be designed to solve the complex pollutants. The rational design and construction of engineering bacteria for typical environmental organic pollutants can effectively promote microbial catabolism of emerging contaminants, providing technical support for environmental remediation in China.

Photochemical Degradation of the Anticancer Drug Bortezomib by V-UV/UV (185/254 nm) Investigated by (1)H NMR Fingerprinting: A Way to Follow Aromaticity Evolution.

PubMed

Martignac, Marion; Balayssac, Stéphane; Gilard, Véronique; Benoit-Marquié, Florence

2015-06-18

We have investigated the removal of bortezomib, an anticancer drug prescribed in multiple myeloma, using the photochemical advanced oxidation process of V-UV/UV (185/254 nm). We used two complementary analytical techniques to follow the removal rate of bortezomib. Nuclear magnetic resonance (NMR) is a nonselective method requiring no prior knowledge of the structures of the byproducts and permits us to provide a spectral signature (fingerprinting approach). This untargeted method provides clues to the molecular structure changes and information on the degradation of the parent drug during the irradiation process. This holistic NMR approach could provide information for monitoring aromaticity evolution. We use liquid chromatography, coupled with high-resolution mass spectrometry (LC-MS), to correlate results obtained by (1)H NMR and for accurate identification of the byproducts, in order to understand the mechanistic degradation pathways of bortezomib. The results show that primary byproducts come from photoassisted deboronation of bortezomib at 254 nm. A secondary byproduct of pyrazinecarboxamide was also identified. We obtained a reliable correlation between these two analytical techniques.

Rescue of compromised lysosomes enhances degradation of photoreceptor outer segments and reduces lipofuscin-like autofluorescence in retinal pigmented epithelial cells.

PubMed

Guha, Sonia; Liu, Ji; Baltazar, Gabe; Laties, Alan M; Mitchell, Claire H

2014-01-01

Healthful cell maintenance requires the efficient degradative processing and removal of waste material. Retinal pigmented epithelial (RPE) cells have the onerous task of degrading both internal cellular debris generated through autophagy as well as phagocytosed photoreceptor outer segments. We propose that the inadequate processing material with the resulting accumulation of cellular waste contributes to the downstream pathologies characterized as age-related macular degeneration (AMD). The lysosomal enzymes responsible for clearance function optimally over a narrow range of acidic pH values; elevation of lysosomal pH by compounds like chloroquine or A2E can impair degradative enzyme activity and lead to a lipofuscin-like autofluorescence. Restoring acidity to the lysosomes of RPE cells can enhance activity of multiple degradative enzymes and is therefore a logical target in early AMD. We have identified several approaches to reacidify lysosomes of compromised RPE cells; stimulation of beta-adrenergic, A2A adenosine and D5 dopamine receptors each lowers lysosomal pH and improves degradation of outer segments. Activation of the CFTR chloride channel also reacidifies lysosomes and increases degradation. These approaches also restore the lysosomal pH of RPE cells from aged ABCA4(-/-) mice with chronically high levels of A2E, suggesting that functional signaling pathways to reacidify lysosomes are retained in aged cells like those in patients with AMD. Acidic nanoparticles transported to RPE lysosomes also lower pH and improve degradation of outer segments. In summary, the ability of diverse approaches to lower lysosomal pH and enhance outer segment degradation support the proposal that lysosomal acidification can prevent the accumulation of lipofuscin-like material in RPE cells.

The use of microcalorimetry and HPLC for the determination of degradation kinetics and thermodynamic parameters of Perindopril Erbumine in aqueous solutions.

PubMed

Simoncic, Z; Roskar, R; Gartner, A; Kogej, K; Kmetec, V

2008-05-22

Perindopril Erbumine (PER) is one of the newly used angiotensin-converting enzyme inhibitors (ACE inhibitors) and is used for the treatment of patients with hypertension and symptomatic heart failure. It has two main degradation pathways, i.e. the degradation by hydrolysis and the degradation by cyclization. An isothermal heat conduction microcalorimetry (MC) and high pressure liquid chromatography (HPLC) were used for the characterization of aqueous solutions of PER and its stability properties. The rates of heat evolved during degradation of perindopril were measured by MC as a function of temperature and pH and from these data rate constant and change in enthalpy of the reactions were determined. With the HPLC method the concentration of perindopril and its degradation products were measured as a function of time in aqueous solutions of different pH that were stored at different temperatures. We demonstrated that reactions of degradation of perindopril at observed conditions follow the first order kinetics. The Arrhenius equation for each pH was determined. At pH 6.8 only one degradation pathway is present, i.e. the degradation by hydrolysis. Degradation constants for this pathway calculated from MC data are in good agreement with those obtained from HPLC. MC as a non-specific technique was shown to be useful in studies of PER when one reaction was present in the sample and also when more chemical and physical processes were simultaneously running.

Neuronal-Targeted TFEB Accelerates Lysosomal Degradation of APP, Reducing Aβ Generation and Amyloid Plaque Pathogenesis.

PubMed

Xiao, Qingli; Yan, Ping; Ma, Xiucui; Liu, Haiyan; Perez, Ronaldo; Zhu, Alec; Gonzales, Ernesto; Tripoli, Danielle L; Czerniewski, Leah; Ballabio, Andrea; Cirrito, John R; Diwan, Abhinav; Lee, Jin-Moo

2015-09-02

In AD, an imbalance between Aβ production and removal drives elevated brain Aβ levels and eventual amyloid plaque deposition. APP undergoes nonamyloidogenic processing via α-cleavage at the plasma membrane, amyloidogenic β- and γ-cleavage within endosomes to generate Aβ, or lysosomal degradation in neurons. Considering multiple reports implicating impaired lysosome function as a driver of increased amyloidogenic processing of APP, we explored the efficacy of targeting transcription factor EB (TFEB), a master regulator of lysosomal pathways, to reduce Aβ levels. CMV promoter-driven TFEB, transduced via stereotactic hippocampal injections of adeno-associated virus particles in APP/PS1 mice, localized primarily to neuronal nuclei and upregulated lysosome biogenesis. This resulted in reduction of APP protein, the α and β C-terminal APP fragments (CTFs), and in the steady-state Aβ levels in the brain interstitial fluid. In aged mice, total Aβ levels and amyloid plaque load were selectively reduced in the TFEB-transduced hippocampi. TFEB transfection in N2a cells stably expressing APP695, stimulated lysosome biogenesis, reduced steady-state levels of APP and α- and β-CTFs, and attenuated Aβ generation by accelerating flux through the endosome-lysosome pathway. Cycloheximide chase assays revealed a shortening of APP half-life with exogenous TFEB expression, which was prevented by concomitant inhibition of lysosomal acidification. These data indicate that TFEB enhances flux through lysosomal degradative pathways to induce APP degradation and reduce Aβ generation. Activation of TFEB in neurons is an effective strategy to attenuate Aβ generation and attenuate amyloid plaque deposition in AD. A key driver for AD pathogenesis is the net balance between production and clearance of Aβ, the major component of amyloid plaques. Here we demonstrate that lysosomal degradation of holo-APP influences Aβ production by limiting the availability of APP for amyloidogenic processing. Using viral gene transfer of transcription factor EB (TFEB), a master regulator of lysosome biogenesis in neurons of APP/PS1 mice, steady-state levels of APP were reduced, resulting in decreased interstitial fluid Aβ levels and attenuated amyloid deposits. These effects were caused by accelerated lysosomal degradation of endocytosed APP, reflected by reduced APP half-life and steady-state levels in TFEB-expressing cells, with resultant decrease in Aβ production and release. Additional studies are needed to explore the therapeutic potential of this approach. Copyright © 2015 the authors 0270-6474/15/3512137-15$15.00/0.

90K Glycoprotein Promotes Degradation of Mutant β-Catenin Lacking the ISGylation or Phosphorylation Sites in the N-terminus.

PubMed

Park, So-Yeon; Yoon, Somy; Kim, Hangun; Kim, Kyung Keun

2016-10-01

β-Catenin is a major transducer of the Wnt signaling pathway, which is aberrantly expressed in colorectal and other cancers. Previously, we showed that β-catenin is downregulated by the 90K glycoprotein via ISGylation-dependent degradation. However, the further mechanisms of β-catenin degradation by 90K-mediated ISGylation pathway were not investigated. This study aimed to identify the β-catenin domain responsible for the action of 90K and to compare the mechanism of 90K on β-catenin degradation with phosphorylation-dependent ubiquitinational degradation of β-catenin. The deletion mutants of β-catenin lacking N- or C-terminal domain or mutating the N-terminal lysine or nonlysine residue were employed to delineate the characteristics of β-catenin degradation by 90K-mediated ISGylation pathway. 90K induced Herc5 and ISG15 expression and reduced β-catenin levels in HeLa and CSC221 cells. The N-terminus of β-catenin is required for 90K-induced β-catenin degradation, but the N-terminus of β-catenin is not essential for interaction with Herc5. However, substituting lysine residues in the N-terminus of β-catenin with arginine or deleting serine or threonine residue containing domains from the N-terminus does not affect 90K-induced β-catenin degradation, indicating that the N-terminal 86 amino acids of β-catenin are crucial for 90K-mediated ISGylation/degradation of β-catenin in which the responsible lysine or nonlysine residues were not identified. Our present results highlight the action of 90K on promoting degradation of mutant β-catenin lacking the phosphorylation sites in the N-terminus. It provides further insights into the discrete pathway downregulating the stabilized β-catenin via acquiring mutations at the serine/threonine residues in the N-terminus. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Anaerobic Biodegradation of Ethylene Glycol within Hydraulic Fracturing Fluid

NASA Astrophysics Data System (ADS)

Heyob, K. M.; Mouser, P. J.

2014-12-01

Ethylene glycol (EG) is a commonly used organic additive in hydraulic fracturing fluids used for shale gas recovery. Under aerobic conditions, this compound readily biodegrades to acetate and CO2 or is oxidized through the glycerate pathway. In the absence of oxygen, organisms within genera Desulfovibrio, Acetobacterium, and others can transform EG to acetaldehyde, a flammable and suspected carcinogenic compound. Acetaldehyde can then be enzymatically degraded to ethanol or acetate and CO2. However, little is known on how EG degrades in the presence of other organic additives, particularly under anaerobic conditions representative of deep groundwater aquifers. To better understand the fate and attenuation of glycols within hydraulic fracturing fluids we are assessing their biodegradation potential and pathways in batch anaerobic microcosm treatments. Crushed Berea sandstone was inoculated with groundwater and incubated with either EG or a synthetic fracturing fluid (SFF) containing EG formulations. We tracked changes in dissolved organic carbon (DOC), EG, and its transformation products over several months. Approximately 41% of bulk DOC in SFF is degraded within 21 days, with 58% DOC still remaining after 63 days. By comparison, this same SFF degrades by 70% within 25 days when inoculated with sediment-groundwater microbial communities, suggesting that bulk DOC degradation occurs at a slower rate and to a lesser extent with bedrock. Aerobic biodegradation of EG occurs rapidly (3-7 days); however anaerobic degradation of EG is much slower, requiring several weeks for substantial DOC loss to be observed. Ongoing experiments are tracking the degradation pathways of EG alone and in the presence of SFF, with preliminary data showing incomplete glycol transformation within the complex hydraulic fracturing fluid mixture. This research will help to elucidate rates, processes, and pathways for EG biodegradation and identify key microbial taxa involved in its degradation.

The N-end rule pathway and regulation by proteolysis

PubMed Central

Varshavsky, Alexander

2011-01-01

The N-end rule relates the regulation of the in vivo half-life of a protein to the identity of its N-terminal residue. Degradation signals (degrons) that are targeted by the N-end rule pathway include a set called N-degrons. The main determinant of an N-degron is a destabilizing N-terminal residue of a protein. In eukaryotes, the N-end rule pathway is a part of the ubiquitin system and consists of two branches, the Ac/N-end rule and the Arg/N-end rule pathways. The Ac/N-end rule pathway targets proteins containing Nα-terminally acetylated (Nt-acetylated) residues. The Arg/N-end rule pathway recognizes unacetylated N-terminal residues and involves N-terminal arginylation. Together, these branches target for degradation a majority of cellular proteins. For example, more than 80% of human proteins are cotranslationally Nt-acetylated. Thus, most proteins harbor a specific degradation signal, termed AcN-degron, from the moment of their birth. Specific N-end rule pathways are also present in prokaryotes and in mitochondria. Enzymes that produce N-degrons include methionine-aminopeptidases, caspases, calpains, Nt-acetylases, Nt-amidases, arginyl-transferases, and leucyl-transferases. Regulated degradation of specific proteins by the N-end rule pathway mediates a legion of physiological functions, including the sensing of heme, oxygen, and nitric oxide; selective elimination of misfolded proteins; the regulation of DNA repair, segregation, and condensation; the signaling by G proteins; the regulation of peptide import, fat metabolism, viral and bacterial infections, apoptosis, meiosis, spermatogenesis, neurogenesis, and cardiovascular development; and the functioning of adult organs, including the pancreas and the brain. Discovered 25 years ago, this pathway continues to be a fount of biological insights. PMID:21633985

Bacteria-mediated bisphenol A degradation.

PubMed

Zhang, Weiwei; Yin, Kun; Chen, Lingxin

2013-07-01

Bisphenol A (BPA) is an important monomer in the manufacture of polycarbonate plastics, food cans, and other daily used chemicals. Daily and worldwide usage of BPA and BPA-contained products led to its ubiquitous distribution in water, sediment/soil, and atmosphere. Moreover, BPA has been identified as an environmental endocrine disruptor for its estrogenic and genotoxic activity. Thus, BPA contamination in the environment is an increasingly worldwide concern, and methods to efficiently remove BPA from the environment are urgently recommended. Although many factors affect the fate of BPA in the environment, BPA degradation is mainly depended on the metabolism of bacteria. Many BPA-degrading bacteria have been identified from water, sediment/soil, and wastewater treatment plants. Metabolic pathways of BPA degradation in specific bacterial strains were proposed, based on the metabolic intermediates detected during the degradation process. In this review, the BPA-degrading bacteria were summarized, and the (proposed) BPA degradation pathway mediated by bacteria were referred.

Inflammasome and Autophagy Regulation: A Two-way Street

PubMed Central

Qian, Sun; Fan, Jie; Billiar, Timothy R; Scott, Melanie J

2017-01-01

Inflammation plays a significant role in protecting hosts against pathogens. Inflammation induced by noninfectious endogenous agents can be detrimental and, if excessive, can result in organ and tissue damage. The inflammasome is a major innate immune pathway that can be activated via both exogenous pathogen-associated molecular patterns (PAMPs) and endogenous damage-associated molecular patterns (DAMPs). Inflammasome activation involves formation and oligomerization of a protein complex including a nucleotide oligomerization domain (NOD)-like receptor (NLR), an adaptor protein and pro-caspase-1. This then allows cleavage and activation of caspase-1, followed by downstream cleavage and release of proinflammatory cytokines interleukin (IL)-1β and IL-18 from innate immune cells. Hyperinflammation caused by unrestrained inflammasome activation is linked with multiple inflammatory diseases, including inflammatory bowel disease, Alzheimer’s disease and multiple sclerosis. So there is an understandable rush to understand mechanisms that regulate such potent inflammatory pathways. Autophagy has now been identified as a main regulator of inflammasomes. Autophagy is a vital intracellular process involved in cellular homeostasis, recycling and removal of damaged organelles (eg, mitochondria) and intracellular pathogens. Autophagy is regulated by proteins that are important in endosomal/phagosomal pathways, as well as by specific autophagy proteins coded for by autophagy-related genes. Cytosolic components are surrounded and contained by a double-membraned vesicle, which then fuses with lysosomes to enable degradation of the contents. Autophagic removal of intracellular DAMPs, inflammasome components or cytokines can reduce inflammasome activation. Similarly, inflammasomes can regulate the autophagic process, allowing for a two-way mutual regulation of inflammation that may hold the key for treatment of multiple diseases. PMID:28741645

Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders.

PubMed

Hu, Ping; Dubinsky, Eric A; Probst, Alexander J; Wang, Jian; Sieber, Christian M K; Tom, Lauren M; Gardinali, Piero R; Banfield, Jillian F; Atlas, Ronald M; Andersen, Gary L

2017-07-11

The Deepwater Horizon (DWH) accident released an estimated 4.1 million barrels of oil and 10 10 mol of natural gas into the Gulf of Mexico, forming deep-sea plumes of dispersed oil droplets and dissolved gases that were largely degraded by bacteria. During the course of this 3-mo disaster a series of different bacterial taxa were enriched in succession within deep plumes, but the metabolic capabilities of the different populations that controlled degradation rates of crude oil components are poorly understood. We experimentally reproduced dispersed plumes of fine oil droplets in Gulf of Mexico seawater and successfully replicated the enrichment and succession of the principal oil-degrading bacteria observed during the DWH event. We recovered near-complete genomes, whose phylogeny matched those of the principal biodegrading taxa observed in the field, including the DWH Oceanospirillales (now identified as a Bermanella species), multiple species of Colwellia , Cycloclasticus , and other members of Gammaproteobacteria, Flavobacteria, and Rhodobacteria. Metabolic pathway analysis, combined with hydrocarbon compositional analysis and species abundance data, revealed substrate specialization that explained the successional pattern of oil-degrading bacteria. The fastest-growing bacteria used short-chain alkanes. The analyses also uncovered potential cooperative and competitive relationships, even among close relatives. We conclude that patterns of microbial succession following deep ocean hydrocarbon blowouts are predictable and primarily driven by the availability of liquid petroleum hydrocarbons rather than natural gases.

Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders

PubMed Central

Hu, Ping; Probst, Alexander J.; Wang, Jian; Sieber, Christian M. K.; Tom, Lauren M.; Gardinali, Piero R.; Banfield, Jillian F.; Atlas, Ronald M.

2017-01-01

The Deepwater Horizon (DWH) accident released an estimated 4.1 million barrels of oil and 1010 mol of natural gas into the Gulf of Mexico, forming deep-sea plumes of dispersed oil droplets and dissolved gases that were largely degraded by bacteria. During the course of this 3-mo disaster a series of different bacterial taxa were enriched in succession within deep plumes, but the metabolic capabilities of the different populations that controlled degradation rates of crude oil components are poorly understood. We experimentally reproduced dispersed plumes of fine oil droplets in Gulf of Mexico seawater and successfully replicated the enrichment and succession of the principal oil-degrading bacteria observed during the DWH event. We recovered near-complete genomes, whose phylogeny matched those of the principal biodegrading taxa observed in the field, including the DWH Oceanospirillales (now identified as a Bermanella species), multiple species of Colwellia, Cycloclasticus, and other members of Gammaproteobacteria, Flavobacteria, and Rhodobacteria. Metabolic pathway analysis, combined with hydrocarbon compositional analysis and species abundance data, revealed substrate specialization that explained the successional pattern of oil-degrading bacteria. The fastest-growing bacteria used short-chain alkanes. The analyses also uncovered potential cooperative and competitive relationships, even among close relatives. We conclude that patterns of microbial succession following deep ocean hydrocarbon blowouts are predictable and primarily driven by the availability of liquid petroleum hydrocarbons rather than natural gases. PMID:28652349

Analysis of EAWAG-BBD pathway prediction system for the identification of malathion degrading microbes

PubMed Central

Sivakumar, Subramaniam; Anitha, Palanivel; Ramesh, Balsubramanian; Suresh, Gopal

2017-01-01

Insecticides are the toxic substances that are used to kill insects. The use of insecticides is believed to be one of the major factors behind the increase in agricultural productivity in the 20th century. The organophosphates are now the largest and most versatile class of insecticide used and Malathion is the predominant type utilized. The accumulation of Malathion in environment is the biggest threat to the environment because of its toxicity. Malathion is lethal to beneficial insects, snails, micro crustaceans, fish, birds, amphibians, and soil microorganisms. Chronic exposure of non-diabetic farmers to organophosphorus Malathion pesticides may induce insulin resistance, which might ultimately results in diabetes mellitus. Given the potential carcinogenic risk from the pesticides there is serious need to develop remediation processes to eliminate or minimize contamination in the environment. Biodegradation could be a reliable and cost effective technique for pesticide abatement. Since today as there were no metabolic pathway predicted for the degradation of organophosphates pesticide Malathion in KEGG database or in any of the other pathway databases. Thus in the present study, an attempt has been made to predict the microbial biodegradation pathway of Malathion using bioinformatics tools. The present study predicted the degradation pathway for Malathion. The present study also identifies, Streptomyces sp. and E.coli are capable of degrading Malathion through pathway prediction system. PMID:28584447

Analysis of EAWAG-BBD pathway prediction system for the identification of malathion degrading microbes.

PubMed

Sivakumar, Subramaniam; Anitha, Palanivel; Ramesh, Balsubramanian; Suresh, Gopal

2017-01-01

Insecticides are the toxic substances that are used to kill insects. The use of insecticides is believed to be one of the major factors behind the increase in agricultural productivity in the 20th century. The organophosphates are now the largest and most versatile class of insecticide used and Malathion is the predominant type utilized. The accumulation of Malathion in environment is the biggest threat to the environment because of its toxicity. Malathion is lethal to beneficial insects, snails, micro crustaceans, fish, birds, amphibians, and soil microorganisms. Chronic exposure of non-diabetic farmers to organophosphorus Malathion pesticides may induce insulin resistance, which might ultimately results in diabetes mellitus. Given the potential carcinogenic risk from the pesticides there is serious need to develop remediation processes to eliminate or minimize contamination in the environment. Biodegradation could be a reliable and cost effective technique for pesticide abatement. Since today as there were no metabolic pathway predicted for the degradation of organophosphates pesticide Malathion in KEGG database or in any of the other pathway databases. Thus in the present study, an attempt has been made to predict the microbial biodegradation pathway of Malathion using bioinformatics tools. The present study predicted the degradation pathway for Malathion. The present study also identifies, Streptomyces sp. and E.coli are capable of degrading Malathion through pathway prediction system.

Direct uptake and degradation of DNA by lysosomes

PubMed Central

Fujiwara, Yuuki; Kikuchi, Hisae; Aizawa, Shu; Furuta, Akiko; Hatanaka, Yusuke; Konya, Chiho; Uchida, Kenko; Wada, Keiji; Kabuta, Tomohiro

2013-01-01

Lysosomes contain various hydrolases that can degrade proteins, lipids, nucleic acids and carbohydrates. We recently discovered “RNautophagy,” an autophagic pathway in which RNA is directly taken up by lysosomes and degraded. A lysosomal membrane protein, LAMP2C, a splice variant of LAMP2, binds to RNA and acts as a receptor for this pathway. In the present study, we show that DNA is also directly taken up by lysosomes and degraded. Like RNautophagy, this autophagic pathway, which we term “DNautophagy,” is dependent on ATP. The cytosolic sequence of LAMP2C also directly interacts with DNA, and LAMP2C functions as a receptor for DNautophagy, in addition to RNautophagy. Similarly to RNA, DNA binds to the cytosolic sequences of fly and nematode LAMP orthologs. Together with the findings of our previous study, our present findings suggest that RNautophagy and DNautophagy are evolutionarily conserved systems in Metazoa. PMID:23839276

Stability control of senna leaves and senna extracts.

PubMed

Goppel, Martin; Franz, Gerhard

2004-05-01

Powdered senna leaves and a commercial methanolic senna leaf extract were investigated for apparent degradation pathways of known constituents. Different defined storage conditions were chosen according to the guidelines of the international conference on harmonization. Analytical fingerprinting was carried out by HPLC with photodiode array detection. Differences in degradation pathways were observed between the powdered herbal drug material and the extract, depending on storage conditions and packaging materials. Within the crude plant material sennosides were shown to be degraded to sennidine monoglycosides, while rhein 8-O-glucoside was hydrolysed to rhein by enzymatic processes. Degradation of the anthranoid compounds was not due to the same pathways in the investigated commercial extracts. Only unspecific alterations of all compounds were observed. Forced decomposition of this herbal drug preparation under high temperature caused oxidative decomposition of the sennosides to rhein 8-O-glucoside. Furthermore flavonoid glycosides decomposition were observed with an apparent increase in the content of flavone aglyca.

Adherens junction turnover: regulating adhesion through cadherin endocytosis, degradation, and recycling

PubMed Central

Nanes, Benjamin A.; Kowalczyk, Andrew P.

2014-01-01

Adherens junctions are important mediators of intercellular adhesion, but they are not static structures. They are regularly formed, broken, and rearranged in a variety of situations, requiring changes in the amount of cadherins, the main adhesion molecule in adherens junctions, present at the cell surface. Thus, endocytosis, degradation, and recycling of cadherins are crucial for dynamic regulation of adherens junctions and control of intercellular adhesion. In this chapter, we review the involvement of cadherin endocytosis in development and disease. We discuss the various endocytic pathways available to cadherins, the adaptors involved, and the sorting of internalized cadherin for recycling or lysosomal degradation. In addition, we review the regulatory pathways controlling cadherin endocytosis and degradation, including regulation of cadherin endocytosis by catenins, cadherin ubiquitination, and growth factor receptor signaling pathways. Lastly, we discuss the proteolytic cleavage of cadherins at the plasma membrane. PMID:22674073

Ligand-independent pathway that controls stability of interferon alpha receptor

PubMed Central

Liu, Jianghuai; Plotnikov, Alexander; Banerjee, Anamika; Kumar, K.G. Suresh; Ragimbeau, Josiane; Marijanovic, Zrinka; Baker, Darren P.; Pellegrini, Sandra; Fuchs, Serge Y.

2008-01-01

SUMMARY Ligand-specific negative regulation of cytokine-induced signaling relies on down regulation of the cytokine receptors. Down regulation of the IFNAR1 sub-unit of the Type I interferon (IFN) receptor proceeds via lysosomal receptor proteolysis, which is triggered by ubiquitination that depends on IFNAR1 serine phosphorylation. While IFN-inducible phosphorylation, ubiquitination and degradation requires the catalytic activity of the Tyk2 Janus kinase, here we found the ligand- and Tyk2-independent pathway that promotes IFNAR1 phosphorylation, ubiquitination, and degradation when IFNAR1 is expressed at high levels. A major cellular kinase activity that is responsible for IFNAR1 phosphorylation in vitro does not depend on either ligand or Tyk2 activity. Inhibition of ligand-independent IFNAR1 degradation suppresses cell proliferation. We discuss the signaling events that might lead to ubiquitination and degradation of IFNAR1 via ligand-dependent and independent pathways and their potential physiologic significance. PMID:18166147

Characterization of Two Novel Propachlor Degradation Pathways in Two Species of Soil Bacteria

PubMed Central

Martin, Margarita; Mengs, Gerardo; Allende, Jose Luis; Fernandez, Javier; Alonso, Ramon; Ferrer, Estrella

1999-01-01

Propachlor (2-chloro-N-isopropylacetanilide) is an acetamide herbicide used in preemergence. In this study, we isolated and characterized a soil bacterium, Acinetobacter strain BEM2, that was able to utilize this herbicide as the sole and limiting carbon source. Identification of the intermediates of propachlor degradation by this strain and characterization of new metabolites in the degradation of propachlor by a previously reported strain of Pseudomonas (PEM1) support two different propachlor degradation pathways. Washed-cell suspensions of strain PEM1 with propachlor accumulated N-isopropylacetanilide, acetanilide, acetamide, and catechol. Pseudomonas strain PEM1 grew on propachlor with a generation time of 3.4 h and a Ks of 0.17 ± 0.04 mM. Acinetobacter strain BEM2 grew on propachlor with a generation time of 3.1 h and a Ks of 0.3 ± 0.07 mM. Incubations with strain BEM2 resulted in accumulation of N-isopropylacetanilide, N-isopropylaniline, isopropylamine, and catechol. Both degradative pathways were inducible, and the principal product of the carbon atoms in the propachlor ring was carbon dioxide. These results and biodegradation experiments with the identified metabolites indicate that metabolism of propachlor by Pseudomonas sp. strain PEM1 proceeds through a different pathway from metabolism by Acinetobacter sp. strain BEM2. PMID:9925619

Quantitative assessment on the contribution of direct photolysis and radical oxidation in photochemical degradation of 4-chlorophenol and oxytetracycline.

PubMed

Liu, Yiqing; He, Xuexiang; Fu, Yongsheng; Dionysiou, Dionysios D

2016-07-01

In UV-254 nm/H2O2 advanced oxidation process (AOP), the potential degradation pathways for organic pollutants include (1) hydrolysis, (2) direct H2O2 oxidation, (3) UV direct photolysis, and (4) hydroxyl radical (HO(•)) reaction. In this study, the contribution of these pathways was quantitatively assessed in the photochemical destruction of 4-chlorophenol (4-CP), demonstrating pathways (3) and (4) to be predominantly responsible for the removal of 4-CP by UV/H2O2 in 50 mM phosphate buffer solution. Increasing reaction pH could significantly enhance the contribution of direct photolysis in UV/H2O2 process. The contribution of HO(•) oxidation was improved with increasing initial H2O2 concentration probably due to the increased formation of HO(•). Presence of sodium carbonate (Na2CO3) as in UV/H2O2/Na2CO3 system promoted the degradation of 4-CP, with carbonate radical (CO3 (•-)) reaction and direct photolysis identified to be the main contributing pathways. The trends in the contribution of each factor were further evaluated and validated on the degradation of the antibiotic compound oxytetracycline (OTC). This study provides valuable information on the relative importance of different reaction pathways on the photochemical degradation of organic contaminants such as 4-CP and OTC in the presence and absence of a CO3 (•-) precursor.

Bacterial Degradation of Phosphonates Bound to High-Molecular-Weight Dissolved Organic Matter Produces Methane and Other Hydrocarbons

NASA Astrophysics Data System (ADS)

Sosa, O.; Ferron Smith, S.; Karl, D. M.; DeLong, E.; Repeta, D.

2016-02-01

The biological degradation of dissolved organic matter (DOM) plays important roles in the carbon cycle and energy balance of the ocean. Yet, the biochemical pathways that drive DOM turnover remain to be fully characterized. In this study, we tested the ability of two open ocean bacterial isolates (a Pseudomonas stutzeri strain (Gammaproteobacteria) and a Sulfitobacter isolate (Alphaproteobacteria)) to degrade DOM phosphonates. Each isolate encoded a complete phosphonate degradation pathway in its genome, and each was able to degrade simple alkyl-phosphonates like methyl phosphonate, releasing methane (or other short chain hydrocarbon gases) as a result. We found that cultures incubated in the presence of HMW DOM polysaccharides also produced methane and other trace gases under aerobic conditions. To demonstrate that phosphonates were the source of these gases, we constructed a P. stutzeri mutant disabled in the phosphonate degradation pathway. Unlike the wild type, the mutant strain was deficient in the production of methane and other gases from HMW DOM-associated phosphonates. These observations support the hypothesis that DOM-bound methyl phosphonates may be a significant source of methane in the water column, and that bacterial degradation of these compounds likely contribute to the subsurface methane maxima observed throughout the world's oceans.

Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane

PubMed Central

Salanenka, Yuliya; Verstraeten, Inge; Löfke, Christian; Tabata, Kaori; Naramoto, Satoshi; Glanc, Matouš; Friml, Jiří

2018-01-01

The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses. PMID:29463731

DFN-M field characterization of sandstone for a process-based site conceptual model and numerical simulations of TCE transport with degradation

NASA Astrophysics Data System (ADS)

Pierce, Amanda A.; Chapman, Steven W.; Zimmerman, Laura K.; Hurley, Jennifer C.; Aravena, Ramon; Cherry, John A.; Parker, Beth L.

2018-05-01

Plumes of trichloroethene (TCE) with degradation products occur at a large industrial site in California where TCE as a dense non-aqueous phase liquid (DNAPL) entered the fractured sandstone bedrock at many locations beginning in the late 1940s. Groundwater flows rapidly in closely spaced fractures but plume fronts are strongly retarded relative to groundwater flow velocities owing largely to matrix diffusion in early decades and degradation processes in later decades and going forward. Multiple data types show field evidence for both biotic and abiotic dechlorination of TCE and its degradation products, resulting in non-chlorinated compounds. Analyses were conducted on groundwater samples from hundreds of monitoring wells and on thousands of rock samples from continuous core over depths ranging from 6 to 426 metres below ground surface. Nearly all of the present-day mass of TCE and degradation products resides in the water-saturated, low-permeability rock matrix blocks. Although groundwater and DNAPL flow primarily occur in the fractures, DNAPL dissolution followed by diffusion and sorption readily transfers contaminant mass into the rock matrix. The presence of non-chlorinated degradation products (ethene, ethane, acetylene) and compound specific isotope analysis (CSIA) of TCE and cis-1,2-dichloroethene (cDCE) indicate at least some complete dechlorination by both biotic and abiotic pathways, consistent with the observed mineralogy and hydrogeochemistry and with published results from crushed rock microcosms. The rock matrix contains abundant iron-bearing minerals and solid-phase organic carbon with large surface areas and long contact times, suggesting degradation processes are occurring in the rock matrix. Multiple, high-resolution datasets provide strong evidence for spatially heterogeneous distributions of TCE and degradation products with varying degrees of degradation observed only when using new methods that achieve better detection of dissolved gases (i.e., Snap Sampler™) and contaminant mass stored in the low permeability rock matrix (i.e., CORE-DFN™). Simulations using a discrete fracture-matrix (DFN-M) numerical model capable of rigorously simulating flow and transport in both the fractures and matrix, including interactions, show that even slow, first-order degradation rates (i.e., 5- to 20-year half-lives) informed by site-derived parameters can contribute strongly to natural attenuation, resulting in TCE plumes that become stationary in space and might even retreat after 50 to 100 years, if the DNAPL sources become depleted due to the combination of diffusion and degradation processes.

DFN-M field characterization of sandstone for a process-based site conceptual model and numerical simulations of TCE transport with degradation.

PubMed

Pierce, Amanda A; Chapman, Steven W; Zimmerman, Laura K; Hurley, Jennifer C; Aravena, Ramon; Cherry, John A; Parker, Beth L

2018-05-01

Plumes of trichloroethene (TCE) with degradation products occur at a large industrial site in California where TCE as a dense non-aqueous phase liquid (DNAPL) entered the fractured sandstone bedrock at many locations beginning in the late 1940s. Groundwater flows rapidly in closely spaced fractures but plume fronts are strongly retarded relative to groundwater flow velocities owing largely to matrix diffusion in early decades and degradation processes in later decades and going forward. Multiple data types show field evidence for both biotic and abiotic dechlorination of TCE and its degradation products, resulting in non-chlorinated compounds. Analyses were conducted on groundwater samples from hundreds of monitoring wells and on thousands of rock samples from continuous core over depths ranging from 6 to 426 metres below ground surface. Nearly all of the present-day mass of TCE and degradation products resides in the water-saturated, low-permeability rock matrix blocks. Although groundwater and DNAPL flow primarily occur in the fractures, DNAPL dissolution followed by diffusion and sorption readily transfers contaminant mass into the rock matrix. The presence of non-chlorinated degradation products (ethene, ethane, acetylene) and compound specific isotope analysis (CSIA) of TCE and cis-1,2-dichloroethene (cDCE) indicate at least some complete dechlorination by both biotic and abiotic pathways, consistent with the observed mineralogy and hydrogeochemistry and with published results from crushed rock microcosms. The rock matrix contains abundant iron-bearing minerals and solid-phase organic carbon with large surface areas and long contact times, suggesting degradation processes are occurring in the rock matrix. Multiple, high-resolution datasets provide strong evidence for spatially heterogeneous distributions of TCE and degradation products with varying degrees of degradation observed only when using new methods that achieve better detection of dissolved gases (i.e., Snap Sampler™) and contaminant mass stored in the low permeability rock matrix (i.e., CORE-DFN™). Simulations using a discrete fracture-matrix (DFN-M) numerical model capable of rigorously simulating flow and transport in both the fractures and matrix, including interactions, show that even slow, first-order degradation rates (i.e., 5- to 20-year half-lives) informed by site-derived parameters can contribute strongly to natural attenuation, resulting in TCE plumes that become stationary in space and might even retreat after 50 to 100 years, if the DNAPL sources become depleted due to the combination of diffusion and degradation processes. Copyright © 2018 Elsevier B.V. All rights reserved.

Coordinated Regulation of Species-Specific Hydroxycinnamic Acid Degradation and Siderophore Biosynthesis Pathways in Agrobacterium fabrum

PubMed Central

Baude, Jessica; Vial, Ludovic; Villard, Camille; Campillo, Tony; Lavire, Céline; Nesme, Xavier

2016-01-01

ABSTRACT The rhizosphere-inhabiting species Agrobacterium fabrum (genomospecies G8 of the Agrobacterium tumefaciens species complex) is known to degrade hydroxycinnamic acids (HCAs), especially ferulic acid and p-coumaric acid, via the novel A. fabrum HCA degradation pathway. Gene expression profiles of A. fabrum strain C58 were investigated in the presence of HCAs, using a C58 whole-genome oligoarray. Both ferulic acid and p-coumaric acid caused variations in the expression of more than 10% of the C58 genes. Genes of the A. fabrum HCA degradation pathway, together with the genes involved in iron acquisition, were among the most highly induced in the presence of HCAs. Two operons coding for the biosynthesis of a particular siderophore, as well as genes of the A. fabrum HCA degradation pathway, have been described as being specific to the species. We demonstrate here their coordinated expression, emphasizing the interdependence between the iron concentration in the growth medium and the rate at which ferulic acid is degraded by cells. The coordinated expression of these functions may be advantageous in HCA-rich but iron-starved environments in which microorganisms have to compete for both iron and carbon sources, such as in plant roots. The present results confirm that there is cooperation between the A. fabrum-specific genes, defining a particular ecological niche. IMPORTANCE We previously identified seven genomic regions in Agrobacterium fabrum that were specifically present in all of the members of this species only. Here we demonstrated that two of these regions, encoding the hydroxycinnamic acid degradation pathway and the iron acquisition pathway, were regulated in a coordinated manner. The coexpression of these functions may be advantageous in hydroxycinnamic acid-rich but iron-starved environments in which microorganisms have to compete for both iron and carbon sources, such as in plant roots. These data support the view that bacterial genomic species emerged from a bacterial population by acquiring specific functions that allowed them to outcompete their closest relatives. In conclusion, bacterial species could be defined not only as genomic species but also as ecological species. PMID:27060117

Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC.

PubMed

Oosterkamp, Margreet J; Boeren, Sjef; Atashgahi, Siavash; Plugge, Caroline M; Schaap, Peter J; Stams, Alfons J M

2015-06-01

Alicycliphilus denitrificans strain BC grows anaerobically on acetone with nitrate as electron acceptor. Comparative proteomics of cultures of A. denitrificans strain BC grown on either acetone or acetate with nitrate was performed to study the enzymes involved in the acetone degradation pathway. In the proposed acetone degradation pathway, an acetone carboxylase converts acetone to acetoacetate, an AMP-dependent synthetase/ligase converts acetoacetate to acetoacetyl-CoA, and an acetyl-CoA acetyltransferase cleaves acetoacetyl-CoA to two acetyl-CoA. We also found a putative aldehyde dehydrogenase associated with acetone degradation. This enzyme functioned as a β-hydroxybutyrate dehydrogenase catalyzing the conversion of surplus acetoacetate to β-hydroxybutyrate that may be converted to the energy and carbon storage compound, poly-β-hydroxybutyrate. Accordingly, we confirmed the formation of poly-β-hydroxybutyrate in acetone-grown cells of strain BC. Our findings provide insight in nitrate-dependent acetone degradation that is activated by carboxylation of acetone. This will aid studies of similar pathways found in other microorganisms degrading acetone with nitrate or sulfate as electron acceptor. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Performance of trichlorfon degradation by a novel Bacillus tequilensis strain PA F-3 and its proposed biodegradation pathway.

PubMed

Tian, Jiang; Yu, Chenlei; Xue, Yingwen; Zhao, Ruixue; Wang, Jing; Chen, Lanzhou

2016-11-01

The novel trichlorfon (TCF)-degrading bacterium PA F-3, identified as Bacillus tequilensis, was isolated from pesticide-polluted soils by using an effective screening and domesticating procedure. The TCF biodegradation pathways of PA F-3 were also systematically elucidated. As revealed by high-performance liquid chromatography, the TCF residues in the mineral salt medium demonstrated that PA F-3 can utilize TCF as its sole carbon source and reach the highest degradation of 71.1 % at an initial TCF concentration of 200 mg/L within 5 days. The TCF degradation conditions were optimized using response surface methodology as follows: temperature, 28 °C; inoculum amount, 4 %; and initial TCF concentration, 125 mg/L. Biodegradation treatments supplemented with exogenous carbon sources and yeast extract markedly increased the microbial dry weights and TCF-degrading performance of PA F-3, respectively. Meanwhile, five metabolic products of TCF were identified through gas chromatography/mass spectrometry, and a biodegradation pathway was proposed. Results indicated that deoxidation and dehydration (including the cleavage of the P-C phosphonate bond and the C-O bond) were the preferred metabolic reactions of TCF in this TCF-degrading bacterium.

Presence or Absence of mlr Genes and Nutrient Concentrations Co-Determine the Microcystin Biodegradation Efficiency of a Natural Bacterial Community

PubMed Central

Lezcano, María Ángeles; Morón-López, Jesús; Agha, Ramsy; López-Heras, Isabel; Nozal, Leonor; Quesada, Antonio; El-Shehawy, Rehab

2016-01-01

The microcystin biodegradation potential of a natural bacterial community coexisting with a toxic cyanobacterial bloom was investigated in a water reservoir from central Spain. The biodegradation capacity was confirmed in all samples during the bloom and an increase of mlrA gene copies was found with increasing microcystin concentrations. Among the 24 microcystin degrading strains isolated from the bacterial community, only 28% showed presence of mlrA gene, strongly supporting the existence and abundance of alternative microcystin degradation pathways in nature. In vitro degradation assays with both mlr+ and mlr− bacterial genotypes (with presence and absence of the complete mlr gene cluster, respectively) were performed with four isolated strains (Sphingopyxis sp. IM-1, IM-2 and IM-3; Paucibacter toxinivorans IM-4) and two bacterial degraders from the culture collection (Sphingosinicella microcystinivorans Y2; Paucibacter toxinivorans 2C20). Differences in microcystin degradation efficiencies between genotypes were found under different total organic carbon and total nitrogen concentrations. While mlr+ strains significantly improved microcystin degradation rates when exposed to other carbon and nitrogen sources, mlr− strains showed lower degradation efficiencies. This suggests that the presence of alternative carbon and nitrogen sources possibly competes with microcystins and impairs putative non-mlr microcystin degradation pathways. Considering the abundance of the mlr− bacterial population and the increasing frequency of eutrophic conditions in aquatic systems, further research on the diversity of this population and the characterization and conditions affecting non-mlr degradation pathways deserves special attention. PMID:27827872

ERManI (Endoplasmic Reticulum Class I α-Mannosidase) Is Required for HIV-1 Envelope Glycoprotein Degradation via Endoplasmic Reticulum-associated Protein Degradation Pathway.

PubMed

Zhou, Tao; Frabutt, Dylan A; Moremen, Kelley W; Zheng, Yong-Hui

2015-09-04

Previously, we reported that the mitochondrial translocator protein (TSPO) induces HIV-1 envelope (Env) degradation via the endoplasmic reticulum (ER)-associated protein degradation (ERAD) pathway, but the mechanism was not clear. Here we investigated how the four ER-associated glycoside hydrolase family 47 (GH47) α-mannosidases, ERManI, and ER-degradation enhancing α-mannosidase-like (EDEM) proteins 1, 2, and 3, are involved in the Env degradation process. Ectopic expression of these four α-mannosidases uncovers that only ERManI inhibits HIV-1 Env expression in a dose-dependent manner. In addition, genetic knock-out of the ERManI gene MAN1B1 using CRISPR/Cas9 technology disrupts the TSPO-mediated Env degradation. Biochemical studies show that HIV-1 Env interacts with ERManI, and between the ERManI cytoplasmic, transmembrane, lumenal stem, and lumenal catalytic domains, the catalytic domain plays a critical role in the Env-ERManI interaction. In addition, functional studies show that inactivation of the catalytic sites by site-directed mutagenesis disrupts the ERManI activity. These studies identify ERManI as a critical GH47 α-mannosidase in the ER-associated protein degradation pathway that initiates the Env degradation and suggests that its catalytic domain and enzymatic activity play an important role in this process. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Infected cell protein 0 functional domains and their coordination in herpes simplex virus replication

PubMed Central

Gu, Haidong

2016-01-01

Herpes simplex virus 1 (HSV-1) is a ubiquitous human pathogen that establishes latent infection in ganglia neurons. Its unique life cycle requires a balanced “conquer and compromise” strategy to deal with the host anti-viral defenses. One of HSV-1 α (immediate early) gene products, infected cell protein 0 (ICP0), is a multifunctional protein that interacts with and modulates a wide range of cellular defensive pathways. These pathways may locate in different cell compartments, which then migrate or exchange factors upon stimulation, for the purpose of a concerted and effective defense. ICP0 is able to simultaneously attack multiple host pathways by either degrading key restrictive factors or modifying repressive complexes. This is a viral protein that contains an E3 ubiquitin ligase, translocates among different cell compartments and interacts with major defensive complexes. The multiple functional domains of ICP0 can work independently and at the same time coordinate with each other. Dissecting the functional domains of ICP0 and delineating the coordination of these domains will help us understand HSV-1 pathogenicity as well as host defense mechanisms. This article focuses on describing individual ICP0 domains, their biochemical properties and their implication in HSV-1 infection. By putting individual domain functions back into the picture of host anti-viral defense network, this review seeks to elaborate the complex interactions between HSV-1 and its host. PMID:26870669

Autophagy and Mis-targeting of Therapeutic Enzyme in Skeletal Muscle in Pompe Disease

PubMed Central

Fukuda, Tokiko; Ahearn, Meghan; Roberts, Ashley; Mattaliano, Robert J.; Zaal, Kristien; Ralston, Evelyn; Plotz, Paul H.; Raben, Nina

2009-01-01

Enzyme replacement therapy (ERT) became a reality for patients with Pompe disease, a fatal cardiomyopathy and skeletal muscle myopathy caused by a deficiency of glycogen-degrading lysosomal enzyme acid alpha-glucosidase (GAA). The therapy, which relies on receptor-mediated endocytosis of recombinant human GAA (rhGAA), appears to be effective in cardiac muscle, but less so in skeletal muscle. We have previously shown a profound disturbance of the lysosomal degradative pathway (autophagy) in therapy-resistant muscle of GAA knockout mice (KO). Our findings here demonstrate a progressive age-dependent autophagic build-up in addition to enlargement of glycogen-filled lysosomes in multiple muscle groups in the KO. Trafficking and processing of the therapeutic enzyme along the endocytic pathway appear to be affected by the autophagy. Confocal microscopy of live single muscle fibers exposed to fluorescently labeled rhGAA indicates that a significant portion of the endocytosed enzyme in the KO was trapped as a partially processed form in the autophagic areas instead of reaching its target – the lysosomes. A fluid-phase endocytic marker was similarly mis-targeted and accumulated in vesicular structures within the autophagic areas. These findings may explain why ERT often falls short of reversing the disease process, and point to new avenues for the development of pharmacological intervention. PMID:17008131

Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase.

PubMed

Sutter, Jan-Moritz; Tästensen, Julia-Beate; Johnsen, Ulrike; Soppa, Jörg; Schönheit, Peter

2016-08-15

The halophilic archaeon Haloferax volcanii has been proposed to degrade glucose via the semiphosphorylative Entner-Doudoroff (spED) pathway. So far, the key enzymes of this pathway, glucose dehydrogenase (GDH), gluconate dehydratase (GAD), and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase (KDPGA), have not been characterized, and their functional involvement in glucose degradation has not been demonstrated. Here we report that the genes HVO_1083 and HVO_0950 encode GDH and KDPGA, respectively. The recombinant enzymes show high specificity for glucose and KDPG and did not convert the corresponding C4 epimers galactose and 2-keto-3-deoxy-6-phosphogalactonate at significant rates. Growth studies of knockout mutants indicate the functional involvement of both GDH and KDPGA in glucose degradation. GAD was purified from H. volcanii, and the encoding gene, gad, was identified as HVO_1488. GAD catalyzed the specific dehydration of gluconate and did not utilize galactonate at significant rates. A knockout mutant of GAD lost the ability to grow on glucose, indicating the essential involvement of GAD in glucose degradation. However, following a prolonged incubation period, growth of the Δgad mutant on glucose was recovered. Evidence is presented that under these conditions, GAD was functionally replaced by xylonate dehydratase (XAD), which uses both xylonate and gluconate as substrates. Together, the characterization of key enzymes and analyses of the respective knockout mutants present conclusive evidence for the in vivo operation of the spED pathway for glucose degradation in H. volcanii The work presented here describes the identification and characterization of the key enzymes glucose dehydrogenase, gluconate dehydratase, and 2-keto-3-deoxy-6-phosphogluconate aldolase and their encoding genes of the proposed semiphosphorylative Entner-Doudoroff pathway in the haloarchaeon Haloferax volcanii The functional involvement of the three enzymes was proven by analyses of the corresponding knockout mutants. These results provide evidence for the in vivo operation of the semiphosphorylative Entner-Doudoroff pathway in haloarchaea and thus expand our understanding of the unusual sugar degradation pathways in the domain Archaea. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Anaerobic Mercury Methylation and Demethylation by Geobacter bemidjiensis Bem

DOE PAGES

Lu, Xia; Liu, Yurong; Johs, Alexander; ...

2016-03-28

Two competing processes controlling the net production and bioaccumulation of neurotoxic methylmercury (MeHg) in natural ecosystems are microbial methylation and demethylation. Though mercury (Hg) methylation by anaerobic microorganisms and demethylation by aerobic Hg-resistant bacteria have both been extensively studied, little attention has been given to MeHg degradation by anaerobic bacteria, particularly the iron-reducing bacterium Geobacter bemidjensis Bem. Here we report, for the first time, that the strain G. bemidjensis Bem can methylate inorganic Hg and degrade MeHg concurrently under anoxic conditions. Our results suggest that G. bemidjensis cells utilize a reductive demethylation pathway to degrade MeHg, with elemental Hg(0) asmore » the major reaction product, possibly due to the presence of homologs encoding both organo-mercurial lyase (MerB) and mercuric reductase (MerA) in this organism. In addition, the cells can mediate multiple reactions including Hg/MeHg sorption, Hg reduction and oxidation, resulting in both time and concentration dependent Hg species transformations. Moderate concentrations (10 500 M) of Hg-binding ligands such as cysteine enhance Hg(II) methylation but inhibit MeHg degradation. These findings indicate a cycle of methylation and demethylation among anaerobic bacteria and suggest that mer-mediated demethylation may play a role in the net balance of MeHg production in anoxic water and sediments.« less

Ferrocene-catalyzed heterogeneous Fenton-like degradation mechanisms and pathways of antibiotics under simulated sunlight: A case study of sulfamethoxazole.

PubMed

Li, Yingjie; Zhang, Biaojun; Liu, Xiangliang; Zhao, Qun; Zhang, Heming; Zhang, Yuechao; Ning, Ping; Tian, Senlin

2018-07-05

Readily-available and efficient catalyst is essential for activating oxidants to produce reactive species for deeply remediating water bodies contaminated by antibiotics. In this study, Ferrocene (Fc) was introduced to establish a heterogeneous photo-Fenton system for the degradation of sulfonamide antibiotics, taking sulfamethoxazole as a representative. Results showed that the removal of sulfamethoxazole was effective in Fc-catalyzed photo-Fenton system. Electron spin resonance and radical scavenging experiments verified that there was a photoindued electron transfer process from Fc to H 2 O 2 and dissolved oxygen resulting in the formation of OH that was primarily responsible for the degradation of sulfamethoxazole. The reactions of OH with substructure model compounds of sulfamethoxazole unveiled that aniline moiety was the preferable reaction site of sulfamethoxazole, which was verified by the formation of hydroxylated product and the dimer of sulfamethoxazole in Fc-catalyzed photo-Fenton system. This heterogeneous photo-Fenton system displayed an effective degradation efficiency even in a complex water matrices, and Fc represented a long-term stability by using the catalyst for multiple cycles. These results demonstrate that Fc-catalyzed photo-Fenton oxidation may be an efficient approach for remediation of wastewater containing antibiotics. Copyright © 2018. Published by Elsevier B.V.

Quality control of mRNP biogenesis: networking at the transcription site.

PubMed

Eberle, Andrea B; Visa, Neus

2014-08-01

Eukaryotic cells carry out quality control (QC) over the processes of RNA biogenesis to inactivate or eliminate defective transcripts, and to avoid their production. In the case of protein-coding transcripts, the quality controls can sense defects in the assembly of mRNA-protein complexes, in the processing of the precursor mRNAs, and in the sequence of open reading frames. Different types of defect are monitored by different specialized mechanisms. Some of them involve dedicated factors whose function is to identify faulty molecules and target them for degradation. Others are the result of a more subtle balance in the kinetics of opposing activities in the mRNA biogenesis pathway. One way or another, all such mechanisms hinder the expression of the defective mRNAs through processes as diverse as rapid degradation, nuclear retention and transcriptional silencing. Three major degradation systems are responsible for the destruction of the defective transcripts: the exosome, the 5'-3' exoribonucleases, and the nonsense-mediated mRNA decay (NMD) machinery. This review summarizes recent findings on the cotranscriptional quality control of mRNA biogenesis, and speculates that a protein-protein interaction network integrates multiple mRNA degradation systems with the transcription machinery. Copyright © 2014 Elsevier Ltd. All rights reserved.

A conformational change within the WAVE2 complex regulates its degradation following cellular activation

PubMed Central

Joseph, Noah; Biber, Guy; Fried, Sophia; Reicher, Barak; Levy, Omer; Sabag, Batel; Noy, Elad; Barda-Saad, Mira

2017-01-01

WASp family Verprolin-homologous protein-2 (WAVE2), a member of the Wiskott-Aldrich syndrome protein (WASp) family of actin nucleation promoting factors, is a central regulator of actin cytoskeleton polymerization and dynamics. Multiple signaling pathways operate via WAVE2 to promote the actin-nucleating activity of the actin-related protein 2/3 (Arp2/3) complex. WAVE2 exists as a part of a pentameric protein complex known as the WAVE regulatory complex (WRC), which is unstable in the absence of its individual proteins. While the involvement of WAVE2 in actin polymerization has been well documented, its negative regulation mechanism is poorly characterized to date. Here, we demonstrate that WAVE2 undergoes ubiquitylation in a T-cell activation dependent manner, followed by proteasomal degradation. The WAVE2 ubiquitylation site was mapped to lysine 45, located at the N-terminus where WAVE2 binds to the WRC. Using Förster resonance energy transfer (FRET), we reveal that the autoinhibitory conformation of the WRC maintains the stability of WAVE2 in resting cells; the release of autoinhibition following T-cell activation facilitates the exposure of WAVE2 to ubiquitylation, leading to its degradation. The dynamic conformational structures of WAVE2 during cellular activation dictate its degradation. PMID:28332566

A conformational change within the WAVE2 complex regulates its degradation following cellular activation.

PubMed

Joseph, Noah; Biber, Guy; Fried, Sophia; Reicher, Barak; Levy, Omer; Sabag, Batel; Noy, Elad; Barda-Saad, Mira

2017-03-23

WASp family Verprolin-homologous protein-2 (WAVE2), a member of the Wiskott-Aldrich syndrome protein (WASp) family of actin nucleation promoting factors, is a central regulator of actin cytoskeleton polymerization and dynamics. Multiple signaling pathways operate via WAVE2 to promote the actin-nucleating activity of the actin-related protein 2/3 (Arp2/3) complex. WAVE2 exists as a part of a pentameric protein complex known as the WAVE regulatory complex (WRC), which is unstable in the absence of its individual proteins. While the involvement of WAVE2 in actin polymerization has been well documented, its negative regulation mechanism is poorly characterized to date. Here, we demonstrate that WAVE2 undergoes ubiquitylation in a T-cell activation dependent manner, followed by proteasomal degradation. The WAVE2 ubiquitylation site was mapped to lysine 45, located at the N-terminus where WAVE2 binds to the WRC. Using Förster resonance energy transfer (FRET), we reveal that the autoinhibitory conformation of the WRC maintains the stability of WAVE2 in resting cells; the release of autoinhibition following T-cell activation facilitates the exposure of WAVE2 to ubiquitylation, leading to its degradation. The dynamic conformational structures of WAVE2 during cellular activation dictate its degradation.

Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine

PubMed Central

Kumar, Ritesh; Zhao, Suwen; Vetting, Matthew W.; Wood, B. McKay; Sakai, Ayano; Cho, Kyuil; Solbiati, José; Almo, Steven C.; Sweedler, Jonathan V.; Jacobson, Matthew P.; Gerlt, John A.; Cronan, John E.

2014-01-01

ABSTRACT Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine. PMID:24520058

One-step prepared cobalt-based nanosheet as an efficient heterogeneous catalyst for activating peroxymonosulfate to degrade caffeine in water.

PubMed

Lin, Kun-Yi Andrew; Lai, Hong-Kai; Tong, Shaoping

2018-03-15

Two-dimensional (2D) planar cobalt-containing materials are promising catalysts for activating peroxymonosulfate (PMS) to degrade contaminants because 2D sheet-like morphology provides large reactive surfaces. However, preparation of these sheet-supported cobaltic materials typically involves multiple steps and complex reagents, making them less practical for PMS activation. In this study, a cobalt-based nanosheet (CoNS) is particularly developed using a one-step hydrothermal process with a single reagent in water. The resulting CoNS can exhibit a thickness as thin as a few nanometers and 2-D morphology. CoNS is also primarily comprised of cobalt species in a coordinated form of Prussian Blue analogue, which consists of both Co 3+ and Co 2+ . These features make CoNS promising for activating PMS in aqueous systems. As degradation of an emerging contaminant, caffeine, is selected as a representative reaction, CoNS not only successfully activates PMS to fully degrade caffeine in 20 min but also exhibits a much higher catalytic activity than the most common PMS activator, Co 3 O 4 . Via studying inhibitive effects of radical scavengers, caffeine degradation by CoNS-activated PMS is primarily attributed to sulfate radicals and hydroxyl radicals to a lesser extent. The degradation products of caffeine by CoNS-activated PMS are also identified and a potential degradation pathway is proposed. Moreover, CoNS could be also re-used to activate PMS for caffeine degradation without activity loss. These results indicate that CoNS is a conveniently prepared and highly effective and stable 2-D catalyst for aqueous chemical oxidation reactions. Copyright © 2017. Published by Elsevier Inc.

Biological Degradation of 2,4,6-Trinitrotoluene

PubMed Central

Esteve-Núñez, Abraham; Caballero, Antonio; Ramos, Juan L.

2001-01-01

Nitroaromatic compounds are xenobiotics that have found multiple applications in the synthesis of foams, pharmaceuticals, pesticides, and explosives. These compounds are toxic and recalcitrant and are degraded relatively slowly in the environment by microorganisms. 2,4,6-Trinitrotoluene (TNT) is the most widely used nitroaromatic compound. Certain strains of Pseudomonas and fungi can use TNT as a nitrogen source through the removal of nitrogen as nitrite from TNT under aerobic conditions and the further reduction of the released nitrite to ammonium, which is incorporated into carbon skeletons. Phanerochaete chrysosporium and other fungi mineralize TNT under ligninolytic conditions by converting it into reduced TNT intermediates, which are excreted to the external milieu, where they are substrates for ligninolytic enzymes. Most if not all aerobic microorganisms reduce TNT to the corresponding amino derivatives via the formation of nitroso and hydroxylamine intermediates. Condensation of the latter compounds yields highly recalcitrant azoxytetranitrotoluenes. Anaerobic microorganisms can also degrade TNT through different pathways. One pathway, found in Desulfovibrio and Clostridium, involves reduction of TNT to triaminotoluene; subsequent steps are still not known. Some Clostridium species may reduce TNT to hydroxylaminodinitrotoluenes, which are then further metabolized. Another pathway has been described in Pseudomonas sp. strain JLR11 and involves nitrite release and further reduction to ammonium, with almost 85% of the N-TNT incorporated as organic N in the cells. It was recently reported that in this strain TNT can serve as a final electron acceptor in respiratory chains and that the reduction of TNT is coupled to ATP synthesis. In this review we also discuss a number of biotechnological applications of bacteria and fungi, including slurry reactors, composting, and land farming, to remove TNT from polluted soils. These treatments have been designed to achieve mineralization or reduction of TNT and immobilization of its amino derivatives on humic material. These approaches are highly efficient in removing TNT, and increasing amounts of research into the potential usefulness of phytoremediation, rhizophytoremediation, and transgenic plants with bacterial genes for TNT removal are being done. PMID:11527999

Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes.

PubMed

Novák, Lukáš; Zubáčová, Zuzana; Karnkowska, Anna; Kolisko, Martin; Hroudová, Miluše; Stairs, Courtney W; Simpson, Alastair G B; Keeling, Patrick J; Roger, Andrew J; Čepička, Ivan; Hampl, Vladimír

2016-10-06

Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.

PINK1 is degraded through the N-end rule pathway

PubMed Central

Yamano, Koji; Youle, Richard J

2013-01-01

PINK1, a mitochondrial serine/threonine kinase, is the product of a gene mutated in an autosomal recessive form of Parkinson disease. PINK1 is constitutively degraded by an unknown mechanism and stabilized selectively on damaged mitochondria where it can recruit the E3 ligase PARK2/PARKIN to induce mitophagy. Here, we show that, under steady-state conditions, endogenous PINK1 is constitutively and rapidly degraded by E3 ubiquitin ligases UBR1, UBR2 and UBR4 through the N-end rule pathway. Following precursor import into mitochondria, PINK1 is cleaved in the transmembrane segment by a mitochondrial intramembrane protease PARL generating an N-terminal destabilizing amino acid and then retrotranslocates from mitochondria to the cytosol for N-end recognition and proteasomal degradation. Thus, sequential actions of mitochondrial import, PARL-processing, retrotranslocation and recognition by N-end rule E3 enzymes for the ubiquitin proteosomal degradation defines the rapid PINK1 turnover. PINK1 steady-state elimination by the N-end rule identifies a novel organelle to cytoplasm turnover pathway that yields a mechanism to flag damaged mitochondria for autophagic elimination. PMID:24121706

Degradation of the chemotherapy drug 5-fluorouracil on medical-grade silver surfaces

NASA Astrophysics Data System (ADS)

Risinggård, Helene Kjær; Cooil, Simon; Mazzola, Federico; Hu, Di; Kjærvik, Marit; Østli, Elise Ramleth; Patil, Nilesh; Preobrajenski, Alexei; Andrew Evans, D.; Breiby, Dag W.; Trinh, Thuat T.; Wells, Justin W.

2018-03-01

The degradation of the chemotherapy drug 5-fluorouracil by a non-pristine metal surfaces is studied. Using density functional theory, X-ray photoelectron spectroscopy and X-ray absorption spectroscopy we show that the drug is entirely degraded by medical-grade silver surfaces, already at body temperature, and that all of the fluorine has left the molecule, presumably as HF. Remarkably, this degradation is even more severe than that reported previously for 5-fluorouracil on a pristine monocrystalline silver surface (in which case 80% of the drug reacted at body temperature) [1]. We conclude that the observed reaction is due to a reaction pathway, driven by H to F attraction between molecules on the surface, which results in the direct formation of HF; a pathway which is favoured when competing pathways involving reactive Ag surface sites are made unavailable by environmental contamination. Our measurements indicate that realistically cleaned, non-pristine silver alloys, which are typically used in medical applications, can result in severe degradation of 5-fluorouracil, with the release of HF - a finding which may have important implications for the handling of chemotherapy drugs.

Magnetic carbon-supported cobalt derived from a Prussian blue analogue as a heterogeneous catalyst to activate peroxymonosulfate for efficient degradation of caffeine in water.

PubMed

Lin, Kun-Yi Andrew; Chen, Bo-Jau

2017-01-15

Extensive usage of caffeine (CAF) as a medicine and additives in beverages has led to increasing presence of CAF in wastewater and even drinking water. To remove CAF, peroxymonosulfate (PMS), is adopted to generate sulfate radical to degrade CAF in water. To facilitate PMS activation, a magnetic carbon-supported cobalt (MC/Co) hybrid material is prepared via carbonization of a cobalt-containing Prussian blue analogue framework (Co 3 [Co(CN) 6 ] 2 ). The resultant MC/Co contains Co and Co 3 O 4 nanoparticles supported on a carbon matrix, making it an attractive magnetic catalyst to activate PMS for degrading CAF. MC/Co-activated PMS was shown to degrade CAF much more effectively than PMS and Co 3 O 4 -activated PMS. Parameters affecting CAF degradation by MC/Co-activated PMS were also examined, including MC/Co and PMS concentrations, temperature, pH, and salt. Effects of radical quenchers were also examined to provide insights into the CAF degradation mechanism. MC/Co-activated PMS was much more favorable at higher temperatures than ambient temperature, and under neutral conditions. Nevertheless, the presence of concentrated NaCl noticeably hindered CAF degradation. Through examining effects of radical quenchers, the mechanism of CAF degradation by MC/Co-activated PMS was attributed primarily to sulfate radicals and hydroxyl radicals to a lesser extent. The degradation products of CAF by MC/Co-activated PMS were also identified and a possible degradation pathway is proposed. MC/Co can activate PMS over multiple cycles without loss of catalytic activity. These findings demonstrate that MC/Co, simply prepared from simple carbonization of Co 3 [Co(CN) 6 ] 2 can be a promising heterogeneous catalyst for activating PMS to degrade CAF. Copyright © 2016 Elsevier Inc. All rights reserved.

The Endoplasmic Reticulum and the Unfolded Protein Response

PubMed Central

Malhotra, Jyoti D.; Kaufman, Randal J.

2009-01-01

The endoplasmic reticulum (ER) is the site where proteins enter the secretory pathway. Proteins are translocated into the ER lumen in an unfolded state and require protein chaperones and catalysts of protein folding to attain their final appropriate conformation. A sensitive surveillance mechanism exists to prevent misfolded proteins from transiting the secretory pathway and ensures that persistently misfolded proteins are directed towards a degradative pathway. In addition, those processes that prevent accumulation of unfolded proteins in the ER lumen are highly regulated by an intracellular signaling pathway known as the unfolded protein response (UPR). The UPR provides a mechanism by which cells can rapidly adapt to alterations in client protein-folding load in the ER lumen by expanding the capacity for protein folding. In addition, a variety of insults that disrupt protein folding in the ER lumen also activate the UPR. These include changes in intralumenal calcium, altered glycosylation, nutrient deprivation, pathogen infection, expression of folding-defective proteins, and changes in redox status. Persistent protein misfolding initiates apoptotic cascades that are now known to play fundamental roles in the pathogenesis of multiple human diseases including diabetes, atherosclerosis and neurodegenerative diseases. PMID:18023214

Proteomic analysis of Bombyx mori molting fluid: Insights into the molting process.

PubMed

Liu, Hua-Wei; Wang, Luo-Ling; Tang, Xin; Dong, Zhao-Ming; Guo, Peng-Chao; Zhao, Dong-Chao; Xia, Qing-You; Zhao, Ping

2018-02-20

Molting is an essential biological process occurring multiple times throughout the life cycle of most Ecdysozoa. Molting fluids accumulate and function in the exuvial space during the molting process. In this study, we used liquid chromatography-tandem mass spectrometry to investigate the molting fluids to analyze the molecular mechanisms of molting in the silkworm, Bombyx mori. In total, 375 proteins were identified in molting fluids from the silkworm at 14-16h before pupation and eclosion, including 12 chitin metabolism-related enzymes, 35 serine proteases, 15 peptidases, and 38 protease inhibitors. Gene ontology analysis indicated that "catalytic" constitutes the most enriched function in the molting fluid. Gene expression patterns and bioinformatic analyses suggested that numerous enzymes are involved in the degradation of cuticle proteins and chitin. Protein-protein interaction network and activity analyses showed that protease inhibitors are involved in the regulation of multiple pathways in molting fluid. Additionally, many immune-related proteins may be involved in the immune defense during molting. These results provide a comprehensive proteomic insight into proteolytic enzymes and protease inhibitors in molting fluid, and will likely improve the current understanding of physiological processes in insect molting. Insect molting constitutes a dynamic physiological process. To better understand this process, we used LC-MS/MS to investigate the proteome of silkworm molting fluids and identified key proteins involved in silkworm molting. The biological processes of the old cuticle degradation pathway and immune defense response were analyzed in the proteome of silkworm molting fluid. We report that protease inhibitors serve as key factors in the regulation of the molting process. The proteomic results provide new insight into biological molting processes in insects. Copyright © 2017 Elsevier B.V. All rights reserved.

Cytokinin levels and signaling respond to wounding and the perception of herbivore elicitors in Nicotiana attenuata

PubMed Central

Schäfer, Martin; Meza-Canales, Ivan D; Navarro-Quezada, Aura; Brütting, Christoph; Vanková, Radomira; Baldwin, Ian T; Meldau, Stefan

2015-01-01

Nearly half a century ago insect herbivores were found to induce the formation of green islands by manipulating cytokinin (CK) levels. However, the response of the CK pathway to attack by chewing insect herbivores remains unclear. Here, we characterize the CK pathway of Nicotiana attenuata (Torr. ex S. Wats.) and its response to wounding and perception of herbivore-associated molecular patterns (HAMPs). We identified 44 genes involved in CK biosynthesis, inactivation, degradation, and signaling. Leaf wounding rapidly induced transcriptional changes in multiple genes throughout the pathway, as well as in the levels of CKs, including isopentenyladenosine and cis-zeatin riboside; perception of HAMPs present in the oral secretions (OS) of the specialist herbivore Manduca sexta amplified these responses. The jasmonate pathway, which triggers many herbivore-induced processes, was not required for these HAMP-triggered changes, but rather suppressed the CK responses. Interestingly CK pathway changes were observed also in systemic leaves in response to wounding and OS application indicating a role of CKs in mediating long distance systemic processes in response to herbivory. Since wounding and grasshopper OS elicited similar accumulations of CKs in Arabidopsis thaliana L., we propose that CKs are integral components of wounding and HAMP-triggered responses in many plant species. PMID:24924599

Extending shikimate pathway for the production of muconic acid and its precursor salicylic acid in Escherichia coli.

PubMed

Lin, Yuheng; Sun, Xinxiao; Yuan, Qipeng; Yan, Yajun

2014-05-01

cis,cis-Muconic acid (MA) and salicylic acid (SA) are naturally-occurring organic acids having great commercial value. MA is a potential platform chemical for the manufacture of several widely-used consumer plastics; while SA is mainly used for producing pharmaceuticals (for example, aspirin and lamivudine) and skincare and haircare products. At present, MA and SA are commercially produced by organic chemical synthesis using petro-derived aromatic chemicals, such as benzene, as starting materials, which is not environmentally friendly. Here, we report a novel approach for efficient microbial production of MA via extending shikimate pathway by introducing the hybrid of an SA biosynthetic pathway with its partial degradation pathway. First, we engineered a well-developed phenylalanine producing Escherichia coli strain into an SA overproducer by introducing isochorismate synthase and isochorismate pyruvate lyase. The engineered strain is able to produce 1.2g/L of SA from simple carbon sources, which is the highest titer reported so far. Further, the partial SA degradation pathway involving salicylate 1-monoxygenase and catechol 1,2-dioxygenase is established to achieve the conversion of SA to MA. Finally, a de novo MA biosynthetic pathway is assembled by integrating the established SA biosynthesis and degradation modules. Modular optimization enables the production of up to 1.5g/L MA within 48h in shake flasks. This study not only establishes an efficient microbial platform for the production of SA and MA, but also demonstrates a generalizable pathway design strategy for the de novo biosynthesis of valuable degradation metabolites. Copyright © 2014. Published by Elsevier Inc.

Degradation of oxcarbazepine by UV-activated persulfate oxidation: kinetics, mechanisms, and pathways.

PubMed

Bu, Lingjun; Zhou, Shiqing; Shi, Zhou; Deng, Lin; Li, Guangchao; Yi, Qihang; Gao, Naiyun

2016-02-01

The degradation kinetics and mechanism of the antiepileptic drug oxcarbazepine (OXC) by UV-activated persulfate oxidation were investigated in this study. Results showed that UV/persulfate (UV/PS) process appeared to be more effective in degrading OXC than UV or PS alone. The OXC degradation exhibited a pseudo-first order kinetics pattern and the degradation rate constants (k obs) were affected by initial OXC concentration, PS dosage, initial pH, and humic acid concentration to different degrees. It was found that low initial OXC concentration, high persulfate dosage, and initial pH enhanced the OXC degradation. Additionally, the presence of humic acid in the solution could greatly inhibit the degradation of OXC. Moreover, hydroxyl radical (OH•) and sulfate radical (SO4 (-)••) were identified to be responsible for OXC degradation and SO4 (-)• made the predominant contribution in this study. Finally, major intermediate products were identified and a preliminary degradation pathway was proposed. Results demonstrated that UV/PS system is a potential technology to control the water pollution caused by emerging contaminants such as OXC.

Cometabolic Degradation of Dibenzofuran and Dibenzothiophene by a Naphthalene-Degrading Comamonas sp. JB.

PubMed

Ji, Xiangyu; Xu, Jing; Ning, Shuxiang; Li, Nan; Tan, Liang; Shi, Shengnan

2017-12-01

Comamonas sp. JB was used to investigate the cometabolic degradation of dibenzofuran (DBF) and dibenzothiophene (DBT) with naphthalene as the primary substrate. Dehydrogenase and ATPase activity of the growing system with the presence of DBF and DBT were decreased when compared to only naphthalene in the growing system, indicating that the presence of DBF and DBT inhibited the metabolic activity of strain JB. The pathways and enzymes involved in the cometabolic degradation were tested. Examination of metabolites elucidated that strain JB cometabolically degraded DBF to 1,2-dihydroxydibenzofuran, subsequently to 2-hydroxy-4-(3'-oxo-3'H-benzofuran-2'-yliden)but-2-enoic acid, and finally to catechol. Meanwhile, strain JB cometabolically degraded DBT to 1,2-dihydroxydibenzothiophene and subsequently to the ring cleavage product. A series of naphthalene-degrading enzymes including naphthalene dioxygenase, 1,2-dihydroxynaphthalene dioxygenase, salicylaldehyde dehydrogenase, salicylate hydroxylase, and catechol 2,3-oxygenase have been detected, confirming that naphthalene was the real inducer of expression the degradation enzymes and metabolic pathways were controlled by naphthalene-degrading enzymes.

Crosstalk of Autophagy and the Secretory Pathway and Its Role in Diseases.

PubMed

Zahoor, Muhammad; Farhan, Hesso

2018-01-01

The secretory and autophagic pathways are two fundamental, evolutionary highly conserved endomembrane processes. Typically, secretion is associated with biosynthesis and delivery of proteins. In contrast, autophagy is usually considered as a degradative pathway. Thus, an analogy to metabolic pathways is evident. Anabolic (biosynthetic) and catabolic (degradative) pathways are usually intimately linked and intertwined, and likewise, the secretory and autophagy pathways are intertwined. Investigation of this link is an emerging area of research, and we will provide an overview of some of the major advances that have been made to contribute to understanding of how secretion regulates autophagy and vice versa. Finally, we will highlight evidence that supports a potential involvement of the autophagy-secretion crosstalk in human diseases. © 2018 Elsevier Inc. All rights reserved.

Effect of phorbol esters on the macrophage-mediated biodegradation of polyurethanes via protein kinase C activation and other pathways.

PubMed

McBane, Joanne Eileen; Santerre, J P; Labow, Rosalind

2009-01-01

It was previously found that re-seeding monocyte-derived macrophages (MDM) on polycarbonate-based polyurethanes (PCNUs) in the presence of the protein kinase C (PKC) activator phorbol myristate acetate (PMA) inhibited MDM-mediated degradation of PCNUs synthesized with 1,6-hexane diisocyanate (HDI), as well as esterase activity and monocyte-specific esterase (MSE) protein. However, no effect on the degradation of a 4,4'-methylene bisphenyl (MDI)-derived PCNU (MDI321) occurred. This finding suggested that oxidation, a process linked to the PKC pathway, was not activated in the same manner for all PCNUs. In the current study MDM were re-seeded onto the above PCNU surfaces with PMA, PKC-inactive 4alphaPMA and the PKC inhibitor bisindolylmaleimide I hydrochloride (BIM) for 48 h before assaying for PCNU degradation, esterase activity, MSE protein, DNA, cell viability and cell morphology. 4alphaPMA did not alter MDM-mediated HDI PCNU degradation but MDI321 degradation increased in this condition. BIM alone had no effect on any parameter; however, when BIM and PMA were added together, the PMA inhibition of biodegradation, esterase activity and MSE protein was partially reversed for MDM on HDI PCNUs only. Adding PMA to MDM on HDI PCNUs increased intercellular connections, whereas 4alphaPMA or BIM+PMA increased cell size. Although this study demonstrated a role for oxidation via a PKC-activated pathway in MDM-mediated PCNU degradation, phorbol esters appear to also activate non-PKC pathways that have roles in biodegradation. Moreover, the sensitivity to material surface chemistry in the MDM response to each PCNU dictates a multi-factorial degradative process involving alternate material specific oxidative and hydrolytic mechanisms.

Degradation Signals Recognized by the Ubc6p-Ubc7p Ubiquitin-Conjugating Enzyme Pair

PubMed Central

Gilon, Tamar; Chomsky, Orna; Kulka, Richard G.

2000-01-01

Proteolysis by the ubiquitin-proteasome system is highly selective. Specificity is achieved by the cooperation of diverse ubiquitin-conjugating enzymes (Ubcs or E2s) with a variety of ubiquitin ligases (E3s) and other ancillary factors. These recognize degradation signals characteristic of their target proteins. In a previous investigation, we identified signals directing the degradation of β-galactosidase and Ura3p fusion proteins via a subsidiary pathway of the ubiquitin-proteasome system involving Ubc6p and Ubc7p. This pathway has recently been shown to be essential for the degradation of misfolded and regulated proteins in the endoplasmic reticulum (ER) lumen and membrane, which are transported to the cytoplasm via the Sec61p translocon. Mutant backgrounds which prevent retrograde transport of ER proteins (hrd1/der3Δ and sec61-2) did not inhibit the degradation of the β-galactosidase and Ura3p fusions carrying Ubc6p/Ubc7p pathway signals. We therefore conclude that the ubiquitination of these fusion proteins takes place on the cytosolic face of the ER without prior transfer to the ER lumen. The contributions of different sequence elements to a 16-amino-acid-residue Ubc6p-Ubc7p-specific signal were analyzed by mutation. A patch of bulky hydrophobic residues was an essential element. In addition, positively charged residues were found to be essential. Unexpectedly, certain substitutions of bulky hydrophobic or positively charged residues with alanine created novel degradation signals, channeling the degradation of fusion proteins to an unidentified proteasomal pathway not involving Ubc6p and Ubc7p. PMID:10982838

The N-end rule pathway catalyzes a major fraction of the protein degradation in skeletal muscle

NASA Technical Reports Server (NTRS)

Solomon, V.; Lecker, S. H.; Goldberg, A. L.

1998-01-01

In skeletal muscle, overall protein degradation involves the ubiquitin-proteasome system. One property of a protein that leads to rapid ubiquitin-dependent degradation is the presence of a basic, acidic, or bulky hydrophobic residue at its N terminus. However, in normal cells, substrates for this N-end rule pathway, which involves ubiquitin carrier protein (E2) E214k and ubiquitin-protein ligase (E3) E3alpha, have remained unclear. Surprisingly, in soluble extracts of rabbit muscle, we found that competitive inhibitors of E3alpha markedly inhibited the 125I-ubiquitin conjugation and ATP-dependent degradation of endogenous proteins. These inhibitors appear to selectively inhibit E3alpha, since they blocked degradation of 125I-lysozyme, a model N-end rule substrate, but did not affect the degradation of proteins whose ubiquitination involved other E3s. The addition of several E2s or E3alpha to the muscle extracts stimulated overall proteolysis and ubiquitination, but only the stimulation by E3alpha or E214k was sensitive to these inhibitors. A similar general inhibition of ubiquitin conjugation to endogenous proteins was observed with a dominant negative inhibitor of E214k. Certain substrates of the N-end rule pathway are degraded after their tRNA-dependent arginylation. We found that adding RNase A to muscle extracts reduced the ATP-dependent proteolysis of endogenous proteins, and supplying tRNA partially restored this process. Finally, although in muscle extracts the N-end rule pathway catalyzes most ubiquitin conjugation, it makes only a minor contribution to overall protein ubiquitination in HeLa cell extracts.

The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader

PubMed Central

Youssef, Noha H.; Couger, M. B.; Struchtemeyer, Christopher G.; Liggenstoffer, Audra S.; Prade, Rolf A.; Najar, Fares Z.; Atiyeh, Hasan K.; Wilkins, Mark R.

2013-01-01

Anaerobic gut fungi represent a distinct early-branching fungal phylum (Neocallimastigomycota) and reside in the rumen, hindgut, and feces of ruminant and nonruminant herbivores. The genome of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, was sequenced using a combination of Illumina and PacBio single-molecule real-time (SMRT) technologies. The large genome (100.95 Mb, 16,347 genes) displayed extremely low G+C content (17.0%), large noncoding intergenic regions (73.1%), proliferation of microsatellite repeats (4.9%), and multiple gene duplications. Comparative genomic analysis identified multiple genes and pathways that are absent in Dikarya genomes but present in early-branching fungal lineages and/or nonfungal Opisthokonta. These included genes for posttranslational fucosylation, the production of specific intramembrane proteases and extracellular protease inhibitors, the formation of a complete axoneme and intraflagellar trafficking machinery, and a near-complete focal adhesion machinery. Analysis of the lignocellulolytic machinery in the C1A genome revealed an extremely rich repertoire, with evidence of horizontal gene acquisition from multiple bacterial lineages. Experimental analysis indicated that strain C1A is a remarkable biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple untreated grasses and crop residues examined, with the process significantly enhanced by mild pretreatments. This capability, acquired during its separate evolutionary trajectory in the rumen, along with its resilience and invasiveness compared to prokaryotic anaerobes, renders anaerobic fungi promising agents for consolidated bioprocessing schemes in biofuels production. PMID:23709508

The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader.

PubMed

Youssef, Noha H; Couger, M B; Struchtemeyer, Christopher G; Liggenstoffer, Audra S; Prade, Rolf A; Najar, Fares Z; Atiyeh, Hasan K; Wilkins, Mark R; Elshahed, Mostafa S

2013-08-01

Anaerobic gut fungi represent a distinct early-branching fungal phylum (Neocallimastigomycota) and reside in the rumen, hindgut, and feces of ruminant and nonruminant herbivores. The genome of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, was sequenced using a combination of Illumina and PacBio single-molecule real-time (SMRT) technologies. The large genome (100.95 Mb, 16,347 genes) displayed extremely low G+C content (17.0%), large noncoding intergenic regions (73.1%), proliferation of microsatellite repeats (4.9%), and multiple gene duplications. Comparative genomic analysis identified multiple genes and pathways that are absent in Dikarya genomes but present in early-branching fungal lineages and/or nonfungal Opisthokonta. These included genes for posttranslational fucosylation, the production of specific intramembrane proteases and extracellular protease inhibitors, the formation of a complete axoneme and intraflagellar trafficking machinery, and a near-complete focal adhesion machinery. Analysis of the lignocellulolytic machinery in the C1A genome revealed an extremely rich repertoire, with evidence of horizontal gene acquisition from multiple bacterial lineages. Experimental analysis indicated that strain C1A is a remarkable biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple untreated grasses and crop residues examined, with the process significantly enhanced by mild pretreatments. This capability, acquired during its separate evolutionary trajectory in the rumen, along with its resilience and invasiveness compared to prokaryotic anaerobes, renders anaerobic fungi promising agents for consolidated bioprocessing schemes in biofuels production.

Degradation of hexane and other recalcitrant hydrocarbons by a novel isolate, Rhodococcus sp. EH831.

PubMed

Lee, Eun-Hee; Kim, Jaisoo; Cho, Kyung-Suk; Ahn, Yun Gyong; Hwang, Geum-Sook

2010-01-01

Hexane, a representative VOC, is used as a solvent for extraction and as an ingredient in gasoline. The degradation of hexane by bacteria is relatively slow due to its low solubility. Moreover, the biodegradation pathway of hexane under aerobic conditions remains to be investigated; therefore, a study relating to aerobic biodegradation mechanisms is required. Consequently, in this study, an effective hexane degrader was isolated and the biodegradation pathway examined for the first time. In addition, the degradation characteristics of a variety of recalcitrant hydrocarbons were qualitatively and quantitatively investigated using the isolate. A hexane-degrading bacterium was isolated from an enrichment culture using petroleum-contaminated soil as an inoculum with hexane as the sole carbon and energy source. The bacterium was also identified using the partial 16S rRNA gene sequence. To test the hexane-degrading capacity of the isolate, 10 ml of an EH831 cell suspension was inoculated into a 600-ml serum bottle with hexane (7.6-75.8 micromol) injected as the sole carbon source. The rates of hexane degradation were determined by analyzing the concentrations of hexane using headspace gas chromatography. In addition, the hexane biodegradation pathway under aerobic conditions was investigated by identifying the metabolites using gas chromatography-mass spectrometry with solid-phase microextraction. 14C-hexane was used to check if EH831 could mineralize hexane in the same experimental system. The degradabilities of other hydrocarbons were examined using EH831 with methanol, ethanol, acetone, cyclohexane, methyl tert-butyl ether (MTBE), dichloromethane (DCM), trichloroethylene, tetrachloroethylene, benzene, toluene, ethylbenzene, xylene (BTEX), pyrene, diesel, lubricant oil, and crude oil as sole carbon sources. A bacterium, EH831, was isolated from the enriched hexane-degrading consortium, which was able to degrade hexane and various hydrocarbons, including alcohols, chlorinated hydrocarbons, cyclic alkanes, ethers, ketones, monoaromatic and polyaromatic hydrocarbons, and petroleum hydrocarbons. The maximum hexane degradation rate (V max) of EH831 was 290 micromol g dry cell weight(-1) h(-1), and the saturation constant (K s) was 15 mM. Using 14C-hexane, EH831 was confirmed to mineralize approximately 49% of the hexane into CO2 and, converted approximately, 46% into biomass; the rest (1.7%) remained as extracellular metabolites in the liquid phase. The degradation pathway was assessed through the qualitative analysis of the hexane intermediates due to EH831, which were 2-hexanol, 2-hexanone, 5-hexen-2-one and 2,5-hexanedione, in that order, followed by 4-methyl-2-pentanone, 3-methyl-1-butanol, 3-methyl-1-butanone and butanal, and finally, CO2. EH831 could degrade methanol, ethanol, acetone, cyclohexane, MTBE, DCM, BTEX, pyrene, diesel, and lubricant oil. EH831 was able to degrade many recalcitrant hydrocarbons at higher degradation rates compared with previous well-known degraders. Furthermore, this study primarily suggested the aerobic biodegradation pathway, which may provide valuable information for researchers and engineers working in the field of environmental engineering. Rhodococcus sp. EH831 is a promising bioresource for removing hexane and other recalcitrant hydrocarbons from a variety of environments. Moreover, the aerobic biodegradation pathway is reported for the first time in this study, which offers valuable information for understanding the microbial degradation of hexane. The utility of the strain isolated in this study needs to be proved by its application to biological process systems, such as biofilters and bioreactors, etc., for the degradation of hexane and many other recalcitrant hydrocarbons. Detailed investigations will also be needed to clarify the enzymatic characteristics relating the degradation of both recalcitrant hydrocarbons and hexane.

Biodegradation of diethyl terephthalate (DET) and polyethylene terephthalate (PET) by a novel identified degrader Delftia sp. WL-3 and its proposed metabolic pathway.

PubMed

Liu, Jiawei; Xu, Guanbao; Dong, Weiliang; Xu, Ning; Xin, Fengxue; Ma, Jiangfeng; Fang, Yan; Zhou, Jie; Jiang, Min

2018-06-01

Polyethylene terephthalate (PET), a synthetic polyester material made of diethyl terephthalate (DET) monomers, is widely used in plastic products of daily life and caused serious pollution to the global environment. Microbial metabolism is the major degradation pathway responsible for DET degradation in natural soil; however, the microbial DET-degradation mechanism remains unclear. In this study, the newly isolated strain WL-3, identified as belonging to the genus Delftia, was found to be able to degrade 94% of 5 g·L -1 of DET and utilize it as the sole carbon source for growth within 7 days. Furthermore, strain WL-3 was capable of stable DET degradation under a wide range of pH values (6.0-9.0) and temperatures (20-42°C) with the optimal pH and temperature of 7.0 and 30°C respectively. Furthermore, the biochemical pathway of DET degradation by strain WL-3 was proposed based on the identified degradation intermediates. DET is first transformed into terephthalic acid (TPA) by the hydrolysis of two ester bonds, which is subsequently converted to protocatechuic acid (PCA) and further mineralized. SEM observations revealed obvious cracks on the surface of PET film after inoculation of 2 months with strain WL-3, indicating the strain's potential for the bioremediation of PET-contaminated environments. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Degradation of clofibric acid in UV/chlorine disinfection process: kinetics, reactive species contribution and pathways

PubMed Central

Tang, Yuqing; Shi, Xueting; Liu, Yongze; Zhang, Liqiu

2018-01-01

As a potential endocrine disruptor, clofibric acid (CA) was investigated in this study for its degradation kinetics and pathways in UV/chlorine process. The results showed that CA in both UV photolysis and UV/chlorine processes could be degraded via pseudo-first-order kinetics, while it almost could not be degraded in the dark chlorination process. The observed rate constant (kobs) in UV photolysis was 0.0078 min−1, and increased to 0.0107 min−1 combining with 0.1 mM chlorine. The kobs increased to 0.0447 min−1 with further increasing the chlorine dosage from 0.1 to 1.0 mM, and reached a plateau at higher dosage (greater than 1.0 mM). The higher kobs was obtained at acid solution rather than basic solution. Moreover, the calculated contributions of radical species to kobs indicated that the HO• contributed significantly to CA degradation in acidic conditions, while the reactive chlorine species and UV direct photolysis dominated in neutral and basic solution. The degradation of CA was slightly inhibited in the presence of HCO3− (1 ∼ 50 mM), barely affected by the presence of Cl− (1 ∼ 200 mM) and greatly suppressed by humic acid (0 ∼ 5 mg l−1). Thirteen main degradation intermediates and three degradation pathways of CA were identified during UV/chlorine process. PMID:29515853

Degradation of 4-chloro-3-nitrophenol via a novel intermediate, 4-chlororesorcinol by Pseudomonas sp. JHN

PubMed Central

Arora, Pankaj Kumar; Srivastava, Alok; Singh, Vijay Pal

2014-01-01

A 4-chloro-3-nitrophenol (4C3NP)-mineralizing bacterium, Pseudomonas sp. JHN was isolated from a waste water sample collected from a chemically-contaminated area, India by an enrichment method. Pseudomonas sp. JHN utilized 4C3NP as a sole carbon and energy source and degraded it with the release of stoichiometric amounts of chloride and nitrite ions. Gas chromatography and gas chromatography-mass spectrometry detected 4-chlororesorcinol as a major metabolite of the 4C3NP degradation pathway. Inhibition studies using 2,2′-dipyridyl showed that 4-chlororesorcinol is a terminal aromatic compound in the degradation pathway of 4C3NP. The activity for 4C3NP-monooxygenase was detected in the crude extracts of the 4C3NP-induced JHN cells that confirmed the formation of 4-chlororesorcinol from 4C3NP. The capillary assay showed that Pseudomonas sp. JHN exhibited chemotaxis toward 4C3NP. The bioremediation capability of Pseudomonas sp. JHN was monitored to carry out the microcosm experiments using sterile and non-sterile soils spiked with 4C3NP. Strain JHN degraded 4C3NP in sterile and non-sterile soil with same degradation rates. This is the first report of (i) bacterial degradation and bioremediation of 4C3NP, (ii) formation of 4-chlororesorcinol in the degradation pathway of 4C3NP, (iii) bacterial chemotaxis toward 4C3NP. PMID:24667329

Degradation of clofibric acid in UV/chlorine disinfection process: kinetics, reactive species contribution and pathways.

PubMed

Tang, Yuqing; Shi, Xueting; Liu, Yongze; Feng, Li; Zhang, Liqiu

2018-02-01

As a potential endocrine disruptor, clofibric acid (CA) was investigated in this study for its degradation kinetics and pathways in UV/chlorine process. The results showed that CA in both UV photolysis and UV/chlorine processes could be degraded via pseudo-first-order kinetics, while it almost could not be degraded in the dark chlorination process. The observed rate constant ( k obs ) in UV photolysis was 0.0078 min -1, and increased to 0.0107 min -1 combining with 0.1 mM chlorine. The k obs increased to 0.0447 min -1 with further increasing the chlorine dosage from 0.1 to 1.0 mM, and reached a plateau at higher dosage (greater than 1.0 mM). The higher k obs was obtained at acid solution rather than basic solution. Moreover, the calculated contributions of radical species to k obs indicated that the HO• contributed significantly to CA degradation in acidic conditions, while the reactive chlorine species and UV direct photolysis dominated in neutral and basic solution. The degradation of CA was slightly inhibited in the presence of [Formula: see text] (1 ∼ 50 mM), barely affected by the presence of Cl - (1 ∼ 200 mM) and greatly suppressed by humic acid (0 ∼ 5 mg l -1 ). Thirteen main degradation intermediates and three degradation pathways of CA were identified during UV/chlorine process.

Oxidatively denatured proteins are degraded by an ATP-independent proteolytic pathway in Escherichia coli.

PubMed

Davies, K J; Lin, S W

1988-01-01

E. coli contains a soluble proteolytic pathway which can recognize and degrade oxidatively denatured proteins and protein fragments, and which may act as a "secondary antioxidant defense." We now provide evidence that this proteolytic pathway is distinct from the previously described ATP-dependent, and protease "La"-dependent, pathway which may degrade other abnormal proteins. Cells (K12) which were depleted of ATP, by arsenate treatment or anaerobic incubation (after growth on succinate), exhibited proteolytic responses to oxidative stress which were indistinguishable from those observed in cells with normal ATP levels. Furthermore, the proteolytic responses to oxidative damage by menadione or H2O2 were almost identical in the isogenic strains RM312 (a K12 derivative) and RM1385 (a lon deletion mutant of RM312). Since the lon (or capR) gene codes for the ATP-dependent protease "La," these results indicate that neither ATP nor protease "La" are required for the degradation of oxidatively denatured proteins. We next prepared cell-free extracts of K12, RM312, and RM1385 and tested the activity of their soluble proteases against proteins (albumin, hemoglobin, superoxide dismutase, catalase) which had been oxidatively denatured (in vitro) by exposure to .OH, .OH + O2- (+O2), H2O2, or ascorbate plus iron. The breakdown of oxidatively denatured proteins was several-fold higher than that of untreated proteins in extracts from all three strains, and ATP did not stimulate degradation. Incubation of extracts at 45 degrees C, which inactivates protease "La," actually stimulated the degradation of oxidatively denatured proteins. Although Ca2+ had little effect on proteolysis, serine reagents, transition metal chelators, and hemin effectively inhibited the degradation of oxidatively denatured proteins in both intact cells and cell-free extracts. Degradation of oxidatively denatured proteins in cell-free extracts was maximal at pH 7.8, and was unaffected by dialysis of the extracts against membranes with molecular weight cutoffs as high as 50,000. Our results indicate the presence of a neutral, ATP- and calcium- independent proteolytic pathway in the E. coli cytosol, which contains serine- and metallo- proteases (with molecular weights greater than 50,000), and which preferentially degrades oxidatively denatured proteins.

Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway.

PubMed

Martínez-Lavanchy, P M; Chen, Z; Lünsmann, V; Marin-Cevada, V; Vilchez-Vargas, R; Pieper, D H; Reiche, N; Kappelmeyer, U; Imparato, V; Junca, H; Nijenhuis, I; Müller, J A; Kuschk, P; Heipieper, H J

2015-09-01

In the present study, microbial toluene degradation in controlled constructed wetland model systems, planted fixed-bed reactors (PFRs), was queried with DNA-based methods in combination with stable isotope fractionation analysis and characterization of toluene-degrading microbial isolates. Two PFR replicates were operated with toluene as the sole external carbon and electron source for 2 years. The bulk redox conditions in these systems were hypoxic to anoxic. The autochthonous bacterial communities, as analyzed by Illumina sequencing of 16S rRNA gene amplicons, were mainly comprised of the families Xanthomonadaceae, Comamonadaceae, and Burkholderiaceae, plus Rhodospirillaceae in one of the PFR replicates. DNA microarray analyses of the catabolic potentials for aromatic compound degradation suggested the presence of the ring monooxygenation pathway in both systems, as well as the anaerobic toluene pathway in the PFR replicate with a high abundance of Rhodospirillaceae. The presence of catabolic genes encoding the ring monooxygenation pathway was verified by quantitative PCR analysis, utilizing the obtained toluene-degrading isolates as references. Stable isotope fractionation analysis showed low-level of carbon fractionation and only minimal hydrogen fractionation in both PFRs, which matches the fractionation signatures of monooxygenation and dioxygenation. In combination with the results of the DNA-based analyses, this suggests that toluene degradation occurs predominantly via ring monooxygenation in the PFRs. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Presence or Absence of mlr Genes and Nutrient Concentrations Co-Determine the Microcystin Biodegradation Efficiency of a Natural Bacterial Community.

PubMed

Lezcano, María Ángeles; Morón-López, Jesús; Agha, Ramsy; López-Heras, Isabel; Nozal, Leonor; Quesada, Antonio; El-Shehawy, Rehab

2016-11-03

The microcystin biodegradation potential of a natural bacterial community coexisting with a toxic cyanobacterial bloom was investigated in a water reservoir from central Spain. The biodegradation capacity was confirmed in all samples during the bloom and an increase of mlr A gene copies was found with increasing microcystin concentrations. Among the 24 microcystin degrading strains isolated from the bacterial community, only 28% showed presence of mlr A gene, strongly supporting the existence and abundance of alternative microcystin degradation pathways in nature. In vitro degradation assays with both mlr ⁺ and mlr - bacterial genotypes (with presence and absence of the complete mlr gene cluster, respectively) were performed with four isolated strains ( Sphingopyxis sp. IM-1, IM-2 and IM-3; Paucibacter toxinivorans IM-4) and two bacterial degraders from the culture collection ( Sphingosinicella microcystinivorans Y2; Paucibacter toxinivorans 2C20). Differences in microcystin degradation efficiencies between genotypes were found under different total organic carbon and total nitrogen concentrations. While mlr ⁺ strains significantly improved microcystin degradation rates when exposed to other carbon and nitrogen sources, mlr - strains showed lower degradation efficiencies. This suggests that the presence of alternative carbon and nitrogen sources possibly competes with microcystins and impairs putative non- mlr microcystin degradation pathways. Considering the abundance of the mlr - bacterial population and the increasing frequency of eutrophic conditions in aquatic systems, further research on the diversity of this population and the characterization and conditions affecting non- mlr degradation pathways deserves special attention.

Characterization of a Pyrethroid-Degrading Pseudomonas fulva Strain P31 and Biochemical Degradation Pathway of D-Phenothrin.

PubMed

Yang, Jingjing; Feng, Yanmei; Zhan, Hui; Liu, Jie; Yang, Fang; Zhang, Kaiyang; Zhang, Lianhui; Chen, Shaohua

2018-01-01

D-phenothrin is one of the most popular pyrethroid insecticides for its broad spectrum and high insecticidal activity. However, continuous use of D-phenothrin has resulted in serious environmental contamination and raised public concern about its impact on human health. Biodegradation of D-phenothrin has never been investigated and its metabolic behaviors remain unknown. Here, a novel bacterial strain P31 was isolated from active sludge, which completely degraded (100%) D-phenothrin at 50 mg⋅L -1 in 72 h. Based on the morphology, 16S rRNA gene and Biolog tests, the strain was identified as Pseudomonas fulva . Biodegradation conditions were optimized as 29.5°C and pH 7.3 by utilizing response surface methodology. Strain P31 depicted high tolerance and strong D-phenothrin degradation ability through hydrolysis pathway. Strain P31 degraded D-phenothrin at inhibition constant ( K i ) of 482.1673 mg⋅L -1 and maximum specific degradation constant ( q max ) of 0.0455 h -1 whereas critical inhibitor concentration remained as 41.1189 mg⋅L -1 . The 3-Phenoxybenzaldehyde and 1,2-benzenedicarboxylic butyl dacyl ester were identified as the major intermediate metabolites of D-phenothrin degradation pathway through high-performance liquid chromatography and gas chromatography-mass spectrometry. Bioaugmentation of D-phenothrin-contaminated soils with strain P31 dramatically enhanced its degradation, and over 75% of D-phenothrin was removed from soils within 10 days. Moreover, the strain illustrated a remarkable capacity to degrade other synthetic pyrethroids, including permethrin, cyhalothrin, β-cypermethrin, deltamethrin, fenpropathrin, and bifenthrin, exhibiting great potential in bioremediation of pyrethroid-contaminated environment.

Chemical intervention in bacterial lignin degradation pathways: Development of selective inhibitors for intradiol and extradiol catechol dioxygenases.

PubMed

Sainsbury, Paul D; Mineyeva, Yelena; Mycroft, Zoe; Bugg, Timothy D H

2015-06-01

Bacterial lignin degradation could be used to generate aromatic chemicals from the renewable resource lignin, provided that the breakdown pathways can be manipulated. In this study, selective inhibitors of enzymatic steps in bacterial degradation pathways were developed and tested for their effects upon lignin degradation. Screening of a collection of hydroxamic acid metallo-oxygenase inhibitors against two catechol dioxygenase enzymes, protocatechuate 3,4-dioxygenase (3,4-PCD) and 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), resulted in the identification of selective inhibitors D13 for 3,4-PCD (IC50 15μM) and D3 for MhpB (IC50 110μM). Application of D13 to Rhodococcus jostii RHA1 in minimal media containing ferulic acid led to the appearance of metabolic precursor protocatechuic acid at low concentration. Application of 1mM disulfiram, an inhibitor of mammalian aldehyde dehydrogenase, to R. jostii RHA1, gave rise to 4-carboxymuconolactone on the β-ketoadipate pathway, whereas in Pseudomonas fluorescens Pf-5 disulfiram treatment gave rise to a metabolite found to be glycine betaine aldehyde. Copyright © 2015 Elsevier Inc. All rights reserved.

TiO2 photocatalytic degradation and transformation of oxazaphosphorine drugs in an aqueous environment.

PubMed

Lai, Webber Wei-Po; Lin, Hank Hui-Hsiang; Lin, Angela Yu-Chen

2015-04-28

This study investigated the TiO2 photocatalytic degradation and transformation of the oxazaphosphorines ifosfamide (IFO), cyclophosphamide (CP) and trofosfamide (TRO). Under the optimum conditions of TiO2=100mg/L, IFO=100μg/L and solution pH=5.5, IFO was completely removed within 10min (k=0.433min(-1)). The results indicated that OHfree radicals generated by valence holes in the bulk solution were the predominant species for the degradation of IFO. At higher initial concentrations of oxazaphosphorines (20mg/L), >50% of TOC remained after 6h of reaction time, indicating that parent compounds were transformed to byproducts, which exhibit higher Microtox acute toxicities; chlorinated byproducts were likely the source of toxicity. Photocatalytic degradation pathways of the three oxazaphosphorines were proposed. IFO, CP and TRO follow very similar pathways and bond-breaking processes: ketonization and breaking of the CCl bond, the PN bond and the CN bond (N-dechloroethylation). Chloride (Cl(-)) release is likely the first and primary step in the decomposition process. Several of the identified byproducts were also metabolites, which implies that photocatalytic oxidation proceeds through pathways that are similar to metabolic pathways. Copyright © 2015 Elsevier B.V. All rights reserved.

Cinnamic Acid, an Autoinducer of Its Own Biosynthesis, Is Processed via Hca Enzymes in Photorhabdus luminescens▿

PubMed Central

Chalabaev, Sabina; Turlin, Evelyne; Bay, Sylvie; Ganneau, Christelle; Brito-Fravallo, Emma; Charles, Jean-François; Danchin, Antoine; Biville, Francis

2008-01-01

Photorhabdus luminescens, an entomopathogenic bacterium and nematode symbiont, has homologues of the Hca and Mhp enzymes. In Escherichia coli, these enzymes catalyze the degradation of the aromatic compounds 3-phenylpropionate (3PP) and cinnamic acid (CA) and allow the use of 3PP as sole carbon source. P. luminescens is not able to use 3PP and CA as sole carbon sources but can degrade them. Hca dioxygenase is involved in this degradation pathway. P. luminescens synthesizes CA from phenylalanine via a phenylalanine ammonia-lyase (PAL) and degrades it via the not-yet-characterized biosynthetic pathway of 3,5-dihydroxy-4-isopropylstilbene (ST) antibiotic. CA induces its own synthesis by enhancing the expression of the stlA gene that codes for PAL. P. luminescens bacteria release endogenous CA into the medium at the end of exponential growth and then consume it. Hca dioxygenase is involved in the consumption of endogenous CA but is not required for ST production. This suggests that CA is consumed via at least two separate pathways in P. luminescens: the biosynthesis of ST and a pathway involving the Hca and Mhp enzymes. PMID:18245247

Chemical Conversion Pathways and Kinetic Modeling for the OH-Initiated Reaction of Triclosan in Gas-Phase

PubMed Central

Zhang, Xue; Zhang, Chenxi; Sun, Xiaomin; Kang, Lingyan; Zhao, Yan

2015-01-01

As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of kadd/ktotal and kabs/ktotal at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin. PMID:25867482

Cytolethal distending toxins require components of the ER-associated degradation pathway for host cell entry.

PubMed

Eshraghi, Aria; Dixon, Shandee D; Tamilselvam, Batcha; Kim, Emily Jin-Kyung; Gargi, Amandeep; Kulik, Julia C; Damoiseaux, Robert; Blanke, Steven R; Bradley, Kenneth A

2014-07-01

Intracellular acting protein exotoxins produced by bacteria and plants are important molecular determinants that drive numerous human diseases. A subset of these toxins, the cytolethal distending toxins (CDTs), are encoded by several Gram-negative pathogens and have been proposed to enhance virulence by allowing evasion of the immune system. CDTs are trafficked in a retrograde manner from the cell surface through the Golgi apparatus and into the endoplasmic reticulum (ER) before ultimately reaching the host cell nucleus. However, the mechanism by which CDTs exit the ER is not known. Here we show that three central components of the host ER associated degradation (ERAD) machinery, Derlin-2 (Derl2), the E3 ubiquitin-protein ligase Hrd1, and the AAA ATPase p97, are required for intoxication by some CDTs. Complementation of Derl2-deficient cells with Derl2:Derl1 chimeras identified two previously uncharacterized functional domains in Derl2, the N-terminal 88 amino acids and the second ER-luminal loop, as required for intoxication by the CDT encoded by Haemophilus ducreyi (Hd-CDT). In contrast, two motifs required for Derlin-dependent retrotranslocation of ERAD substrates, a conserved WR motif and an SHP box that mediates interaction with the AAA ATPase p97, were found to be dispensable for Hd-CDT intoxication. Interestingly, this previously undescribed mechanism is shared with the plant toxin ricin. These data reveal a requirement for multiple components of the ERAD pathway for CDT intoxication and provide insight into a Derl2-dependent pathway exploited by retrograde trafficking toxins.

Cytolethal Distending Toxins Require Components of the ER-Associated Degradation Pathway for Host Cell Entry

PubMed Central

Eshraghi, Aria; Dixon, Shandee D.; Tamilselvam, Batcha; Kim, Emily Jin-Kyung; Gargi, Amandeep; Kulik, Julia C.; Damoiseaux, Robert; Blanke, Steven R.; Bradley, Kenneth A.

2014-01-01

Intracellular acting protein exotoxins produced by bacteria and plants are important molecular determinants that drive numerous human diseases. A subset of these toxins, the cytolethal distending toxins (CDTs), are encoded by several Gram-negative pathogens and have been proposed to enhance virulence by allowing evasion of the immune system. CDTs are trafficked in a retrograde manner from the cell surface through the Golgi apparatus and into the endoplasmic reticulum (ER) before ultimately reaching the host cell nucleus. However, the mechanism by which CDTs exit the ER is not known. Here we show that three central components of the host ER associated degradation (ERAD) machinery, Derlin-2 (Derl2), the E3 ubiquitin-protein ligase Hrd1, and the AAA ATPase p97, are required for intoxication by some CDTs. Complementation of Derl2-deficient cells with Derl2:Derl1 chimeras identified two previously uncharacterized functional domains in Derl2, the N-terminal 88 amino acids and the second ER-luminal loop, as required for intoxication by the CDT encoded by Haemophilus ducreyi (Hd-CDT). In contrast, two motifs required for Derlin-dependent retrotranslocation of ERAD substrates, a conserved WR motif and an SHP box that mediates interaction with the AAA ATPase p97, were found to be dispensable for Hd-CDT intoxication. Interestingly, this previously undescribed mechanism is shared with the plant toxin ricin. These data reveal a requirement for multiple components of the ERAD pathway for CDT intoxication and provide insight into a Derl2-dependent pathway exploited by retrograde trafficking toxins. PMID:25078082

Autophagy degrades hypoxia inducible factors

PubMed Central

DePavia, Adela; Jonasch, Eric; Liu, Xian-De

2016-01-01

ABSTRACT Hypoxia inducible factors are subjected to degradation by the ubiquitin-proteasome system (UPS), macroautophagy, and chaperone-mediated autophagy. The E3 ligases, ubiquitination, autophagy receptor proteins, and oxygen are determinants that direct hypoxia-inducible factors to different degradation pathways. PMID:27308629

Mass dependent stable isotope fractionation of mercury during mer mediated microbial degradation of monomethylmercury

NASA Astrophysics Data System (ADS)

Kritee, K.; Barkay, Tamar; Blum, Joel D.

2009-03-01

Controlling bioaccumulation of toxic monomethylmercury (MMHg) in aquatic food chains requires differentiation between biotic and abiotic pathways that lead to its production and degradation. Recent mercury (Hg) stable isotope measurements of natural samples suggest that Hg isotope ratios can be a powerful proxy for tracing dominant Hg transforming pathways in aquatic ecosystems. Specifically, it has been shown that photo-degradation of MMHg causes both mass dependent (MDF) and mass independent fractionation (MIF) of Hg isotopes. Because the extent of MDF and MIF observed in natural samples (e.g., fish, soil and sediments) can potentially be used to determine the relative importance of pathways leading to MMHg accumulation, it is important to determine the potential role of microbial pathways in contributing to the fractionation, especially MIF, observed in these samples. This study reports the extent of fractionation of Hg stable isotopes during degradation of MMHg to volatile elemental Hg and methane via the microbial Hg resistance ( mer) pathway in Escherichia coli carrying a mercury resistance ( mer) genetic system on a multi-copy plasmid. During experimental microbial degradation of MMHg, MMHg remaining in reactors became progressively heavier (increasing δ202Hg) with time and underwent mass dependent Rayleigh fractionation with a fractionation factor α202/198 = 1.0004 ± 0.0002 (2SD). However, MIF was not observed in any of the microbial MMHg degradation experiments indicating that the isotopic signature left by mer mediated MMHg degradation is significantly different from fractionation observed during DOC mediated photo-degradation of MMHg. Additionally, a clear suppression of Hg isotope fractionation, both during reduction of Hg(II) and degradation of MMHg, was observed when the cell densities increased, possibly due to a reduction in substrate bioavailability. We propose a multi-step framework for understanding the extent of fractionation seen in our MMHg degradation experiments and, based on estimates of the rates of the various steps involved in this mer mediated pathway, suggest which steps in the process could contribute towards the observed extent of fractionation. This framework suggests that at lower cell densities catalysis by MerB was the rate limiting step while at higher cell densities transport into the cell, which does not cause fractionation, became the rate limiting step. In addition to presenting evidence for absence of MIF during mer mediated Hg transformations, based on the nature of Hg compounds and microbe-Hg interactions, we suggest that the nuclear spin dependent MIF (i.e., the magnetic isotope effect) is also unlikely to occur during other non mer mediated 'dark' microbial Hg transformations (e.g., formation of MMHg and oxidative degradation of MMHg). Because of the important implications of the absence of MIF during biological processes on Hg isotope systematics, we discuss theoretical considerations and experimental strategies that could be used to confirm this suggestion.

Ascorbate degradation in tomato leads to accumulation of oxalate, threonate and oxalyl threonate.

PubMed

Truffault, Vincent; Fry, Stephen C; Stevens, Rebecca G; Gautier, Hélène

2017-03-01

Ascorbate content in plants is controlled by its synthesis from carbohydrates, recycling of the oxidized forms and degradation. Of these pathways, ascorbate degradation is the least studied and represents a lack of knowledge that could impair improvement of ascorbate content in fruits and vegetables as degradation is non-reversible and leads to a depletion of the ascorbate pool. The present study revealed the nature of degradation products using [ 14 C]ascorbate labelling in tomato, a model plant for fleshy fruits; oxalate and threonate are accumulated in leaves, as is oxalyl threonate. Carboxypentonates coming from diketogulonate degradation were detected in relatively insoluble (cell wall-rich) leaf material. No [ 14 C]tartaric acid was found in tomato leaves. Ascorbate degradation was stimulated by darkness, and the degradation rate was evaluated at 63% of the ascorbate pool per day, a percentage that was constant and independent of the initial ascorbate or dehydroascorbic acid concentration over periods of 24 h or more. Furthermore, degradation could be partially affected by the ascorbate recycling pathway, as lines under-expressing monodehydroascorbate reductase showed a slight decrease in degradation product accumulation. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Significance of duon mutations in cancer genomes

NASA Astrophysics Data System (ADS)

Yadav, Vinod Kumar; Smith, Kyle S.; Flinders, Colin; Mumenthaler, Shannon M.; de, Subhajyoti

2016-06-01

Functional mutations in coding regions not only affect the structure and function of the protein products, but may also modulate their expression in some cases. This class of mutations, recently dubbed “duon mutations” due to their dual roles, can potentially have major impacts on downstream pathways. However their significance in diseases such as cancer remain unclear. In a survey covering 4606 samples from 19 cancer types, and integrating allelic expression, overall mRNA expression, regulatory motif perturbation, and chromatin signatures in one composite index called REDACT score, we identified potential duon mutations. Several such mutations are detected in known cancer genes in multiple cancer types. For instance a potential duon mutation in TP53 is associated with increased expression of the mutant allelic gene copy, thereby possibly amplifying the functional effects on the downstream pathways. Another potential duon mutation in SF3B1 is associated with abnormal splicing and changes in angiogenesis and matrix degradation related pathways. Our findings emphasize the need to interrogate the mutations in coding regions beyond their obvious effects on protein structures.

Dissecting the Molecular Pathway Involved in PLK2 Kinase-mediated α-Synuclein-selective Autophagic Degradation.

PubMed

Dahmene, Manel; Bérard, Morgan; Oueslati, Abid

2017-03-03

Increasing lines of evidence support the causal link between α-synuclein (α-syn) accumulation in the brain and Parkinson's disease (PD) pathogenesis. Therefore, lowering α-syn protein levels may represent a viable therapeutic strategy for the treatment of PD and related disorders. We recently described a novel selective α-syn degradation pathway, catalyzed by the activity of the Polo-like kinase 2 (PLK2), capable of reducing α-syn protein expression and suppressing its toxicity in vivo However, the exact molecular mechanisms underlying this degradation route remain elusive. In the present study we report that among PLK family members, PLK3 is also able to catalyze α-syn phosphorylation and degradation in living cells. Using pharmacological and genetic approaches, we confirmed the implication of the macroautophagy on PLK2-mediated α-syn turnover, and our observations suggest a concomitant co-degradation of these two proteins. Moreover, we showed that the N-terminal region of α-syn is important for PLK2-mediated α-syn phosphorylation and degradation and is implicated in the physical interaction between the two proteins. We also demonstrated that PLK2 polyubiquitination is important for PLK2·α-syn protein complex degradation, and we hypothesize that this post-translational modification may act as a signal for the selective recognition by the macroautophagy machinery. Finally, we observed that the PD-linked mutation E46K enhances PLK2-mediated α-syn degradation, suggesting that this mutated form is a bona fide substrate of this degradation pathway. In conclusion, our study provides a detailed description of the new degradation route of α-syn and offers new opportunities for the development of therapeutic strategies aiming to reduce α-syn protein accumulation and toxicity. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Characterization of nitrite degradation by Lactobacillus casei subsp. rhamnosus LCR 6013.

PubMed

Liu, Dong-mei; Wang, Pan; Zhang, Xin-yue; Xu, Xi-lin; Wu, Hui; Li, Li

2014-01-01

Nitrites are potential carcinogens. Therefore, limiting nitrites in food is critically important for food safety. The nitrite degradation capacity of Lactobacillus casei subsp. rhamnosus LCR 6013 was investigated in pickle fermentation. After LCR 6013 fermentation for 120 h at 37°C, the nitrite concentration in the fermentation system was significantly lower than that in the control sample without the LCR 6013 strain. The effects of NaCl and Vc on nitrite degradation by LCR 6013 in the De Man, Rogosa and Sharpe (MRS) medium were also investigated. The highest nitrite degradations, 9.29 mg/L and 9.89 mg/L, were observed when NaCl and Vc concentrations were 0.75% and 0.02%, respectively in the MRS medium, which was significantly higher than the control group (p ≤ 0.01). Electron capture/gas chromatography and indophenol blue staining were used to study the nitrite degradation pathway of LCR 6013. The nitrite degradation products contained N2O, but no NH4(+). The LCR 6013 strain completely degraded all NaNO2 (50.00 mg/L) after 16 h of fermentation. The enzyme activity of NiR in the periplasmic space was 2.5 times of that in the cytoplasm. Our results demonstrated that L. casei subsp. rhamnosus LCR 6013 can effectively degrade nitrites in both the pickle fermentation system and in MRS medium by NiR. Nitrites are degraded by the LCR 6013 strain, likely via the nitrate respiration pathway (NO2(-)>NO->N2O->N2), rather than the aammonium formation pathway (dissimilatory nitrate reduction to ammonium, DNRA), because the degradation products contain N2O, but not NH4(+).

In-situ multianalytical approach to analyze and compare the degradation pathways jeopardizing two murals exposed to different environments (Ariadne House, Pompeii, Italy).

PubMed

Veneranda, M; Prieto-Taboada, N; Fdez-Ortiz de Vallejuelo, S; Maguregui, M; Morillas, H; Marcaida, I; Castro, K; Garcia-Diego, F-J; Osanna, M; Madariaga, J M

2018-05-29

This study aimed at using portable analytical techniques to characterize original and decayed materials from two murals paintings of Ariadne House (archaeological site of Pompeii, Italy) and define the degradation pathways threatening their conservation. The first wall, located in an outdoor environment, has been directly exposed to degradation processes triggered by weathering and atmospheric pollution. The second wall, placed in a basement under the ground floor, has been constantly sheltered from sunlight exposure and drastic temperature fluctuations. The analytical data obtained in-situ by using Raman spectroscopy and Laser Induced Breakdown Spectroscopy (LIBS) correlates the degradation patterns affecting the two surfaces to their environmental context. The deterioration processes detected on the outdoor wall, which entailed the complete loss of the paint layer, were mostly related to leaching and thermal fluctuation phenomena. The mural painting from the basement instead, showed deep degradation issues due to soluble salt infiltration and biological colonization. The results obtained from this unique case of study highlight the indispensable role of in-situ spectroscopic analysis to understand and predict the degradation pathways jeopardizing the cultural heritage and provide to the Archaeological Park of Pompeii important inference to consider in future conservation projects. Copyright © 2018. Published by Elsevier B.V.

Degradation of ibuprofen by hydrodynamic cavitation: Reaction pathways and effect of operational parameters.

PubMed

Musmarra, Dino; Prisciandaro, Marina; Capocelli, Mauro; Karatza, Despina; Iovino, Pasquale; Canzano, Silvana; Lancia, Amedeo

2016-03-01

Ibuprofen (IBP) is an anti-inflammatory drug whose residues can be found worldwide in natural water bodies resulting in harmful effects to aquatic species even at low concentrations. This paper deals with the degradation of IBP in water by hydrodynamic cavitation in a convergent-divergent nozzle. Over 60% of ibuprofen was degraded in 60 min with an electrical energy per order (EEO) of 10.77 kWh m(-3) at an initial concentration of 200 μg L(-1) and a relative inlet pressure pin=0.35 MPa. Five intermediates generated from different hydroxylation reactions were identified; the potential mechanisms of degradation were sketched and discussed. The reaction pathways recognized are in line with the relevant literature, both experimental and theoretical. By varying the pressure upstream the constriction, different degradation rates were observed. This effect was discussed according to a numerical simulation of the hydroxyl radical production identifying a clear correspondence between the maximum kinetic constant kOH and the maximum calculated OH production. Furthermore, in the investigated experimental conditions, the pH parameter was found not to affect the extent of degradation; this peculiar feature agrees with a recently published kinetic insight and has been explained in the light of the intermediates of the different reaction pathways. Copyright © 2015 Elsevier B.V. All rights reserved.

Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment

PubMed Central

Yang, Fu-Chun; Chen, Yi-Lung; Tang, Sen-Lin; Yu, Chang-Ping; Wang, Po-Hsiang; Ismail, Wael; Wang, Chia-Hsiang; Ding, Jiun-Yan; Yang, Cheng-Yu; Yang, Chia-Ying; Chiang, Yin-Ru

2016-01-01

Steroid hormones, such as androgens, are common surface-water contaminants. However, literature on the ecophysiological relevance of steroid-degrading organisms in the environment, particularly in anoxic ecosystems, is extremely limited. We previously reported that Steroidobacter denitrificans anaerobically degrades androgens through the 2,3-seco pathway. In this study, the genome of Sdo. denitrificans was completely sequenced. Transcriptomic data revealed gene clusters that were distinctly expressed during anaerobic growth on testosterone. We isolated and characterized the bifunctional 1-testosterone hydratase/dehydrogenase, which is essential for anaerobic degradation of steroid A-ring. Because of apparent substrate preference of this molybdoenzyme, corresponding genes, along with the signature metabolites of the 2,3-seco pathway, were used as biomarkers to investigate androgen biodegradation in the largest sewage treatment plant in Taipei, Taiwan. Androgen metabolite analysis indicated that denitrifying bacteria in anoxic sewage use the 2,3-seco pathway to degrade androgens. Metagenomic analysis and PCR-based functional assays showed androgen degradation in anoxic sewage by Thauera spp. through the action of 1-testosterone hydratase/dehydrogenase. Our integrative ‘omics' approach can be used for culture-independent investigations of the microbial degradation of structurally complex compounds where isotope-labeled substrates are not easily available. PMID:26872041

Targeting the Autophagy/Lysosomal Degradation Pathway in Parkinson's Disease.

PubMed

Rivero-Ríos, Pilar; Madero-Pérez, Jesús; Fernández, Belén; Hilfiker, Sabine

2016-01-01

Autophagy is a cellular quality control mechanism crucial for neuronal homeostasis. Defects in autophagy are critically associated with mechanisms underlying Parkinson's disease (PD), a common and debilitating neurodegenerative disorder. Autophagic dysfunction in PD can occur at several stages of the autophagy/lysosomal degradative machinery, contributing to the formation of intracellular protein aggregates and eventual neuronal cell death. Therefore, autophagy inducers may comprise a promising new therapeutic approach to combat neurodegeneration in PD. Several currently available FDA-approved drugs have been shown to enhance autophagy, which may allow for their repurposing for use in novel clinical conditions including PD. This review summarizes our current knowledge of deficits in the autophagy/lysosomal degradation pathways associated with PD, and highlight current approaches which target this pathway as possible means towards novel therapeutic strategies.

Characterization of methyl parathion degradation by a Burkholderia zhejiangensis strain, CEIB S4-3, isolated from agricultural soils.

PubMed

Popoca-Ursino, Elida C; Martínez-Ocampo, Fernando; Dantán-González, Edgar; Sánchez-Salinas, Enrique; Ortiz-Hernández, Ma Laura

2017-12-01

Through the use of an enrichment technique, we isolated from the agricultural soils of Morelos in central México a strain of Burkholderia zhejiangensis identified as CEIB S4-3, it's could use the pesticide methyl parathion (MP) as the only source of carbon and degrade completely p-nitrophenol (PNP). For more efficient MP and PNP degradation by the CEIB S4-3 strain, the absence of an extra carbon source, a large inoculum and an MP concentration up to 50 mg/l are required. Sequence and annotation analysis of the draft genome, showed presence of mpd functional gene, which was expressed and its activity on the MP was confirmed. Additionally, the genes coding for enzymes in the benzoquinone pathway (conducted by Gram-negative bacteria) and the benzenotriol pathway (conducted by Gram-positive bacteria) were found, which was corroborated by identification of intermediary metabolites by HPLC. Thus, we propose that B. zhejiangensis CEIB S4-3 uses both degradation pathways.

Metabolites of the phenylurea herbicides chlorotoluron, diuron, isoproturon and linuron produced by the soil fungus Mortierella sp.

PubMed

Badawi, Nora; Rønhede, Stig; Olsson, Stefan; Kragelund, Birthe B; Johnsen, Anders H; Jacobsen, Ole Stig; Aamand, Jens

2009-10-01

Phenylurea herbicides are used worldwide, and often pollute surface- and groundwater in concentrations exceeding the limit value for drinking water (0.1 microg l(-1)). Bacteria degrade phenylurea herbicides by successive N-dealkylation to substituted aniline products. Little is known about the corresponding fungal pathways, however. We here report degradation of chlorotoluron, diuron, isoproturon and linuron by the soil fungus Mortierella sp. Gr4. Degradation was fastest with linuron and resulted in successively dealkylated metabolites and 3,4-dichloroaniline. A major new metabolite was detected that has not yet been fully identified. Thin layer chromatography and nuclear magnetic resonance spectroscopy indicate that it is a non-aromatic diol. Degradation of isoproturon, chlorotoluron and diuron involved successive N-demethylation and, in the case of isoproturon and chlorotoluron, additional hydroxylation. A new hydroxylated isoproturon metabolite was detected. The study thus shows that the fungal pathways differ from the bacterial pathways and yield new metabolites of possible environmental concern.

[Combined application of multiple fluorescence in research on the degradation of fluoranthene by potassium ferrate].

PubMed

Li, Si; Yu, Dan-Ni; Ji, Fang-Ying; Zhou, Guang-Ming; He, Qiang

2012-11-01

The degradation of fluoranthene was researched by combined means of multiple fluorescence spectra, including emission, synchronous, excitation emission matrix (EEM), time-scan and photometry. The characteristics of the degradation and fluoranthene molecular changes within the degradation's process were also discussed according to the information about the degradation provided by all of the fluorescence spectra mentioned above. The equations of fluoranthene's degradation by potassium ferrate were obtained on the bases of fitting time-scan fluorescence curves at different time, and the degradation's kinetic was speculated accordingly. From the experimental results, multiple fluorescence data commonly reflected that it had same degradation rate at the same reaction time. t = 10 s, and the degradation rate is -55%, t = 25 s, -81%, t = 40 s, -91%. No new fluorescent characteristic was observed within every degradation' stage. The reaction stage during t < or = 20 s was crucial, in which the degradation process is closest to linear relationship. After this beginning stage, the linear relationship deviated gradually with the development of the degradation process. The degradation of fluoranthene by potassium ferrate was nearly in accord with the order of the first order reaction.

Degradation of Glyphosate by Mn-Oxide May Bypass Sarcosine and Form Glycine Directly after C-N Bond Cleavage.

PubMed

Li, Hui; Wallace, Adam F; Sun, Mingjing; Reardon, Patrick; Jaisi, Deb P

2018-02-06

Glyphosate is the active ingredient of the common herbicide Roundup. The increasing presence of glyphosate and its byproducts has raised concerns about its potential impact on the environment and human health. In this research, we investigated abiotic pathways of glyphosate degradation as catalyzed by birnessite under aerobic and neutral pH conditions to determine whether certain pathways have the potential to generate less harmful intermediate products. Nuclear magnetic resonance (NMR) spectroscopy and high-performance liquid chromatography (HPLC) were utilized to identify and quantify reaction products, and density functional theory (DFT) calculations were used to investigate the bond critical point (BCP) properties of the C-N bond in glyphosate and Mn(IV)-complexed glyphosate. We found that sarcosine, the commonly recognized precursor to glycine, was not present at detectable levels in any of our experiments despite the fact that its half-life (∼13.6 h) was greater than our sampling intervals. Abiotic degradation of glyphosate largely followed the glycine pathway rather than the AMPA (aminomethylphosphonic acid) pathway. Preferential cleavage of the phosphonate adjacent C-N bond to form glycine directly was also supported by our BCP analysis, which revealed that this C-N bond was disproportionately affected by the interaction of glyphosate with Mn(IV). Overall, these results provide useful insights into the potential pathways through which glyphosate may degrade via relatively benign intermediates.

[Dysregulation of the mTOR signaling pathway in the pathogenesis of autism spectrum disorders].

PubMed

Gabryel, Bożena; Kapałka, Agata; Sobczyk, Wojciech; Łabuzek, Krzysztof; Gawęda, Agnieszka; Janas-Kozik, Małgorzata

2014-04-10

Mammalian target of rapamycin (mTor) plays multiple role in central nervous system and is involved in regulation of cell viability, differentiation, transcription, translation, protein degradation, actin cytoskeletal organization and autophagy. Recent experimental and clinical studies reveal that disturbances of mTOR signaling are involved in the pathogenesis of autism spectrum disorders (ASD). This article reviews current data on the alteration in the mTOR transduction cascade, which may contribute to common neurobehavioral disorders typical for ASD. Moreover, the results of the latest experimental studies on the potential of mTOR inhibitors for the treatment of ASD are reviewed.

Biodegradation pathway of an anionic surfactant (Igepon TC-42) during recycling waste water through plant hydroponics for advanced life support during long-duration space missions

NASA Astrophysics Data System (ADS)

Levine, L. H.; Kagie, H. R.; Garland, J. L.

The degradation of an anionic surfactant (Igepon TC-42) was investigated as part of an integrated study of direct recycling of human hygiene water through hydroponic plant growth systems. Several chemical approaches were developed to characterize the degradation of Igepon and to measure the accumulation of intermediates such as fatty acids and methyl taurine. Igepon was rapidly degraded as indicated by the reduction of methylene blue active substances (MBAS) and component fatty acids. The Igepon degradation rate continued to increase over a period of several weeks following repeated daily exposure to 18 μg/l Igepon. The accumulation of free fatty acids and methyl taurine was also observed during decomposition of Igepon. The concentration of methyl taurine was below detection limit (0.2 nmol/ml) during the slow phase of Igepon degradation, and increased to 1-2 nmol/ml during the phase of rapid degradation. These findings support a degradation pathway involving initial hydrolysis of amide to release fatty acids and methyl taurine, and subsequent degradation of these intermediates.

Kinetic and mechanistic study of microcystin-LR degradation by nitrous acid under ultraviolet irradiation.

PubMed

Ma, Qingwei; Ren, Jing; Huang, Honghui; Wang, Shoubing; Wang, Xiangrong; Fan, Zhengqiu

2012-05-15

Degradation of microcystin-LR (MC-LR) in the presence of nitrous acid (HNO(2)) under irradiation of 365nm ultraviolet (UV) was studied for the first time. The influence of initial conditions including pH value, NaNO(2) concentration, MC-LR concentration and UV intensity were studied. MC-LR was degraded in the presence of HNO(2); enhanced degradation of MC-LR was observed with 365nm UV irradiation, caused by the generation of hydroxyl radicals through the photolysis of HNO(2). The degradation processes of MC-LR could well fit the pseudo-first-order kinetics. Mass spectrometry was applied for identification of the byproducts and the analysis of degradation mechanisms. Major degradation pathways were proposed according to the results of LC-MS analysis. The degradation of MC-LR was initiated via three major pathways: attack of hydroxyl radicals on the conjugated carbon double bonds of Adda, attack of hydroxyl radicals on the benzene ring of Adda, and attack of nitrosonium ion on the benzene ring of Adda. Copyright © 2012 Elsevier B.V. All rights reserved.

Degraded iota-carrageenan can induce apoptosis in human osteosarcoma cells via the Wnt/β-catenin signaling pathway.

PubMed

Jin, Zhe; Han, Ya-Xin; Han, Xiao-Rui

2013-01-01

Osteosarcoma (OS) is a high-grade malignant bone tumor. Therefore, using both in vitro and in vivo assays, the effects of degraded iota-Carrageenan (ι-CGN) on a human osteosarcoma cell line, HOS, were examined. Degraded ι-CGN was observed to induce apoptosis and G(1) phase arrest in HOS cells. Moreover, degraded ι-CGN suppressed tumor growth in established xenograft tumor models. Accordingly, the survival rate of these mice was significantly higher than that of mice bearing tumors treated with native ι-CGN or PBS. In addition, the formation of intratumoral microvessels was inhibited following treatment with degraded ι-CGN. In Western blot assays, degraded ι-CGN was found to inhibit the Wnt/β-catenin signaling pathway. Overall, these studies demonstrate the antitumor activity of degraded ι-CGN toward the OS cell line, HOS. Moreover, valuable insight into the mechanisms mediated by degraded ι-CGN was obtained, potentially leading to the identification of novel treatments for OS. However, additional studies are needed to confirm these results in other cell types, particularly in human umbilical vein endothelial cells.

Novel strategy for a bispecific antibody: induction of dual target internalization and degradation.

PubMed

Lee, J M; Lee, S H; Hwang, J-W; Oh, S J; Kim, B; Jung, S; Shim, S-H; Lin, P W; Lee, S B; Cho, M-Y; Koh, Y J; Kim, S Y; Ahn, S; Lee, J; Kim, K-M; Cheong, K H; Choi, J; Kim, K-A

2016-08-25

Activation of the extensive cross-talk among the receptor tyrosine kinases (RTKs), particularly ErbB family-Met cross-talk, has emerged as a likely source of drug resistance. Notwithstanding brilliant successes were attained while using small-molecule inhibitors or antibody therapeutics against specific RTKs in multiple cancers over recent decades, a high recurrence rate remains unsolved in patients treated with these targeted inhibitors. It is well aligned with multifaceted properties of cancer and cross-talk and convergence of signaling pathways of RTKs. Thereby many therapeutic interventions have been actively developed to overcome inherent or acquired resistance. To date, no bispecific antibody (BsAb) showed complete depletion of dual RTKs from the plasma membrane and efficient dual degradation. In this manuscript, we report the first findings of a target-specific dual internalization and degradation of membrane RTKs induced by designed BsAbs based on the internalizing monoclonal antibodies and the therapeutic values of these BsAbs. Leveraging the anti-Met mAb able to internalize and degrade by a unique mechanism, we generated the BsAbs for Met/epidermal growth factor receptor (EGFR) and Met/HER2 to induce an efficient EGFR or HER2 internalization and degradation in the presence of Met that is frequently overexpressed in the invasive tumors and involved in the resistance against EGFR- or HER2-targeted therapies. We found that Met/EGFR BsAb ME22S induces dissociation of the Met-EGFR complex from Hsp90, followed by significant degradation of Met and EGFR. By employing patient-derived tumor models we demonstrate therapeutic potential of the BsAb-mediated dual degradation in various cancers.

Ferrocene-functionalized graphitic carbon nitride as an enhanced heterogeneous catalyst of Fenton reaction for degradation of Rhodamine B under visible light irradiation.

PubMed

Lin, Kun-Yi Andrew; Lin, Jyun-Ting

2017-09-01

To enhance degradation of Rhodamine B (RhB), a toxic xanthene dye, an iron-doped graphitic carbon nitride (CN) is prepared by establishing a covalent bond (-CN-) bridging ferrocene (Fc) and CN via a Schiff base reaction. The π-conjugation between the aromatic Fc and CN can be much enhanced by the covalent bond, thereby facilitating the bulk-to-surface charge transfer and separation as well as reversible photo-redox reactions during photocatalytic reactions. Thus, the resulting Fc-CN exhibits a much higher catalytic activity than CN to activate hydrogen peroxide (HP) for RhB degradation, because the photocatalytically generated electrons from CN can activate HP and effectively maintain the bivalence state of Fe in Fc, which also induces the activation of HP. The RhB degradation by the Fc-CN activated HP process (Fc-CN-HP) is validated to involve OH • by examining the effect of radical probe agent as well as electron paramagnetic resonance (EPR) spectroscopic analysis. Fc-CN is also proven to activate HP for RhB degradation over multiple times without loss of catalytic activity. Through determining the degradation intermediates, RhB is indeed fully decomposed by Fc-CN-HP into much lower-molecular-weight organic compounds. These features indicate that Fc-functionalization can be an advantageous technique to enhance the catalytic activity of CN for activating HP. The results obtained in this study are essential to further design and utilize Fc-functionalized CN for Fenton-like reactions. The findings shown here, especially the degradation mechanism and pathway, are also quite important for treating xanthene dyes in wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

Chemical approaches to targeted protein degradation through modulation of the ubiquitin-proteasome pathway.

PubMed

Collins, Ian; Wang, Hannah; Caldwell, John J; Chopra, Raj

2017-03-15

Manipulation of the ubiquitin-proteasome system to achieve targeted degradation of proteins within cells using chemical tools and drugs has the potential to transform pharmacological and therapeutic approaches in cancer and other diseases. An increased understanding of the molecular mechanism of thalidomide and its analogues following their clinical use has unlocked small-molecule modulation of the substrate specificity of the E3 ligase cereblon (CRBN), which in turn has resulted in the advancement of new immunomodulatory drugs (IMiDs) into the clinic. The degradation of multiple context-specific proteins by these pleiotropic small molecules provides a means to uncover new cell biology and to generate future drug molecules against currently undruggable targets. In parallel, the development of larger bifunctional molecules that bring together highly specific protein targets in complexes with CRBN, von Hippel-Lindau, or other E3 ligases to promote ubiquitin-dependent degradation has progressed to generate selective chemical compounds with potent effects in cells and in vivo models, providing valuable tools for biological target validation and with future potential for therapeutic use. In this review, we survey recent breakthroughs achieved in these two complementary methods and the discovery of new modes of direct and indirect engagement of target proteins with the proteasome. We discuss the experimental characterisation that validates the use of molecules that promote protein degradation as chemical tools, the preclinical and clinical examples disclosed to date, and the future prospects for this exciting area of chemical biology. © 2017 The Author(s).

Dynamics of Multiple lin Gene Expression in Sphingomonas paucimobilis B90A in Response to Different Hexachlorocyclohexane Isomers

PubMed Central

Suar, Mrutyunjay; van der Meer, Jan Roelof; Lawlor, Kirsten; Holliger, Christof; Lal, Rup

2004-01-01

Sphingomonas paucimobilis B90A is able to degrade the α-, β-, γ-, and δ-isomers of hexachlorocyclohexane (HCH). It contains the genes linA, linB, linC, linD, linE, and linR, which have been implicated in HCH degradation. In this study, dynamic expression of the lin genes was measured in chemostat-grown S. paucimobilis B90A by RNA dot blot hybridization and real-time reverse transcriptase PCR upon exposure to a pulse of different HCH isomers. Irrespective of the addition of HCH, linA, linB, and linC were all expressed constitutively. In contrast, linD and linE were induced with α-HCH (2 mg/liter) and γ-HCH (7 mg/liter). A sharp increase in mRNA levels for linD and linE was observed from 10 to 45 min after the addition of α- or γ-HCH. Induction of linD and linE was not detectable upon the addition of 0.7 mg of γ-HCH per liter, although the compound was degraded by the cells. The addition of β-HCH (5 mg/liter) or δ-HCH (20 mg/liter) did not lead to linE and linD induction, despite the fact that 50% of the compounds were degraded. This suggests that degradation of β- and δ-HCH proceeds by a different pathway than that of α- and γ-HCH. PMID:15528530

Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders

DOE PAGES

Hu, Ping; Dubinsky, Eric A.; Probst, Alexander J.; ...

2017-06-26

The Deepwater Horizon (DWH) accident released an estimated 4.1 million barrels of oil and 10 10 mol of natural gas into the Gulf of Mexico, forming deep-sea plumes of dispersed oil droplets and dissolved gases that were largely degraded by bacteria. During the course of this 3-mo disaster a series of different bacterial taxa were enriched in succession within deep plumes, but the metabolic capabilities of the different populations that controlled degradation rates of crude oil components are poorly understood. We experimentally reproduced dispersed plumes of fine oil droplets in Gulf of Mexico seawater and successfully replicated the enrichment andmore » succession of the principal oil-degrading bacteria observed during the DWH event. We recovered near-complete genomes, whose phylogeny matched those of the principal biodegrading taxa observed in the field, including the DWH Oceanospirillales (now identified as a Bermanella species), multiple species of Colwellia, Cycloclasticus, and other members of Gammaproteobacteria, Flavobacteria, and Rhodobacteria. Metabolic pathway analysis, combined with hydrocarbon compositional analysis and species abundance data, revealed substrate specialization that explained the successional pattern of oil-degrading bacteria. The fastest-growing bacteria used short-chain alkanes. The analyses also uncovered potential cooperative and competitive relationships, even among close relatives. We conclude that patterns of microbial succession following deep ocean hydrocarbon blowouts are predictable and primarily driven by the availability of liquid petroleum hydrocarbons rather than natural gases.« less

Facile Fabrication of 100% Bio-Based and Degradable Ternary Cellulose/PHBV/PLA Composites

PubMed Central

Wang, Jinwu

2018-01-01

Modifying bio-based degradable polymers such as polylactide (PLA) and poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV) with non-degradable agents will compromise the 100% degradability of their resultant composites. This work developed a facile and solvent-free route in order to fabricate 100% bio-based and degradable ternary cellulose/PHBV/PLA composite materials. The effects of ball milling on the physicochemical properties of pulp cellulose fibers, and the ball-milled cellulose particles on the morphology and mechanical properties of PHBV/PLA blends, were investigated experimentally and statistically. The results showed that more ball-milling time resulted in a smaller particle size and lower crystallinity by way of mechanical disintegration. Filling PHBV/PLA blends with the ball-milled celluloses dramatically increased the stiffness at all of the levels of particle size and filling content, and improved their elongation at the break and fracture work at certain levels of particle size and filling content. It was also found that the high filling content of the ball-milled cellulose particles was detrimental to the mechanical properties for the resultant composite materials. The ternary cellulose/PHBV/PLA composite materials have some potential applications, such as in packaging materials and automobile inner decoration parts. Furthermore, filling content contributes more to the variations of their mechanical properties than particle size does. Statistical analysis combined with experimental tests provide a new pathway to quantitatively evaluate the effects of multiple variables on a specific property, and figure out the dominant one for the resultant composite materials. PMID:29495315

Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Ping; Dubinsky, Eric A.; Probst, Alexander J.

The Deepwater Horizon (DWH) accident released an estimated 4.1 million barrels of oil and 10 10 mol of natural gas into the Gulf of Mexico, forming deep-sea plumes of dispersed oil droplets and dissolved gases that were largely degraded by bacteria. During the course of this 3-mo disaster a series of different bacterial taxa were enriched in succession within deep plumes, but the metabolic capabilities of the different populations that controlled degradation rates of crude oil components are poorly understood. We experimentally reproduced dispersed plumes of fine oil droplets in Gulf of Mexico seawater and successfully replicated the enrichment andmore » succession of the principal oil-degrading bacteria observed during the DWH event. We recovered near-complete genomes, whose phylogeny matched those of the principal biodegrading taxa observed in the field, including the DWH Oceanospirillales (now identified as a Bermanella species), multiple species of Colwellia, Cycloclasticus, and other members of Gammaproteobacteria, Flavobacteria, and Rhodobacteria. Metabolic pathway analysis, combined with hydrocarbon compositional analysis and species abundance data, revealed substrate specialization that explained the successional pattern of oil-degrading bacteria. The fastest-growing bacteria used short-chain alkanes. The analyses also uncovered potential cooperative and competitive relationships, even among close relatives. We conclude that patterns of microbial succession following deep ocean hydrocarbon blowouts are predictable and primarily driven by the availability of liquid petroleum hydrocarbons rather than natural gases.« less

Process optimization for microcystin-LR degradation by Response Surface Methodology and mechanism analysis in gas-liquid hybrid discharge system.

PubMed

Zhang, Yi; Wei, Hanyu; Xin, Qing; Wang, Mingang; Wang, Qi; Wang, Qiang; Cong, Yanqing

2016-12-01

A gas-liquid hybrid discharge system was applied to microcystin-LR (MC-LR) degradation. MC-LR degradation was completed after 1 min under a pulsed high voltage of 16 kV, gas-liquid interface gap of 10 mm and oxygen flow rate of 160 L/h. The Box-Behnken Design was proposed in Response Surface Methodology to evaluate the influence of pulsed high voltage, electrode distance and oxygen flow rate on MC-LR removal efficiency. Multiple regression analysis, focused on multivariable factors, was employed and a reduced cubic model was developed. The ANOVA analysis shows that the model is significant and the model prediction on MC-LR removal was also validated with experimental data. The optimum conditions for the process are obtained at pulsed voltage of 16 kV, gas-liquid interface gap of 10 mm and oxygen flow rate of 120 L/h with ta removal efficiency of MC-LR of 96.6%. The addition of catalysts (TiO 2 or Fe 2+ ) in the gas-liquid hybrid discharge system was found to enhance the removal of MC-LR. The intermediates of MC-LR degradation were analyzed by liquid chromatography/mass spectrometry. The degradation pathway proposed envisaged the oxidation of hydroxyl radicals and ozone, and attack of high-energy electrons on the unsaturated double bonds of Adda and Mdha, with MC-LR finally decomposing into small molecular products. Copyright © 2016 Elsevier Ltd. All rights reserved.

A qrr noncoding RNA deploys four different regulatory mechanisms to optimize quorum-sensing dynamics.

PubMed

Feng, Lihui; Rutherford, Steven T; Papenfort, Kai; Bagert, John D; van Kessel, Julia C; Tirrell, David A; Wingreen, Ned S; Bassler, Bonnie L

2015-01-15

Quorum sensing is a cell-cell communication process that bacteria use to transition between individual and social lifestyles. In vibrios, homologous small RNAs called the Qrr sRNAs function at the center of quorum-sensing pathways. The Qrr sRNAs regulate multiple mRNA targets including those encoding the quorum-sensing regulatory components luxR, luxO, luxM, and aphA. We show that a representative Qrr, Qrr3, uses four distinct mechanisms to control its particular targets: the Qrr3 sRNA represses luxR through catalytic degradation, represses luxM through coupled degradation, represses luxO through sequestration, and activates aphA by revealing the ribosome binding site while the sRNA itself is degraded. Qrr3 forms different base-pairing interactions with each mRNA target, and the particular pairing strategy determines which regulatory mechanism occurs. Combined mathematical modeling and experiments show that the specific Qrr regulatory mechanism employed governs the potency, dynamics, and competition of target mRNA regulation, which in turn, defines the overall quorum-sensing response. Copyright © 2015 Elsevier Inc. All rights reserved.

The mitochondrial translocator protein, TSPO, inhibits HIV-1 envelope glycoprotein biosynthesis via the endoplasmic reticulum-associated protein degradation pathway.

PubMed

Zhou, Tao; Dang, Ying; Zheng, Yong-Hui

2014-03-01

The HIV-1 Env glycoprotein is folded in the endoplasmic reticulum (ER), which is necessary for viral entry and replication. Currently, it is still unclear how this process is regulated. The glycoprotein folding in the ER is controlled by the ER-associated protein degradation (ERAD) pathway, which specifically targets misfolded proteins for degradation. Previously, we reported that HIV-1 replication is restricted in the human CD4(+) T cell line CEM.NKR (NKR). To understand this mechanism, we first analyzed cellular protein expression in NKR cells and discovered that levels of the mitochondrial translocator protein TSPO were upregulated by ∼64-fold. Notably, when NKR cells were treated with TSPO antagonist PK-11195, Ro5-4864, or diazepam, HIV restriction was completely disrupted, and TSPO knockdown by short hairpin RNAs (shRNAs) achieved a similar effect. We next analyzed viral protein expression, and, interestingly, we discovered that Env expression was specifically inhibited. Both TSPO knockdown and treatment with TSPO antagonist could restore Env expression in NKR cells. We further discovered that Env proteins were rapidly degraded and that kifunensine, an ERAD pathway inhibitor, could restore Env expression and viral replication, indicating that Env proteins were misfolded and degraded through the ERAD pathway in NKR cells. We also knocked out the TSPO gene in 293T cells using CRISPR/Cas9 (clustered, regularly interspaced, short palindromic repeat [CRISPR]/CRISPR-associated-9) technology and found that TSPO could similarly inhibit Env expression in these cells. Taken together, these results demonstrate that TSPO inhibits Env protein expression through the ERAD pathway and suggest that mitochondria play an important role in regulating the Env folding process. The HIV-1 Env glycoprotein is absolutely required for viral infection, and an understanding of its expression pathway in infected cells will identify new targets for antiretroviral therapies. Env proteins are folded in the ER and secreted through the classical secretory pathway. The Env folding process involves extensive cross-linking of 10 Cys residues by disulfide bond formation and heavy N-glycosylation on ∼30 Asn residues. Currently, it is still unclear how this process is regulated. Here, we studied this mechanism in the HIV nonpermissive human CD4(+) T cell line CEM.NKR. We found that Env proteins were rapidly degraded through a cellular pathway that specifically targets misfolded proteins, resulting in inhibition of Env expression. Importantly, we have identified a mitochondrial translocator protein, TSPO, which could trigger this degradation by interfering with the Env folding process. Further characterization of TSPO antiviral activity will reveal a novel antiretroviral mechanism that targets the Env protein.

[Microbial degradation of 3-phenoxybenzoic acid--A review].

PubMed

Deng, Weiqin; Liu, Shuliang; Yao, Kai

2015-09-04

3-phenoxybenzoic acid (3-PBA) with estrogen toxicity is one of the intermediate products of most pyrethroid pesticides. 3-PBA is difficult to degrade in the natural environment, and threatens food safety and human health. Microbial degradation of pyrethroids and their intermediate product (3-PBA) has become a hot topic in recent years. Here, we reviewed microbial species, degrading enzymes and degradation genes, degradation pathways of 3-PBA degrading and the application of 3-PBA degradation strains. This article provides references for the study of 3-PBA degradation by microorganisms.

Distinctive Roles for Periplasmic Proteases in the Maintenance of Essential Outer Membrane Protein Assembly.

PubMed

Soltes, Garner R; Martin, Nicholas R; Park, Eunhae; Sutterlin, Holly A; Silhavy, Thomas J

2017-10-15

Outer membrane protein (OMP) biogenesis in Escherichia coli is a robust process essential to the life of the organism. It is catalyzed by the β-barrel assembly machine (Bam) complex, and a number of quality control factors, including periplasmic chaperones and proteases, maintain the integrity of this trafficking pathway. Little is known, however, about how periplasmic proteases recognize and degrade OMP substrates when assembly is compromised or whether different proteases recognize the same substrate at distinct points in the assembly pathway. In this work, we use well-defined assembly-defective mutants of LptD, the essential lipopolysaccharide assembly translocon, to show that the periplasmic protease DegP degrades substrates with assembly defects that prevent or impair initial contact with Bam, causing the mutant protein to accumulate in the periplasm. In contrast, another periplasmic protease, BepA, degrades a LptD mutant substrate that has engaged the Bam complex and formed a nearly complete barrel. Furthermore, we describe the role of the outer membrane lipoprotein YcaL, a protease of heretofore unknown function, in the degradation of a LptD substrate that has engaged the Bam complex but is stalled at an earlier step in the assembly process that is not accessible to BepA. Our results demonstrate that multiple periplasmic proteases monitor OMPs at distinct points in the assembly process. IMPORTANCE OMP assembly is catalyzed by the essential Bam complex and occurs in a cellular environment devoid of energy sources. Assembly intermediates that misfold can compromise this essential molecular machine. Here we demonstrate distinctive roles for three different periplasmic proteases that can clear OMP substrates with folding defects that compromise assembly at three different stages. These quality control factors help ensure the integrity of the permeability barrier that contributes to the intrinsic resistance of Gram-negative organisms to many antibiotics. Copyright © 2017 American Society for Microbiology.

Computer-assisted engineering of the synthetic pathway for biodegradation of a toxic persistent pollutant.

PubMed

Kurumbang, Nagendra Prasad; Dvorak, Pavel; Bendl, Jaroslav; Brezovsky, Jan; Prokop, Zbynek; Damborsky, Jiri

2014-03-21

Anthropogenic halogenated compounds were unknown to nature until the industrial revolution, and microorganisms have not had sufficient time to evolve enzymes for their degradation. The lack of efficient enzymes and natural pathways can be addressed through a combination of protein and metabolic engineering. We have assembled a synthetic route for conversion of the highly toxic and recalcitrant 1,2,3-trichloropropane to glycerol in Escherichia coli, and used it for a systematic study of pathway bottlenecks. Optimal ratios of enzymes for the maximal production of glycerol, and minimal toxicity of metabolites were predicted using a mathematical model. The strains containing the expected optimal ratios of enzymes were constructed and characterized for their viability and degradation efficiency. Excellent agreement between predicted and experimental data was observed. The validated model was used to quantitatively describe the kinetic limitations of currently available enzyme variants and predict improvements required for further pathway optimization. This highlights the potential of forward engineering of microorganisms for the degradation of toxic anthropogenic compounds.

Chemotaxis and degradation of organophosphate compound by a novel moderately thermo-halo tolerant Pseudomonas sp. strain BUR11: evidence for possible existence of two pathways for degradation.

PubMed

Pailan, Santanu; Saha, Pradipta

2015-01-01

An organophosphate (OP) degrading chemotactic bacterial strain BUR11 isolated from an agricultural field was identified as a member of Pseudomonas genus on the basis of its 16S rRNA gene sequence. The strain could utilize parathion, chlorpyrifos and their major hydrolytic intermediates as sole source of carbon for its growth and exhibited positive chemotactic response towards most of them. Optimum concentration of parathion for its growth was recorded to be 200 ppm and 62% of which was degraded within 96 h at 37 °C. Growth studies indicated the strain to be moderately thermo-halo tolerant in nature. Investigation based on identification of intermediates of parathion degradation by thin layer chromatography (TLC), high performance liquid chromatography (HPLC), gas chromatography (GC) and liquid chromatography mass spectrometry (LC-MS/MS) provided evidence for possible existence of two pathways. The first pathway proceeds via 4-nitrophenol (4-NP) while the second proceeds through formation of 4-aminoparathion (4-APar), 4-aminophenol (4-AP) and parabenzoquinone (PBQ). This is the first report of chemotaxis towards organophosphate compound by a thermo-halo tolerant bacterium.

Chemotaxis and degradation of organophosphate compound by a novel moderately thermo-halo tolerant Pseudomonas sp. strain BUR11: evidence for possible existence of two pathways for degradation

PubMed Central

Pailan, Santanu

2015-01-01

An organophosphate (OP) degrading chemotactic bacterial strain BUR11 isolated from an agricultural field was identified as a member of Pseudomonas genus on the basis of its 16S rRNA gene sequence. The strain could utilize parathion, chlorpyrifos and their major hydrolytic intermediates as sole source of carbon for its growth and exhibited positive chemotactic response towards most of them. Optimum concentration of parathion for its growth was recorded to be 200 ppm and 62% of which was degraded within 96 h at 37 °C. Growth studies indicated the strain to be moderately thermo-halo tolerant in nature. Investigation based on identification of intermediates of parathion degradation by thin layer chromatography (TLC), high performance liquid chromatography (HPLC), gas chromatography (GC) and liquid chromatography mass spectrometry (LC-MS/MS) provided evidence for possible existence of two pathways. The first pathway proceeds via 4-nitrophenol (4-NP) while the second proceeds through formation of 4-aminoparathion (4-APar), 4-aminophenol (4-AP) and parabenzoquinone (PBQ). This is the first report of chemotaxis towards organophosphate compound by a thermo-halo tolerant bacterium. PMID:26587344

Emerging branches of the N-end rule pathways are revealing the sequence complexities of N-termini dependent protein degradation.

PubMed

Eldeeb, Mohamed A; Leitao, Luana C A; Fahlman, Richard P

2018-06-01

The N-end rule links the identity of the N-terminal amino acid of a protein to its in vivo half-life, as some N-terminal residues confer metabolic instability to a protein via their recognition by the cellular machinery that targets them for degradation. Since its discovery, the N-end rule has generally been defined as set of rules of whether an N-terminal residue is stabilizing or not. However, recent studies are revealing that the N-terminal code of amino acids conferring protein instability is more complex than previously appreciated, as recent investigations are revealing that the identity of adjoining downstream residues can also influence the metabolic stability of N-end rule substrate. This is exemplified by the recent discovery of a new branch of N-end rule pathways that target proteins bearing N-terminal proline. In addition, recent investigations are demonstrating that the molecular machinery in N-termini dependent protein degradation may also target proteins for lysosomal degradation, in addition to proteasome-dependent degradation. Herein, we describe some of the recent advances in N-end rule pathways and discuss some of the implications regarding the emerging additional sequence requirements.

Tipping the balance of RNA stability by 3' editing of the transcriptome.

PubMed

Chung, Christina Z; Seidl, Lauren E; Mann, Mitchell R; Heinemann, Ilka U

2017-11-01

The regulation of active microRNAs (miRNAs) and maturation of messenger RNAs (mRNAs) that are competent for translation is a crucial point in the control of all cellular processes, with established roles in development and differentiation. Terminal nucleotidyltransferases (TNTases) are potent regulators of RNA metabolism. TNTases promote the addition of single or multiple nucleotides to an RNA transcript that can rapidly alter transcript stability. The well-known polyadenylation promotes transcript stability while the newly discovered but ubiquitious 3'-end polyuridylation marks RNA for degradation. Monoadenylation and uridylation are essential control mechanisms balancing mRNA and miRNA homeostasis. This review discusses the multiple functions of non-canonical TNTases, focusing on their substrate range, biological functions, and evolution. TNTases directly control mRNA and miRNA levels, with diverse roles in transcriptome stabilization, maturation, silencing, or degradation. We will summarize the current state of knowledge on non-canonical nucleotidyltransferases and their function in regulating miRNA and mRNA metabolism. We will review the discovery of uridylation as an RNA degradation pathway and discuss the evolution of nucleotidyltransferases along with their use in RNA labeling and future applications as therapeutic targets. The biochemically and evolutionarily highly related adenylyl- and uridylyltransferases play antagonizing roles in the cell. In general, RNA adenylation promotes stability, while uridylation marks RNA for degradation. Uridylyltransferases evolved from adenylyltransferases in multiple independent evolutionary events by the insertion of a histidine residue into the active site, altering nucleotide, but not RNA specificity. Understanding the mechanisms regulating RNA stability in the cell and controlling the transcriptome is essential for efforts aiming to influence cellular fate. Selectively enhancing or reducing RNA stability allows for alterations in the transcriptome, proteome, and downstream cellular processes. Genetic, biochemical, and clinical data suggest TNTases are potent targets for chemotherapeutics and have been exploited for RNA labeling applications. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

Wnt/β-catenin signaling: new (and old) players and new insights

PubMed Central

Huang, He; He, Xi

2008-01-01

Wnt/β-catenin signaling has central roles in embryogenesis and human diseases including cancer. A central scheme of the Wnt pathway is to stabilize the transcription coactivator β-catenin by preventing its phosphorylation-dependent degradation. Significant progress has been made towards the understanding of this critical regulatory pathway, including the protein complex that promotes β-catenin phosphorylation-degradation, and the mechanism by which the extracellular Wnt ligand engages cell surface receptors to inhibit β-catenin phosphorylation-degradation. Here we review some recent discoveries in these two areas, and highlight some critical questions that remain to be resolved. PMID:18339531

Sugar suppresses cell death caused by disruption of fumarylacetoacetate hydrolase in Arabidopsis.

PubMed

Zhi, Tiantian; Zhou, Zhou; Huang, Yi; Han, Chengyun; Liu, Yan; Zhu, Qi; Ren, Chunmei

2016-09-01

Sugar negatively regulates cell death resulting from the loss of fumarylacetoacetate hydrolase that catalyzes the last step in the Tyr degradation pathway in Arabidopsis . Fumarylacetoacetate hydrolase (FAH) hydrolyzes fumarylacetoacetate to fumarate and acetoacetate, the final step in the tyrosine (Tyr) degradation pathway that is essential to animals. Previously, we first found that the Tyr degradation pathway plays an important role in plants. Mutation of the SSCD1 gene encoding FAH in Arabidopsis leads to spontaneous cell death under short-day conditions. In this study, we presented that the lethal phenotype of the short-day sensitive cell death1 (sscd1) seedlings was suppressed by sugars including sucrose, glucose, fructose, and maltose in a dose-dependent manner. Real-time quantitative PCR (RT-qPCR) analysis showed the expression of Tyr degradation pathway genes homogentisate dioxygenase and maleylacetoacetate isomerase, and sucrose-processing genes cell-wall invertase 1 and alkaline/neutral invertase G, was up-regulated in the sscd1 mutant, however, this up-regulation could be repressed by sugar. In addition, a high concentration of sugar attenuated cell death of Arabidopsis wild-type seedlings caused by treatment with exogenous succinylacetone, an abnormal metabolite resulting from the loss of FAH in the Tyr degradation pathway. These results indicated that (1) sugar could suppress cell death in sscd1, which might be because sugar supply enhances the resistance of Arabidopsis seedlings to toxic effects of succinylacetone and reduces the accumulation of Tyr degradation intermediates, resulting in suppression of cell death; and (2) sucrose-processing genes cell-wall invertase 1 and alkaline/neutral invertase G might be involved in the cell death in sscd1. Our work provides insights into the relationship between sugar and sscd1-mediated cell death, and contributes to elucidation of the regulation of cell death resulting from the loss of FAH in plants.

Ubiquitination in the antiviral immune response.

PubMed

Davis, Meredith E; Gack, Michaela U

2015-05-01

Ubiquitination has long been known to regulate fundamental cellular processes through the induction of proteasomal degradation of target proteins. More recently, 'atypical' non-degradative types of polyubiquitin chains have been appreciated as important regulatory moieties by modulating the activity or subcellular localization of key signaling proteins. Intriguingly, many of these non-degradative types of ubiquitination regulate the innate sensing pathways initiated by pattern recognition receptors (PRRs), ultimately coordinating an effective antiviral immune response. Here we discuss recent advances in understanding the functional roles of degradative and atypical types of ubiquitination in innate immunity to viral infections, with a specific focus on the signaling pathways triggered by RIG-I-like receptors, Toll-like receptors, and the intracellular viral DNA sensor cGAS. Copyright © 2015 Elsevier Inc. All rights reserved.

Use of dual carbon-chlorine isotope analysis to assess the degradation pathways of 1,1,1-trichloroethane in groundwater.

PubMed

Palau, Jordi; Jamin, Pierre; Badin, Alice; Vanhecke, Nicolas; Haerens, Bruno; Brouyère, Serge; Hunkeler, Daniel

2016-04-01

Compound-specific isotope analysis (CSIA) is a powerful tool to track contaminant fate in groundwater. However, the application of CSIA to chlorinated ethanes has received little attention so far. These compounds are toxic and prevalent groundwater contaminants of environmental concern. The high susceptibility of chlorinated ethanes like 1,1,1-trichloroethane (1,1,1-TCA) to be transformed via different competing pathways (biotic and abiotic) complicates the assessment of their fate in the subsurface. In this study, the use of a dual C-Cl isotope approach to identify the active degradation pathways of 1,1,1-TCA is evaluated for the first time in an aerobic aquifer impacted by 1,1,1-TCA and trichloroethylene (TCE) with concentrations of up to 20 mg/L and 3.4 mg/L, respectively. The reaction-specific dual carbon-chlorine (C-Cl) isotope trends determined in a recent laboratory study illustrated the potential of a dual isotope approach to identify contaminant degradation pathways of 1,1,1-TCA. Compared to the dual isotope slopes (Δδ(13)C/Δδ(37)Cl) previously determined in the laboratory for dehydrohalogenation/hydrolysis (DH/HY, 0.33 ± 0.04) and oxidation by persulfate (∞), the slope determined from field samples (0.6 ± 0.2, r(2) = 0.75) is closer to the one observed for DH/HY, pointing to DH/HY as the predominant degradation pathway of 1,1,1-TCA in the aquifer. The observed deviation could be explained by a minor contribution of additional degradation processes. This result, along with the little degradation of TCE determined from isotope measurements, confirmed that 1,1,1-TCA is the main source of the 1,1-dichlorethylene (1,1-DCE) detected in the aquifer with concentrations of up to 10 mg/L. This study demonstrates that a dual C-Cl isotope approach can strongly improve the qualitative and quantitative assessment of 1,1,1-TCA degradation processes in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ubiquitin-proteasomal degradation of COX-2 in TGF-β stimulated human endometrial cells is mediated through endoplasmic reticulum mannosidase I.

PubMed

Singh, Mohan; Chaudhry, Parvesh; Parent, Sophie; Asselin, Eric

2012-01-01

Cyclooxygenase (COX)-2 is a key regulatory enzyme in the production of prostaglandins (PG) during various physiological processes. Mechanisms of COX-2 regulation in human endometrial stromal cells (human endometrial stromal cells) are not fully understood. In this study, we investigate the role of TGF-β in the regulation of COX-2 in human uterine stromal cells. Each TGF-β isoform decreases COX-2 protein level in human uterine stromal cells in Smad2/3-dependent manner. The decrease in COX-2 is accompanied by a decrease in PG synthesis. Knockdown of Smad4 using specific small interfering RNA prevents the decrease in COX-2 protein, confirming that Smad pathway is implicated in the regulation of COX-2 expression in human endometrial stromal cells. Pretreatment with 26S proteasome inhibitor, MG132, significantly restores COX-2 protein and PG synthesis, indicating that COX-2 undergoes proteasomal degradation in the presence of TGF-β. In addition, each TGF-β isoform up-regulates endoplasmic reticulum (ER)-mannosidase I (ERManI) implying that COX-2 degradation is mediated through ER-associated degradation pathway in these cells. Furthermore, inhibition of ERManI activity using the mannosidase inhibitor (kifunensine), or small interfering RNA-mediated knockdown of ERManI, prevents TGF-β-induced COX-2 degradation. Taken together, these studies suggest that TGF-β promotes COX-2 degradation in a Smad-dependent manner by up-regulating the expression of ERManI and thereby enhancing ER-associated degradation and proteasomal degradation pathways.

Compound specific isotope analysis to investigate pesticide degradation in lysimeter experiments at field conditions

NASA Astrophysics Data System (ADS)

Ryabenko, Evgenia; Elsner, Martin; Bakkour, Rani; Hofstetter, Thomas; Torrento, Clara; Hunkeler, Daniel

2015-04-01

The frequent detection of organic micropollutants such as pesticides, consumer care products or pharmaceuticals in water is an increasing concern for human and ecosystem health. Degradation analysis of these compounds can be challenging in complex systems due to the fact that metabolites are not always found and mass balances frequently cannot be closed. Many abiotic and biotic degradation pathways cause, however, distinct isotope fractionation, where light isotopes are transferred preferentially from the reactant to the product pool (normal isotope fractionation). Compound-specific isotope analysis (CSIA) of multiple elements is a particularly powerful method to evaluate organic micropollutant transformation, because it can even give pathway-specific isotope fractionation (1,2). Available CSIA field studies, however, have focused almost exclusively on volatile petroleum and chlorinated hydrocarbons, which are present in high concentrations in the environment and can be extracted easily from water for GC-IRMS analysis. In the case of micropollutants, such as pesticides, CSIA in more challenging since it needs to be conducted at lower concentrations and requires pre-concentration, purification and high chromatographic performance (3). In this study we used lysimeters experiments to analyze transformation of atrazine, acetochlor, metolachlor and chloridazone by studying associated isotope fractionation. The project combines a) analytical method development for CSIA, b) identification of pathways of micropollutant degradation and c) quantification of transformation processes under field condition. The pesticides were applied both, at the soil surface and below the top soil under field-relevant concentrations in May 2014. After typical irrigation of the lysimeters, seepage water was collected in 50L bottles and stored for further SPE and CSIA. Here we present the very first result of a) analytical method development, b) improvement of SPE methods for complex pesticide mixtures and c) transformation of pesticides in lysimeters during the year 2014. 1 Elsner, M. Stable isotope fractionation to investigate natural transformation mechanisms of organic contaminants: principles, prospects and limitations. J. Environ. Monit. 12, 2005-2031 (2010). 2 Hofstetter, T. B. & Berg, M. Assessing transformation processes of organic contaminants by compound-specific stable isotope analysis. TrAC Trends in Analytical Chemistry 30, 618-627 (2011). 3 Elsner, M. et al. Current challenges in compound-specific stable isotope analysis of environmental organic contaminants. Anal. Bioanal. Chem. 403, 2471-2491, doi:10.1007/s00216-011-5683-y (2012).

In vivo degeneration and the fate of inorganic nanoparticles.

PubMed

Feliu, Neus; Docter, Dominic; Heine, Markus; Del Pino, Pablo; Ashraf, Sumaira; Kolosnjaj-Tabi, Jelena; Macchiarini, Paolo; Nielsen, Peter; Alloyeau, Damien; Gazeau, Florence; Stauber, Roland H; Parak, Wolfgang J

2016-05-03

What happens to inorganic nanoparticles (NPs), such as plasmonic gold or silver, superparamagnetic iron oxide, or fluorescent quantum dot NPs after they have been administrated to a living being? This review discusses the integrity, biodistribution, and fate of NPs after in vivo administration. The hybrid nature of the NPs is described, conceptually divided into the inorganic core, the engineered surface coating comprising of the ligand shell and optionally also bio-conjugates, and the corona of adsorbed biological molecules. Empirical evidence shows that all of these three compounds may degrade individually in vivo and can drastically modify the life cycle and biodistribution of the whole heterostructure. Thus, the NPs may be decomposed into different parts, whose biodistribution and fate would need to be analyzed individually. Multiple labeling and quantification strategies for such a purpose will be discussed. All reviewed data indicate that NPs in vivo should no longer be considered as homogeneous entities, but should be seen as inorganic/organic/biological nano-hybrids with complex and intricately linked distribution and degradation pathways.

Dense fibrillar collagen is a potent inducer of invadopodia via a specific signaling network

PubMed Central

Swatkoski, Stephen; Matsumoto, Kazue; Campbell, Catherine B.; Petrie, Ryan J.; Dimitriadis, Emilios K.; Li, Xin; Mueller, Susette C.; Bugge, Thomas H.; Gucek, Marjan

2015-01-01

Cell interactions with the extracellular matrix (ECM) can regulate multiple cellular activities and the matrix itself in dynamic, bidirectional processes. One such process is local proteolytic modification of the ECM. Invadopodia of tumor cells are actin-rich proteolytic protrusions that locally degrade matrix molecules and mediate invasion. We report that a novel high-density fibrillar collagen (HDFC) matrix is a potent inducer of invadopodia, both in carcinoma cell lines and in primary human fibroblasts. In carcinoma cells, HDFC matrix induced formation of invadopodia via a specific integrin signaling pathway that did not require growth factors or even altered gene and protein expression. In contrast, phosphoproteomics identified major changes in a complex phosphosignaling network with kindlin2 serine phosphorylation as a key regulatory element. This kindlin2-dependent signal transduction network was required for efficient induction of invadopodia on dense fibrillar collagen and for local degradation of collagen. This novel phosphosignaling mechanism regulates cell surface invadopodia via kindlin2 for local proteolytic remodeling of the ECM. PMID:25646088

Multifunctional Mitochondrial AAA Proteases

PubMed Central

Glynn, Steven E.

2017-01-01

Mitochondria perform numerous functions necessary for the survival of eukaryotic cells. These activities are coordinated by a diverse complement of proteins encoded in both the nuclear and mitochondrial genomes that must be properly organized and maintained. Misregulation of mitochondrial proteostasis impairs organellar function and can result in the development of severe human diseases. ATP-driven AAA+ proteins play crucial roles in preserving mitochondrial activity by removing and remodeling protein molecules in accordance with the needs of the cell. Two mitochondrial AAA proteases, i-AAA and m-AAA, are anchored to either face of the mitochondrial inner membrane, where they engage and process an array of substrates to impact protein biogenesis, quality control, and the regulation of key metabolic pathways. The functionality of these proteases is extended through multiple substrate-dependent modes of action, including complete degradation, partial processing, or dislocation from the membrane without proteolysis. This review discusses recent advances made toward elucidating the mechanisms of substrate recognition, handling, and degradation that allow these versatile proteases to control diverse activities in this multifunctional organelle. PMID:28589125

Multifunctional Mitochondrial AAA Proteases.

PubMed

Glynn, Steven E

2017-01-01

Mitochondria perform numerous functions necessary for the survival of eukaryotic cells. These activities are coordinated by a diverse complement of proteins encoded in both the nuclear and mitochondrial genomes that must be properly organized and maintained. Misregulation of mitochondrial proteostasis impairs organellar function and can result in the development of severe human diseases. ATP-driven AAA+ proteins play crucial roles in preserving mitochondrial activity by removing and remodeling protein molecules in accordance with the needs of the cell. Two mitochondrial AAA proteases, i-AAA and m-AAA, are anchored to either face of the mitochondrial inner membrane, where they engage and process an array of substrates to impact protein biogenesis, quality control, and the regulation of key metabolic pathways. The functionality of these proteases is extended through multiple substrate-dependent modes of action, including complete degradation, partial processing, or dislocation from the membrane without proteolysis. This review discusses recent advances made toward elucidating the mechanisms of substrate recognition, handling, and degradation that allow these versatile proteases to control diverse activities in this multifunctional organelle.

Kinetic models and pathways of ronidazole degradation by chlorination, UV irradiation and UV/chlorine processes.

PubMed

Qin, Lang; Lin, Yi-Li; Xu, Bin; Hu, Chen-Yan; Tian, Fu-Xiang; Zhang, Tian-Yang; Zhu, Wen-Qian; Huang, He; Gao, Nai-Yun

2014-11-15

Degradation kinetics and pathways of ronidazole (RNZ) by chlorination (Cl2), UV irradiation and combined UV/chlorine processes were investigated in this paper. The degradation kinetics of RNZ chlorination followed a second-order behavior with the rate constants calculated as (2.13 ± 0.15) × 10(2) M(-2) s(-1), (0.82 ± 0.52) × 10(-2) M(-1) s(-1) and (2.06 ± 0.09) × 10(-1) M(-1) s(-1) for the acid-catalyzed reaction, as well as the reactions of RNZ with HOCl and OCl(-), respectively. Although UV irradiation degraded RNZ more effectively than chlorination did, very low quantum yield of RNZ at 254 nm was obtained as 1.02 × 10(-3) mol E(-1). RNZ could be efficiently degraded and mineralized in the UV/chlorine process due to the generation of hydroxyl radicals. The second-order rate constant between RNZ and hydroxyl radical was determined as (2.92 ± 0.05) × 10(9) M(-1) s(-1). The degradation intermediates of RNZ during the three processes were identified with Ultra Performance Liquid Chromatography - Electrospray Ionization - mass spectrometry and the degradation pathways were then proposed. Moreover, the variation of chloropicrin (TCNM) and chloroform (CF) formation after the three processes were further evaluated. Enhanced formation of CF and TCNM precursors during UV/chlorine process deserves extensive attention in drinking water treatment. Copyright © 2014 Elsevier Ltd. All rights reserved.

Synergetic effect of alkaline earth metal oxides and iron oxides on the degradation of hexachlorobenzene and its degradation pathway.

PubMed

Su, Guijin; Liu, Yexuan; Huang, Linyan; Shi, Yali; Zhang, Aiqian; Zhang, Lixia; Liu, Wenbin; Gao, Lirong; Zheng, Minghui

2013-01-01

The degradation of hexachlorobenzene (HCB) was carried out over physical mixtures of a series of alkaline earth metal oxides (MO: M=Mg, Ca, Sr, Ba) and iron oxides with different crystal types (Fe(x)O(y):Fe(2)O(3) or Fe(3)O(4)) at 300°C. These physical mixtures all showed a synergetic effect toward the degradation of HCB. A range of degradation products were identified by various methods, including tri- to penta-chlorobenzenes by gas chromatography/mass spectrometry (GC-MS), tri- to penta-chlorophenols, tetrachlorocatechol (TCC) and tetrachlorohydroquinone (TCHQ) by GC-MS after derivatization, and formic and acetic acids by ion chromatography. Two degradation pathways, hydrodechlorination and oxidative degradation, appear to occur competitively. However, more sequential chlorinated benzene and phenol congeners were formed over mixed MO/Fe(3)O(4) than over mixed MO/Fe(2)O(3) under the same conditions. The oxidative reaction dominated over mixed MO/Fe(2)O(3) and was promoted as the major reaction by the synergetic effect, while both the oxidative and hydrodechlorination reactions were important over mixed MO/Fe(3)O(4), and both pathways are remarkably promoted by the synergetic effect. The enhanced hydrodechlorination may be attributed to free electrons generated by the transformation of Fe(3)O(4) into Fe(2)O(3), and hydrogen provided by water adsorbed on the MO. Copyright © 2012 Elsevier Ltd. All rights reserved.

Emerging roles of protein kinase CK2 in abscisic acid signaling.

PubMed

Vilela, Belmiro; Pagès, Montserrat; Riera, Marta

2015-01-01

The phytohormone abscisic acid (ABA) regulates many aspects of plant growth and development as well as responses to multiple stresses. Post-translational modifications such as phosphorylation or ubiquitination have pivotal roles in the regulation of ABA signaling. In addition to the positive regulator sucrose non-fermenting-1 related protein kinase 2 (SnRK2), the relevance of the role of other protein kinases, such as CK2, has been recently highlighted. We have recently established that CK2 phosphorylates the maize ortholog of open stomata 1 OST1, ZmOST1, suggesting a role of CK2 phosphorylation in the control of ZmOST1 protein degradation (Vilela et al., 2015). CK2 is a pleiotropic enzyme involved in multiple developmental and stress-responsive pathways. This review summarizes recent advances that taken together suggest a prominent role of protein kinase CK2 in ABA signaling and related processes.

A comparative intracellular proteomic profiling of Pseudomonas aeruginosa strain ASP-53 grown on pyrene or glucose as sole source of carbon and identification of some key enzymes of pyrene biodegradation pathway.

PubMed

Mukherjee, Ashis K; Bhagowati, Pabitra; Biswa, Bhim Bahadur; Chanda, Abhishek; Kalita, Bhargab

2017-09-07

Pseudomonas aeruginosa strain ASP-53, isolated from a petroleum oil-contaminated soil sample, was found to be an efficient degrader of pyrene. PCR amplification of selected hydrocarbon catabolic genes (alkB gene, which encodes for monooxygenase, and the C12O, C23O, and PAH-RHDα genes encoding for the dioxygenase enzyme) from the genomic DNA of P. aeruginosa strain ASP-53 suggested its hydrocarbon degradation potential. The GC-MS analysis demonstrated 30.1% pyrene degradation by P. aeruginosa strain ASP-53 after 144h of incubation at pH6.5, 37°C. Expressions of 115 and 196 intracellular proteins were unambiguously identified and quantitated by shotgun proteomics analysis when the isolate was grown in medium containing pyrene and glucose, respectively. The pyrene-induced uniquely expressed and up-regulated proteins in P. aeruginosa strain ASP-53 in addition to substrate (pyrene) metabolism are also likely to be associated with different cellular functions for example-related to protein folding (molecular chaperone), stress response, metabolism of carbohydrate, proteins and amino acids, and fatty acids; transport of metabolites, energy generation such as ATP synthesis, electron transport and nitrate assimilation, and other oxidation-reduction reactions. Proteomic analyses identified some important enzymes involved in pyrene degradation by P. aeruginosa ASP-53 which shows that this bacterium follows the salicylate pathway of pyrene degradation. This study is the first report on proteomic analysis of pyrene biodegradation pathway by Pseudomonas aeruginosa, isolated from a petroleum-oil contaminated soil sample. The pathway displays partial similarity with deduced pyrene degradation mechanisms of Mycobacterium vanbaalenii PYR-1. The GC-MS analysis as well as PCR amplification of hydrocarbon catabolic genes substantiated the potency of the bacterium under study to effectively degrade high molecular weight, toxic PAH such as pyrene for its filed scale bioremediation experiments. The proteomics approach (LC-MS/MS analysis) identified the differentially regulated intracellular proteins of the isolate P. aeruginosa ASP-53 when grown in pyrene medium. This study identified some important pyrene biodegradation enzymes in Pseudomonas aeruginosa ASP-53 and highlights that the bacterium follows salicylate pathway for pyrene degradation. Copyright © 2017 Elsevier B.V. All rights reserved.

Identification of an itaconic acid degrading pathway in itaconic acid producing Aspergillus terreus.

PubMed

Chen, Mei; Huang, Xuenian; Zhong, Chengwei; Li, Jianjun; Lu, Xuefeng

2016-09-01

Itaconic acid, one of the most promising and flexible bio-based chemicals, is mainly produced by Aspergillus terreus. Previous studies to improve itaconic acid production in A. terreus through metabolic engineering were mainly focused on its biosynthesis pathway, while the itaconic acid-degrading pathway has largely been ignored. In this study, we used transcriptomic, proteomic, bioinformatic, and in vitro enzymatic analyses to identify three key enzymes, itaconyl-CoA transferase (IctA), itaconyl-CoA hydratase (IchA), and citramalyl-CoA lyase (CclA), that are involved in the catabolic pathway of itaconic acid in A. terreus. In the itaconic acid catabolic pathway in A. terreus, itaconic acid is first converted by IctA into itaconyl-CoA with succinyl-CoA as the CoA donor, and then itaconyl-CoA is hydrated into citramalyl-CoA by IchA. Finally, citramalyl-CoA is cleaved into acetyl-CoA and pyruvate by CclA. Moreover, IctA can also catalyze the reaction between citramalyl-CoA and succinate to generate succinyl-CoA and citramalate. These results, for the first time, identify the three key enzymes, IctA, IchA, and CclA, involved in the itaconic acid degrading pathway in itaconic acid producing A. terreus. The results will facilitate the improvement of itaconic acid production by metabolically engineering the catabolic pathway of itaconic acid in A. terreus.

Investigating the control of chlorophyll degradation by genomic correlation mining

USDA-ARS?s Scientific Manuscript database

Chlorophyll degradation is an intricate process that is critical in a variety of plant tissues at different times during the plant life cycle. Many of the photoactive chlorophyll degradation intermediates are exceptionally cytotoxic necessitating that the pathway be carefully coordinated and regulat...

Characterization of a novel oxyfluorfen-degrading bacterial strain Chryseobacterium aquifrigidense and its biochemical degradation pathway.

PubMed

Zhao, Huanhuan; Xu, Jun; Dong, Fengshou; Liu, Xingang; Wu, Yanbing; Wu, Xiaohu; Zheng, Yongquan

2016-08-01

Persistent use of the diphenyl ether herbicides oxyfluorfen may seriously increase the health risks and ecological safety problems. A newly bacterium R-21 isolated from active soil was able to degrade and utilize oxyfluorfen as the sole carbon source. R-21 was identified as Chryseobacterium aquifrigidense by morphology, physiobiochemical characteristics, and genetic analysis. Under the optimum cultural conditions (pH 6.9, temperature 33.4 °C, and inoculum size 0.2 g L(-1)), R-21 could degrade 92.1 % of oxyfluorfen at 50 mg L(-1) within 5 days. During oxyfluorfen degradation, six metabolites were detected and identified by atmospheric pressure gas chromatography coupled to quadrupole-time of flight mass spectrometry and ultra-performance liquid chromatography coupled to quadrupole-time of flight mass spectrometry, and a plausible degradation pathway was deduced. Strain R-21 is a promising potential in bioremediation of oxyfluorfen-contaminated environments.

Degradation of Chloronitrobenzenes by a Coculture of Pseudomonas putida and a Rhodococcus sp.

PubMed Central

Park, Hee-Sung; Lim, Sung-Jin; Chang, Young Keun; Livingston, Andrew G.; Kim, Hak-Sung

1999-01-01

A single microorganism able to mineralize chloronitrobenzenes (CNBs) has not been reported, and degradation of CNBs by coculture of two microbial strains was attempted. Pseudomonas putida HS12 was first isolated by analogue enrichment culture using nitrobenzene (NB) as the substrate, and this strain was observed to possess a partial reductive pathway for the degradation of NB. From high-performance liquid chromatography-mass spectrometry and 1H nuclear magnetic resonance analyses, NB-grown cells of P. putida HS12 were found to convert 3- and 4-CNBs to the corresponding 5- and 4-chloro-2-hydroxyacetanilides, respectively, by partial reduction and subsequent acetylation. For the degradation of CNBs, Rhodococcus sp. strain HS51, which degrades 4- and 5-chloro-2-hydroxyacetanilides, was isolated and combined with P. putida HS12 to give a coculture. This coculture was confirmed to mineralize 3- and 4-CNBs in the presence of an additional carbon source. A degradation pathway for 3- and 4-CNBs by the two isolated strains was also proposed. PMID:10049867

Robust Ordering of Anaphase Events by Adaptive Thresholds and Competing Degradation Pathways.

PubMed

Kamenz, Julia; Mihaljev, Tamara; Kubis, Armin; Legewie, Stefan; Hauf, Silke

2015-11-05

The splitting of chromosomes in anaphase and their delivery into the daughter cells needs to be accurately executed to maintain genome stability. Chromosome splitting requires the degradation of securin, whereas the distribution of the chromosomes into the daughter cells requires the degradation of cyclin B. We show that cells encounter and tolerate variations in the abundance of securin or cyclin B. This makes the concurrent onset of securin and cyclin B degradation insufficient to guarantee that early anaphase events occur in the correct order. We uncover that the timing of chromosome splitting is not determined by reaching a fixed securin level, but that this level adapts to the securin degradation kinetics. In conjunction with securin and cyclin B competing for degradation during anaphase, this provides robustness to the temporal order of anaphase events. Our work reveals how parallel cell-cycle pathways can be temporally coordinated despite variability in protein concentrations. Copyright © 2015 Elsevier Inc. All rights reserved.

Degradation of N-heterocyclic indole by a novel endophytic fungus Phomopsis liquidambari.

PubMed

Chen, Yan; Xie, Xing-Guang; Ren, Cheng-Gang; Dai, Chuan-Chao

2013-02-01

A broad-spectrum endophytic Phomopsis liquidambari, was used to degrade environmental pollutant indole. In the condition of using indole as sole carbon and nitrogen source, the optimum concentration of indole supplied was determined to be 100 mg L(-1), with 41.7% ratio of indole degradation within 120 h. Exogenous addition of plant litter significantly increased indole degradation to 99.1% within 60 h. Indole oxidation to oxindole and isatin were the key steps limiting indole degradation. Plant litter addition induced fungus to produce laccase and LiP to non-specific oxidize indole. The results of fungal metabolites pathway through HPLC-MS and NMR analysis showed that indole was firstly oxidized to oxindole and isatin, and deoxidated to indolenie-2-dione, then hydroxylated to 2-dioxindole, which pyridine ring were cleaved through C-N position and changed to 2-aminobenzoic acid. Such metabolic pathway was similar with bacterial degradation of indole-3-acetic acid in plant. Copyright © 2012 Elsevier Ltd. All rights reserved.

A Decade of Boon or Burden: What Has the CHIP Ever Done for Cellular Protein Quality Control Mechanism Implicated in Neurodegeneration and Aging?

PubMed Central

Joshi, Vibhuti; Amanullah, Ayeman; Upadhyay, Arun; Mishra, Ribhav; Kumar, Amit; Mishra, Amit

2016-01-01

Cells regularly synthesize new proteins to replace old and abnormal proteins for normal cellular functions. Two significant protein quality control pathways inside the cellular milieu are ubiquitin proteasome system (UPS) and autophagy. Autophagy is known for bulk clearance of cytoplasmic aggregated proteins, whereas the specificity of protein degradation by UPS comes from E3 ubiquitin ligases. Few E3 ubiquitin ligases, like C-terminus of Hsc70-interacting protein (CHIP) not only take part in protein quality control pathways, but also plays a key regulatory role in other cellular processes like signaling, development, DNA damage repair, immunity and aging. CHIP targets misfolded proteins for their degradation through proteasome, as well as autophagy; simultaneously, with the help of chaperones, it also regulates folding attempts for misfolded proteins. The broad range of CHIP substrates and their associations with multiple pathologies make it a key molecule to work upon and focus for future therapeutic interventions. E3 ubiquitin ligase CHIP interacts and degrades many protein inclusions formed in neurodegenerative diseases. The presence of CHIP at various nodes of cellular protein-protein interaction network presents this molecule as a potential candidate for further research. In this review, we have explored a wide range of functionality of CHIP inside cells by a detailed presentation of its co-chaperone, E3 and E4 enzyme like functions, with central focus on its protein quality control roles in neurodegenerative diseases. We have also raised many unexplored but expected fundamental questions regarding CHIP functions, which generate hopes for its future applications in research, as well as drug discovery. PMID:27757073

The RNA Silencing Pathway: The Bits and Pieces That Matter

PubMed Central

Groenenboom, Marian A. C; Marée, Athanasius F. M; Hogeweg, Paulien

2005-01-01

Cellular pathways are generally proposed on the basis of available experimental knowledge. The proposed pathways, however, may be inadequate to describe the phenomena they are supposed to explain. For instance, by means of concise mathematical models we are able to reveal shortcomings in the current description of the pathway of RNA silencing. The silencing pathway operates by cleaving siRNAs from dsRNA. siRNAs can associate with RISC, leading to the degradation of the target mRNA. We propose and analyze a few small extensions to the pathway: a siRNA degrading RNase, primed amplification of aberrant RNA pieces, and cooperation between aberrant RNA to trigger amplification. These extensions allow for a consistent explanation for various types of silencing phenomena, such as virus induced silencing, transgene and transposon induced silencing, and avoidance of self-reactivity, as well as for differences found between species groups. PMID:16110335

Identification and analysis of the RNA degrading complexes and machinery of Giardia lamblia using an in silico approach.

PubMed

Williams, Christopher W; Elmendorf, Heidi G

2011-11-29

RNA degradation is critical to the survival of all cells. With increasing evidence for pervasive transcription in cells, RNA degradation has gained recognition as a means of regulating gene expression. Yet, RNA degradation machinery has been studied extensively in only a few eukaryotic organisms, including Saccharomyces cerevisiae and humans. Giardia lamblia is a parasitic protist with unusual genomic traits: it is binucleated and tetraploid, has a very compact genome, displays a theme of genomic minimalism with cellular machinery commonly comprised of a reduced number of protein components, and has a remarkably large population of long, stable, noncoding, antisense RNAs. Here we use in silico approaches to investigate the major RNA degradation machinery in Giardia lamblia and compare it to a broad array of other parasitic protists. We have found key constituents of the deadenylation and decapping machinery and of the 5'-3' RNA degradation pathway. We have similarly found that all of the major 3'-5' RNA degradation pathways are present in Giardia, including both exosome-dependent and exosome-independent machinery. However, we observe significant loss of RNA degradation machinery genes that will result in important differences in the protein composition, and potentially functionality, of the various RNA degradation pathways. This is most apparent in the exosome, the central mediator of 3'-5' degradation, which apparently contains an altered core configuration in both Giardia and Plasmodium, with only four, instead of the canonical six, distinct subunits. Additionally the exosome in Giardia is missing both the Rrp6, Nab3, and Nrd1 proteins, known to be key regulators of noncoding transcript stability in other cells. These findings suggest that although the full complement of the major RNA degradation mechanisms were present - and likely functional - early in eukaryotic evolution, the composition and function of the complexes is more variable than previously appreciated. We suggest that the missing components of the exosome complex provide an explanation for the stable abundance of sterile RNA species in Giardia.

Novel Strategy for Tracking the Microbial Degradation of Azo Dyes with Different Polarities in Living Cells.

PubMed

Liu, Fei; Xu, Meiying; Chen, Xingjuan; Yang, Yonggang; Wang, Haiji; Sun, Guoping

2015-10-06

Direct visualization evidence is important for understanding the microbial degradation mechanisms. To track the microbial degradation pathways of azo dyes with different polar characterizations, sensors based on the fluorescence resonance energy transfer (FRET) from 1,8-naphthalimide to azo dyes were synthesized, in which the quenched fluorescence will recover when the azo bond was cleaved. In living cells, the sensor-tracking experiment showed that the low polarity and hydrophobic azo dye can be taken up into the cells and reduced inside the cells, whereas the high polarity and hydrophilic azo dye can be reduced only outside the cells because of the selective permeability of the cell membranes. These results indicated that there were two different bacterial degradation pathways available for different polarity azo dyes. To our knowledge, no fluorescent sensor has yet been designed for illuminating the microbial degradation mechanisms of organic pollutants with different characteristics.

Retinoic acid induces proteasome-dependent degradation of retinoic acid receptor α (RARα) and oncogenic RARα fusion proteins

PubMed Central

Zhu, Jun; Gianni, Maurizio; Kopf, Eliezer; Honoré, Nicole; Chelbi-Alix, Mounira; Koken, Marcel; Quignon, Frédérique; Rochette-Egly, Cécile; de Thé, Hugues

1999-01-01

Analyzing the pathways by which retinoic acid (RA) induces promyelocytic leukemia/retinoic acid receptor α (PML/RARα) catabolism in acute promyelocytic leukemia (APL), we found that, in addition to caspase-mediated PML/RARα cleavage, RA triggers degradation of both PML/RARα and RARα. Similarly, in non-APL cells, RA directly targeted RARα and RARα fusions to the proteasome degradation pathway. Activation of either RARα or RXRα by specific agonists induced degradation of both proteins. Conversely, a mutation in RARα that abolishes heterodimer formation and DNA binding, blocked both RARα and RXRα degradation. Mutations in the RARα DNA-binding domain or AF-2 transcriptional activation region also impaired RARα catabolism. Hence, our results link transcriptional activation to receptor catabolism and suggest that transcriptional up-regulation of nuclear receptors by their ligands may be a feedback mechanism allowing sustained target-gene activation. PMID:10611294

Novel degradation pathway and kinetic analysis for buprofezin removal by newly isolated Bacillus sp.

PubMed

Wang, Guangli; Xu, Dayong; Xiong, Minghua; Zhang, Hui; Li, Feng; Liu, Yuan

2016-09-15

Given the intensive and widespread application of the pesticide, buprofezin, its environmental residues potentially pose a problem; yet little is known about buprofezin's kinetic and metabolic behaviors. In this study, a novel gram-positive strain, designated BF-5, isolated from aerobic activated sludge, was found to be capable of metabolizing buprofezin as its sole energy, carbon, and nitrogen source. Based on its physiological and biochemical characteristics, other aspects of its phenotype, and a phylogenetic analysis, strain BF-5 was identified as Bacillus sp. This study investigated the effect of culture conditions on bacterial growth and substrate degradation, such as pH, temperature, initial concentration, different nitrogen source, and additional nitrogen sources as co-substrates. The degradation rate parameters, qmax, Ks, Ki and Sm were determined to be 0.6918 h(-1), 105.4 mg L(-1), 210.5 mg L(-1), and 148.95 mg L(-1) respectively. The capture of unpublished potential metabolites by gas chromatography-mass spectrometry (GC-MS) analysis has led to the proposal of a novel degradation pathway. Taken together, our results clarify buprofezin's biodegradation pathway(s) and highlight the promising potential of strain BF-5 in bioremediation of buprofezin-contaminated environments. Copyright © 2016 Elsevier Ltd. All rights reserved.

Disassembly of the lens fiber cell nucleus to create a clear lens: The p27 descent.

PubMed

Rowan, Sheldon; Chang, Min-Lee; Reznikov, Natalie; Taylor, Allen

2017-03-01

The eye lens is unique among tissues: it is transparent, does not form tumors, and the majority of its cells degrade their organelles, including their cell nuclei. A mystery for over a century, there has been considerable recent progress in elucidating mechanisms of lens fiber cell denucleation (LFCD). In contrast to the disassembly and reassembly of the cell nucleus during mitosis, LFCD is a unidirectional process that culminates in destruction of the fiber cell nucleus. Whereas p27 Kip1 , the cyclin-dependent kinase inhibitor, is upregulated during formation of LFC in the outermost cortex, in the inner cortex, in the nascent organelle free zone, p27 Kip1 is degraded, markedly activating cyclin-dependent kinase 1 (Cdk1). This process results in phosphorylation of nuclear Lamins, dissociation of the nuclear membrane, and entry of lysosomes that liberate DNaseIIβ (DLAD) to cleave chromatin. Multiple cellular pathways, including the ubiquitin proteasome system and the unfolded protein response, converge on post-translational regulation of p27 Kip1 . Mutations that impair these pathways are associated with congenital cataracts and loss of LFCD. These findings highlight new regulatory nodes in the lens and suggest that we are close to understanding this fascinating terminal differentiation process. Such knowledge may offer a new means to confront proliferative diseases including cancer. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3

PubMed Central

Xiao, Jingfa; Hao, Lirui; Crowley, David E.; Zhang, Zhewen; Yu, Jun; Huang, Ning; Huo, Mingxin; Wu, Jiayan

2015-01-01

Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals. PMID:26301592

Chemical evolution of Macondo crude oil during laboratory degradation as characterized by fluorescence EEMs and hydrocarbon composition.

PubMed

Zhou, Zhengzhen; Liu, Zhanfei; Guo, Laodong

2013-01-15

The fluorescence EEM technique, PARAFAC modeling, and hydrocarbon composition were used to characterize oil components and to examine the chemical evolution and degradation pathways of Macondo crude oil under controlled laboratory conditions. Three major fluorescent oil components were identified, with Ex/Em maxima at 226/328, 262/315, and 244/366 nm, respectively. An average degradation half-life of ∼20 d was determined for the oil components based on fluorescence EEM and hydrocarbon composition measurements, showing a dynamic chemical evolution and transformation of the oil during degradation. Dispersants appeared to change the chemical characteristics of oil, to shift the fluorescence EEM spectra, and to enhance the degradation of low-molecular-weight hydrocarbons. Photochemical degradation played a dominant role in the transformation of oil components, likely an effective degradation pathway of oil in the water column. Results from laboratory experiments should facilitate the interpretation of field-data and provide insights for understanding the fate and transport of oil components in the Gulf of Mexico. Copyright © 2012 Elsevier Ltd. All rights reserved.

A vacuolar carboxypeptidase mutant of Arabidopsis thaliana is degraded by the ERAD pathway independently of its N-glycan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamamoto, Masaya; Kawanabe, Mitsuyoshi; Hayashi, Yoko

2010-03-12

Misfolded proteins produced in the endoplasmic reticulum (ER) are degraded by a mechanism, the ER-associated degradation (ERAD). Here we report establishment of the experimental system to analyze the ERAD in plant cells. Carboxypeptidase Y (CPY) is a vacuolar enzyme and its mutant CPY* is degraded by the ERAD in yeast. Since Arabidopsis thaliana has AtCPY, an ortholog of yeast CPY, we constructed and expressed fusion proteins consisting of AtCPY and GFP and of AtCPY*, which carries a mutation homologous to yeast CPY*, and GFP in A. thaliana cells. While AtCPY-GFP was efficiently transported to the vacuole, AtCPY*-GFP was retained inmore » the ER to be degraded in proteasome- and Cdc48-dependent manners. We also found that AtCPY*-GFP was degraded by the ERAD in yeast cells, but that its single N-glycan did not function as a degradation signal in yeast or plant cells. Therefore, AtCPY*-GFP can be used as a marker protein to analyze the ERAD pathway, likely for nonglycosylated substrates, in plant cells.« less

Kinetics and degradation pathways of photolytic and photocatalytic oxidation of the anthelmintic drug praziquantel.

PubMed

Čizmić, Mirta; Ljubas, Davor; Ćurković, Lidija; Škorić, Irena; Babić, Sandra

2017-02-05

In this study, an anthelmintic drug, praziquantel(PZQ), was degraded using the direct photolysis, photocatalysis, and oxidation processes including UV radiation, TiO 2 film, and hydrogen peroxide. The photolytic degradation with predominant wavelengths of 185/254nm (UV-C) proved to be more efficient with a half-life of 3.13min compared to the radiation of 365nm (UV-A) where the degradation did not occur. In order to enhance the rate of PZQ photolytic degradation, H 2 O 2 was added, which resulted in two to three times higher degradation rates. In the photocatalytic degradation, TiO 2 film was used as catalyst. The degradation was ten times faster in the photocatalytic experiments where UV-C light (k=0.2390min -1 ) was used than in those with UV-A (k=0.0201min -1 ). Comparing the results from all performed experiments it can be concluded that the UV-C/TiO 2 /H 2 O 2 process yielded the highest degradation rate and complete degradation of PZQ was obtained in less than 7min. The degradation of PZQ followed the first order kinetics in all the experiments. The photo degradation was inhibited in the presence of methanol. The degradation pathways and the structural formulae of five degradation products (m/z 273, 269, 189, 147, 132) were proposed based on the liquid chromatography tandem mass spectrometry analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

A review of bacterial methyl halide degradation: biochemistry, genetics and molecular ecology

USGS Publications Warehouse

McDonald, I.R.; Warner, K.L.; McAnulla, C.; Woodall, C.A.; Oremland, R.S.; Murrell, J.C.

2002-01-01

Methyl halide-degrading bacteria are a diverse group of organisms that are found in both terrestrial and marine environments. They potentially play an important role in mitigating ozone depletion resulting from methyl chloride and methyl bromide emissions. The first step in the pathway(s) of methyl halide degradation involves a methyltransferase and, recently, the presence of this pathway has been studied in a number of bacteria. This paper reviews the biochemistry and genetics of methyl halide utilization in the aerobic bacteria Methylobacterium chloromethanicum CM4T, Hyphomicrobium chloromethanicum CM2T, Aminobacter strain IMB-1 and Aminobacter strain CC495. These bacteria are able to use methyl halides as a sole source of carbon and energy, are all members of the α-Proteobacteria and were isolated from a variety of polluted and pristine terrestrial environments. An understanding of the genetics of these bacteria identified a unique gene (cmuA) involved in the degradation of methyl halides, which codes for a protein (CmuA) with unique methyltransferase and corrinoid functions. This unique functional gene, cmuA, is being used to develop molecular ecology techniques to examine the diversity and distribution of methyl halide-utilizing bacteria in the environment and hopefully to understand their role in methyl halide degradation in different environments. These techniques will also enable the detection of potentially novel methyl halide-degrading bacteria.

Biodegradability of HCH in agricultural soils from Guadeloupe (French West Indies): identification of the lin genes involved in the HCH degradation pathway.

PubMed

Laquitaine, L; Durimel, A; de Alencastro, L F; Jean-Marius, C; Gros, O; Gaspard, S

2016-01-01

Banana has been a main agricultural product in the French West Indies (Guadeloupe and Martinique) since the 1960s. This crop requires the intensive use of pesticides to prevent attacks by insect pests. Chlorinated pesticides, such as hexachlorocyclohexane (HCH), chlordecone and dieldrin, were used until the beginning of the 1990s, resulting in a generalized diffuse contamination of the soil and water in the areas of banana production, hence the need to develop solutions for cleanup of the polluted sites. The aims of this work were (i) to assess lindane degradation in soil slurry microcosms treated with lindane at 10 mg/L and (ii) to detect the catabolic genes involved in the HCH degradation pathway. The soil slurry microcosm system showed a 40% lindane degradation efficiency at the end of a 30-day experiment. Lower lindane removal was also detected in the abiotic controls, probably caused by pesticide adsorption to soil particles. Indeed, the lindane concentration decreased from 6000 to 1330 ng/mL and from 800 to 340 ng/mL for the biotic and abiotic soils, respectively. Nevertheless, some of the genes involved in the HCH degradation pathway were amplified by polymerase chain reaction (PCR) from crude deoxyribonucleic acid (DNA) extracted from the Guadeloupe agricultural soil, suggesting that HCH degradation is probably mediated by bacteria closely related to the family Sphingomonadaceae.

The Cys-Arg/N-End Rule Pathway Is a General Sensor of Abiotic Stress in Flowering Plants.

PubMed

Vicente, Jorge; Mendiondo, Guillermina M; Movahedi, Mahsa; Peirats-Llobet, Marta; Juan, Yu-Ting; Shen, Yu-Yen; Dambire, Charlene; Smart, Katherine; Rodriguez, Pedro L; Charng, Yee-Yung; Gray, Julie E; Holdsworth, Michael J

2017-10-23

Abiotic stresses impact negatively on plant growth, profoundly affecting yield and quality of crops. Although much is known about plant responses, very little is understood at the molecular level about the initial sensing of environmental stress. In plants, hypoxia (low oxygen, which occurs during flooding) is directly sensed by the Cys-Arg/N-end rule pathway of ubiquitin-mediated proteolysis, through oxygen-dependent degradation of group VII Ethylene Response Factor transcription factors (ERFVIIs) via amino-terminal (Nt-) cysteine [1, 2]. Using Arabidopsis (Arabidopsis thaliana) and barley (Hordeum vulgare), we show that the pathway regulates plant responses to multiple abiotic stresses. In Arabidopsis, genetic analyses revealed that response to these stresses is controlled by N-end rule regulation of ERFVII function. Oxygen sensing via the Cys-Arg/N-end rule in higher eukaryotes is linked through a single mechanism to nitric oxide (NO) sensing [3, 4]. In plants, the major mechanism of NO synthesis is via NITRATE REDUCTASE (NR), an enzyme of nitrogen assimilation [5]. Here, we identify a negative relationship between NR activity and NO levels and stabilization of an artificial Nt-Cys substrate and ERFVII function in response to environmental changes. Furthermore, we show that ERFVIIs enhance abiotic stress responses via physical and genetic interactions with the chromatin-remodeling ATPase BRAHMA. We propose that plants sense multiple abiotic stresses through the Cys-Arg/N-end rule pathway either directly (via oxygen sensing) or indirectly (via NO sensing downstream of NR activity). This single mechanism can therefore integrate environment and response to enhance plant survival. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Chemical conversion pathways and kinetic modeling for the OH-initiated reaction of triclosan in gas-phase.

PubMed

Zhang, Xue; Zhang, Chenxi; Sun, Xiaomin; Kang, Lingyan; Zhao, Yan

2015-04-10

As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of k add/k total and k abs/k total at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin.

Biochemistry of Microbial Degradation of Hexachlorocyclohexane and Prospects for Bioremediation

PubMed Central

Lal, Rup; Pandey, Gunjan; Sharma, Pooja; Kumari, Kirti; Malhotra, Shweta; Pandey, Rinku; Raina, Vishakha; Kohler, Hans-Peter E.; Holliger, Christof; Jackson, Colin; Oakeshott, John G.

2010-01-01

Summary: Lindane, the γ-isomer of hexachlorocyclohexane (HCH), is a potent insecticide. Purified lindane or unpurified mixtures of this and α-, β-, and δ-isomers of HCH were widely used as commercial insecticides in the last half of the 20th century. Large dumps of unused HCH isomers now constitute a major hazard because of their long residence times in soil and high nontarget toxicities. The major pathway for the aerobic degradation of HCH isomers in soil is the Lin pathway, and variants of this pathway will degrade all four of the HCH isomers although only slowly. Sequence differences in the primary LinA and LinB enzymes in the pathway play a key role in determining their ability to degrade the different isomers. LinA is a dehydrochlorinase, but little is known of its biochemistry. LinB is a hydrolytic dechlorinase that has been heterologously expressed and crystallized, and there is some understanding of the sequence-structure-function relationships underlying its substrate specificity and kinetics, although there are also some significant anomalies. The kinetics of some LinB variants are reported to be slow even for their preferred isomers. It is important to develop a better understanding of the biochemistries of the LinA and LinB variants and to use that knowledge to build better variants, because field trials of some bioremediation strategies based on the Lin pathway have yielded promising results but would not yet achieve economic levels of remediation. PMID:20197499

Unveiling New Degradation Intermediates/Pathways from the Photocatalytic Degradation of Microcystin-LR

EPA Science Inventory

This study focuses on the identification of reaction intermediates formed during the photocatalytic degradation of the cyanotoxin microcystin-LR with immobilized TiO₂ Tphotocatalysts at neutral pH. To differentiate between impurities already existing in the MC-LR stand...

Pathway for recovery of photo-degraded polymer solar cells by post degradation thermal anneal

DOE PAGES

Bhattacharya, J.; Joshi, P. H.; Biswas, Rana; ...

2017-02-16

The photo-degradation of polymer solar cells is a critical challenge preventing its commercial deployment. We experimentally fabricate organic solar cells and characterize their degradation under solar simulators in an environmental chamber under nitrogen flow, without exposure to oxygen and moisture. We have developed a thermally stable inverted organic solar cell architecture in which light induced degradation of device characteristics can be reversibly annealed to the pristine values. The stable inverted cells utilized MoO x layers that are thermally treated immediately after their deposition on the organic layer, and before metal cathode deposition. Organic solar cells that are photo-degraded in themore » presence of oxygen, however show irreversible degradation that cannot be thermally recovered. The decrease of organic solar cell characteristics correlates with increases in mid-gap electronic states, measured using capacitance spectroscopy and dark current. It is likely the photo-induced defect states caused by local H motion from the alkyl chains to the aromatic backbone, can be reversibly annealed at elevated temperatures after photo-degradation. Finally, our results provide a pathway for improving the stability of organic photovoltaics.« less

Biodegradation pathway of an anionic surfactant (Igepon TC-42) during recycling waste water through plant hydroponics for advanced life support during long-duration space missions.

PubMed

Levine, L H; Kagie, H R; Garland, J L

2003-01-01

The degradation of an anionic surfactant (Igepon TC-42) was investigated as part of an integrated study of direct recycling of human hygiene water through hydroponic plant growth systems. Several chemical approaches were developed to characterize the degradation of Igepon and to measure the accumulation of intermediates such as fatty acids and methyl taurine. Igepon was rapidly degraded as indicated by the reduction of methylene blue active substances (MBAS) and component fatty acids. The Igepon degradation rate continued to increase over a period of several weeks following repeated daily exposure to 18 micrograms/l Igepon. The accumulation of free fatty acids and methyl taurine was also observed during decomposition of Igepon. The concentration of methyl taurine was below detection limit (0.2 nmol/ml) during the slow phase of Igepon degradation, and increased to 1-2 nmol/ml during the phase of rapid degradation. These findings support a degradation pathway involving initial hydrolysis of amide to release fatty acids and methyl taurine, and subsequent degradation of these intermediates. Published by Elsevier Science Ltd on behalf of COSPAR.

Biodegradation pathway of an anionic surfactant (Igepon TC-42) during recycling waste water through plant hydroponics for advanced life support during long-duration space missions

NASA Technical Reports Server (NTRS)

Levine, L. H.; Kagie, H. R.; Garland, J. L.

2003-01-01

The degradation of an anionic surfactant (Igepon TC-42) was investigated as part of an integrated study of direct recycling of human hygiene water through hydroponic plant growth systems. Several chemical approaches were developed to characterize the degradation of Igepon and to measure the accumulation of intermediates such as fatty acids and methyl taurine. Igepon was rapidly degraded as indicated by the reduction of methylene blue active substances (MBAS) and component fatty acids. The Igepon degradation rate continued to increase over a period of several weeks following repeated daily exposure to 18 micrograms/l Igepon. The accumulation of free fatty acids and methyl taurine was also observed during decomposition of Igepon. The concentration of methyl taurine was below detection limit (0.2 nmol/ml) during the slow phase of Igepon degradation, and increased to 1-2 nmol/ml during the phase of rapid degradation. These findings support a degradation pathway involving initial hydrolysis of amide to release fatty acids and methyl taurine, and subsequent degradation of these intermediates. Published by Elsevier Science Ltd on behalf of COSPAR.

Pathway for recovery of photo-degraded polymer solar cells by post degradation thermal anneal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhattacharya, J.; Joshi, P. H.; Biswas, Rana

The photo-degradation of polymer solar cells is a critical challenge preventing its commercial deployment. We experimentally fabricate organic solar cells and characterize their degradation under solar simulators in an environmental chamber under nitrogen flow, without exposure to oxygen and moisture. We have developed a thermally stable inverted organic solar cell architecture in which light induced degradation of device characteristics can be reversibly annealed to the pristine values. The stable inverted cells utilized MoO x layers that are thermally treated immediately after their deposition on the organic layer, and before metal cathode deposition. Organic solar cells that are photo-degraded in themore » presence of oxygen, however show irreversible degradation that cannot be thermally recovered. The decrease of organic solar cell characteristics correlates with increases in mid-gap electronic states, measured using capacitance spectroscopy and dark current. It is likely the photo-induced defect states caused by local H motion from the alkyl chains to the aromatic backbone, can be reversibly annealed at elevated temperatures after photo-degradation. Finally, our results provide a pathway for improving the stability of organic photovoltaics.« less

Metagenomic Analysis of a Biphenyl-Degrading Soil Bacterial Consortium Reveals the Metabolic Roles of Specific Populations

PubMed Central

Garrido-Sanz, Daniel; Manzano, Javier; Martín, Marta; Redondo-Nieto, Miguel; Rivilla, Rafael

2018-01-01

Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source. This consortium is able to grow on biphenyl, benzoate, and protocatechuate. Whole-community DNA extracted from the consortium was used to analyze biodiversity by Illumina sequencing of a 16S rRNA gene amplicon library and to determine the metagenome by whole-genome shotgun Illumina sequencing. Biodiversity analysis shows that the consortium consists of 24 operational taxonomic units (≥97% identity). The consortium is dominated by strains belonging to the genus Pseudomonas, but also contains betaproteobacteria and Rhodococcus strains. whole-genome shotgun (WGS) analysis resulted in contigs containing 78.3 Mbp of sequenced DNA, representing around 65% of the expected DNA in the consortium. Bioinformatic analysis of this metagenome has identified the genes encoding the enzymes implicated in three pathways for the conversion of biphenyl to benzoate and five pathways from benzoate to tricarboxylic acid (TCA) cycle intermediates, allowing us to model the whole biodegradation network. By genus assignment of coding sequences, we have also been able to determine that the three biphenyl to benzoate pathways are carried out by Rhodococcus strains. In turn, strains belonging to Pseudomonas and Bordetella are the main responsible of three of the benzoate to TCA pathways while the benzoate conversion into TCA cycle intermediates via benzoyl-CoA and the catechol meta-cleavage pathways are carried out by beta proteobacteria belonging to genera such as Achromobacter and Variovorax. We have isolated a Rhodococcus strain WAY2 from the consortium which contains the genes encoding the three biphenyl to benzoate pathways indicating that this strain is responsible for all the biphenyl to benzoate transformations. The presented results show that metagenomic analysis of consortia allows the identification of bacteria active in biodegradation processes and the assignment of specific reactions and pathways to specific bacterial groups. PMID:29497412

Pathways for degradation of lignin in bacteria and fungi.

PubMed

Bugg, Timothy D H; Ahmad, Mark; Hardiman, Elizabeth M; Rahmanpour, Rahman

2011-11-01

Lignin is a heterogeneous aromatic polymer found as 10-35% of lignocellulose, found in plant cell walls. The bio-conversion of plant lignocellulose to glucose is an important part of second generation biofuel production, but the resistance of lignin to breakdown is a major obstacle in this process, hence there is considerable interest in the microbial breakdown of lignin. White-rot fungi are known to break down lignin with the aid of extracellular peroxidase and laccase enzymes. There are also reports of bacteria that can degrade lignin, and recent work indicates that bacterial lignin breakdown may be more significant than previously thought. The review will discuss the enzymes for lignin breakdown in fungi and bacteria, and the catabolic pathways for breakdown of the β-aryl ether, biphenyl and other components of lignin in bacteria and fungi. The review will also discuss small molecule phenolic breakdown products from lignin that have been identified from lignin-degrading microbes, and includes a bioinformatic analysis of the occurrence of known lignin-degradation pathways in Gram-positive and Gram-negative bacteria.

Degradation pathway of 2-chloroethanol in Pseudomonas stutzeri strain JJ under denitrifying conditions.

PubMed

Dijk, John A; Gerritse, Jan; Schraa, Gosse; Stams, Alfons J M

2004-12-01

The pathway of 2-chloroethanol degradation in the denitrifying Pseudomonas stutzeri strain JJ was investigated. In cell-free extracts, activities of a phenazine methosulfate (PMS)-dependent chloroethanol dehydrogenase, an NAD-dependent chloroacetaldehyde dehydrogenase, and a chloroacetate dehalogenase were detected. This suggested that the 2-chloroethanol degradation pathway in this denitrifying strain is the same as found in aerobic bacteria that degrade chloroethanol. Activity towards primary alcohols, secondary alcohols, diols, and other chlorinated alcohols could be measured in cell-free extracts with chloroethanol dehydrogenase (CE-DH) activity. PMS and phenazine ethosulfate (PES) were used as primary electron acceptors, but not NAD, NADP or ferricyanide. Cells of strain JJ cultured in a continuous culture under nitrate limitation exhibited chloroethanol dehydrogenase activity that was a 12 times higher than in cells grown in batch culture. However, under chloroethanol-limiting conditions, CE-DH activity was in the same range as in batch culture. Cells grown on ethanol did not exhibit CE-DH activity. Instead, NAD-dependent ethanol dehydrogenase (E-DH) activity and PMS-dependent E-DH activity were detected.

(Per)Chlorate-Reducing Bacteria Can Utilize Aerobic and Anaerobic Pathways of Aromatic Degradation with (Per)Chlorate as an Electron Acceptor

PubMed Central

Carlström, Charlotte I.; Loutey, Dana; Bauer, Stefan; Clark, Iain C.; Rohde, Robert A.; Iavarone, Anthony T.; Lucas, Lauren

2015-01-01

ABSTRACT The pathways involved in aromatic compound oxidation under perchlorate and chlorate [collectively known as (per)chlorate]-reducing conditions are poorly understood. Previous studies suggest that these are oxygenase-dependent pathways involving O2 biogenically produced during (per)chlorate respiration. Recently, we described Sedimenticola selenatireducens CUZ and Dechloromarinus chlorophilus NSS, which oxidized phenylacetate and benzoate, two key intermediates in aromatic compound catabolism, coupled to the reduction of perchlorate or chlorate, respectively, and nitrate. While strain CUZ also oxidized benzoate and phenylacetate with oxygen as an electron acceptor, strain NSS oxidized only the latter, even at a very low oxygen concentration (1%, vol/vol). Strains CUZ and NSS contain similar genes for both the anaerobic and aerobic-hybrid pathways of benzoate and phenylacetate degradation; however, the key genes (paaABCD) encoding the epoxidase of the aerobic-hybrid phenylacetate pathway were not found in either genome. By using transcriptomics and proteomics, as well as by monitoring metabolic intermediates, we investigated the utilization of the anaerobic and aerobic-hybrid pathways on different electron acceptors. For strain CUZ, the results indicated utilization of the anaerobic pathways with perchlorate and nitrate as electron acceptors and of the aerobic-hybrid pathways in the presence of oxygen. In contrast, proteomic results suggest that strain NSS may use a combination of the anaerobic and aerobic-hybrid pathways when growing on phenylacetate with chlorate. Though microbial (per)chlorate reduction produces molecular oxygen through the dismutation of chlorite (ClO2−), this study demonstrates that anaerobic pathways for the degradation of aromatics can still be utilized by these novel organisms. PMID:25805732

The alignment of enzymatic steps reveals similar metabolic pathways and probable recruitment events in Gammaproteobacteria.

PubMed

Poot-Hernandez, Augusto Cesar; Rodriguez-Vazquez, Katya; Perez-Rueda, Ernesto

2015-11-17

It is generally accepted that gene duplication followed by functional divergence is one of the main sources of metabolic diversity. In this regard, there is an increasing interest in the development of methods that allow the systematic identification of these evolutionary events in metabolism. Here, we used a method not based on biomolecular sequence analysis to compare and identify common and variable routes in the metabolism of 40 Gammaproteobacteria species. The metabolic maps deposited in the KEGG database were transformed into linear Enzymatic Step Sequences (ESS) by using the breadth-first search algorithm. These ESS represent subsequent enzymes linked to each other, where their catalytic activities are encoded in the Enzyme Commission numbers. The ESS were compared in an all-against-all (pairwise comparisons) approach by using a dynamic programming algorithm, leaving only a set of significant pairs. From these comparisons, we identified a set of functionally conserved enzymatic steps in different metabolic maps, in which cell wall components and fatty acid and lysine biosynthesis were included. In addition, we found that pathways associated with biosynthesis share a higher proportion of similar ESS than degradation pathways and secondary metabolism pathways. Also, maps associated with the metabolism of similar compounds contain a high proportion of similar ESS, such as those maps from nucleotide metabolism pathways, in particular the inosine monophosphate pathway. Furthermore, diverse ESS associated with the low part of the glycolysis pathway were identified as functionally similar to multiple metabolic pathways. In summary, our comparisons may help to identify similar reactions in different metabolic pathways and could reinforce the patchwork model in the evolution of metabolism in Gammaproteobacteria.

Degradation of Nicotine in Chlorinated Water: Pathways and ...

EPA Pesticide Factsheets

Report The objective of the study is to illustrate how drinking water would affect alkaloid pesticides, and to address the issue by (a) investigating the fate of nicotine in chlorinated drinking water and deionized water, (b) determining the reaction rate and pathway of the reaction between nicotine and aqueous chlorine, (c) identifying nicotine’s degradation products, and (d) providing data that can be used to assess the potential threat from nicotine in drinking water.

Parkin and PINK1 function in a vesicular trafficking pathway regulating mitochondrial quality control

PubMed Central

McLelland, Gian-Luca; Soubannier, Vincent; Chen, Carol X; McBride, Heidi M; Fon, Edward A

2014-01-01

Mitochondrial dysfunction has long been associated with Parkinson's disease (PD). Parkin and PINK1, two genes associated with familial PD, have been implicated in the degradation of depolarized mitochondria via autophagy (mitophagy). Here, we describe the involvement of parkin and PINK1 in a vesicular pathway regulating mitochondrial quality control. This pathway is distinct from canonical mitophagy and is triggered by the generation of oxidative stress from within mitochondria. Wild-type but not PD-linked mutant parkin supports the biogenesis of a population of mitochondria-derived vesicles (MDVs), which bud off mitochondria and contain a specific repertoire of cargo proteins. These MDVs require PINK1 expression and ultimately target to lysosomes for degradation. We hypothesize that loss of this parkin- and PINK1-dependent trafficking mechanism impairs the ability of mitochondria to selectively degrade oxidized and damaged proteins leading, over time, to the mitochondrial dysfunction noted in PD. PMID:24446486

Sono-activated persulfate oxidation of diclofenac: Degradation, kinetics, pathway and contribution of the different radicals involved.

PubMed

Monteagudo, J M; El-Taliawy, H; Durán, A; Caro, G; Bester, K

2018-06-20

Degradation of a diclofenac aqueous solution was performed using persulfate anions activated by ultrasound. The objective of this study was to analyze different parameters affecting the diclofenac (DCF) removal reaction by the ultrasonic persulfate (US/PS) process and to evaluate the role played by various intermediate oxidative species such as hydroxyl- and sulfate radicals, superoxide radical anion or singlet oxygen in the removal process as well as to determine a possible reaction pathway. The effects of pH, initial persulfate anion concentration, ultrasonic amplitude and temperature on DCF degradation were examined. Sulfate and hydroxyl radicals were involved in the main reaction pathway of diclofenac. Diclofenac amide and three hydroxy-diclofenac isomers (3´-hydroxy diclofenac, 4´-hydroxy diclofenac and 5-hydroxy diclofenac) were identified as reaction intermediates. Copyright © 2018 Elsevier B.V. All rights reserved.

Natural Antioxidants: Multiple Mechanisms to Protect Skin From Solar Radiation

PubMed Central

Dunaway, Spencer; Odin, Rachel; Zhou, Linli; Ji, Liyuan; Zhang, Yuhang; Kadekaro, Ana L.

2018-01-01

Human skin exposed to solar ultraviolet radiation (UVR) results in a dramatic increase in the production of reactive oxygen species (ROS). The sudden increase in ROS shifts the natural balance toward a pro-oxidative state, resulting in oxidative stress. The detrimental effects of oxidative stress occur through multiple mechanisms that involve alterations to proteins and lipids, induction of inflammation, immunosuppression, DNA damage, and activation of signaling pathways that affect gene transcription, cell cycle, proliferation, and apoptosis. All of these alterations promote carcinogenesis and therefore, regulation of ROS levels is critical to the maintenance of normal skin homeostasis. Several botanical products have been found to exhibit potent antioxidant capacity and the ability to counteract UV-induced insults to the skin. These natural products exert their beneficial effects through multiple pathways, including some known to be negatively affected by solar UVR. Aging of the skin is also accelerated by UVR exposure, in particular UVA rays that penetrate deep into the epidermis and the dermis where it causes the degradation of collagen and elastin fibers via oxidative stress and activation of matrix metalloproteinases (MMPs). Because natural compounds are capable of attenuating some of the UV-induced aging effects in the skin, increased attention has been generated in the area of cosmetic sciences. The focus of this review is to cover the most prominent phytoproducts with potential to mitigate the deleterious effects of solar UVR and suitability for use in topical application. PMID:29740318

Small heat shock proteins target mutant cystic fibrosis transmembrane conductance regulator for degradation via a small ubiquitin-like modifier–dependent pathway

PubMed Central

Ahner, Annette; Gong, Xiaoyan; Schmidt, Bela Z.; Peters, Kathryn W.; Rabeh, Wael M.; Thibodeau, Patrick H.; Lukacs, Gergely L.; Frizzell, Raymond A.

2013-01-01

Small heat shock proteins (sHsps) bind destabilized proteins during cell stress and disease, but their physiological functions are less clear. We evaluated the impact of Hsp27, an sHsp expressed in airway epithelial cells, on the common protein misfolding mutant that is responsible for most cystic fibrosis. F508del cystic fibrosis transmembrane conductance regulator (CFTR), a well-studied protein that is subject to cytosolic quality control, selectively associated with Hsp27, whose overexpression preferentially targeted mutant CFTR to proteasomal degradation. Hsp27 interacted physically with Ubc9, the small ubiquitin-like modifier (SUMO) E2 conjugating enzyme, implying that F508del SUMOylation leads to its sHsp-mediated degradation. Enhancing or disabling the SUMO pathway increased or blocked Hsp27’s ability to degrade mutant CFTR. Hsp27 promoted selective SUMOylation of F508del NBD1 in vitro and of full-length F508del CFTR in vivo, which preferred endogenous SUMO-2/3 paralogues that form poly-chains. The SUMO-targeted ubiquitin ligase (STUbL) RNF4 recognizes poly-SUMO chains to facilitate nuclear protein degradation. RNF4 overexpression elicited F508del degradation, whereas Hsp27 knockdown blocked RNF4’s impact on mutant CFTR. Similarly, the ability of Hsp27 to degrade F508del CFTR was lost during overexpression of dominant-negative RNF4. These findings link sHsp-mediated F508del CFTR degradation to its SUMOylation and to STUbL-mediated targeting to the ubiquitin–proteasome system and thereby implicate this pathway in the disposal of an integral membrane protein. PMID:23155000

Anaerobic bioremediation of RDX by ovine whole rumen fluid and pure culture isolates.

PubMed

Eaton, H L; Duringer, J M; Murty, L D; Craig, A M

2013-04-01

The ability of ruminal microbes to degrade the explosive compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in ovine whole rumen fluid (WRF) and as 24 bacterial isolates was examined under anaerobic conditions. Compound degradation was monitored by high-performance liquid chromatography analysis, followed by liquid chromatography-tandem mass spectrometry identification of metabolites. Organisms in WRF microcosms degraded 180 μM RDX within 4 h. Nitroso-intermediates hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX), hexahydro-1,3-dinitroso-5-nitro-1,3,5-triazine (DNX), and hexahydro-1,3,5-trinitroso-1,3,5-triazine (TNX) were present as early as 0.25 h and were detected throughout the 24-h incubation period, representing one reductive pathway of ring cleavage. Following reduction to MNX, peaks consistent with m/z 193 and 174 were also produced, which were unstable and resulted in rapid ring cleavage to a common metabolite consistent with an m/z of 149. These represent two additional reductive pathways for RDX degradation in ovine WRF, which have not been previously reported. The 24 ruminal isolates degraded RDX with varying efficiencies (0-96 %) over 120 h. Of the most efficient degraders identified, Clostridium polysaccharolyticum and Desulfovibrio desulfuricans subsp. desulfuricans degraded RDX when medium was supplemented with both nitrogen and carbon, while Anaerovibrio lipolyticus, Prevotella ruminicola, and Streptococcus bovis IFO utilized RDX as a sole source of nitrogen. This study showed that organisms in whole rumen fluid, as well as several ruminal isolates, have the ability to degrade RDX in vitro and, for the first time, delineated the metabolic pathway for its biodegradation.

Protection of scaffold protein Isu from degradation by the Lon protease Pim1 as a component of Fe-S cluster biogenesis regulation.

PubMed

Ciesielski, Szymon J; Schilke, Brenda; Marszalek, Jaroslaw; Craig, Elizabeth A

2016-04-01

Iron-sulfur (Fe-S) clusters, essential protein cofactors, are assembled on the mitochondrial scaffold protein Isu and then transferred to recipient proteins via a multistep process in which Isu interacts sequentially with multiple protein factors. This pathway is in part regulated posttranslationally by modulation of the degradation of Isu, whose abundance increases >10-fold upon perturbation of the biogenesis process. We tested a model in which direct interaction with protein partners protects Isu from degradation by the mitochondrial Lon-type protease. Using purified components, we demonstrated that Isu is indeed a substrate of the Lon-type protease and that it is protected from degradation by Nfs1, the sulfur donor for Fe-S cluster assembly, as well as by Jac1, the J-protein Hsp70 cochaperone that functions in cluster transfer from Isu. Nfs1 and Jac1 variants known to be defective in interaction with Isu were also defective in protecting Isu from degradation. Furthermore, overproduction of Jac1 protected Isu from degradation in vivo, as did Nfs1. Taken together, our results lead to a model of dynamic interplay between a protease and protein factors throughout the Fe-S cluster assembly and transfer process, leading to up-regulation of Isu levels under conditions when Fe-S cluster biogenesis does not meet cellular demands. © 2016 Ciesielski et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Assessment of the roles of reactive oxygen species in the UV and visible light photocatalytic degradation of cyanotoxins and water taste and odor compounds using C-TiO2.

PubMed

Fotiou, Theodora; Triantis, Theodoros M; Kaloudis, Triantafyllos; O'Shea, Kevin E; Dionysiou, Dionysios D; Hiskia, Anastasia

2016-03-01

Visible light (VIS) photocatalysis has large potential as a sustainable water treatment process, however the reaction pathways and degradation processes of organic pollutants are not yet clearly defined. The presence of cyanobacteria cause water quality problems since several genera can produce potent cyanotoxins, harmful to human health. In addition, cyanobacteria produce taste and odor compounds, which pose serious aesthetic problems in drinking water. Although photocatalytic degradation of cyanotoxins and taste and odor compounds have been reported under UV-A light in the presence of TiO2, limited studies have been reported on their degradation pathways by VIS photocatalysis of these problematic compounds. The main objectives of this work were to study the VIS photocatalytic degradation process, define the reactive oxygen species (ROS) involved and elucidate the reaction mechanisms. We report carbon doped TiO2 (C-TiO2) under VIS leads to the slow degradation of cyanotoxins, microcystin-LR (MC-LR) and cylindrospermopsin (CYN), while taste and odor compounds, geosmin and 2-methylisoborneol, were not appreciably degraded. Further studies were carried-out employing several specific radical scavengers (potassium bromide, isopropyl alcohol, sodium azide, superoxide dismutase and catalase) and probes (coumarin) to assess the role of different ROS (hydroxyl radical OH, singlet oxygen (1)O2, superoxide radical anion [Formula: see text] ) in the degradation processes. Reaction pathways of MC-LR and CYN were defined through identification and monitoring of intermediates using liquid chromatography tandem mass spectrometry (LC-MS/MS) for VIS in comparison with UV-A photocatalytic treatment. The effects of scavengers and probes on the degradation process under VIS, as well as the differences in product distributions under VIS and UV-A, suggested that the main species in VIS photocatalysis is [Formula: see text] , with OH and (1)O2 playing minor roles in the degradation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nitric Oxide–Triggered Remodeling of Chloroplast Bioenergetics and Thylakoid Proteins upon Nitrogen Starvation in Chlamydomonas reinhardtii[W

PubMed Central

Wei, Lili; Derrien, Benoit; Gautier, Arnaud; Houille-Vernes, Laura; Boulouis, Alix; Saint-Marcoux, Denis; Malnoë, Alizée; Rappaport, Fabrice; de Vitry, Catherine; Vallon, Olivier; Choquet, Yves; Wollman, Francis-André

2014-01-01

Starving microalgae for nitrogen sources is commonly used as a biotechnological tool to boost storage of reduced carbon into starch granules or lipid droplets, but the accompanying changes in bioenergetics have been little studied so far. Here, we report that the selective depletion of Rubisco and cytochrome b6f complex that occurs when Chlamydomonas reinhardtii is starved for nitrogen in the presence of acetate and under normoxic conditions is accompanied by a marked increase in chlororespiratory enzymes, which converts the photosynthetic thylakoid membrane into an intracellular matrix for oxidative catabolism of reductants. Cytochrome b6f subunits and most proteins specifically involved in their biogenesis are selectively degraded, mainly by the FtsH and Clp chloroplast proteases. This regulated degradation pathway does not require light, active photosynthesis, or state transitions but is prevented when respiration is impaired or under phototrophic conditions. We provide genetic and pharmacological evidence that NO production from intracellular nitrite governs this degradation pathway: Addition of a NO scavenger and of two distinct NO producers decrease and increase, respectively, the rate of cytochrome b6f degradation; NO-sensitive fluorescence probes, visualized by confocal microscopy, demonstrate that nitrogen-starved cells produce NO only when the cytochrome b6f degradation pathway is activated. PMID:24474630

Molecular assessment of glyphosate-degradation pathway via sarcosine intermediate in Lysinibacillus sphaericus.

PubMed

González-Valenzuela, Laura E; Dussán, Jenny

2018-05-31

The widespread use of glyphosate has permeated not only small- and large-scale agriculture, but also the fight against drug trafficking and illicit crops. Health, alimentary security, and the rights of peasant and indigenous communities have been compromised in countries with intensive use of glyphosate-based herbicides. In 2015, the International Agency for Research on Cancer classified this substance as probably carcinogenic to humans, leading to the suspension of aerial glyphosate spraying the same year in countries like Colombia, where glyphosate has been extensively used in illicit crop eradication. Notwithstanding, according to a study of the U.S. Geological Survey, traces of glyphosate and its main degradation product, AMPA, remain in soil year after year. This underscores the urgency and importance of assessing new technologies to degrade glyphosate present in soils and waterbodies without leaving persistent byproducts. The aim of this study was to evaluate Lysinibacillus sphaericus' glyphosate uptake as a carbon and phosphorous source by a sarcosine-mediated metabolic pathway that releases glycine as final degradation product. To accomplish this, molecular and analytic evidence were collected in vitro from sarcosine oxidase activity, a key enzyme of a degradation pathway which releases byproducts that are easy to incorporate into natural biosynthesis routes.

PML-RARα stabilized by zinc in human acute promyelocytic leukemia NB4 cells.

PubMed

Zhu, Bo; Wang, Jia-Yu; Zhou, Jun-Jie; Zhou, Feng; Cheng, Wei; Liu, Ying-Ting; Wang, Jie; Chen, Xiao; Chen, Dian-Hua; Luo, Lan; Hua, Zi-Chun

2017-10-01

Acute promyelocytic leukemia (APL) is characterized and driven by the promyelocytic leukemia protein-retinoic acid receptor alpha (PML-RARα) fusion gene. Previous studies have highlighted the importance of PML-RARα degradation in the treatment against APL. Considering the presence of two zinc fingers in the PML-RARα fusion protein, we explored the function of zinc homeostasis in maintaining PML-RARα stability. We demonstrated for the first time that zinc depletion by its chelator N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN) triggered PML-RARα degradation in NB4 APL cells via the proteasome pathway rather than the autophagy-lysosomal pathway. In contrast, autophagy protected TPEN-mediated PML-RARα degradation in NB4 APL cells. We further demonstrated that crosstalk between zinc homeostasis and nitric oxide pathway played a key role in maintaining PML-RARα stability in NB4 APL cells. These results demonstrate that zinc homeostasis is vital for maintaining PML-RARα stability, and zinc depletion by TPEN may be useful as a potential strategy to trigger PML-RARα degradation in APL cells. We also found that TPEN triggered apoptosis of NB4 APL cells in a time-dependent manner. The relationship between PML-RARα degradation and apoptosis triggered by TPEN deserves further study. Copyright © 2017 Elsevier Inc. All rights reserved.

Unraveling Alzheimer's: Making Sense of the Relationship between Diabetes and Alzheimer's Disease1.

PubMed

Schilling, Melissa A

2016-01-01

Numerous studies have documented a strong association between diabetes and Alzheimer's disease (AD). The nature of the relationship, however, has remained a puzzle, in part because of seemingly incongruent findings. For example, some studies have concluded that insulin deficiency is primarily at fault, suggesting that intranasal insulin or inhibiting the insulin-degrading enzyme (IDE) could be beneficial. Other research has concluded that hyperinsulinemia is to blame, which implies that intranasal insulin or the inhibition of IDE would exacerbate the disease. Such antithetical conclusions pose a serious obstacle to making progress on treatments. However, careful integration of multiple strands of research, with attention to the methods used in different studies, makes it possible to disentangle the research on AD. This integration suggests that there is an important relationship between insulin, IDE, and AD that yields multiple pathways to AD depending on the where deficiency or excess in the cycle occurs. I review evidence for each of these pathways here. The results suggest that avoiding excess insulin, and supporting robust IDE levels, could be important ways of preventing and lessening the impact of AD. I also describe what further tests need to be conducted to verify the arguments made in the paper, and their implications for treating AD.

Abeta-degrading enzymes in Alzheimer's disease.

PubMed

Miners, James Scott; Baig, Shabnam; Palmer, Jennifer; Palmer, Laura E; Kehoe, Patrick G; Love, Seth

2008-04-01

In Alzheimer's disease (AD) Abeta accumulates because of imbalance between the production of Abeta and its removal from the brain. There is increasing evidence that in most sporadic forms of AD, the accumulation of Abeta is partly, if not in some cases solely, because of defects in its removal--mediated through a combination of diffusion along perivascular extracellular matrix, transport across vessel walls into the blood stream and enzymatic degradation. Multiple enzymes within the central nervous system (CNS) are capable of degrading Abeta. Most are produced by neurons or glia, but some are expressed in the cerebral vasculature, where reduced Abeta-degrading activity may contribute to the development of cerebral amyloid angiopathy (CAA). Neprilysin and insulin-degrading enzyme (IDE), which have been most extensively studied, are expressed both neuronally and within the vasculature. The levels of both of these enzymes are reduced in AD although the correlation with enzyme activity is still not entirely clear. Other enzymes shown capable of degrading Abetain vitro or in animal studies include plasmin; endothelin-converting enzymes ECE-1 and -2; matrix metalloproteinases MMP-2, -3 and -9; and angiotensin-converting enzyme (ACE). The levels of plasmin and plasminogen activators (uPA and tPA) and ECE-2 are reported to be reduced in AD. Reductions in neprilysin, IDE and plasmin in AD have been associated with possession of APOEepsilon4. We found no change in the level or activity of MMP-2, -3 or -9 in AD. The level and activity of ACE are increased, the level being directly related to Abeta plaque load. Up-regulation of some Abeta-degrading enzymes may initially compensate for declining activity of others, but as age, genetic factors and diseases such as hypertension and diabetes diminish the effectiveness of other Abeta-clearance pathways, reductions in the activity of particular Abeta-degrading enzymes may become critical, leading to the development of AD and CAA.

Autophagy-deficient mice develop multiple liver tumors

PubMed Central

Takamura, Akito; Komatsu, Masaaki; Hara, Taichi; Sakamoto, Ayako; Kishi, Chieko; Waguri, Satoshi; Eishi, Yoshinobu; Hino, Okio; Tanaka, Keiji; Mizushima, Noboru

2011-01-01

Autophagy is a major pathway for degradation of cytoplasmic proteins and organelles, and has been implicated in tumor suppression. Here, we report that mice with systemic mosaic deletion of Atg5 and liver-specific Atg7−/− mice develop benign liver adenomas. These tumor cells originate autophagy-deficient hepatocytes and show mitochondrial swelling, p62 accumulation, and oxidative stress and genomic damage responses. The size of the Atg7−/− liver tumors is reduced by simultaneous deletion of p62. These results suggest that autophagy is important for the suppression of spontaneous tumorigenesis through a cell-intrinsic mechanism, particularly in the liver, and that p62 accumulation contributes to tumor progression. PMID:21498569

Metabolism of 2-Chloro-4-Nitroaniline via Novel Aerobic Degradation Pathway by Rhodococcus sp. Strain MB-P1

PubMed Central

Khan, Fazlurrahman; Pal, Deepika; Vikram, Surendra; Cameotra, Swaranjit Singh

2013-01-01

2-chloro-4-nitroaniline (2-C-4-NA) is used as an intermediate in the manufacture of dyes, pharmaceuticals, corrosion inhibitor and also used in the synthesis of niclosamide, a molluscicide. It is marked as a black-listed substance due to its poor biodegradability. We report biodegradation of 2-C-4-NA and its pathway characterization by Rhodococcus sp. strain MB-P1 under aerobic conditions. The strain MB-P1 utilizes 2-C-4-NA as the sole carbon, nitrogen, and energy source. In the growth medium, the degradation of 2-C-4-NA occurs with the release of nitrite ions, chloride ions, and ammonia. During the resting cell studies, the 2-C-4-NA-induced cells of strain MB-P1 transformed 2-C-4-NA stoichiometrically to 4-amino-3-chlorophenol (4-A-3-CP), which subsequently gets transformed to 6-chlorohydroxyquinol (6-CHQ) metabolite. Enzyme assays by cell-free lysates prepared from 2-C-4-NA-induced MB-P1 cells, demonstrated that the first enzyme in the 2-C-4-NA degradation pathway is a flavin-dependent monooxygenase that catalyzes the stoichiometric removal of nitro group and production of 4-A-3-CP. Oxygen uptake studies on 4-A-3-CP and related anilines by 2-C-4-NA-induced MB-P1 cells demonstrated the involvement of aniline dioxygenase in the second step of 2-C-4-NA degradation. This is the first report showing 2-C-4-NA degradation and elucidation of corresponding metabolic pathway by an aerobic bacterium. PMID:23614030

The Application of the Weighted k-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways.

PubMed

Chen, Wenbin; Hendrix, William; Samatova, Nagiza F

2017-12-01

The problem of aligning multiple metabolic pathways is one of very challenging problems in computational biology. A metabolic pathway consists of three types of entities: reactions, compounds, and enzymes. Based on similarities between enzymes, Tohsato et al. gave an algorithm for aligning multiple metabolic pathways. However, the algorithm given by Tohsato et al. neglects the similarities among reactions, compounds, enzymes, and pathway topology. How to design algorithms for the alignment problem of multiple metabolic pathways based on the similarity of reactions, compounds, and enzymes? It is a difficult computational problem. In this article, we propose an algorithm for the problem of aligning multiple metabolic pathways based on the similarities among reactions, compounds, enzymes, and pathway topology. First, we compute a weight between each pair of like entities in different input pathways based on the entities' similarity score and topological structure using Ay et al.'s methods. We then construct a weighted k-partite graph for the reactions, compounds, and enzymes. We extract a mapping between these entities by solving the maximum-weighted k-partite matching problem by applying a novel heuristic algorithm. By analyzing the alignment results of multiple pathways in different organisms, we show that the alignments found by our algorithm correctly identify common subnetworks among multiple pathways.

Degradation of polyvinyl alcohol (PVA) by UV/chlorine oxidation: Radical roles, influencing factors, and degradation pathway.

PubMed

Ye, Bei; Li, Yue; Chen, Zhuo; Wu, Qian-Yuan; Wang, Wen-Long; Wang, Ting; Hu, Hong-Ying

2017-11-01

Polyvinyl alcohol (PVA) is widely used in industry but is difficult to degrade. In this study, the synergistic effect of UV irradiation and chlorination on degradation of PVA was investigated. UV irradiation or chlorination alone did not degrade PVA. By contrast, UV/chlorine oxidation showed good efficiency for PVA degradation via generation of active free radicals, such as OH and Cl. The relative importance of these two free radicals in the oxidation process was evaluated, and it was shown that OH contributed more to PVA degradation than Cl did. The degradation of PVA followed pseudo first order kinetics. The rate constant k increased linearly from 0 min -1 to 0.3 min -1 with increasing chlorine dosage in range of 0 mg/L to 20 mg/L. However, when the chlorine dosage was increased above 20 mg/L, scavenging effect of free radicals occurred, and the degradation efficiency of PVA did not increase much more. Acidic media increased the degradation efficiency of PVA by UV/chlorine oxidation more than basic or neutral media because of the higher ratio of [HOCl]/[OCl - ], higher free radical quantum yields, and the lower free radical quenching effect under acidic conditions. Results of Fourier Transform Infrared Spectroscopy showed that carbonyl groups in degradation products were formed during UV/chlorine oxidation, and a possible degradation pathway via alcohol to carbonyl was proposed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Estimating pathway-specific contributions to biodegradation in aquifers based on dual isotope analysis: theoretical analysis and reactive transport simulations.

PubMed

Centler, Florian; Heße, Falk; Thullner, Martin

2013-09-01

At field sites with varying redox conditions, different redox-specific microbial degradation pathways contribute to total contaminant degradation. The identification of pathway-specific contributions to total contaminant removal is of high practical relevance, yet difficult to achieve with current methods. Current stable-isotope-fractionation-based techniques focus on the identification of dominant biodegradation pathways under constant environmental conditions. We present an approach based on dual stable isotope data to estimate the individual contributions of two redox-specific pathways. We apply this approach to carbon and hydrogen isotope data obtained from reactive transport simulations of an organic contaminant plume in a two-dimensional aquifer cross section to test the applicability of the method. To take aspects typically encountered at field sites into account, additional simulations addressed the effects of transverse mixing, diffusion-induced stable-isotope fractionation, heterogeneities in the flow field, and mixing in sampling wells on isotope-based estimates for aerobic and anaerobic pathway contributions to total contaminant biodegradation. Results confirm the general applicability of the presented estimation method which is most accurate along the plume core and less accurate towards the fringe where flow paths receive contaminant mass and associated isotope signatures from the core by transverse dispersion. The presented method complements the stable-isotope-fractionation-based analysis toolbox. At field sites with varying redox conditions, it provides a means to identify the relative importance of individual, redox-specific degradation pathways. © 2013.

A novel method to identify hub pathways of rheumatoid arthritis based on differential pathway networks.

PubMed

Wei, Shi-Tong; Sun, Yong-Hua; Zong, Shi-Hua

2017-09-01

The aim of the current study was to identify hub pathways of rheumatoid arthritis (RA) using a novel method based on differential pathway network (DPN) analysis. The present study proposed a DPN where protein‑protein interaction (PPI) network was integrated with pathway‑pathway interactions. Pathway data was obtained from background PPI network and the Reactome pathway database. Subsequently, pathway interactions were extracted from the pathway data by building randomized gene‑gene interactions and a weight value was assigned to each pathway interaction using Spearman correlation coefficient (SCC) to identify differential pathway interactions. Differential pathway interactions were visualized using Cytoscape to construct a DPN. Topological analysis was conducted to identify hub pathways that possessed the top 5% degree distribution of DPN. Modules of DPN were mined according to ClusterONE. A total of 855 pathways were selected to build pathway interactions. By filtrating pathway interactions of weight values >0.7, a DPN with 312 nodes and 791 edges was obtained. Topological degree analysis revealed 15 hub pathways, such as heparan sulfate/heparin‑glycosaminoglycan (HS‑GAG) degradation, HS‑GAG metabolism and keratan sulfate degradation for RA based on DPN. Furthermore, hub pathways were also important in modules, which validated the significance of hub pathways. In conclusion, the proposed method is a computationally efficient way to identify hub pathways of RA, which identified 15 hub pathways that may be potential biomarkers and provide insight to future investigation and treatment of RA.

Novel Aspects of Degradation of T Cell Receptor Subunits from the Endoplasmic Reticulum (ER) in T Cells: Importance of Oligosaccharide Processing, Ubiquitination, and Proteasome-dependent Removal from ER Membranes

PubMed Central

Yang, Mei; Omura, Satoshi; Bonifacino, Juan S.; Weissman, Allan M.

1998-01-01

Expression of the T cell antigen receptor (TCR) on the surface of thymocytes and mature T cells is dependent on the assembly of receptor subunits into TCRs in the endoplasmic reticulum (ER) and their successful traversal of the secretory pathway to the plasma membrane. TCR subunits that fail to exit the ER for the Golgi complex are degraded by nonlysosomal processes that have been referred to as “ER degradation”. The molecular basis for the loss of the TCR CD3-δ and TCR-α subunits from the ER was investigated in lymphocytes. For CD3-δ, we describe a process leading to its degradation that includes trimming of mannose residues from asparagine-linked (N-linked) oligosaccharides, generation of ubiquitinated membrane-bound intermediates, and proteasome-dependent removal from the ER membrane. When either mannosidase activity or the catalytic activity of proteasomes was inhibited, loss of CD3-δ was markedly curtailed and CD3-δ remained membrane bound in a complex with CD3-ε. TCR-α was also found to be degraded in a proteasome-dependent manner with ubiquitinated intermediates. However, no evidence of a role for mannosidases was found for TCR-α, and significant retrograde movement through the ER membrane took place even when proteasome function was inhibited. These findings provide new insights into mechanisms employed to regulate levels of TCRs, and underscore that cells use multiple mechanisms to target proteins from the ER to the cytosol for degradation. PMID:9500786

Quantum chemical investigation on photodegradation mechanisms of sulfamethoxypyridazine with dissolved inorganic matter and hydroxyl radical.

PubMed

Shah, Shaheen; Hao, Ce

2017-07-01

Sulfamethoxypyridazine (SMP) is one of the commonly used sulfonamide antibiotics (SAs). SAs are mainly studied to undergo triplet-sensitized photodegradation in water under natural sunlight with other coexisting aquatic environmental organic pollutants. In this work, SMP was selected as a representative of SAs. We studied the mechanisms of triplet-sensitized photodegradation of SMP and the influence of selected dissolved inorganic matter, i.e., anions (Br - , Cl - , and NO 3 - ) and cations ions (Ca 2+ , Mg 2+ , and Zn 2+ ) on SMP photodegradation mechanism by quantum chemical methods. In addition, the degradation mechanisms of SMP by hydroxyl radical (OH) were also investigated. The creation of SO 2 extrusion product was accessed with two different energy pathways (pathway-1 and pathway-2) by following two steps (step-I and step-II) in the triplet-sensitized photodegradation of SMP. Due to low activation energy, the pathway-1 was considered as the main pathway to obtain SO 2 extrusion product. Step-II of pathway-1 was measured to be the rate-limiting step (RLS) of SMP photodegradation mechanism and the effect of the selected anions and cations was estimated for this step. All selected anions and cations promoted photodegradation of SMP by dropping the activation energy of pathway-1. The estimated low activation energies of different degradation pathways of SMP with OH radical indicate that OH radical is a very powerful oxidizing agent for SMP degradation via attack through benzene derivative and pyridazine derivative ring. Copyright © 2016. Published by Elsevier B.V.

Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway.

PubMed Central

Abril, M A; Michan, C; Timmis, K N; Ramos, J L

1989-01-01

The TOL plasmid upper pathway operon encodes enzymes involved in the catabolism of aromatic hydrocarbons such as toluene and xylenes. The regulator of the gene pathway, the XylR protein, exhibits a very broad effector specificity, being able to recognize as effectors not only pathway substrates but also a wide variety of mono- and disubstituted methyl-, ethyl-, and chlorotoluenes, benzyl alcohols, and p-chlorobenzaldehyde. Benzyl alcohol dehydrogenase and benzaldehyde dehydrogenase, two upper pathway enzymes, exhibit very broad substrate specificities and transform unsubstituted substrates and m- and p-methyl-, m- and p-ethyl-, and m- and p-chloro-substituted benzyl alcohols and benzaldehydes, respectively, at a high rate. In contrast, toluene oxidase only oxidizes toluene, m- and p-xylene, m-ethyltoluene, and 1,2,4-trimethylbenzene [corrected], also at a high rate. A biological test showed that toluene oxidase attacks m- and p-chlorotoluene, albeit at a low rate. No evidence for the transformation of p-ethyltoluene by toluene oxidase has been found. Hence, toluene oxidase acts as the bottleneck step for the catabolism of p-ethyl- and m- and p-chlorotoluene through the TOL upper pathway. A mutant toluene oxidase able to transform p-ethyltoluene was isolated, and a mutant strain capable of fully degrading p-ethyltoluene was constructed with a modified TOL plasmid meta-cleavage pathway able to mineralize p-ethylbenzoate. By transfer of a TOL plasmid into Pseudomonas sp. strain B13, a clone able to slowly degrade m-chlorotoluene was also obtained. PMID:2687253

Rhodococcus erythropolis DCL14 Contains a Novel Degradation Pathway for Limonene

PubMed Central

van der Werf, Mariët J.; Swarts, Henk J.; de Bont, Jan A. M.

1999-01-01

Strain DCL14, which is able to grow on limonene as a sole source of carbon and energy, was isolated from a freshwater sediment sample. This organism was identified as a strain of Rhodococcus erythropolis by chemotaxonomic and genetic studies. R. erythropolis DCL14 also assimilated the terpenes limonene-1,2-epoxide, limonene-1,2-diol, carveol, carvone, and (−)-menthol, while perillyl alcohol was not utilized as a carbon and energy source. Induction tests with cells grown on limonene revealed that the oxygen consumption rates with limonene-1,2-epoxide, limonene-1,2-diol, 1-hydroxy-2-oxolimonene, and carveol were high. Limonene-induced cells of R. erythropolis DCL14 contained the following four novel enzymatic activities involved in the limonene degradation pathway of this microorganism: a flavin adenine dinucleotide- and NADH-dependent limonene 1,2-monooxygenase activity, a cofactor-independent limonene-1,2-epoxide hydrolase activity, a dichlorophenolindophenol-dependent limonene-1,2-diol dehydrogenase activity, and an NADPH-dependent 1-hydroxy-2-oxolimonene 1,2-monooxygenase activity. Product accumulation studies showed that (1S,2S,4R)-limonene-1,2-diol, (1S,4R)-1-hydroxy-2-oxolimonene, and (3R)-3-isopropenyl-6-oxoheptanoate were intermediates in the (4R)-limonene degradation pathway. The opposite enantiomers [(1R,2R,4S)-limonene-1,2-diol, (1R,4S)-1-hydroxy-2-oxolimonene, and (3S)-3-isopropenyl-6-oxoheptanoate] were found in the (4S)-limonene degradation pathway, while accumulation of (1R,2S,4S)-limonene-1,2-diol from (4S)-limonene was also observed. These results show that R. erythropolis DCL14 metabolizes both enantiomers of limonene via a novel degradation pathway that starts with epoxidation at the 1,2 double bond forming limonene-1,2-epoxide. This epoxide is subsequently converted to limonene-1,2-diol, 1-hydroxy-2-oxolimonene, and 7-hydroxy-4-isopropenyl-7-methyl-2-oxo-oxepanone. This lactone spontaneously rearranges to form 3-isopropenyl-6-oxoheptanoate. In the presence of coenzyme A and ATP this acid is converted further, and this finding, together with the high levels of isocitrate lyase activity in extracts of limonene-grown cells, suggests that further degradation takes place via the β-oxidation pathway. PMID:10224006

Investigating microbial cycling of recalcitrant organic matter in marine sediments using natural isotope respirometry in a novel, carbon-free bioreactor

NASA Astrophysics Data System (ADS)

Mahmoudi, N.; Beaupre, S. R.; Pearson, A.

2016-02-01

Marine sediments harbor complex microbial communities that play a key role in the cycling of carbon and nutrients. Reactions initiated by microbial enzymes at the molecular scale drive the rate and extent of organic matter degradation to CO2 and CH4. Organic matter is comprised of multiple carbon pools with different intrinsic turnover times. It is hypothesized that microbes will degrade younger pools with more labile compounds, while older pools with refractory compounds will remain unutilized. However, many studies have shown that microbes are capable of respiring older, refractory pools of organic matter in a number of environments. In order to better understand microbial carbon cycling and the fate of recalcitrant organic matter, we constructed a novel bioreactor system to measure carbon isotopes during microbial degradation of complex organic matter. This system enables us to measure the natural isotopic signature (δ13C and Δ14C ) of microbially-respired CO2, thereby allowing us to determine the age of the organic matter that is being respired. We investigated microbial carbon utilization in sediments from Falmouth, MA and observed a pattern of successive microbial respiration such that several peaks appear over the course of a 7-day incubation. Δ14C signatures of CO2 fractions collected during incubation ranged from -185 to +70‰ with the majority of CO2 appearing to be modern. This indicates that the microbial community is primarily are respiring labile organic matter from fast cycling pools. Interestingly, the observation of multiple peaks with similar Δ14C signatures suggests that organic matter is degraded in a step-wise manner by a succession of microbial taxa. Illumina sequencing of 16S rRNA genes will identify these successions of bacteria (and archaea), while enzymatic analyses may help determine the metabolic pathways that correspond to each peak. Our study will provide a molecular-level framework for organic matter degradation and provide insight into patterns of microbial carbon utilization, linking these observations to genomic and metabolomics information.

The potential role of bortezomib in combination with chemotherapy and radiation in non-small-cell lung cancer.

PubMed

Edelman, Martin J

2005-10-01

The combination of chemotherapy and radiation has been validated for the treatment of locally advanced non-small-cell lung cancer (NSCLC). However, the results are still unsatisfactory, and there is a need to improve current treatment. One approach is to use new agents that have the potential to enhance the efficacy of chemotherapy, radiation therapy (RT), or both. One potential target is the ubiquitin-proteasome pathway. This pathway plays an essential role in the degradation of most short- and long-lived intracellular proteins in eukaryotic cells and therefore regulating the cell cycle, neoplastic growth, and metastasis. Bortezomib is a selective 26S proteasome inhibitor that has been approved for the treatment of multiple myeloma. Bortezomib has demonstrated in vitro chemotherapy- and RT-sensitizing properties as well as single-agent activity in lung cancer. This article will review the rationale for the use of bortezomib as part of the chemotherapy/RT strategy for the treatment of NSCLC.

Granzyme B Disrupts Central Metabolism and Protein Synthesis in Bacteria to Promote an Immune Cell Death Program.

PubMed

Dotiwala, Farokh; Sen Santara, Sumit; Binker-Cosen, Andres Ariel; Li, Bo; Chandrasekaran, Sriram; Lieberman, Judy

2017-11-16

Human cytotoxic lymphocytes kill intracellular microbes. The cytotoxic granule granzyme proteases released by cytotoxic lymphocytes trigger oxidative bacterial death by disrupting electron transport, generating superoxide anion and inactivating bacterial oxidative defenses. However, they also cause non-oxidative cell death because anaerobic bacteria are also killed. Here, we use differential proteomics to identify granzyme B substrates in three unrelated bacteria: Escherichia coli, Listeria monocytogenes, and Mycobacteria tuberculosis. Granzyme B cleaves a highly conserved set of proteins in all three bacteria, which function in vital biosynthetic and metabolic pathways that are critical for bacterial survival under diverse environmental conditions. Key proteins required for protein synthesis, folding, and degradation are also substrates, including multiple aminoacyl tRNA synthetases, ribosomal proteins, protein chaperones, and the Clp system. Because killer cells use a multipronged strategy to target vital pathways, bacteria may not easily become resistant to killer cell attack. Copyright © 2017 Elsevier Inc. All rights reserved.

Ultralow-power switching via defect engineering in germanium telluride phase-change memory devices.

PubMed

Nukala, Pavan; Lin, Chia-Chun; Composto, Russell; Agarwal, Ritesh

2016-01-25

Crystal-amorphous transformation achieved via the melt-quench pathway in phase-change memory involves fundamentally inefficient energy conversion events; and this translates to large switching current densities, responsible for chemical segregation and device degradation. Alternatively, introducing defects in the crystalline phase can engineer carrier localization effects enhancing carrier-lattice coupling; and this can efficiently extract work required to introduce bond distortions necessary for amorphization from input electrical energy. Here, by pre-inducing extended defects and thus carrier localization effects in crystalline GeTe via high-energy ion irradiation, we show tremendous improvement in amorphization current densities (0.13-0.6 MA cm(-2)) compared with the melt-quench strategy (∼50 MA cm(-2)). We show scaling behaviour and good reversibility on these devices, and explore several intermediate resistance states that are accessible during both amorphization and recrystallization pathways. Existence of multiple resistance states, along with ultralow-power switching and scaling capabilities, makes this approach promising in context of low-power memory and neuromorphic computation.

Ultralow-power switching via defect engineering in germanium telluride phase-change memory devices

PubMed Central

Nukala, Pavan; Lin, Chia-Chun; Composto, Russell; Agarwal, Ritesh

2016-01-01

Crystal–amorphous transformation achieved via the melt-quench pathway in phase-change memory involves fundamentally inefficient energy conversion events; and this translates to large switching current densities, responsible for chemical segregation and device degradation. Alternatively, introducing defects in the crystalline phase can engineer carrier localization effects enhancing carrier–lattice coupling; and this can efficiently extract work required to introduce bond distortions necessary for amorphization from input electrical energy. Here, by pre-inducing extended defects and thus carrier localization effects in crystalline GeTe via high-energy ion irradiation, we show tremendous improvement in amorphization current densities (0.13–0.6 MA cm−2) compared with the melt-quench strategy (∼50 MA cm−2). We show scaling behaviour and good reversibility on these devices, and explore several intermediate resistance states that are accessible during both amorphization and recrystallization pathways. Existence of multiple resistance states, along with ultralow-power switching and scaling capabilities, makes this approach promising in context of low-power memory and neuromorphic computation. PMID:26805748

Assessment of groundwater pathways and contaminant transport in Florida and Georgia using multiple chemical and microbiological indicators

USGS Publications Warehouse

Mahon, Gary L.

2011-01-01

The hydrogeology of Florida, especially in the northern part of the state, and southwestern Georgia is characterized by a predominance of limestone aquifers overlain by varying amounts of sands, silts, and clays. This karstic system of aquifers and their associated springs is particularly vulnerable to contamination from various anthropogenic activities at the land surface. Numerous sinkholes, disappearing streams, and conduit systems or dissolution pathways, often associated with large spring systems, allow rapid movement of contaminants from the land surface to the groundwater system with little or no attenuation or degradation. The fate of contaminants in the groundwater system is not fully understood, but traveltimes from sources are greatly reduced when conduits are intercepted by pumping wells and springs. Contaminant introduction to groundwater systems in Florida and Georgia is not limited to seepage from land surface, but can be associated with passive (drainage wells) and forced subsurface injection (aquifer storage and recovery, waste-water disposal).

Pathway and Molecular Mechanisms for Malachite Green Biodegradation in Exiguobacterium sp. MG2

PubMed Central

Wang, Ji’ai; Gao, Feng; Liu, Zhongzhong; Qiao, Min; Niu, Xuemei; Zhang, Ke-Qin; Huang, Xiaowei

2012-01-01

Malachite green (MG), N-methylated diaminotriphenylmethane, is one of the most common dyes in textile industry and has also been used as an effective antifungal agent. However, due to its negative impact on the environment and carcinogenic effects to mammalian cells, there is a significant interest in developing microbial agents to degrade this type of recalcitrant molecules. Here, an Exiguobacterium sp. MG2 was isolated from a river in Yunnan Province of China as one of the best malachite green degraders. This strain had a high decolorization capability even at the concentration of 2500 mg/l and maintained its stable activity within the pH range from 5.0 to 9.0. High-pressure liquid chromatography, liquid chromatography-mass spectrometry and gas chromatography–mass spectrometry were employed to detect the catabolic pathway of MG. Six intermediate products were identified and a potential biodegradation pathway was proposed. This pathway involves a series of reactions of N-demethylation, reduction, benzene ring-removal, and oxidation, which eventually converted N-methylated diaminotriphenylmethane into N, N-dimethylaniline that is the key precursor to MG. Furthermore, our molecular biology experiments suggested that both triphenylmethane reductase gene tmr and cytochrome P450 participated in MG degradation, consistent with their roles in the proposed pathway. Collectively, our investigation is the first report on a biodegradation pathway of triphenylmethane dye MG in bacteria. PMID:23251629

Evidence for the Existence in Arabidopsis thaliana of the Proteasome Proteolytic Pathway

PubMed Central

Polge, Cécile; Jaquinod, Michel; Holzer, Frances; Bourguignon, Jacques; Walling, Linda; Brouquisse, Renaud

2009-01-01

Heavy metals are known to generate reactive oxygen species that lead to the oxidation and fragmentation of proteins, which become toxic when accumulated in the cell. In this study, we investigated the role of the proteasome during cadmium stress in the leaves of Arabidopsis thaliana plants. Using biochemical and proteomics approaches, we present the first evidence of an active proteasome pathway in plants. We identified and characterized the peptidases acting sequentially downstream from the proteasome in animal cells as follows: tripeptidyl-peptidase II, thimet oligopeptidase, and leucine aminopeptidase. We investigated the proteasome proteolytic pathway response in the leaves of 6-week-old A. thaliana plants grown hydroponically for 24, 48, and 144 h in the presence or absence of 50 μm cadmium. The gene expression and proteolytic activity of the proteasome and the different proteases of the pathway were found to be up-regulated in response to cadmium. In an in vitro assay, oxidized bovine serum albumin and lysozyme were more readily degraded in the presence of 20 S proteasome and tripeptidyl-peptidase II than their nonoxidized form, suggesting that oxidized proteins are preferentially degraded by the Arabidopsis 20 S proteasome pathway. These results show that, in response to cadmium, the 20 S proteasome proteolytic pathway is up-regulated at both RNA and activity levels in Arabidopsis leaves and may play a role in degrading oxidized proteins generated by the stress. PMID:19822524

Correlated noise-based switches and stochastic resonance in a bistable genetic regulation system

NASA Astrophysics Data System (ADS)

Wang, Can-Jun; Yang, Ke-Li

2016-07-01

The correlated noise-based switches and stochastic resonance are investigated in a bistable single gene switching system driven by an additive noise (environmental fluctuations), a multiplicative noise (fluctuations of the degradation rate). The correlation between the two noise sources originates from on the lysis-lysogeny pathway system of the λ phage. The steady state probability distribution is obtained by solving the time-independent Fokker-Planck equation, and the effects of noises are analyzed. The effects of noises on the switching time between the two stable states (mean first passage time) is investigated by the numerical simulation. The stochastic resonance phenomenon is analyzed by the power amplification factor. The results show that the multiplicative noise can induce the switching from "on" → "off" of the protein production, while the additive noise and the correlation between the noise sources can induce the inverse switching "off" → "on". A nonmonotonic behaviour of the average switching time versus the multiplicative noise intensity, for different cross-correlation and additive noise intensities, is observed in the genetic system. There exist optimal values of the additive noise, multiplicative noise and cross-correlation intensities for which the weak signal can be optimal amplified.

Anaerobic Degradation Pathway of the Novel Chiral Insecticide Paichongding and Its Impact on Bacterial Communities in Soils.

PubMed

Cai, Zhiqiang; Wang, Jing; Ma, Jiangtao; Zhu, Xiaolin; Cai, Jinyan; Yang, Guanghua

2015-08-19

To comprehensively understand anaerobic degradation of the novel cis-nitromethylene neonicotinoid insecticide Paichongding (IPP) and its impacts on microbial communities in anaerobic soils, we investigated IPP degradation characteristics, kinetics, and pathway in four different soils. The bacterial community in response to the application of IPP using pyrosequencing of 16S rRNA gene amplicons was also studied. The removal ratio of IPP stereoisomers (RR-IPP, SS-IPP, RS-IPP, and SR-IPP) reached >90% at 60 days after IPP treatment (DAT) in yellow loam soil (F) and paddy field on desalting muddy polder (C), whereas the degradation ratios of RR-IPP and SS-IPP were <30% at 60 DAT in Huangshi soil (J) and yellow paddy soil (H). The results showed that the anaerobic degradation rate of IPP and its stereoisomers was strongly affected by soil physical-chemical characteristics. Furthermore, on the basis of the six metabolites (M1-M6) identified by LC-MS/MS and their behavior, the anaerobic degradation pathway of IPP in soils was proposed. Biodegradation of IPP involved continuous biocatalytic reactions such as nitro reduction and elimination, hydrolysis, demethyl, and ether cleavage reactions. A higher richness of operational taxonomic units (OTUs) was found in soils without IPP application than in soils with IPP application. Both the rarefaction curves and Shannon-Wiener diversity index in anaerobic soils had significant difference after IPP application, and the community composition also differed at both the phyla and genus levels.

Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oosterkamp, Margreet J.; Veuskens, Teun; Saia, Flavia Talarico

2013-01-01

The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacteriummore » that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.« less

Genome Analysis and Physiological Comparison of Alicycliphilus denitrificans Strains BC and K601T

PubMed Central

Talarico Saia, Flávia; Weelink, Sander A. B.; Goodwin, Lynne A.; Daligault, Hajnalka E.; Bruce, David C.; Detter, John C.; Tapia, Roxanne; Han, Cliff S.; Land, Miriam L.; Hauser, Loren J.; Langenhoff, Alette A. M.; Gerritse, Jan; van Berkel, Willem J. H.; Pieper, Dietmar H.; Junca, Howard; Smidt, Hauke; Schraa, Gosse; Davids, Mark; Schaap, Peter J.; Plugge, Caroline M.; Stams, Alfons J. M.

2013-01-01

The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far. PMID:23825601

KCTD1 Suppresses Canonical Wnt Signaling Pathway by Enhancing β-catenin Degradation

PubMed Central

Wang, Fangmei; Huang, Wenhuan; Liang, Zhongheng; Xiao, Yuzhong; Wei, Ke; Wan, Zhenxing; Hu, Xiang; Xiang, Shuanglin; Ding, Xiaofeng; Zhang, Jian

2014-01-01

The canonical Wnt signaling pathway controls normal embryonic development, cellular proliferation and growth, and its aberrant activity results in human carcinogenesis. The core component in regulation of this pathway is β-catenin, but molecular regulation mechanisms of β-catenin stability are not completely known. Here, our recent studies have shown that KCTD1 strongly inhibits TCF/LEF reporter activity. Moreover, KCTD1 interacted with β-catenin both in vivo by co-immunoprecipitation as well as in vitro through GST pull-down assays. We further mapped the interaction regions to the 1-9 armadillo repeats of β-catenin and the BTB domain of KCTD1, especially Position Ala-30 and His-33. Immunofluorescence analysis indicated that KCTD1 promotes the cytoplasmic accumulation of β-catenin. Furthermore, protein stability assays revealed that KCTD1 enhances the ubiquitination/degradation of β-catenin in a concentration-dependent manner in HeLa cells. And the degradation of β-catenin mediated by KCTD1 was alleviated by the proteasome inhibitor, MG132. In addition, KCTD1-mediated β-catenin degradation was dependent on casein kinase 1 (CK1)- and glycogen synthase kinase-3β (GSK-3β)-mediated phosphorylation and enhanced by the E3 ubiquitin ligase β-transducin repeat-containing protein (β-TrCP). Moreover, KCTD1 suppressed the expression of endogenous Wnt downstream genes and transcription factor AP-2α. Finally, we found that Wnt pathway member APC and tumor suppressor p53 influence KCTD1-mediated downregulation of β-catenin. These results suggest that KCTD1 functions as a novel inhibitor of Wnt signaling pathway. PMID:24736394

Lignolytic-consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization.

PubMed

Moraes, Eduardo C; Alvarez, Thabata M; Persinoti, Gabriela F; Tomazetto, Geizecler; Brenelli, Livia B; Paixão, Douglas A A; Ematsu, Gabriela C; Aricetti, Juliana A; Caldana, Camila; Dixon, Neil; Bugg, Timothy D H; Squina, Fabio M

2018-01-01

Lignin is a heterogeneous polymer representing a renewable source of aromatic and phenolic bio-derived products for the chemical industry. However, the inherent structural complexity and recalcitrance of lignin makes its conversion into valuable chemicals a challenge. Natural microbial communities produce biocatalysts derived from a large number of microorganisms, including those considered unculturable, which operate synergistically to perform a variety of bioconversion processes. Thus, metagenomic approaches are a powerful tool to reveal novel optimized metabolic pathways for lignin conversion and valorization. The lignin-degrading consortium (LigMet) was obtained from a sugarcane plantation soil sample. The LigMet taxonomical analyses (based on 16S rRNA) indicated prevalence of Proteobacteria , Actinobacteria and Firmicutes members, including the Alcaligenaceae and Micrococcaceae families, which were enriched in the LigMet compared to sugarcane soil. Analysis of global DNA sequencing revealed around 240,000 gene models, and 65 draft bacterial genomes were predicted. Along with depicting several peroxidases, dye-decolorizing peroxidases, laccases, carbohydrate esterases, and lignocellulosic auxiliary (redox) activities, the major pathways related to aromatic degradation were identified, including benzoate (or methylbenzoate) degradation to catechol (or methylcatechol), catechol ortho-cleavage, catechol meta-cleavage, and phthalate degradation. A novel Paenarthrobacter strain harboring eight gene clusters related to aromatic degradation was isolated from LigMet and was able to grow on lignin as major carbon source. Furthermore, a recombinant pathway for vanillin production was designed based on novel gene sequences coding for a feruloyl-CoA synthetase and an enoyl-CoA hydratase/aldolase retrieved from the metagenomic data set. The enrichment protocol described in the present study was successful for a microbial consortium establishment towards the lignin and aromatic metabolism, providing pathways and enzyme sets for synthetic biology engineering approaches. This work represents a pioneering study on lignin conversion and valorization strategies based on metagenomics, revealing several novel lignin conversion enzymes, aromatic-degrading bacterial genomes, and a novel bacterial strain of potential biotechnological interest. The validation of a biosynthetic route for vanillin synthesis confirmed the applicability of the targeted metagenome discovery approach for lignin valorization strategies.

Survival and Energy Producing Strategies of Alkane Degraders Under Extreme Conditions and Their Biotechnological Potential.

PubMed

Park, Chulwoo; Park, Woojun

2018-01-01

Many petroleum-polluted areas are considered as extreme environments because of co-occurrence of low and high temperatures, high salt, and acidic and anaerobic conditions. Alkanes, which are major constituents of crude oils, can be degraded under extreme conditions, both aerobically and anaerobically by bacteria and archaea of different phyla. Alkane degraders possess exclusive metabolic pathways and survival strategies, which involve the use of protein and RNA chaperones, compatible solutes, biosurfactants, and exopolysaccharide production for self-protection during harsh environmental conditions such as oxidative and osmotic stress, and ionic nutrient-shortage. Recent findings suggest that the thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus uses a novel alkylsuccinate synthase for long-chain alkane degradation, and the thermophilic Candidatus Syntrophoarchaeum butanivorans anaerobically oxidizes butane via alkyl-coenzyme M formation. In addition, gene expression data suggest that extremophiles produce energy via the glyoxylate shunt and the Pta-AckA pathway when grown on a diverse range of alkanes under stress conditions. Alkane degraders possess biotechnological potential for bioremediation because of their unusual characteristics. This review will provide genomic and molecular insights on alkane degraders under extreme conditions.

[Furfural degradation by filamentous fungus Amorphotheca resinae ZN1].

PubMed

Wang, Xiaofeng; Zhang, Jian; Xin, Xiujuan; Bao, Jie

2012-09-01

Some degradation products from lignocellulose pretreatment strongly inhibit the activities of cellulolytic enzymes and ethanol fermentation strains, thus the efficient removal of the inhibitor substances ("detoxification") is the inevitable step for the biotransformation processes. In this study, the biological detoxification of furfural by a newly isolated fungus, Amorphotheca resinae ZN1, was studied and the metabolic pathways of furfural degradation was analyzed. The metabolic pathway of furfural degradation in A. resinae ZN1 was described as follows: first, furfural was quickly converted into the low toxic furfuryl alcohol; then the furfuryl alcohol was gradually converted into furfural again but under the low concentration under aerobic condition, which was not lethal to the growth of the fungi; furfural continued to be oxidized to furoic acid by A. resinae ZN1. It is likely that furoic acid was further degraded in the TCA cycle to complete the biological degradation of furfural. The present study provided the important experimental basis for speeding up the biodetoxification of furfural by A. resinae ZN1 and the rate-limiting step in the lignocellulose biotransformation to ethanol.

Tau protein degradation is catalyzed by the ATP/ubiquitin-independent 20S proteasome under normal cell conditions

PubMed Central

Grune, Tilman; Botzen, Diana; Engels, Martina; Voss, Peter; Kaiser, Barbara; Jung, Tobias; Grimm, Stefanie; Ermak, Gennady; Davies, Kelvin J. A.

2010-01-01

Tau is the major protein exhibiting intracellular accumulation in Alzheimer disease. The mechanisms leading to its accumulation are not fully understood. It has been proposed that the proteasome is responsible for degrading tau but, since proteasomal inhibitors block both the ubiquitin-dependent 26S proteasome and the ubiqutin-independent 20S proteasome pathways, it is not clear which of these pathways is involved in tau degradation. Some involvement of the ubiquitin ligase, CHIP in tau degradation has also been postulated during stress. In the current studies, we utilized HT22 cells and tau-transfected E36 cells in order to test the relative importance or possible requirement of the ubiquitin-dependent 26S proteasomal system versus the ubiquitin-independent 20S proteasome, in tau degradation. By means of ATP-depletion, ubiquitinylation-deficient E36ts20 cells, a 19S proteasomal regulator subunit MSS1-siRNA approaches, and in vitro ubiquitinylation studies, we were able to demonstrate that ubiquitinylation is not required for normal tau degradation. PMID:20478262

New insights into the enhanced performance of high solid anaerobic digestion with dewatered sludge by thermal hydrolysis: Organic matter degradation and methanogenic pathways.

PubMed

Chen, Sisi; Li, Ning; Dong, Bin; Zhao, Wentao; Dai, Lingling; Dai, Xiaohu

2018-01-15

Two lab-scale high solid anaerobic digesters fed with untreated sludge (R1) and thermally hydrolyzed sludge (R2) were operated to investigate the influence of thermal hydrolysis pretreatment (THP) on the degradation of individual macromolecular organic components (MOCs), as well as the functional and metabolic responses of microbes during anaerobic digestion (AD). The degradation of MOCs was improved by THP at different rates, in which improved degradation of proteins (by 49.0%) and hemicelluloses (by 25.0%) were the main factors contributing to the increase in volatile solids (VS) reduction. However, no enhancement of final degradation extent of MOCs was observed. With a more densified microbial population, R2 was also enriched in genes involved in amino acid and carbohydrate metabolism, reflected in the enhanced degradation of proteins and carbohydrates. After THP, the methanogenic pathway shifted from strict acetoclastic methanogenesis to acetoclastic/hydrogenotrophic methanogenesis, consistent with the enhanced methane production and the increase of methane content. Copyright © 2017 Elsevier B.V. All rights reserved.

Cigarette smoke exposure reveals a novel role for the MEK/ERK1/2 MAPK pathway in regulation of CFTR

PubMed Central

Xu, Xiaohua; Balsiger, Robert; Tyrrell, Jean; Boyaka, Prosper N.; Tarran, Robert; Cormet-Boyaka, Estelle

2015-01-01

Background CFTR plays a key role in maintenance of lung fluid homeostasis. Cigarette smoke decreases CFTR expression in the lung but neither the mechanisms leading to CFTR loss, nor potential ways to prevent its loss have been identified to date. Methods The molecular mechanisms leading to down-regulation of CFTR by cigarette smoke were determined using pharmacologic inhibitors and silencing RNAs. Results Using human bronchial epithelial cells, here we show that cigarette smoke induces degradation of CFTR that is attenuated by the lysosomal inhibitors, but not proteasome inhibitors. Cigarette smoke can activate multiple signaling pathways in airway epithelial cells, including the MEK/Erk1/2 MAPK pathway regulating cell survival. Interestingly, pharmacological inhibition of the MEK/Erk1/2 MAPK pathway prevented the loss of plasma membrane CFTR upon cigarette smoke exposure. Similarly, decreased expression of Erk1/2 using silencing RNAs prevented the suppression of CFTR protein by cigarette smoke. Conversely, specific inhibitors of the JNK or p38 MAPK pathways had no effect on CFTR decrease after cigarette smoke exposure. In addition, inhibition of the MEK/Erk1/2 MAPK pathway prevented the reduction of the airway surface liquid observed upon cigarette smoke exposure of primary human airway epithelial cells. Finally, addition of the antioxidant NAC inhibited activation of Erk1/2 by cigarette smoke and precluded the cigarette smoke-induced decrease of CFTR. Conclusions These results show that the MEK/Erk1/2 MAPK pathway regulates plasma membrane CFTR in human airway cells. General Significance The MEK/Erk1/2 MAPK pathway should be considered as a target for strategies to maintain/restore CFTR expression in the lung of smokers. PMID:25697727

Characterization of naphthalene degradation by Streptomyces sp. QWE-5 isolated from active sludge.

PubMed

Xu, Peng; Ma, Wencheng; Han, Hongjun; Hou, Baolin; Jia, Shengyong

2014-01-01

A bacterial strain, QWE-5, which utilized naphthalene as its sole carbon and energy source, was isolated and identified as Streptomyces sp. It was a Gram-positive, spore-forming bacterium with a flagellum, with whole, smooth, convex and wet colonies. The optimal temperature and pH for QWE-5 were 35 °C and 7.0, respectively. The QWE-5 strain was capable of completely degrading naphthalene at a concentration as high as 100 mg/L. At initial naphthalene concentrations of 10, 20, 50, 80 and 100 mg/L, complete degradation was achieved within 32, 56, 96, 120 and 144 h, respectively. Kinetics of naphthalene degradation was described using the Andrews equation. The kinetic parameters were as follows: qmax (maximum specific degradation rate) = 1.56 h⁻¹, Ks (half-rate constant) = 60.34 mg/L, and KI (substrate-inhibition constant) = 81.76 mg/L. Metabolic intermediates were identified by gas chromatography and mass spectrometry, allowing a new degradation pathway for naphthalene to be proposed. In this pathway, monooxygenation of naphthalene yielded naphthalen-1-ol. Further degradation by Streptomyces sp. QWE-5 produced acetophenone, followed by adipic acid, which was produced as a combination of decarboxylation and hydroxylation processes.

The balance of protein expression and degradation: an ESCRTs point of view.

PubMed

Babst, Markus; Odorizzi, Greg

2013-08-01

Endosomal sorting complexes required for transport (ESCRTs) execute the biogenesis of late endosomal multivesicular bodies (MVBs). The ESCRT pathway has traditionally been viewed as a means by which transmembrane proteins are degraded in vacuoles/lysosomes. More recent studies aimed at understanding the broader functions of ESCRTs have uncovered unexpected links with pathways that control cellular metabolism. Central to this communication is TORC1, the kinase complex that controls many of the catabolic and anabolic systems. The connection between TORC1 activity and ESCRTs allows cells to quickly adapt to the stress of nutrient limitations until the longer-term autophagic pathway is activated. Increasing evidence also points to ESCRTs regulating RNA interference (RNAi) pathways that control translation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Viral degradasome hijacks mitochondria to suppress innate immunity

PubMed Central

Goswami, Ramansu; Majumdar, Tanmay; Dhar, Jayeeta; Chattopadhyay, Saurabh; Bandyopadhyay, Sudip K; Verbovetskaya, Valentina; Sen, Ganes C; Barik, Sailen

2013-01-01

The balance between the innate immunity of the host and the ability of a pathogen to evade it strongly influences pathogenesis and virulence. The two nonstructural (NS) proteins, NS1 and NS2, of respiratory syncytial virus (RSV) are critically required for RSV virulence. Together, they strongly suppress the type I interferon (IFN)-mediated innate immunity of the host cells by degrading or inhibiting multiple cellular factors required for either IFN induction or response pathways, including RIG-I, IRF3, IRF7, TBK1 and STAT2. Here, we provide evidence for the existence of a large and heterogeneous degradative complex assembled by the NS proteins, which we named “NS-degradasome” (NSD). The NSD is roughly ∼300-750 kD in size, and its degradative activity was enhanced by the addition of purified mitochondria in vitro. Inside the cell, the majority of the NS proteins and the substrates of the NSD translocated to the mitochondria upon RSV infection. Genetic and pharmacological evidence shows that optimal suppression of innate immunity requires mitochondrial MAVS and mitochondrial motility. Together, we propose a novel paradigm in which the mitochondria, known to be important for the innate immune activation of the host, are also important for viral suppression of the innate immunity. PMID:23877405

Advances of naphthalene degradation in Pseudomonas putida ND6

NASA Astrophysics Data System (ADS)

Song, Fu; Shi, Yifei; Jia, Shiru; Tan, Zhilei; Zhao, Huabing

2018-03-01

Naphthalene is one of the most common and simple polycyclic aromatic hydrocarbons. Degradation of naphthalene has been greatly concerned due to its economic, free-pollution and its fine effect in Pseudomonas putida ND6. This review summarizes the development history of naphthalene degradation, the research progress of naphthalene degrading gene and naphthalene degradation pathway of Pseudomonas putida ND6, and the researching path of this strain. Although the study of naphthalene degradation is not consummate in Pseudomonas putida ND6, there is a potential capability for Pseudomonas putida ND6 to degrade the naphthalene in the further research.

Mammalian proapoptotic factor ChaC1 and its homologues function as γ-glutamyl cyclotransferases acting specifically on glutathione

PubMed Central

Kumar, Akhilesh; Tikoo, Shweta; Maity, Shuvadeep; Sengupta, Shantanu; Sengupta, Sagar; Kaur, Amandeep; Kumar Bachhawat, Anand

2012-01-01

ChaC1 is a mammalian proapoptic protein of unknown function induced during endoplasmic reticulum stress. We show using in vivo studies and novel in vitro assays that the ChaC family of proteins function as γ-glutamyl cyclotransferases acting specifically to degrade glutathione but not other γ-glutamyl peptides. The overexpression of these proteins (but not the catalytically dead E>Q mutants) led to glutathione depletion and enhanced apoptosis in yeast. The ChaC family is conversed across all phyla and represents a new pathway for glutathione degradation in living cells, and the first cytosolic pathway for glutathione degradation in mammalian cells. PMID:23070364

Modelling anaerobic digestion acclimatisation to a biodegradable toxicant: application to cyanide.

PubMed

Zaher, U; Moussa, M S; Widyatmika, I N; van Der Steen, P; Gijzen, H J; Vanrolleghem, P A

2006-01-01

The observed acclimatisation to biodegradable toxicants in anaerobic cassava wastewater treatment is explained by modelling anaerobic cyanide degradation. A complete degradation pathway is proposed for cyanide. Cyanide degradation is modelled as enzymatic hydrolysis to formate and ammonia. Ammonia is added to the inorganic nitrogen content of the digester while formate is degraded by the hydrogenotrophic methanogens. Cyanide irreversible enzyme inhibition is modelled as an inhibition factor to acetate uptake processes. Cyanide irreversible toxicity is modelled as a decay factor to the acetate degraders. Cyanide as well as added phosphorus buffer solution were considered in the chemical equilibrium calculations of pH. The observed reversible effect after acclimatisation of sludge is modelled by a population shift between two aceticlastic methanogens that have different tolerance to cyanide toxicity. The proposed pathway is added to the IWA Anaerobic Digestion Model no.1 (ADM1). The ADM1 model with the designed extension is validated by an experiment using three lab-scale upflow anaerobic sludge bed reactors which were exposed to different cyanide loadings.

Simultaneous degradation of toxic refractory organic pesticide and bioelectricity generation using a soil microbial fuel cell.

PubMed

Cao, Xian; Song, Hai-Liang; Yu, Chun-Yan; Li, Xian-Ning

2015-01-01

In this study, the soil microbial fuel cells (MFCs) were constructed in the topsoil contaminated with toxic refractory organic pesticide, hexachlorobenzene (HCB). The performance of electricity generation and HCB degradation in the soil-MFCs were investigated. The HCB degradation pathway was analyzed based on the determination of degradation products and intermediates. Experimental results showed that the HCB removal efficiencies in the three groups (soil MFCs group, open circuit control group and no adding anaerobic sludge blank group) were 71.15%, 52.49% and 38.92%, respectively. The highest detected power density was 77.5 mW/m(2) at the external resistance of 1000 Ω. HCB was degraded via the reductive dechlorination pathway in the soil MFC under anaerobic condition. The existence of the anode promoted electrogenic bacteria to provide more electrons to increase the metabolic reactions rates of anaerobic bacteria was the main way which could promote the removal efficiencies of HCB in soil MFC. Copyright © 2015 Elsevier Ltd. All rights reserved.

Characterization of para-Nitrophenol-Degrading Bacterial Communities in River Water by Using Functional Markers and Stable Isotope Probing.

PubMed

Kowalczyk, Agnieszka; Eyice, Özge; Schäfer, Hendrik; Price, Oliver R; Finnegan, Christopher J; van Egmond, Roger A; Shaw, Liz J; Barrett, Glyn; Bending, Gary D

2015-10-01

Microbial degradation is a major determinant of the fate of pollutants in the environment. para-Nitrophenol (PNP) is an EPA-listed priority pollutant with a wide environmental distribution, but little is known about the microorganisms that degrade it in the environment. We studied the diversity of active PNP-degrading bacterial populations in river water using a novel functional marker approach coupled with [(13)C6]PNP stable isotope probing (SIP). Culturing together with culture-independent terminal restriction fragment length polymorphism analysis of 16S rRNA gene amplicons identified Pseudomonas syringae to be the major driver of PNP degradation in river water microcosms. This was confirmed by SIP-pyrosequencing of amplified 16S rRNA. Similarly, functional gene analysis showed that degradation followed the Gram-negative bacterial pathway and involved pnpA from Pseudomonas spp. However, analysis of maleylacetate reductase (encoded by mar), an enzyme common to late stages of both Gram-negative and Gram-positive bacterial PNP degradation pathways, identified a diverse assemblage of bacteria associated with PNP degradation, suggesting that mar has limited use as a specific marker of PNP biodegradation. Both the pnpA and mar genes were detected in a PNP-degrading isolate, P. syringae AKHD2, which was isolated from river water. Our results suggest that PNP-degrading cultures of Pseudomonas spp. are representative of environmental PNP-degrading populations. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Understanding the similarities and differences between ozone and peroxone in the degradation of naphthenic acids: Comparative performance for potential treatment.

PubMed

Meshref, Mohamed N A; Klamerth, Nikolaus; Islam, Md Shahinoor; McPhedran, Kerry N; Gamal El-Din, Mohamed

2017-08-01

Ozonation at high doses is a costly treatment for oil sands process-affected water (OSPW) naphthenic acids (NAs) degradation. To decrease costs and limit doses, different peroxone (hydrogen peroxide/ozone; H 2 O 2 :O 3 ) processes using mild-ozone doses of 30 and 50 mg/L were investigated. The degradation efficiency of O x -NAs (classical (O 2 -NAs) + oxidized NAs) improved from 58% at 30 mg/L ozone to 59%, 63% and 76% at peroxone (1:1), 50 mg/L ozone, and peroxone (1:2), respectively. Suppressing the hydroxyl radical (•OH) pathway by adding tert-butyl alcohol did significantly reduce the degradation in all treatments, while molecular ozone contribution was around 50% and 34% for O 2 -NAs and O x -NAs, respectively. Structure reactivity toward degradation was observed with degradation increase for both O 2 -NAs and O x -NAs with increase of both carbon (n) and hydrogen deficiency/or |-Z| numbers in all treatments. However, the combined effect of n and Z showed specific insights and differences between ozone and peroxone treatments. The degradation pathway for |-Z|≥10 isomers in ozone treatments through molecular ozone was significant compared to •OH. Though peroxone (1:2) highly reduced the fluorophore organics and toxicity to Vibrio fischeri, the best oxidant utilization in the degradation of O 2 -NAs (mg/L) per ozone dose (mg/L) was observed in the peroxone (1:1) (0.91) and 30 mg/L ozone treatments (0.92). At n = 9-11, peroxone (1:1) had similar or enhanced effect on the O 2 -NAs degradation compared to 50 mg/L ozone. Enhancing •OH pathway through peroxone versus ozone may be an effective OSPW treatment that will allow its safe release into receiving environments with marginal cost addition. Copyright © 2017 Elsevier Ltd. All rights reserved.

Degradation of paracetamol by pure bacterial cultures and their microbial consortium.

PubMed

Zhang, Lili; Hu, Jun; Zhu, Runye; Zhou, Qingwei; Chen, Jianmeng

2013-04-01

Three bacterial strains utilizing paracetamol as the sole carbon, nitrogen, and energy source were isolated from a paracetamol-degrading aerobic aggregate, and assigned to species of the genera Stenotrophomonas and Pseudomonas. The Stenotrophomonas species have not included any known paracetamol degraders until now. In batch cultures, the organisms f1, f2, and fg-2 could perform complete degradation of paracetamol at concentrations of 400, 2,500, and 2,000 mg/L or below, respectively. A combination of three microbial strains resulted in significantly improved degradation and mineralization of paracetamol. The co-culture was able to use paracetamol up to concentrations of 4,000 mg/L, and mineralized 87.1 % of the added paracetamol at the initial of 2,000 mg/L. Two key metabolites of the biodegradation pathway of paracetamol, 4-aminophenol, and hydroquinone were detected. Paracetamol was degraded predominantly via 4-aminophenol to hydroquinone with subsequent ring fission, suggesting new pathways for paracetamol-degrading bacteria. The degradation of paracetamol could thus be performed by the single isolates, but is stimulated by a synergistic interaction of the three-member consortium, suggesting a possible complementary interaction among the various isolates. The exact roles of each of the strains in the consortium need to be further elucidated.

Sirtuin 6 prevents matrix degradation through inhibition of the NF-κB pathway in intervertebral disc degeneration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Liang; Hu, Jia; Weng, Yuxiong

Intervertebral disc degeneration (IDD) is marked by imbalanced metabolism of the extracellular matrix (ECM) in the nucleus pulposus (NP) of intervertebral discs. This study aimed to determine whether sirtuin 6 (SIRT6), a member of the sirtuin family of nicotinamide adenine dinucleotide-dependent deacetylases, protects the NP from ECM degradation in IDD. Our study showed that expression of SIRT6 markedly decreased during IDD progression. Overexpression of wild-type SIRT6, but not a catalytically inactive mutant, prevented IL-1β-induced NP ECM degradation. SIRT6 depletion by RNA interference in NP cells caused ECM degradation. Moreover, SIRT6 physically interacted with nuclear factor-κB (NF-κB) catalytic subunit p65, transcriptionalmore » activity of which was significantly suppressed by SIRT6 overexpression. These results suggest that SIRT6 prevented NP ECM degradation in vitro via inhibiting NF-κB-dependent transcriptional activity and that this effect depended on its deacetylase activity. - Highlights: • SIRT6 expression is decreased in degenerative nucleus pulposus (NP) tissues. • SIRT6 overexpression lowers IL-1β-induced matrix degradation of NP. • SIRT6 inhibition induces matrix degradation of NP. • SIRT6 prevents matrix degradation of NP via the NF-κB signaling pathway.« less

Multitiered and Cooperative Surveillance of Mitochondrial Phosphatidylserine Decarboxylase 1.

PubMed

Ogunbona, Oluwaseun B; Onguka, Ouma; Calzada, Elizabeth; Claypool, Steven M

2017-09-01

Phosphatidylserine decarboxylase 1 (Psd1p), an ancient enzyme that converts phosphatidylserine to phosphatidylethanolamine in the inner mitochondrial membrane, must undergo an autocatalytic self-processing event to gain activity. Autocatalysis severs the protein into a large membrane-anchored β subunit that noncovalently associates with the small α subunit on the intermembrane space side of the inner membrane. Here, we determined that a temperature sensitive ( ts ) PSD1 allele is autocatalytically impaired and that its fidelity is closely monitored throughout its life cycle by multiple mitochondrial quality control proteases. Interestingly, the proteases involved in resolving misfolded Psd1 ts vary depending on its autocatalytic status. Specifically, the degradation of a Psd1 ts precursor unable to undergo autocatalysis requires the unprecedented cooperative and sequential actions of two inner membrane proteases, Oma1p and Yme1p. In contrast, upon heat exposure postautocatalysis, Psd1 ts β subunits accumulate in protein aggregates that are resolved by Yme1p acting alone, while the released α subunit is degraded in parallel by an unidentified protease. Importantly, the stability of endogenous Psd1p is also influenced by Yme1p. We conclude that Psd1p, the key enzyme required for the mitochondrial pathway of phosphatidylethanolamine production, is closely monitored at several levels and by multiple mitochondrial quality control mechanisms present in the intermembrane space. Copyright © 2017 American Society for Microbiology.

Enzymes involved in the biodegradation of hexachlorocyclohexane: a mini review.

PubMed

Camacho-Pérez, Beni; Ríos-Leal, Elvira; Rinderknecht-Seijas, Noemí; Poggi-Varaldo, Héctor M

2012-03-01

The scope of this paper encompasses the following subjects: (i) aerobic and anaerobic degradation pathways of γ-hexachlorocyclohexane (HCH); (ii) important genes and enzymes involved in the metabolic pathways of γ-HCH degradation; (iii) the instrumental methods for identifying and quantifying intermediate metabolites, such as gas chromatography coupled to mass spectrometry (GC-MS) and other techniques. It can be concluded that typical anaerobic and aerobic pathways of γ-HCH are well known for a few selected microbial strains, although less is known for anaerobic consortia where the possibility of synergism, antagonism, and mutualism can lead to more particular routes and more effective degradation of γ-HCH. Conversion and removals in the range 39%-100% and 47%-100% have been reported for aerobic and anaerobic cultures, respectively. Most common metabolites reported for aerobic degradation of lindane are γ-pentachlorocyclohexene (γ-PCCH), 2,5-dichlorobenzoquinone (DCBQ), Chlorohydroquinone (CHQ), chlorophenol, and phenol, whereas PCCH, isomers of trichlorobenzene (TCB), chlorobenzene, and benzene are the most typical metabolites found in anaerobic pathways. Enzyme and genetic characterization of the involved molecular mechanisms are in their early infancy; more work is needed to elucidate them in the future. Advances have been made on identification of enzymes of Sphingomonas paucimobilis where the gene LinB codifies for the enzyme haloalkane dehalogenase that acts on 1,3,4,6-tetrachloro 1,4-cyclohexadiene, thus debottlenecking the pathway. Other more common enzymes such as phenol hydroxylase, catechol 1,2-dioxygenase, catechol 2,3-dioxygenase are also involved since they attack intermediate metabolites of lindane such as catechol and less substituted chlorophenols. Chromatography coupled to mass spectrometric detector, especially GC-MS, is the most used technique for resolving for γ-HCH metabolites, although there is an increased participation of HPLC-MS methods. Scintillation methods are very useful to assess final degradation of γ-HCH. Copyright © 2011 Elsevier Ltd. All rights reserved.

Identification and analysis of the RNA degrading complexes and machinery of Giardia lamblia using an in silico approach

PubMed Central

2011-01-01

Background RNA degradation is critical to the survival of all cells. With increasing evidence for pervasive transcription in cells, RNA degradation has gained recognition as a means of regulating gene expression. Yet, RNA degradation machinery has been studied extensively in only a few eukaryotic organisms, including Saccharomyces cerevisiae and humans. Giardia lamblia is a parasitic protist with unusual genomic traits: it is binucleated and tetraploid, has a very compact genome, displays a theme of genomic minimalism with cellular machinery commonly comprised of a reduced number of protein components, and has a remarkably large population of long, stable, noncoding, antisense RNAs. Results Here we use in silico approaches to investigate the major RNA degradation machinery in Giardia lamblia and compare it to a broad array of other parasitic protists. We have found key constituents of the deadenylation and decapping machinery and of the 5'-3' RNA degradation pathway. We have similarly found that all of the major 3'-5' RNA degradation pathways are present in Giardia, including both exosome-dependent and exosome-independent machinery. However, we observe significant loss of RNA degradation machinery genes that will result in important differences in the protein composition, and potentially functionality, of the various RNA degradation pathways. This is most apparent in the exosome, the central mediator of 3'-5' degradation, which apparently contains an altered core configuration in both Giardia and Plasmodium, with only four, instead of the canonical six, distinct subunits. Additionally the exosome in Giardia is missing both the Rrp6, Nab3, and Nrd1 proteins, known to be key regulators of noncoding transcript stability in other cells. Conclusions These findings suggest that although the full complement of the major RNA degradation mechanisms were present - and likely functional - early in eukaryotic evolution, the composition and function of the complexes is more variable than previously appreciated. We suggest that the missing components of the exosome complex provide an explanation for the stable abundance of sterile RNA species in Giardia. PMID:22126454

Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester

PubMed Central

Hagen, Live H.; Frank, Jeremy A.; Zamanzadeh, Mirzaman; Eijsink, Vincent G. H.; Pope, Phillip B.; Arntzen, Magnus Ø.

2016-01-01

ABSTRACT In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor with food waste as the dominant feedstock, operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg/liter NH3-N). The microbial community was strongly dominated (76% of all 16S rRNA amplicon sequences) by populations closely related to the proteolytic bacterium Coprothermobacter proteolyticus. Multiple Coprothermobacter-affiliated strains were detected, introducing an additional level of complexity seldom explored in biogas studies. Genome reconstructions provided metabolic insight into the microbes that performed biomass deconstruction and fermentation, including the deeply branching phyla Dictyoglomi and Planctomycetes and the candidate phylum “Atribacteria.” These biomass degraders were complemented by a synergistic network of microorganisms that convert key fermentation intermediates (fatty acids) via syntrophic interactions with hydrogenotrophic methanogens to ultimately produce methane. Interpretation of the proteomics data also suggested activity of a Methanosaeta phylotype acclimatized to high ammonia levels. In particular, we report multiple novel phylotypes proposed as syntrophic acetate oxidizers, which also exert expression of enzymes needed for both the Wood-Ljungdahl pathway and β-oxidation of fatty acids to acetyl coenzyme A. Such an arrangement differs from known syntrophic oxidizing bacteria and presents an interesting hypothesis for future studies. Collectively, these findings provide increased insight into active metabolic roles of uncultured phylotypes and presents new synergistic relationships, both of which may contribute to the stability of the biogas reactor. IMPORTANCE Biogas production through anaerobic digestion of organic waste provides an attractive source of renewable energy and a sustainable waste management strategy. A comprehensive understanding of the microbial community that drives anaerobic digesters is essential to ensure stable and efficient energy production. Here, we characterize the intricate microbial networks and metabolic pathways in a thermophilic biogas reactor. We discuss the impact of frequently encountered microbial populations as well as the metabolism of newly discovered novel phylotypes that seem to play distinct roles within key microbial stages of anaerobic digestion in this stable high-temperature system. In particular, we draft a metabolic scenario whereby multiple uncultured syntrophic acetate-oxidizing bacteria are capable of syntrophically oxidizing acetate as well as longer-chain fatty acids (via the β-oxidation and Wood-Ljundahl pathways) to hydrogen and carbon dioxide, which methanogens subsequently convert to methane. PMID:27815274

Knockdown of Akt1 promotes Akt2 upregulation and resistance to oxidative-stress-induced apoptosis through control of multiple signaling pathways.

PubMed

Zhang, Lan; Sun, Shuming; Zhou, Jie; Liu, Jiao; Lv, Jia-Han; Yu, Xiang-Qiang; Li, Chi; Gong, Lili; Yan, Qin; Deng, Mi; Xiao, Ling; Ma, Haili; Liu, Jin-Ping; Peng, Yun-Lei; Wang, Dao; Liao, Gao-Peng; Zou, Li-Jun; Liu, Wen-Bin; Xiao, Ya-Mei; Li, David Wan-Cheng

2011-07-01

The Akt signaling pathway plays a key role in promoting the survival of various types of cells from stress-induced apoptosis, and different members of the Akt family display distinct physiological roles. Previous studies have shown that in response to UV irradiation, Akt2 is sensitized to counteract the induced apoptosis. However, in response to oxidative stress such as hydrogen peroxide, it remains to be elucidated what member of the Akt family would be activated to initiate the signaling cascades leading to resistance of the induced apoptosis. In the present study, we present the first evidence that knockdown of Akt1 enhances cell survival under exposure to 50 μM H(2)O(2). This survival is derived from selective upregulation and activation of Akt2 but not Akt3, which initiates 3 major signaling cascades. First, murine double minute 2 (MDM2) is hyperphosphorylated, which promotes p53 degradation and attenuates its Ser-15 phosphorylation, significantly attenuating Bcl-2 homologous antagonist killer (Bak) upregulation. Second, Akt2 activation inactivates glycogen synthase kinase 3 beta (GSK-3β) to promote stability of myeloid leukemia cell differentiation protein 1 (MCL-1). Finally, Akt2 activation promotes phosphorylation of FOXO3A toward cytosolic export and thus downregulates Bim expression. Overexpression of Bim enhances H(2)O(2)-induced apoptosis. Together, our results demonstrate that among the Akt family members, Akt2 is an essential kinase in counteracting oxidative-stress-induced apoptosis through multiple signaling pathways.

Nck adaptor proteins link Tks5 to invadopodia actin regulation and ECM degradation.

PubMed

Stylli, Stanley S; Stacey, T T I; Verhagen, Anne M; Xu, San San; Pass, Ian; Courtneidge, Sara A; Lock, Peter

2009-08-01

Invadopodia are actin-based projections enriched with proteases, which invasive cancer cells use to degrade the extracellular matrix (ECM). The Phox homology (PX)-Src homology (SH)3 domain adaptor protein Tks5 (also known as SH3PXD2A) cooperates with Src tyrosine kinase to promote invadopodia formation but the underlying pathway is not clear. Here we show that Src phosphorylates Tks5 at Y557, inducing it to associate directly with the SH3-SH2 domain adaptor proteins Nck1 and Nck2 in invadopodia. Tks5 mutants unable to bind Nck show reduced matrix degradation-promoting activity and recruit actin to invadopodia inefficiently. Conversely, Src- and Tks5-driven matrix proteolysis and actin assembly in invadopodia are enhanced by Nck1 or Nck2 overexpression and inhibited by Nck1 depletion. We show that clustering at the plasma membrane of the Tks5 inter-SH3 region containing Y557 triggers phosphorylation at this site, facilitating Nck recruitment and F-actin assembly. These results identify a Src-Tks5-Nck pathway in ECM-degrading invadopodia that shows parallels with pathways linking several mammalian and pathogen-derived proteins to local actin regulation.

High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism.

PubMed

Bao, Yun-Juan; Xu, Zixiang; Li, Yang; Yao, Zhi; Sun, Jibin; Song, Hui

2017-06-01

The soil with petroleum contamination is one of the most studied soil ecosystems due to its rich microorganisms for hydrocarbon degradation and broad applications in bioremediation. However, our understanding of the genomic properties and functional traits of the soil microbiome is limited. In this study, we used high-throughput metagenomic sequencing to comprehensively study the microbial community from petroleum-contaminated soils near Tianjin Dagang oilfield in eastern China. The analysis reveals that the soil metagenome is characterized by high level of community diversity and metabolic versatility. The metageome community is predominated by γ-Proteobacteria and α-Proteobacteria, which are key players for petroleum hydrocarbon degradation. The functional study demonstrates over-represented enzyme groups and pathways involved in degradation of a broad set of xenobiotic aromatic compounds, including toluene, xylene, chlorobenzoate, aminobenzoate, DDT, methylnaphthalene, and bisphenol. A composite metabolic network is proposed for the identified pathways, thus consolidating our identification of the pathways. The overall data demonstrated the great potential of the studied soil microbiome in the xenobiotic aromatics degradation. The results not only establish a rich reservoir for novel enzyme discovery but also provide putative applications in bioremediation. Copyright © 2016. Published by Elsevier B.V.

Bioconversion of dieldrin by wood-rotting fungi and metabolite detection.

PubMed

Kamei, Ichiro; Takagi, Kazuhiro; Kondo, Ryuichiro

2010-08-01

Dieldrin is one of the most persistent organochlorine pesticides, listed as one of the 12 persistent organic pollutants in the Stockholm Convention. Although microbial degradation is an effective way to remediate environmental pollutants, reports on aerobic microbial degradation of dieldrin are limited. Wood-rotting fungi can degrade a wide spectrum of recalcitrant organopollutants, and an attempt has been made to select wood-rotting fungi that can degrade dieldrin, and to identify the metabolite. Thirty-four isolates of wood-rotting fungi were investigated for their ability to degrade dieldrin. Strain YK543 degraded 39.1 +/- 8.8% of dieldrin during 30 days of incubation. Phylogenetic analysis demonstrated that strain YK543 was closely related to the fungus Phlebia brevispora Nakasone TMIC33929, which has been reported as a fungus that can degrade chlorinated dioxins and polychlorinated biphenyls. 9-Hydroxydieldrin was detected as a metabolite in the cultures of strain YK543. It is important to select the microorganisms that degrade organic pollutants, and to identify the metabolic pathway for the development of bioremediation methods. Strain YK543 was selected as a fungus capable of degrading dieldrin. The metabolic pathway includes 9-hydroxylation reported in rat's metabolism catalysed by liver microsomal monooxygenase. This is the first report of transformation of dieldrin to 9-hydroxydieldrin by a microorganism. Copyright (c) 2010 Society of Chemical Industry.

Biodegradation of RDX and MNX with Rhodococcus sp. Strain DN22: New Insights into the Degradation Pathway

DTIC Science & Technology

2010-11-15

denitrosation of MNX by DN22 did not involve direct participation of either oxygen or water, but both played major roles in subsequent secondary chemical and... secondary reactions and products distributions would pro- vide new insights into the degradation pathway of RDX and thus help in the development of...not involve direct participation of either oxygen or water, but both played major roles in subsequent secondary chemical and biochemical reactions of

Oxidative degradation of chlorophenol derivatives promoted by microwaves or power ultrasound: a mechanism investigation.

PubMed

Cravotto, Giancarlo; Binello, Arianna; Di Carlo, Stefano; Orio, Laura; Wu, Zhi-Lin; Ondruschka, Bernd

2010-03-01

Phenols are the most common pollutants in industrial wastewaters (particularly from oil refineries, resin manufacture, and coal processing). In the last two decades, it has become common knowledge that they can be effectively destroyed by nonconventional techniques such as power ultrasound (US) and/or microwave (MW) irradiation. Both techniques may strongly promote advanced oxidation processes (AOPs). The present study aimed to shed light on the effect and mechanism of US- and MW-promoted oxidative degradation of chlorophenols; 2,4-dichlorophenoxyacetic acid (2,4-D), a pesticide widespread in the environment, was chosen as the model compound. 2,4-D degradation by AOPs was carried out either under US (20 and 300 kHz) in aqueous solutions (with and without the addition of Fenton reagent) or solvent-free under MW with sodium percarbonate (SPC). All these reactions were monitored by gas chromatography-mass spectrometry (GC-MS) analysis and compared with the classical Fenton reaction in water under magnetic stirring. The same set of treatments was also applied to 2,4-dichlorophenol (2,4-DCP) and phenol, the first two products that occur a step down in the degradation sequence. Fenton and Fenton-like reagents were employed at the lowest active concentration. The effects of US and MW irradiation were investigated and compared with those of conventional treatments. Detailed mechanisms of Fenton-type reactions were suggested for 2,4-D, 2,4-DCP, and phenol, underlining the principal degradation products identified. MW-promoted degradation under solvent-free conditions with solid Fenton-like reagents (viz. SPC) is extremely efficient and mainly follows pyrolytic pathways. Power US strongly accelerates the degradation of 2,4-D in water through a rapid generation of highly reactive radicals; it does not lead to the formation of more toxic dimers. We show that US and MW enhance the oxidative degradation of 2,4-D and that a considerable saving of oxidants and cutting down of reaction times is thereby achieved. The results support the interpretation of previously published data and improve the understanding of the factors of direct degradation along different pathways. Oxidative pathways for 2,4-D, 2,4-DCP, and phenol were proposed by a careful monitoring of the reactions and detection of intermediates by GC-MS. The understanding of the factors that affect chlorophenols degradation along different pathways may facilitate the optimization of the treatment. Type of energy source (US or MW), power, and frequency to be applied could be designed in function of the operative scenario (amount of pollutant in soil, water, or oils).

Role of sulfate, chloride, and nitrate anions on the degradation of fluoroquinolone antibiotics by photoelectro-Fenton.

PubMed

Villegas-Guzman, Paola; Hofer, Florian; Silva-Agredo, Javier; Torres-Palma, Ricardo A

2017-12-01

Taking ciprofloxacin (CIP) as a fluoroquinolone antibiotic model, this work explores the role of common anions (sulfate, nitrate, and chloride) during the application of photoelectro-Fenton (PEF) at natural pH to degrade this type of compound in water. The system was composed of an IrO 2 anode, Ti, or gas diffusion electrode (GDE) as cathode, Fe 2+ , and UV (254 nm). To determine the implications of these anions, the degradation pathway and efficiency of the PEF sub-processes (UV photolysis, anodic oxidation, and electro-Fenton at natural pH) were studied in the individual presence of the anions. The results highlight that degradation routes and kinetics are strongly dependent on electrolytes. When chloride and nitrate ions were present, indirect electro-chemical oxidation was identified by electro-generated HOCl and nitrogenated oxidative species, respectively. Additionally, direct photolysis and direct oxidation at the anode surface were identified as degradation routes. As a consequence of the different pathways, six primary CIP by-products were identified. Therefore, a scheme was proposed representing the pathways involved in the degradation of CIP when submitted to PEF in water with chloride, nitrate, and sulfate ions, showing the complexity of this process. Promoted by individual and synergistic actions of this process, the PEF system leads to a complete elimination of CIP with total removal of antibiotic activity against Staphylococcus aureus and Escherichia coli, and significant mineralization. Finally, the role of the anions was tested in seawater containing CIP, in which the positive contributions of the anions were partially suppressed by its OH radical scavenger action. The findings are of interest for the understanding of the degradation of antibiotics via the PEF process in different matrices containing sulfate, nitrate, and chloride ions.

Biodegradation of the Allelopathic Chemical m-Tyrosine by Bacillus aquimaris SSC5 Involves the Homogentisate Central Pathway

PubMed Central

Khan, Fazlurrahman; Kumari, Munesh; Cameotra, Swaranjit Singh

2013-01-01

m-Tyrosine is an amino acid analogue, exuded from the roots of fescue grasses, which acts as a potent allelopathic and a broad spectrum herbicidal chemical. Although the production and toxic effects of m-tyrosine are known, its microbial degradation has not been documented yet. A soil microcosm study showed efficient degradation of m-tyrosine by the inhabitant microorganisms. A bacterial strain designated SSC5, that was able to utilize m-tyrosine as the sole source of carbon, nitrogen, and energy, was isolated from the soil microcosm and was characterized as Bacillus aquimaris. Analytical methods such as HPLC, GC-MS, and 1H-NMR performed on the resting cell samples identified the formation of 3-hydroxyphenylpyruvate (3-OH-PPA), 3-hydroxyphenylacetate (3-OH-PhAc), and homogentisate (HMG) as major intermediates in the m-tyrosine degradation pathway. Enzymatic assays carried out on cell-free lysates of m-tyrosine-induced cells confirmed transamination reaction as the first step of m-tyrosine degradation. The intermediate 3-OH-PhAc thus obtained was further funneled into the HMG central pathway as revealed by a hydroxylase enzyme assay. Subsequent degradation of HMG occurred by ring cleavage catalyzed by the enzyme homogentisate 1, 2-dioxygenase. This study has significant implications in terms of understanding the environmental fate of m-tyrosine as well as regulation of its phytotoxic effect by soil microorganisms. PMID:24098407

Developability studies before initiation of process development: improving manufacturability of monoclonal antibodies.

PubMed

Yang, Xiaoyu; Xu, Wei; Dukleska, Svetlana; Benchaar, Sabrina; Mengisen, Selina; Antochshuk, Valentyn; Cheung, Jason; Mann, Leslie; Babadjanova, Zulfia; Rowand, Jason; Gunawan, Rico; McCampbell, Alexander; Beaumont, Maribel; Meininger, David; Richardson, Daisy; Ambrogelly, Alexandre

2013-01-01

Monoclonal antibodies constitute a robust class of therapeutic proteins. Their stability, resistance to stress conditions and high solubility have allowed the successful development and commercialization of over 40 antibody-based drugs. Although mAbs enjoy a relatively high probability of success compared with other therapeutic proteins, examples of projects that are suspended due to the instability of the molecule are not uncommon. Developability assessment studies have therefore been devised to identify early during process development problems associated with stability, solubility that is insufficient to meet expected dosing or sensitivity to stress. This set of experiments includes short-term stability studies at 2-8 þC, 25 þC and 40 þC, freeze-thaw studies, limited forced degradation studies and determination of the viscosity of high concentration samples. We present here three case studies reflecting three typical outcomes: (1) no major or unexpected degradation is found and the study results are used to inform early identification of degradation pathways and potential critical quality attributes within the Quality by Design framework defined by US Food and Drug Administration guidance documents; (2) identification of specific degradation pathway(s) that do not affect potency of the molecule, with subsequent definition of proper process control and formulation strategies; and (3) identification of degradation that affects potency, resulting in program termination and reallocation of resources.

Iohexol degradation in wastewater and urine by UV-based Advanced Oxidation Processes (AOPs): Process modeling and by-products identification.

PubMed

Giannakis, Stefanos; Jovic, Milica; Gasilova, Natalia; Pastor Gelabert, Miquel; Schindelholz, Simon; Furbringer, Jean-Marie; Girault, Hubert; Pulgarin, César

2017-06-15

In this work, an Iodinated Contrast Medium (ICM), Iohexol, was subjected to treatment by 3 Advanced Oxidation Processes (AOPs) (UV, UV/H 2 O 2 , UV/H 2 O 2 /Fe 2+ ). Water, wastewater and urine were spiked with Iohexol, in order to investigate the treatment efficiency of AOPs. A tri-level approach has been deployed to assess the UV-based AOPs efficacy. The treatment was heavily influenced by the UV transmittance and the organics content of the matrix, as dilution and acidification improved the degradation but iron/H 2 O 2 increase only moderately. Furthermore, optimization of the treatment conditions, as well as modeling of the degradation was performed, by step-wise constructed quadratic or product models, and determination of the optimal operational regions was achieved through desirability functions. Finally, global chemical parameters (COD, TOC and UV-Vis absorbance) were followed in parallel with specific analyses to elucidate the degradation process of Iohexol by UV-based AOPs. Through HPLC/MS analysis the degradation pathway and the effects the operational parameters were monitored, thus attributing the pathways the respective modifications. The addition of iron in the UV/H 2 O 2 process inflicted additional pathways beneficial for both Iohexol and organics removal from the matrix. Copyright © 2016 Elsevier Ltd. All rights reserved.

A novel controlled release formulation of the Pin1 inhibitor ATRA to improve liver cancer therapy by simultaneously blocking multiple cancer pathways.

PubMed

Yang, Dayun; Luo, Wensong; Wang, Jichuang; Zheng, Min; Liao, Xin-Hua; Zhang, Nan; Lu, Wenxian; Wang, Long; Chen, Ai-Zheng; Wu, Wen-Guo; Liu, Hekun; Wang, Shi-Bin; Zhou, Xiao Zhen; Lu, Kun Ping

2018-01-10

Hepatocellular carcinoma (HCC) is the second leading cause of cancer deaths worldwide largely due to lack of effective targeted drugs to simultaneously block multiple cancer-driving pathways. The identification of all-trans retinoic acid (ATRA) as a potent Pin1 inhibitor provides a promising candidate for HCC targeted therapy because Pin1 is overexpressed in most HCC and activates numerous cancer-driving pathways. However, the efficacy of ATRA against solid tumors is limited due to its short half-life of 45min in humans. A slow-releasing ATRA formulation inhibits solid tumors such as HCC, but can be used only in animals. Here, we developed a one-step, cost-effective route to produce a novel biocompatible, biodegradable, and non-toxic controlled release formulation of ATRA for effective HCC therapy. We used supercritical carbon dioxide process to encapsulate ATRA in largely uniform poly L-lactic acid (PLLA) microparticles, with the efficiency of 91.4% and yield of 68.3%, and ~4-fold higher C max and AUC over the slow-releasing ATRA formulation. ATRA-PLLA microparticles had good biocompatibility, and significantly enhanced the inhibitory potency of ATRA on HCC cell growth, improving IC 50 by over 3-fold. ATRA-PLLA microparticles exerted its efficacy likely through degrading Pin1 and inhibiting multiple Pin1-regulated cancer pathways and cell cycle progression. Indeed, Pin1 knock-down abolished ATRA inhibitory effects on HCC cells and ATRA-PLLA did not inhibit normal liver cells, as expected because ATRA selectively inhibits active Pin1 in cancer cells. Moreover ATRA-PLLA microparticles significantly enhanced the efficacy of ATRA against HCC tumor growth in mice through reducing Pin1, with a better potency than the slow-releasing ATRA formulation, consistent with its improved pharmacokinetic profiles. This study illustrates an effective platform to produce controlled release formulation of anti-cancer drugs, and ATRA-PLLA microparticles might be a promising targeted drug for HCC therapy as PLLA is biocompatible, biodegradable and nontoxic to humans. Copyright © 2017 Elsevier B.V. All rights reserved.

Proteomic characterization of Withaferin A-targeted protein networks for the treatment of monoclonal myeloma gammopathies.

PubMed

Dom, Martin; Offner, Fritz; Vanden Berghe, Wim; Van Ostade, Xaveer

2018-05-15

Withaferin A (WA), a natural steroid lactone from the plant Withania somnifera, is often studied because of its antitumor properties. Although many in vitro and in vivo studies have been performed, the identification of Withaferin A protein targets and its mechanism of antitumor action remain incomplete. We used quantitative chemoproteomics and differential protein expression analysis to characterize the WA antitumor effects on a multiple myeloma cell model. Identified relevant targets were further validated by Ingenuity Pathway Analysis and Western blot and indicate that WA targets protein networks that are specific for monoclonal gammopathy of undetermined significance (MGUS) and other closely related disorders, such as multiple myeloma (MM) and Waldenström macroglobulinemia (WM). By blocking the PSMB10 proteasome subunit, downregulation of ANXA4, potential association with HDAC6 and upregulation of HMOX1, WA puts a massive blockage on both proteotoxic and oxidative stress responses pathways, leaving cancer cells defenseless against WA induced stresses. These results indicate that WA mediated apoptosis is preceded by simultaneous targeting of cellular stress response pathways like proteasome degradation, autophagy and unfolded protein stress response and thus suggests that WA can be used as an effective treatment for MGUS and other closely related disorders. Multifunctional antitumor compounds are of great potential since they reduce the risk of multidrug resistance in chemotherapy. Unfortunately, characterization of all protein targets of a multifunctional compound is lacking. Therefore, we optimized an SILAC quantitative chemoproteomics workflow to identify the potential protein targets of Withaferin A (WA), a natural multifunctional compound with promising antitumor properties. To further understand the antitumor mechanisms of WA, we performed a differential protein expression analysis and combined the altered expression data with chemoproteome WA target data in the highly curated Ingenuity Pathway database. We provide a first global overview on how WA kills multiple myeloma cancer cells and serve as a starting point for further in depth experiments. Furthermore, the combined approach can be used for other types of cancer and/or other promising multifunctional compounds, thereby increasing the potential development of new antitumor therapies. Copyright © 2018 Elsevier B.V. All rights reserved.

Description of toluene inhibition of methyl bromide biodegradation in seawater and isolation of a marine toluene oxidizer that degrades methyl bromide.

PubMed

Goodwin, Kelly D; Tokarczyk, Ryszard; Stephens, F Carol; Saltzman, Eric S

2005-07-01

Methyl bromide (CH3Br) and methyl chloride (CH3Cl) are important precursors for destruction of stratospheric ozone, and oceanic uptake is an important component of the biogeochemical cycle of these methyl halides. In an effort to identify and characterize the organisms mediating halocarbon biodegradation, we surveyed the effect of potential cometabolic substrates on CH3Br biodegradation using a 13CH3Br incubation technique. Toluene (160 to 200 nM) clearly inhibited CH3Br and CH3Cl degradation in seawater samples from the North Atlantic, North Pacific, and Southern Oceans. Furthermore, a marine bacterium able to co-oxidize CH3Br while growing on toluene was isolated from subtropical Western Atlantic seawater. The bacterium, Oxy6, was also able to oxidize o-xylene and the xylene monooxygenase (XMO) pathway intermediate 3-methylcatechol. Patterns of substrate oxidation, lack of acetylene inhibition, and the inability of the toluene 4-monooxygenase (T4MO)-containing bacterium Pseudomonas mendocina KR1 to degrade CH3Br ruled out participation of the T4MO pathway in Oxy6. Oxy6 also oxidized a variety of toluene (TOL) pathway intermediates such as benzyl alcohol, benzylaldehyde, benzoate, and catechol, but the inability of Pseudomonas putida mt-2 to degrade CH3Br suggested that the TOL pathway might not be responsible for CH3Br biodegradation. Molecular phylogenetic analysis identified Oxy6 to be a member of the family Sphingomonadaceae related to species within the Porphyrobacter genus. Although some Sphingomonadaceae can degrade a variety of xenobiotic compounds, this appears to be the first report of CH3Br degradation for this class of organism. The widespread inhibitory effect of toluene on natural seawater samples and the metabolic capabilities of Oxy6 indicate a possible link between aromatic hydrocarbon utilization and the biogeochemical cycle of methyl halides.

Removal of antibiotic cloxacillin by means of electrochemical oxidation, TiO2 photocatalysis, and photo-Fenton processes: analysis of degradation pathways and effect of the water matrix on the elimination of antimicrobial activity.

PubMed

Serna-Galvis, Efraim A; Giraldo-Aguirre, Ana L; Silva-Agredo, Javier; Flórez-Acosta, Oscar A; Torres-Palma, Ricardo A

2017-03-01

This study evaluates the treatment of the antibiotic cloxacillin (CLX) in water by means of electrochemical oxidation, TiO 2 photocatalysis, and the photo-Fenton system. The three treatments completely removed cloxacillin and eliminated the residual antimicrobial activity from synthetic pharmaceutical wastewater containing the antibiotic, commercial excipients, and inorganic ions. However, significant differences in the degradation routes were found. In the photo-Fenton process, the hydroxyl radical was involved in the antibiotic removal, while in the TiO 2 photocatalysis process, the action of both the holes and the adsorbed hydroxyl radicals degraded the pollutant. In the electrochemical treatment (using a Ti/IrO 2 anode in sodium chloride as supporting electrolyte), oxidation via HClO played the main role in the removal of CLX. The analysis of initial by-products showed five different mechanistic pathways: oxidation of the thioether group, opening of the central β-lactam ring, breakdown of the secondary amide, hydroxylation of the aromatic ring, and decarboxylation. All the oxidation processes exhibited the three first pathways. Moreover, the aromatic ring hydroxylation was found in both photochemical treatments, while the decarboxylation of the pollutant was only observed in the TiO 2 photocatalysis process. As a consequence of the degradation routes and mechanistic pathways, the elimination of organic carbon was different. After 480 and 240 min, the TiO 2 photocatalysis and photo-Fenton processes achieved ∼45 and ∼15 % of mineralization, respectively. During the electrochemical treatment, 100 % of the organic carbon remained even after the antibiotic was treated four times the time needed to degrade it. In contrast, in all processes, a natural matrix (mineral water) did not considerably inhibit pollutant elimination. However, the presence of glucose in the water significantly affected the degradation of CLX by means of TiO 2 photocatalysis.

Draft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium Arthrobacter sp. Strain SJCon

PubMed Central

Vikram, Surendra; Kumar, Shailesh; Vaidya, Bhumika; Pinnaka, Anil Kumar

2013-01-01

We report the 4.39-Mb draft genome sequence of the 2-chloro-4-nitrophenol-degrading bacterium Arthrobacter sp. strain SJCon, isolated from a pesticide-contaminated site. The draft genome sequence of strain SJCon will be helpful in studying the genetic pathways involved in the degradation of several aromatic compounds. PMID:23516196

Degradation mechanisms of Microcystin-LR during UV-B photolysis and UV/H2O2 processes: Byproducts and pathways.

PubMed

Moon, Bo-Ram; Kim, Tae-Kyoung; Kim, Moon-Kyung; Choi, Jaewon; Zoh, Kyung-Duk

2017-10-01

The removal and degradation pathways of microcystin-LR (MC-LR, [M+H] +  = 995.6) in UV-B photolysis and UV-B/H 2 O 2 processes were examined using liquid chromatography-tandem mass spectrometry. The UV/H 2 O 2 process was more efficient than UV-B photolysis for MC-LR removal. Eight by-products were newly identified in the UV-B photolysis ([M+H] +  = 414.3, 417.3, 709.6, 428.9, 608.6, 847.5, 807.4, and 823.6), and eleven by-products were identified in the UV-B/H 2 O 2 process ([M+H] +  = 707.4, 414.7, 429.3, 445.3, 608.6, 1052.0, 313.4, 823.6, 357.3, 245.2, and 805.7). Most of the MC-LR by-products had lower [M+H] + values than the MC-LR itself during both processes, except for the [M+H] + value of 1052.0 during UV-B photolysis. Based on identified by-products and peak area patterns, we proposed potential degradation pathways during the two processes. Bond cleavage and intramolecular electron rearrangement by electron pair in the nitrogen atom were the major reactions during UV-B photolysis and UV-B/H 2 O 2 processes, and hydroxylation by OH radical and the adduct formation reaction between the produced by-products were identified as additional pathways during the UV-B/H 2 O 2 process. Meanwhile, the degradation by-products identified from MC-LR during UV-B/H 2 O 2 process can be further degraded by increasing H 2 O 2 dose. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multi-functional regulation of 4E-BP gene expression by the Ccr4-Not complex.

PubMed

Okada, Hirokazu; Schittenhelm, Ralf B; Straessle, Anna; Hafen, Ernst

2015-01-01

The mechanistic target of rapamycin (mTOR) signaling pathway is highly conserved from yeast to humans. It senses various environmental cues to regulate cellular growth and homeostasis. Deregulation of the pathway has been implicated in many pathological conditions including cancer. Phosphorylation cascades through the pathway have been extensively studied but not much is known about the regulation of gene expression of the pathway components. Here, we report that the mRNA level of eukaryotic translation initiation factor (eIF) subunit 4E-binding protein (4E-BP) gene, one of the key mTOR signaling components, is regulated by the highly conserved Ccr4-Not complex. RNAi knockdown of Not1, a putative scaffold protein of this protein complex, increases the mRNA level of 4E-BP in Drosophila Kc cells. Examination of the gene expression mechanism using reporter swap constructs reveals that Not1 depletion increases reporter mRNAs with the 3'UTR of 4E-BP gene, but decreases the ones with the 4E-BP promoter region, suggesting that Ccr4-Not complex regulates both degradation and transcription of 4E-BP mRNA. These results indicate that the Ccr4-Not complex controls expression of a single gene at multiple levels and adjusts the magnitude of the total effect. Thus, our study reveals a novel regulatory mechanism of a key component of the mTOR signaling pathway at the level of gene expression.

Entner–Doudoroff pathway for sulfoquinovose degradation in Pseudomonas putida SQ1

PubMed Central

Felux, Ann-Katrin; Spiteller, Dieter; Klebensberger, Janosch; Schleheck, David

2015-01-01

Sulfoquinovose (SQ; 6-deoxy-6-sulfoglucose) is the polar head group of the plant sulfolipid SQ-diacylglycerol, and SQ comprises a major proportion of the organosulfur in nature, where it is degraded by bacteria. A first degradation pathway for SQ has been demonstrated recently, a “sulfoglycolytic” pathway, in addition to the classical glycolytic (Embden–Meyerhof) pathway in Escherichia coli K-12; half of the carbon of SQ is abstracted as dihydroxyacetonephosphate (DHAP) and used for growth, whereas a C3-organosulfonate, 2,3-dihydroxypropane sulfonate (DHPS), is excreted. The environmental isolate Pseudomonas putida SQ1 is also able to use SQ for growth, and excretes a different C3-organosulfonate, 3-sulfolactate (SL). In this study, we revealed the catabolic pathway for SQ in P. putida SQ1 through differential proteomics and transcriptional analyses, by in vitro reconstitution of the complete pathway by five heterologously produced enzymes, and by identification of all four organosulfonate intermediates. The pathway follows a reaction sequence analogous to the Entner–Doudoroff pathway for glucose-6-phosphate: It involves an NAD+-dependent SQ dehydrogenase, 6-deoxy-6-sulfogluconolactone (SGL) lactonase, 6-deoxy-6-sulfogluconate (SG) dehydratase, and 2-keto-3,6-dideoxy-6-sulfogluconate (KDSG) aldolase. The aldolase reaction yields pyruvate, which supports growth of P. putida, and 3-sulfolactaldehyde (SLA), which is oxidized to SL by an NAD(P)+-dependent SLA dehydrogenase. All five enzymes are encoded in a single gene cluster that includes, for example, genes for transport and regulation. Homologous gene clusters were found in genomes of other P. putida strains, in other gamma-Proteobacteria, and in beta- and alpha-Proteobacteria, for example, in genomes of Enterobacteria, Vibrio, and Halomonas species, and in typical soil bacteria, such as Burkholderia, Herbaspirillum, and Rhizobium. PMID:26195800

Degradation of paracetamol by Pseudomonas aeruginosa strain HJ1012.

PubMed

Hu, Jun; Zhang, Li L; Chen, Jian M; Liu, Yu

2013-01-01

Pseudomonas aeruginosa strain HJ1012 was isolated on paracetamol as a sole carbon and energy source. This organism could completely degrade paracetamol as high as 2200 mg/L. Following paracetamol consumption, a CO₂ yield rate up to 71.4% proved that the loss of paracetamol was mainly via mineralization. Haldane's equation adequately described the relationship between the specific growth rate and substrate concentration. The maximum specific growth rate and yield coefficient were 0.201 g-Paracetamol/g-VSS·h and 0.101 mg of biomass yield/mg of paracetamol consumed, respectively. A total of 8 metabolic intermediates was identified and classified into aromatic compounds, carboxylic acids, and inorganic species (nitrite and nitrate ions). P-aminophenol and hydroquinone are the two key metabolites of the initial steps in the paracetamol catabolic pathway. Paracetamol is degraded predominantly via p-aminophenol to hydroquinone with subsequent ring fission, suggesting partially new pathways for paracetamol-degrading bacteria.

The IRAK homolog Pelle is the functional counterpart of IκB kinase in the Drosophila Toll pathway.

PubMed

Daigneault, Jessica; Klemetsaune, Liv; Wasserman, Steven A

2013-01-01

Toll receptors transduce signals that activate Rel-family transcription factors, such as NF-κB, by directing proteolytic degradation of inhibitor proteins. In mammals, the IκB Kinase (IKK) phosphorylates the inhibitor IκBα. A βTrCP protein binds to phosphorylated IκBα, triggering ubiquitination and proteasome mediated degradation. In Drosophila, Toll signaling directs Cactus degradation via a sequence motif that is highly similar to that in IκBα, but without involvement of IKK. Here we show that Pelle, the homolog of a mammalian regulator of IKK, acts as a Cactus kinase. We further find that the fly βTrCP protein Slimb is required in cultured cells to mediate Cactus degradation. These findings enable us for the first time to trace an uninterrupted pathway from the cell surface to the nucleus for Drosophila Toll signaling.

The IRAK Homolog Pelle Is the Functional Counterpart of IκB Kinase in the Drosophila Toll Pathway

PubMed Central

Daigneault, Jessica; Klemetsaune, Liv; Wasserman, Steven A.

2013-01-01

Toll receptors transduce signals that activate Rel-family transcription factors, such as NF-κB, by directing proteolytic degradation of inhibitor proteins. In mammals, the IκB Kinase (IKK) phosphorylates the inhibitor IκBα. A βTrCP protein binds to phosphorylated IκBα, triggering ubiquitination and proteasome mediated degradation. In Drosophila, Toll signaling directs Cactus degradation via a sequence motif that is highly similar to that in IκBα, but without involvement of IKK. Here we show that Pelle, the homolog of a mammalian regulator of IKK, acts as a Cactus kinase. We further find that the fly βTrCP protein Slimb is required in cultured cells to mediate Cactus degradation. These findings enable us for the first time to trace an uninterrupted pathway from the cell surface to the nucleus for Drosophila Toll signaling. PMID:24086459

Modulation of fatty acid synthase degradation by concerted action of p38 MAP kinase, E3 ligase COP1, and SH2-tyrosine phosphatase Shp2.

PubMed

Yu, Jianxiu; Deng, Rong; Zhu, Helen H; Zhang, Sharon S; Zhu, Changhong; Montminy, Marc; Davis, Roger; Feng, Gen-Sheng

2013-02-08

The Src-homology 2 (SH2) domain-containing tyrosine phosphatase Shp2 has been known to regulate various signaling pathways triggered by receptor and cytoplasmic tyrosine kinases. Here we describe a novel function of Shp2 in control of lipid metabolism by mediating degradation of fatty acid synthase (FASN). p38-phosphorylated COP1 accumulates in the cytoplasm and subsequently binds FASN through Shp2 here as an adapter, leading to FASN-Shp2-COP1 complex formation and FASN degradation mediated by ubiquitination pathway. By fasting p38 is activated and stimulates FASN protein degradation in mice. Consistently, the FASN protein levels are dramatically elevated in mouse liver and pancreas in which Shp2/Ptpn11 is selectively deleted. Thus, this study identifies a new activity for Shp2 in lipid metabolism.

An integrated multiple-analyte pharmacokinetic model to characterize trastuzumab emtansine (T-DM1) clearance pathways and to evaluate reduced pharmacokinetic sampling in patients with HER2-positive metastatic breast cancer.

PubMed

Lu, Dan; Joshi, Amita; Wang, Bei; Olsen, Steve; Yi, Joo-Hee; Krop, Ian E; Burris, Howard A; Girish, Sandhya

2013-08-01

Trastuzumab emtansine (T-DM1) is an antibody-drug conjugate recently approved by the US Food and Drug Administration for the treatment of human epidermal growth factor receptor 2 (HER2)-positive metastatic breast cancer previously treated with trastuzumab and taxane chemotherapy. It comprises the microtubule inhibitory cytotoxic agent DM1 conjugated to the HER2-targeted humanized monoclonal antibody trastuzumab via a stable linker. To characterize the pharmacokinetics of T-DM1 in patients with metastatic breast cancer, concentrations of multiple analytes were quantified, including serum concentrations of T-DM1 conjugate and total trastuzumab (the sum of conjugated and unconjugated trastuzumab), as well as plasma concentrations of DM1. The clearance of T-DM1 conjugate is approximately 2 to 3 times faster than its parent antibody, trastuzumab. However, the clearance pathways accounting for this faster clearance rate are unclear. An integrated population pharmacokinetic model that simultaneously fits the pharmacokinetics of T-DM1 conjugate and total trastuzumab can help to elucidate the clearance pathways of T-DM1. The model can also be used to predict total trastuzumab pharmacokinetic profiles based on T-DM1 conjugate pharmacokinetic data and sparse total trastuzumab pharmacokinetic data, thereby reducing the frequency of pharmacokinetic sampling. T-DM1 conjugate and total trastuzumab serum concentration data, including baseline trastuzumab concentrations prior to T-DM1 treatment, from phase I and II studies were used to develop this integrated population pharmacokinetic model. Based on a hypothetical T-DM1 catabolism scheme, two-compartment models for T-DM1 conjugate and trastuzumab were integrated by assuming a one-step deconjugation clearance from T-DM1 conjugate to trastuzumab. The ability of the model to predict the total trastuzumab pharmacokinetic profile based on T-DM1 conjugate pharmacokinetics and various sampling schemes of total trastuzumab pharmacokinetics was assessed to evaluate total trastuzumab sampling schemes. The final model reflects a simplified catabolism scheme of T-DM1, suggesting that T-DM1 clearance pathways include both deconjugation and proteolytic degradation. The model fits T-DM1 conjugate and total trastuzumab pharmacokinetic data simultaneously. The deconjugation clearance of T-DM1 was estimated to be ~0.4 L/day. Proteolytic degradation clearances for T-DM1 and trastuzumab were similar (~0.3 L/day). This model accurately predicts total trastuzumab pharmacokinetic profiles based on T-DM1 conjugate pharmacokinetic data and sparse total trastuzumab pharmacokinetic data sampled at preinfusion and end of infusion in cycle 1, and in one additional steady state cycle. This semi-mechanistic integrated model links T-DM1 conjugate and total trastuzumab pharmacokinetic data, and supports the inclusion of both proteolytic degradation and deconjugation as clearance pathways in the hypothetical T-DM1 catabolism scheme. The model attributes a faster T-DM1 conjugate clearance versus that of trastuzumab to the presence of a deconjugation process and suggests a similar proteolytic clearance of T-DM1 and trastuzumab. Based on the model and T-DM1 conjugate pharmacokinetic data, a sparse pharmacokinetic sampling scheme for total trastuzumab provides an entire pharmacokinetic profile with similar predictive accuracy to that of a dense pharmacokinetic sampling scheme.

Atg6/UVRAG/Vps34-Containing Lipid Kinase Complex Is Required for Receptor Downregulation through Endolysosomal Degradation and Epithelial Polarity during Drosophila Wing Development

PubMed Central

Szatmári, Zsuzsanna; Sass, Miklós

2014-01-01

Atg6 (Beclin 1 in mammals) is a core component of the Vps34 PI3K (III) complex, which promotes multiple vesicle trafficking pathways. Atg6 and Vps34 form two distinct PI3K (III) complexes in yeast and mammalian cells, either with Atg14 or with UVRAG. The functions of these two complexes are not entirely clear, as both Atg14 and UVRAG have been suggested to regulate both endocytosis and autophagy. In this study, we performed a microscopic analysis of UVRAG, Atg14, or Atg6 loss-of-function cells in the developing Drosophila wing. Both autophagy and endocytosis are seriously impaired and defective endolysosomes accumulate upon loss of Atg6. We show that Atg6 is required for the downregulation of Notch and Wingless signaling pathways; thus it is essential for normal wing development. Moreover, the loss of Atg6 impairs cell polarity. Atg14 depletion results in autophagy defects with no effect on endocytosis or cell polarity, while the silencing of UVRAG phenocopies all but the autophagy defect of Atg6 depleted cells. Thus, our results indicate that the UVRAG-containing PI3K (III) complex is required for receptor downregulation through endolysosomal degradation and for the establishment of proper cell polarity in the developing wing, while the Atg14-containing complex is involved in autophagosome formation. PMID:25006588

Biosolid-borne tetracyclines and sulfonamides in plants.

PubMed

Mathews, Shiny; Reinhold, Dawn

2013-07-01

Tetracyclines and sulfonamides used in human and animal medicine are released to terrestrial ecosystems from wastewater treatment plants or by direct manure application. The interactions between plants and these antibiotics are numerous and complex, including uptake and accumulation, phytometabolism, toxicity responses, and degradation in the rhizosphere. Uptake and accumulation of antibiotics have been studied in plants such as wheat, maize, potato, vegetables, and ornamentals. Once accumulated in plant tissue, organic contaminants can be metabolized through a sequential process of transformation, conjugation through glycosylation and glutathione pathways, and ultimately sequestration into plant tissue. While studies have yet to fully elucidate the phytometabolism of tetracyclines and sulfonamides, an in-depth review of plant and mammalian studies suggest multiple potential transformation and conjugation pathways for tetracyclines and sulfonamides. The presence of contaminants in the vicinity or within the plants can elicit stress responses and defense mechanisms that can help tolerate the negative effects of contaminants. Antibiotics can change microbial communities and enzyme activity in the rhizosphere, potentially inducing microbial antibiotic resistance. On the other hand, the interaction of microbes and root exudates on pharmaceuticals in the rhizosphere can result in degradation of the parent molecule to less toxic compounds. To fully characterize the environmental impacts of increased antibiotic use in human medicine and animal production, further research is essential to understand the effects of different antibiotics on plant physiology and productivity, uptake, translocation, and phytometabolism of antibiotics, and the role of antibiotics in the rhizosphere.

Energy balance associated with the degradation of lignocellulosic material by white-rot and brown-rot fungi.

NASA Astrophysics Data System (ADS)

Derrien, Delphine; Bédu, Hélène; Buée, Marc; Kohler, Annegret; Goodell, Barry; Gelhaye, Eric

2017-04-01

Forest soils cover about 30% of terrestrial area and comprise between 50 and 80% of the global stock of soil organic carbon (SOC). The major precursor for this forest SOC is lignocellulosic material, which is made of polysaccharides and lignin. Lignin has traditionally been considered as a recalcitrant polymer that hinders access to the much more labile structural polysaccharides. This view appears to be partly incorrect from a microbiology perspective yet, as substrate alteration depends on the metabolic potential of decomposers. In forest ecosystems the wood-rotting Basidiomycota fungi have developed two different strategies to attack the structure of lignin and gain access to structural polysaccharides. White-rot fungi degrade all components of plant cell walls, including lignin, using enzymatic systems. Brown-rot fungi do not remove lignin. They generate oxygen-derived free radicals, such as the hydroxyl radical produced by the Fenton reaction, that disrupt the lignin polymer and depolymerize polysaccharides which then diffuse out to where the enzymes are located The objective of this study was to develop a model to investigate whether the lignin relative persistence could be related to the energetic advantage of brown-rot degradative pathway in comparison to white-rot degradative pathway. The model simulates the changes in substrate composition over time, and determines the energy gained from the conversion of the lost substrate into CO2. The energy cost for the production of enzymes involved in substrate alteration is assessed using information derived from genome and secretome analysis. For brown-rot fungus specifically, the energy cost related to the production of OH radicals is also included. The model was run, using data from the literature on populous wood degradation by Trametes versicolor, a white-rot fungus, and Gloeophyllum trabeum, a brown-rot fungus. It demonstrates that the brown-rot fungus (Gloeophyllum trabeum) was more efficient than the white-rot fungus (Trametes versicolor). The energy advantage could explain the emergence of the brown-rot degradative pathway from a white-rot degradative pathway and subsequently, the relative persistence of lignin in soil.

Transgenic plants for enhanced biodegradation and phytoremediation of organic xenobiotics.

PubMed

Abhilash, P C; Jamil, Sarah; Singh, Nandita

2009-01-01

Phytoremediation--the use of plants to clean up polluted soil and water resources--has received much attention in the last few years. Although plants have the inherent ability to detoxify xenobiotics, they generally lack the catabolic pathway for the complete degradation of these compounds compared to microorganisms. There are also concerns over the potential for the introduction of contaminants into the food chain. The question of how to dispose of plants that accumulate xenobiotics is also a serious concern. Hence the feasibility of phytoremediation as an approach to remediate environmental contamination is still somewhat in question. For these reasons, researchers have endeavored to engineer plants with genes that can bestow superior degradation abilities. A direct method for enhancing the efficacy of phytoremediation is to overexpress in plants the genes involved in metabolism, uptake, or transport of specific pollutants. Furthermore, the expression of suitable genes in root system enhances the rhizodegradation of highly recalcitrant compounds like PAHs, PCBs etc. Hence, the idea to amplify plant biodegradation of xenobiotics by genetic manipulation was developed, following a strategy similar to that used to develop transgenic crops. Genes from human, microbes, plants, and animals are being used successfully for this venture. The introduction of these genes can be readily achieved for many plant species using Agrobacterium tumefaciens-mediated plant transformation or direct DNA methods of gene transfer. One of the promising developments in transgenic technology is the insertion of multiple genes (for phase 1 metabolism (cytochrome P450s) and phase 2 metabolism (GSH, GT etc.) for the complete degradation of the xenobiotics within the plant system. In addition to the use of transgenic plants overexpressed with P450 and GST genes, various transgenic plants expressing bacterial genes can be used for the enhanced degradation and remediation of herbicides, explosives, PCBs etc. Another approach to enhancing phytoremediation ability is the construction of plants that secrete chemical degrading enzymes into the rhizosphere. Recent studies revealed that accelerated ethylene production in response to stress induced by contaminants is known to inhibit root growth and is considered as major limitation in improving phytoremediation efficiency. However, this can be overcome by the selective expression of bacterial ACC deaminase (which regulates ethylene levels in plants) in plants together with multiple genes for the different phases of xenobiotic degradation. This review examines the recent developments in use of transgenic-plants for the enhanced metabolism, degradation and phytoremediation of organic xenobiotics and its future directions.

Skp1 Independent Function of Cdc53/Cul1 in F-box Protein Homeostasis.

PubMed

Mathur, Radhika; Yen, James L; Kaiser, Peter

2015-12-01

Abundance of substrate receptor subunits of Cullin-RING ubiquitin ligases (CRLs) is tightly controlled to maintain the full repertoire of CRLs. Unbalanced levels can lead to sequestration of CRL core components by a few overabundant substrate receptors. Numerous diseases, including cancer, have been associated with misregulation of substrate receptor components, particularly for the largest class of CRLs, the SCF ligases. One relevant mechanism that controls abundance of their substrate receptors, the F-box proteins, is autocatalytic ubiquitylation by intact SCF complex followed by proteasome-mediated degradation. Here we describe an additional pathway for regulation of F-box proteins on the example of yeast Met30. This ubiquitylation and degradation pathway acts on Met30 that is dissociated from Skp1. Unexpectedly, this pathway required the cullin component Cdc53/Cul1 but was independent of the other central SCF component Skp1. We demonstrated that this non-canonical degradation pathway is critical for chromosome stability and effective defense against heavy metal stress. More importantly, our results assign important biological functions to a sub-complex of cullin-RING ligases that comprises Cdc53/Rbx1/Cdc34, but is independent of Skp1.

Photodegradation of diclofenac in aqueous solution by simulated sunlight irradiation: kinetics, thermodynamics and pathways.

PubMed

Zhang, N; Li, J M; Liu, G G; Chen, X L; Jiang, K

2017-05-01

Diclofenac (DCF) is one of the most frequently detected pharmaceuticals in various water samples. This paper studied the effects of aquatic environmental factors (pH, temperature and dissolved organic matter) on photodegradation of DCF under simulated sunlight. The results demonstrate that degradation pathways proceed via pseudo first-order kinetics in all cases and the photodegradation of DCF by simulated sunlight. Thermodynamic study indicated that the photodegradation course is spontaneous, exothermic and irreversible. The rate constant gradually increased when the pH increased from 3 to 5, then decreased when the pH increased from 5 to 8, and finally increased when the pH further increased from 8 to 12. Humic acid inhibited the photodegradation of DCF. Three kinds of main degradation products were observed by high performance liquid chromatography/mass spectrometry and the degradation pathways were suggested. A toxicity test using Photobacterium phosphoreum T 3 Sp indicated the generation of some more toxic products than DCF.

5-Hydroxytryptophan, a major product of tryptophan degradation, is essential for optimal replication of human parainfluenza virus.

PubMed

Rabbani, M A G; Barik, Sailen

2017-03-01

Interferon (IFN) exerts its antiviral effect by inducing a large family of cellular genes, named interferon (IFN)-stimulated genes (ISGs). An intriguing member of this family is indoleamine 2,3-dioxygenase (IDO), which catalyzes the first and rate-limiting step of the main branch of tryptophan (Trp) degradation, the kynurenine pathway. We recently showed that IDO strongly inhibits human parainfluenza virus type 3 (PIV3), a significant respiratory pathogen. Here, we show that 5-hydoxytryptophan (5-HTP), the first product of an alternative branch of Trp degradation and a serotonin precursor, is essential to protect virus growth against IDO in cell culture. We also show that the apparent antiviral effect of IDO on PIV3 is not due to the generation of the kynurenine pathway metabolites, but rather due to the depletion of intracellular Trp by IDO, as a result of which this rare amino acid becomes unavailable for the alternative, proviral 5-HTP pathway. Copyright © 2017 Elsevier Inc. All rights reserved.

Autophagy: not good OR bad, but good AND bad.

PubMed

Altman, Brian J; Rathmell, Jeffrey C

2009-05-01

Autophagy is a well-established mechanism to degrade intracellular components and provide a nutrient source to promote survival of cells in metabolic distress. Such stress can be caused by a lack of available nutrients or by insufficient rates of nutrient uptake. Indeed, growth factor deprivation leads to internalization and degradation of nutrient transporters, leaving cells with limited means to access extracellular nutrients even when plentiful.This loss of growth factor signaling and extracellular nutrients ultimately leads to apoptosis, but also activates autophagy, which may degrade intracellular components and provide fuel for mitochondrial bioenergetics. The precise metabolic role of autophagy and how it intersects with the apoptotic pathways in growth factor withdrawal, however, has been uncertain. Our recent findings ingrowth factor-deprived hematopoietic cells show that autophagy can simultaneously contribute to cell metabolism and initiate a pathway to sensitize cells to apoptotic death. This pathway may promote tissue homeostasis by ensuring that only cells with high resistance to apoptosis may utilize autophagy as a survival mechanism when growth factors are limiting and nutrient uptake decreases.

Coformer selection based on degradation pathway of drugs: a case study of adefovir dipivoxil-saccharin and adefovir dipivoxil-nicotinamide cocrystals.

PubMed

Gao, Yuan; Gao, Jing; Liu, Ziling; Kan, Hongliang; Zu, Hui; Sun, Wanjin; Zhang, Jianjun; Qian, Shuai

2012-11-15

Adefovir dipivoxil (AD) is a bis(pivaloyloxymethyl) prodrug of adefovir with chemical stability problem. It undergoes two degradation pathways including hydrolysis and dimerization during storage. Pharmaceutical cocrystallization exhibits a promising approach to enhance aqueous solubility as well as physicochemical stability. In this study we attempted to prepare and investigate the physiochemical properties of AD cocrystals, which were formed with two coformers having different acidity and alkalinity (weakly acidic saccharin (SAC) and weakly basic nicotinamide (NCT)). The presence of different coformer molecules along with AD resulted in altered physicochemical properties. AD-SAC cocrystal showed great improvement in solubility and chemical stability, while AD-NCT did not. Several potential factors giving rise to different solid-state properties were summarized. Different coformers resulted in different cocrystal formation, packing style and hydrogen bond formation. This study could provide the coformer selection strategy based on degradation pathways for some unstable drugs in pharmaceutical cocrystal design. Copyright © 2012 Elsevier B.V. All rights reserved.

Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae

PubMed Central

Neymotin, Benjamin; Ettorre, Victoria; Gresham, David

2016-01-01

Degradation of mRNA contributes to variation in transcript abundance. Studies of individual mRNAs have shown that both cis and trans factors affect mRNA degradation rates. However, the factors underlying transcriptome-wide variation in mRNA degradation rates are poorly understood. We investigated the contribution of different transcript properties to transcriptome-wide degradation rate variation in the budding yeast, Saccharomyces cerevisiae, using multiple regression analysis. We find that multiple transcript properties are significantly associated with variation in mRNA degradation rates, and that a model incorporating these properties explains ∼50% of the genome-wide variance. Predictors of mRNA degradation rates include transcript length, ribosome density, biased codon usage, and GC content of the third position in codons. To experimentally validate these factors, we studied individual transcripts expressed from identical promoters. We find that decreasing ribosome density by mutating the first translational start site of a transcript increases its degradation rate. Using coding sequence variants of green fluorescent protein (GFP) that differ only at synonymous sites, we show that increased GC content of the third position of codons results in decreased rates of mRNA degradation. Thus, in steady-state conditions, a large fraction of genome-wide variation in mRNA degradation rates is determined by inherent properties of transcripts, many of which are related to translation, rather than specific regulatory mechanisms. PMID:27633789

Hydrogen Isotope Fractionation during the Biodegradation of 1,2-Dichloroethane: Potential for Pathway Identification Using a Multi-element (C, Cl, and H) Isotope Approach.

PubMed

Palau, Jordi; Shouakar-Stash, Orfan; Hatijah Mortan, Siti; Yu, Rong; Rosell, Monica; Marco-Urrea, Ernest; Freedman, David L; Aravena, Ramon; Soler, Albert; Hunkeler, Daniel

2017-09-19

Even though multi-element isotope fractionation patterns provide crucial information with which to identify contaminant degradation pathways in the field, those involving hydrogen are still lacking for many halogenated groundwater contaminants and degradation pathways. This study investigates for the first time hydrogen isotope fractionation during both aerobic and anaerobic biodegradation of 1,2-dichloroethane (1,2-DCA) using five microbial cultures. Transformation-associated isotope fractionation values (ε bulk H ) were -115 ± 18‰ (aerobic C-H bond oxidation), -34 ± 4‰ and -38 ± 4‰ (aerobic C-Cl bond cleavage via hydrolytic dehalogenation), and -57 ± 3‰ and -77 ± 9‰ (anaerobic C-Cl bond cleavage via reductive dihaloelimination). The dual-element C-H isotope approach (Λ C-H = Δδ 2 H/Δδ 13 C ≈ ε bulk H /ε bulk C , where Δδ 2 H and Δδ 13 C are changes in isotope ratios during degradation) resulted in clearly different Λ C-H values: 28 ± 4 (oxidation), 0.7 ± 0.1 and 0.9 ± 0.1 (hydrolytic dehalogenation), and 1.76 ± 0.05 and 3.5 ± 0.1 (dihaloelimination). This result highlights the potential of this approach to identify 1,2-DCA degradation pathways in the field. In addition, distinct trends were also observed in a multi- (i.e., Δδ 2 H versus Δδ 37 Cl versus Δδ 13 C) isotope plot, which opens further possibilities for pathway identification in future field studies. This is crucial information to understand the mechanisms controlling natural attenuation of 1,2-DCA and to design appropriate strategies to enhance biodegradation.

Analysis of aromatic catabolic pathways in Pseudomonas putida KT 2440 using a combined proteomic approach: 2-DE/MS and cleavable isotope-coded affinity tag analysis.

PubMed

Kim, Young Hwan; Cho, Kun; Yun, Sung-Ho; Kim, Jin Young; Kwon, Kyung-Hoon; Yoo, Jong Shin; Kim, Seung Il

2006-02-01

Proteomic analysis of Pseudomonas putida KT2440 cultured in monocyclic aromatic compounds was performed using 2-DE/MS and cleavable isotope-coded affinity tag (ICAT) to determine whether proteins involved in aromatic compound degradation pathways were altered as predicted by genomic analysis (Jiménez et al., Environ Microbiol. 2002, 4, 824-841). Eighty unique proteins were identified by 2-DE/MS or MS/MS analysis from P. putida KT2440 cultured in the presence of six different organic compounds. Benzoate dioxygenase (BenA, BenD) and catechol 1,2-dioxygenase (CatA) were induced by benzoate. Protocatechuate 3,4-dixoygenase (PcaGH) was induced by p-hydroxybenzoate and vanilline. beta-Ketoadipyl CoA thiolase (PcaF) and 3-oxoadipate enol-lactone hydrolase (PcaD) were induced by benzoate, p-hydroxybenzoate and vanilline, suggesting that benzoate, p-hydroxybenzoate and vanilline were degraded by different dioxygenases and then converged in the same beta-ketoadipate degradation pathway. An additional 110 proteins, including 19 proteins from 2-DE analysis, were identified by cleavable ICAT analysis for benzoate-induced proteomes, which complemented the 2-DE results. Phenylethylamine exposure induced beta-ketoacyl CoA thiolase (PhaD) and ring-opening enzyme (PhaL), both enzymes of the phenylacetate (pha) biodegradation pathway. Phenylalanine induced 4-hydroxyphenyl-pyruvate dioxygenase (Hpd) and homogentisate 1,2-dioxygenase (HmgA), key enzymes in the homogentisate degradation pathway. Alkyl hydroperoxide reductase (AphC) was induced under all aromatic compounds conditions. These results suggest that proteome analysis complements and supports predictive information obtained by genomic sequence analysis.

Benzoate Metabolism Intermediate Benzoyl Coenzyme A Affects Gentisate Pathway Regulation in Comamonas testosteroni

PubMed Central

Chen, Dong-Wei; Zhang, Yun; Jiang, Cheng-Ying

2014-01-01

A previous study showed that benzoate was catabolized via a coenzyme A (CoA)-dependent epoxide pathway in Azoarcus evansii (R. Niemetz, U. Altenschmidt, S. Brucker, and G. Fuchs, Eur. J. Biochem. 227:161-168, 1995), but gentisate 1,2-dioxygenase was induced. Similarly, we found that the Comamonas testosteroni strain CNB-1 degraded benzoate via a CoA-dependent epoxide pathway and that gentisate 1,2-dioxygenase (GenA) was also induced when benzoate or 3-hydroxybenzoate served as a carbon source for growth. Genes encoding the CoA-dependent epoxide (box genes) and gentisate (gen genes) pathways were identified. Genetic disruption revealed that the gen genes were not involved in benzoate and 3-hydroxybenzoate degradation. Hence, we investigated gen gene regulation in the CNB-1 strain. The PgenA promoter, a MarR-type regulator (GenR), and the GenR binding site were identified. We found that GenR took gentisate, 3-hydroxybenzoate, and benzoyl-CoA as effectors and that binding of GenR to its target DNA sequence was prohibited when these effectors were present. In vivo studies showed that the CNB-1 mutant that lost benzoyl-CoA synthesis was not able to activate PgenA promoter, while transcription of genA was upregulated in another CNB-1 mutant that lost the ability to degrade benzoyl-CoA. The finding that benzoyl-CoA (a metabolic intermediate of benzoate degradation) and 3-hydroxybenzoate function as GenR effectors explains why GenA was induced when CNB-1 grew on benzoate or 3-hydroxybenzoate. Regulation of gentisate pathways by MarR-, LysR-, and IclR-type regulators in diverse bacterial groups is discussed in detail. PMID:24771026

A Comprehensive Study on Chlorella pyrenoidosa for Phenol Degradation and its Potential Applicability as Biodiesel Feedstock and Animal Feed.

PubMed

Das, Bhaskar; Mandal, Tapas K; Patra, Sanjukta

2015-07-01

The present work evaluates the phenol degradative performance of microalgae Chlorella pyrenoidosa. High-performance liquid chromatography (HPLC) analysis showed that C. pyrenoidosa degrades phenol completely up to 200 mg/l. It could also metabolize phenol in refinery wastewater. Biokinetic parameters obtained are the following: growth kinetics, μ max (media) > μ max (refinery wastewater), K s(media) < K s(refinery wastewater), K I(media) > K I(refinery wastewater); degradation kinetics, q max (media) > q max (refinery wastewater), K s(media) < K s(refinery wastewater), K I(media) > K I(refinery wastewater). The microalgae could cometabolize the alkane components present in refinery wastewater. Fourier transform infrared (FTIR) fingerprinting of biomass indicates intercellular phenol uptake and breakdown into its intermediates. Phenol was metabolized as an organic carbon source leading to higher specific growth rate of biomass. Phenol degradation pathway was elucidated using HPLC, liquid chromatography-mass spectrometry (LC-MS) and ultraviolet-visible (UV-visible) spectrophotometry. It involved both ortho- and meta-pathway with prominence of ortho-pathway. SEM analysis shows that cell membrane gets wrinkled on phenol exposure. Phenol degradation was growth and photodependent. Infrared analysis shows increased intracellular accumulation of neutral lipids opening possibility for utilization of spent biomass as biodiesel feedstock. The biomass after lipid extraction could be used as protein supplement in animal feed owing to enhanced protein content. The phenol remediation ability coupled with potential applicability of the spent biomass as biofuel feedstock and animal feed makes it a potential candidate for an environmentally sustainable process.

Application of isotopic labeling, and gas chromatography mass spectrometry, to understanding degradation products and pathways in the thermal-oxidative aging of Nylon 6.6

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Gregory Von; Clough, Roger L.; Hochrein, James M.

2013-12-01

Nylon 6.6 containing 13C isotopic labels at specific positions along the macromolecular backbone has been subjected to extensive thermal-oxidative aging at 138 °C for time periods up to 243 days. In complementary experiments, unlabeled Nylon 6.6 was subjected to the same aging conditions under an atmosphere of 18O 2. Volatile organic degradation products were analyzed by cryofocusing gas chromatography mass spectrometry (cryo-GC/MS) to identify the isotopic labeling. The labeling results, combined with basic considerations of free radical reaction chemistry, provided insights to the origin of degradation species, with respect to the macromolecular structure. A number of inferences on chemical mechanismsmore » were drawn, based on 1) the presence (or absence) of the isotopic labels in the various products, 2) the location of the isotope within the product molecule, and 3) the relative abundance of products as indicated by large differences in peak intensities in the gas chromatogram. The overall degradation results can be understood in terms of free radical pathways originating from initial attacks on three different positions along the nylon chain which include hydrogen abstraction from: the (CH 2) group adjacent to the nitrogen atom, at the (CH 2) adjacent the carbonyl group, and direct radical attack on the carbonyl. Understanding the pathways which lead to Nylon 6.6 degradation ultimately provides new insight into changes that can be leveraged to detect and reduce early aging and minimize problems associated with material degradation.« less

Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation.

PubMed

Guerra, Alaine B; Oliveira, Jorge S; Silva-Portela, Rita C B; Araújo, Wydemberg; Carlos, Aline C; Vasconcelos, Ana Tereza R; Freitas, Ana Teresa; Domingos, Yldeney Silva; de Farias, Mirna Ferreira; Fernandes, Glauber José Turolla; Agnez-Lima, Lucymara F

2018-04-01

Drill cuttings leave behind thousands of tons of residues without adequate treatment, generating a large environmental liability. Therefore knowledge about the microbial community of drilling residue may be useful for developing bioremediation strategies. In this work, samples of drilling residue were enriched in different culture media in the presence of petroleum, aiming to select potentially oil-degrading bacteria and biosurfactant producers. Total DNA was extracted directly from the drill cutting samples and from two enriched consortia and sequenced using the Ion Torrent platform. Taxonomic analysis revealed the predominance of Proteobacteria in the metagenome from the drill cuttings, while Firmicutes was enriched in consortia samples. Functional analysis using the Biosurfactants and Biodegradation Database (BioSurfDB) revealed a similar pattern among the three samples regarding hydrocarbon degradation and biosurfactants production pathways. However, some statistical differences were observed between samples. Namely, the pathways related to the degradation of fatty acids, chloroalkanes, and chloroalkanes were enriched in consortia samples. The degradation colorimetric assay using dichlorophenolindophenol as an indicator was positive for several hydrocarbon substrates. The consortia were also able to produce biosurfactants, with biosynthesis of iturin, lichnysin, and surfactin among the more abundant pathways. A microcosms assay followed by gas chromatography analysis showed the efficacy of the consortia in degrading alkanes, as we observed a reduction of around 66% and 30% for each consortium in total alkanes. These data suggest the potential use of these consortia in the bioremediation of drilling residue based on autochthonous bioaugmentation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Ribosomal protein-Mdm2-p53 pathway coordinates nutrient stress with lipid metabolism by regulating MCD and promoting fatty acid oxidation.

PubMed

Liu, Yong; He, Yizhou; Jin, Aiwen; Tikunov, Andrey P; Zhou, Lishi; Tollini, Laura A; Leslie, Patrick; Kim, Tae-Hyung; Li, Lei O; Coleman, Rosalind A; Gu, Zhennan; Chen, Yong Q; Macdonald, Jeffrey M; Graves, Lee M; Zhang, Yanping

2014-06-10

The tumor suppressor p53 has recently been shown to regulate energy metabolism through multiple mechanisms. However, the in vivo signaling pathways related to p53-mediated metabolic regulation remain largely uncharacterized. By using mice bearing a single amino acid substitution at cysteine residue 305 of mouse double minute 2 (Mdm2(C305F)), which renders Mdm2 deficient in binding ribosomal proteins (RPs) RPL11 and RPL5, we show that the RP-Mdm2-p53 signaling pathway is critical for sensing nutrient deprivation and maintaining liver lipid homeostasis. Although the Mdm2(C305F) mutation does not significantly affect growth and development in mice, this mutation promotes fat accumulation under normal feeding conditions and hepatosteatosis under acute fasting conditions. We show that nutrient deprivation inhibits rRNA biosynthesis, increases RP-Mdm2 interaction, and induces p53-mediated transactivation of malonyl-CoA decarboxylase (MCD), which catalyzes the degradation of malonyl-CoA to acetyl-CoA, thus modulating lipid partitioning. Fasted Mdm2(C305F) mice demonstrate attenuated MCD induction and enhanced malonyl-CoA accumulation in addition to decreased oxidative respiration and increased fatty acid accumulation in the liver. Thus, the RP-Mdm2-p53 pathway appears to function as an endogenous sensor responsible for stimulating fatty acid oxidation in response to nutrient depletion.

Photo-fenton degradation of diclofenac: identification of main intermediates and degradation pathway.

PubMed

Pérez-Estrada, Leónidas A; Malato, Sixto; Gernjak, Wolfgang; Agüera, Ana; Thurman, E Michael; Ferrer, Imma; Fernández-Alba, Amadeo R

2005-11-01

In recent years, the presence of pharmaceuticals in the aquatic environment has been of growing interest. These new contaminants are important because many of them are not degraded under the typical biological treatments applied in the wastewater treatment plants and represent a continuous input into the environment. Thus, compounds such as diclofenac are present in surface waters in all Europe and a crucial need for more enhanced technologies that can reduce its presence in the environment has become evident. In this sense, advanced oxidation processes (AOPs) represent a good choice for the treatment of hazardous nonbiodegradable pollutants. This work deals with the solar photodegradation of diclofenac, an antiinflammatory drug, in aqueous solutions by photo-Fenton reaction. A pilot-scale facility using a compound parabolic collector (CPC) reactor was used for this study. Results obtained show rapid and complete oxidation of diclofenac after 60 min, and total mineralization (disappearance of dissolved organic carbon, DOC) after 100 min of exposure to sunlight. Although diclofenac precipitates during the process at low pH, its degradation takes place in the homogeneous phase governed by a precipitation-redissolution-degradation process. Establishment of the reaction pathway was made possible by a thorough analysis of the reaction mixture identifying the main intermediate products generated. Gas chromatography-mass spectrometry (GC/ MS) and liquid chromatography coupled with time-of-flight mass spectrometry (LC/TOF-MS) were used to identify 18 intermediates, in two tentative degradation routes. The main one was based on the initial hydroxylation of the phenylacetic acid moiety in the C-4 position and subsequent formation of a quinone imine derivative that was the starting point for further multistep degradation involving hydroxylation, decarboxylation, and oxidation reactions. An alternative route was based on the transient preservation of the biphenyl amino moiety that underwent a similar oxidative process of C-N bond cleavage. The proposed degradation route differs from those previously reported involving alternative degradation processes (ozonization, UV/H2O2, or photolysis), indicating that diclofenac degradation follows different pathways, depending on the treatment applied.

Methoxyflavones from New Lingzhi Medicinal Mushroom, Ganoderma lingzhi (Agaricomycetes).

PubMed

Shimizu, Kuniyoshi; Amen, Yhiya M; Kaifuchi, Satoru

2016-01-01

Ganoderma lingzhi is one of the most famous medicinal fungi in the world. It has been used in folk medicine, especially in East Asian countries. It is also a white-rot fungus with strong wood degradation ability, especially against lignin. Different classes of bioactive natural products have been reported in Ganoderma, including triterpenes, polysaccharides, sterols, and peptides. The triterpenes and polysaccharides are the primary bioactive compounds of Ganoderma. We report for the first time the presence of 3 methoxyflavones as minor constituents in G. linghzi. The 3 compounds were identified based on different spectroscopic techniques, including 1- and 2-dimensional nuclear magnetic resonance (1H-1H correlation spectroscopy, heteronuclear single quantum coherence, and heteronuclear multiple bond correlation) and mass spectrometry (high-resolution electrospray ionization mass spectrometry). Our report provides an approach to a possible biosynthetic pathway for biosynthetic genes in the mushrooms. Another great possibility is that these compounds may exist or be formed through degradation of the components in the woody substrate, such as lignin, and then subsequently translocate to the fruiting bodies.

DNA repair in mammalian mitochondria: Much more than we thought?

PubMed

Liu, Pingfang; Demple, Bruce

2010-06-01

For many years, the repair of most damage in mitochondrial DNA (mtDNA) was thought limited to short-patch base excision repair (SP-BER), which replaces a single nucleotide by the sequential action of DNA glycosylases, an apurinic/apyrimidinic (AP) endonuclease, the mitochondrial DNA polymerase gamma, an abasic lyase activity, and mitochondrial DNA ligase. However, the likely array of lesions inflicted on mtDNA by oxygen radicals and the possibility of replication errors and disruptions indicated that such a restricted repair repertoire would be inadequate. Recent studies have considerably expanded our knowledge of mtDNA repair to include long-patch base excision repair (LP-BER), mismatch repair, and homologous recombination and nonhomologous end-joining. In addition, elimination of mutagenic 8-oxodeoxyguanosine triphosphate (8-oxodGTP) helps prevent cell death due to the accumulation of this oxidation product in mtDNA. Although it was suspected for many years that irreparably damaged mtDNA might be targeted for degradation, only recently was clear evidence provided for this hypothesis. Therefore, multiple DNA repair pathways and controlled degradation of mtDNA function together to maintain the integrity of mitochondrial genome.

PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3

DOE PAGES

Ni, Weimin; Xu, Shou-Ling; González-Grandío, Eduardo; ...

2017-05-11

Upon light-induced nuclear translocation, phytochrome (phy) sensory photoreceptors interact with, and induce rapid phosphorylation and consequent ubiquitin-mediated degradation of, transcription factors, called PIFs, thereby regulating target gene expression and plant development. Nevertheless, the biochemical mechanism of phy-induced PIF phosphorylation has remained ill-defined. Here in this paper we identify a family of nuclear protein kinases, designated Photoregulatory Protein Kinases (PPK1–4; formerly called MUT9-Like Kinases (MLKs)), that interact with PIF3 and phyB in a light-induced manner in vivo. Genetic analyses demonstrate that the PPKs are collectively necessary for the normal light-induced phosphorylation and degradation of PIF3. PPK1 directly phosphorylates PIF3 in vitro,more » with a phosphosite pattern that strongly mimics the light-induced pattern in vivo. These data establish that the PPKs are directly involved in catalysing the photoactivated-phy-induced phosphorylation of PIF3 in vivo, and thereby are critical components of a transcriptionally centred signalling hub that pleiotropically regulates plant growth and development in response to multiple signalling pathways.« less

Adenosine monophosphate-activated protein kinase attenuates cardiomyocyte hypertrophy through regulation of FOXO3a/MAFbx signaling pathway.

PubMed

Chen, Baolin; Wu, Qiang; Xiong, Zhaojun; Ma, Yuedong; Yu, Sha; Chen, Dandan; Huang, Shengwen; Dong, Yugang

2016-09-01

Control of cardiac muscle mass is thought to be determined by a dynamic balance of protein synthesis and degradation. Recent studies have demonstrated that atrophy-related forkhead box O 3a (FOXO3a)/muscle atrophy F-box (MAFbx) signaling pathway plays a central role in the modulation of proteolysis and exert inhibitory effect on cardiomyocyte hypertrophy. In this study, we tested the hypothesis that adenosine monophosphate-activated protein kinase (AMPK) activation attenuates cardiomyocyte hypertrophy by regulating FOXO3a/MAFbx signaling pathway and its downstream protein degradation. The results showed that activation of AMPK with 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR) attenuated cardiomyocyte hypertrophy induced by angiotensin II (Ang II). The antihypertrophic effects of AICAR were blunted by AMPK inhibitor Compound C. In addition, AMPK dramatically increased the activity of transcription factor FOXO3a, up-regulated the expression of its downstream ubiquitin ligase MAFbx, and enhanced cardiomyocyte proteolysis. Meanwhile, the effects of AMPK on protein degradation and cardiomyocyte hypertrophy were blocked after MAFbx was silenced by transfection of cardiomyocytes with MAFbx-siRNA. These results indicate that AMPK plays an important role in the inhibition of cardiomyocyte hypertrophy by activating protein degradation via FOXO3a/MAFbx signaling pathway. © The Author 2016. Published by Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Identification of a novel TIF-IA-NF-κB nucleolar stress response pathway.

PubMed

Chen, Jingyu; Lobb, Ian T; Morin, Pierre; Novo, Sonia M; Simpson, James; Kennerknecht, Kathrin; von Kriegsheim, Alex; Batchelor, Emily E; Oakley, Fiona; Stark, Lesley A

2018-06-05

p53 as an effector of nucleolar stress is well defined, but p53 independent mechanisms are largely unknown. Like p53, the NF-κB transcription factor plays a critical role in maintaining cellular homeostasis under stress. Many stresses that stimulate NF-κB also disrupt nucleoli. However, the link between nucleolar function and activation of the NF-κB pathway is as yet unknown. Here we demonstrate that artificial disruption of the PolI complex stimulates NF-κB signalling. Unlike p53 nucleolar stress response, this effect does not appear to be linked to inhibition of rDNA transcription. We show that specific stress stimuli of NF-κB induce degradation of a critical component of the PolI complex, TIF-IA. This degradation precedes activation of NF-κB and is associated with increased nucleolar size. It is mimicked by CDK4 inhibition and is dependent upon a novel pathway involving UBF/p14ARF and S44 of the protein. We show that blocking TIF-IA degradation blocks stress effects on nucleolar size and NF-κB signalling. Finally, using ex vivo culture, we show a strong correlation between degradation of TIF-IA and activation of NF-κB in freshly resected, human colorectal tumours exposed to the chemopreventative agent, aspirin. Together, our study provides compelling evidence for a new, TIF-IA-NF-κB nucleolar stress response pathway that has in vivo relevance and therapeutic implications.

Reconstructing metabolic pathways of a member of the genus Pelotomaculum suggesting its potential to oxidize benzene to carbon dioxide with direct reduction of sulfate.

PubMed

Dong, Xiyang; Dröge, Johannes; von Toerne, Christine; Marozava, Sviatlana; McHardy, Alice C; Meckenstock, Rainer U

2017-03-01

The enrichment culture BPL is able to degrade benzene with sulfate as electron acceptor and is dominated by an organism of the genus Pelotomaculum. Members of Pelotomaculum are usually known to be fermenters, undergoing syntrophy with anaerobic respiring microorganisms or methanogens. By using a metagenomic approach, we reconstructed a high-quality genome (∼2.97 Mbp, 99% completeness) for Pelotomaculum candidate BPL. The proteogenomic data suggested that (1) anaerobic benzene degradation was activated by a yet unknown mechanism for conversion of benzene to benzoyl-CoA; (2) the central benzoyl-CoA degradation pathway involved reductive dearomatization by a class II benzoyl-CoA reductase followed by hydrolytic ring cleavage and modified β-oxidation; (3) the oxidative acetyl-CoA pathway was utilized for complete oxidation to CO2. Interestingly, the genome of Pelotomaculum candidate BPL has all the genes for a complete sulfate reduction pathway including a similar electron transfer mechanism for dissimilatory sulfate reduction as in other Gram-positive sulfate-reducing bacteria. The proteome analysis revealed that the essential enzymes for sulfate reduction were all formed during growth with benzene. Thus, our data indicated that, besides its potential to anaerobically degrade benzene, Pelotomaculum candidate BPL is the first member of the genus that can perform sulfate reduction. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Biodegradation of 2-nitrotoluene by Micrococcus sp. strain SMN-1.

PubMed

Mulla, Sikandar I; Hoskeri, Robertcyril S; Shouche, Yogesh S; Ninnekar, Harichandra Z

2011-02-01

A bacterial consortium capable of degrading nitroaromatic compounds was isolated from pesticide-contaminated soil samples by selective enrichment on 2-nitrotoluene as a sole source of carbon and energy. The three different bacterial isolates obtained from bacterial consortium were identified as Bacillus sp. (A and C), Bacillus flexus (B) and Micrococcus sp. (D) on the basis of their morphological and biochemical characteristics and by phylogenetic analysis based on 16S rRNA gene sequences. The pathway for the degradation of 2-nitrotoluene by Micrococcus sp. strain SMN-1 was elucidated by the isolation and identification of metabolites, growth and enzymatic studies. The organism degraded 2-nitrotoluene through 3-methylcatechol by a meta-cleavage pathway, with release of nitrite.

Bovine Intestinal Bacteria Inactivate and Degrade Ceftiofur and Ceftriaxone with Multiple β-Lactamases▿

PubMed Central

Wagner, R. Doug; Johnson, Shemedia J.; Cerniglia, Carl E.; Erickson, Bruce D.

2011-01-01

The veterinary cephalosporin drug ceftiofur is rapidly degraded in the bovine intestinal tract. A cylinder-plate assay was used to detect microbiologically active ceftiofur, and high-performance liquid chromatography-mass spectrometry analysis was used to quantify the amount of ceftiofur remaining after incubation with bovine intestinal anaerobic bacteria, which were isolated from colon contents or feces from 8 cattle. Ninety-six percent of the isolates were able to inactivate ceftiofur to some degree, and 54% actually degraded the drug. None of 9 fungal isolates inactivated or degraded ceftiofur. Facultative and obligate anaerobic bacterial species that inactivated or degraded ceftiofur were identified with Vitek and Biolog systems, respectively. A subset of ceftiofur degraders also degraded the chemically similar drug ceftriaxone. Most of the species of bacteria that degraded ceftiofur belonged to the genera Bacillus and Bacteroides. PCR analysis of bacterial DNA detected specific β-lactamase genes. Bacillus cereus and B. mycoides isolates produced extended-spectrum β-lactamases and metallo-β-lactamases. Seven isolates of Bacteroides spp. produced multiple β-lactamases, including possibly CepA, and metallo-β-lactamases. Isolates of Eubacterium biforme, Bifidobacterium breve, and several Clostridium spp. also produced ceftiofur-degrading β-lactamases. An agar gel overlay technique on isoelectric focusing separations of bacterial lysates showed that β-lactamase enzymes were sufficient to degrade ceftiofur. These results suggest that ceftiofur is inactivated nonenzymatically and degraded enzymatically by multiple β-lactamases from bacteria in the large intestines of cattle. PMID:21876048

Bovine intestinal bacteria inactivate and degrade ceftiofur and ceftriaxone with multiple beta-lactamases.

PubMed

Wagner, R Doug; Johnson, Shemedia J; Cerniglia, Carl E; Erickson, Bruce D

2011-11-01

The veterinary cephalosporin drug ceftiofur is rapidly degraded in the bovine intestinal tract. A cylinder-plate assay was used to detect microbiologically active ceftiofur, and high-performance liquid chromatography-mass spectrometry analysis was used to quantify the amount of ceftiofur remaining after incubation with bovine intestinal anaerobic bacteria, which were isolated from colon contents or feces from 8 cattle. Ninety-six percent of the isolates were able to inactivate ceftiofur to some degree, and 54% actually degraded the drug. None of 9 fungal isolates inactivated or degraded ceftiofur. Facultative and obligate anaerobic bacterial species that inactivated or degraded ceftiofur were identified with Vitek and Biolog systems, respectively. A subset of ceftiofur degraders also degraded the chemically similar drug ceftriaxone. Most of the species of bacteria that degraded ceftiofur belonged to the genera Bacillus and Bacteroides. PCR analysis of bacterial DNA detected specific β-lactamase genes. Bacillus cereus and B. mycoides isolates produced extended-spectrum β-lactamases and metallo-β-lactamases. Seven isolates of Bacteroides spp. produced multiple β-lactamases, including possibly CepA, and metallo-β-lactamases. Isolates of Eubacterium biforme, Bifidobacterium breve, and several Clostridium spp. also produced ceftiofur-degrading β-lactamases. An agar gel overlay technique on isoelectric focusing separations of bacterial lysates showed that β-lactamase enzymes were sufficient to degrade ceftiofur. These results suggest that ceftiofur is inactivated nonenzymatically and degraded enzymatically by multiple β-lactamases from bacteria in the large intestines of cattle.

Brassinosteroid-Induced Transcriptional Repression and Dephosphorylation-Dependent Protein Degradation Negatively Regulate BIN2-Interacting AIF2 (a BR Signaling-Negative Regulator) bHLH Transcription Factor.

PubMed

Kim, Yoon; Song, Ji-Hye; Park, Seon-U; Jeong, You-Seung; Kim, Soo-Hwan

2017-02-01

Brassinosteroids (BRs) are plant polyhydroxy-steroids that play important roles in plant growth and development via extensive signal integration through direct interactions between regulatory components of different signaling pathways. Recent studies have shown that diverse helix-loop-helix/basic helix-loop-helix (HLH/bHLH) family proteins are actively involved in control of BR signaling pathways and interact with other signaling pathways. In this study, we show that ATBS1-INTERACTING FACTOR 2 (AIF2), a nuclear-localized atypical bHLH transcription factor, specifically interacts with BRASSINOSTEROID-INSENSITIVE 2 (BIN2) among other BR signaling molecules. Overexpression of AIF2 down-regulated transcript expression of growth-promoting genes, thus resulting in retardation of growth. AIF2 renders plants hyposensitive to BR-induced root growth inhibition, but shows little effects on BR-promoted hypocotyl elongation. Notably, AIF2 was dephosphorylated by BR, and the dephosphorylated AIF2 was subject to proteasome-mediated degradation. AIF2 degradation was greatly induced by BR and ABA, but relatively slightly by other hormones such as auxin, gibberellin, cytokinin and ethylene. Moreover, AIF2 transcription was significantly suppressed by a BRI1/BZR1-mediated BR signaling pathway through a direct binding of BRASSINAZOLE RESISTANT 1 (BZR1) to the BR response element (BRRE) region of the AIF2 promoter. In conclusion, our study suggests that BIN2-driven AIF2 phosphorylation could augment the BIN2/AIF2-mediated negative circuit of BR signaling pathways, and the BR-induced transcriptional repression and protein degradation negatively regulate AIF2 transcription factor, reinforcing the BZR1/BES1-mediated positive BR signaling pathway. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Land cover effects on infiltration and preferential flow pathways in the high rainfall zone of Madagascar

NASA Astrophysics Data System (ADS)

Zwartendijk, Bob; van Meerveld, Ilja; Ravelona, Maafaka; Razakamanarivo, Herintsitohaina; Ghimire, Chandra; Bruijnzeel, Sampurno; Jones, Julia

2015-04-01

Shortened slash-and-burn cycles exhaust agricultural land and have resulted in extensive tracts of highly degraded land across the tropics. Land degradation typically results in decreased rainfall infiltration due to a reduced field-saturated hydraulic conductivity of the topsoil because of a progressive decline in soil organic matter, exposure to raindrop impact, surface sealing and compaction. This results, in turn, in enhanced surface runoff and erosion, and consequently less subsurface flow and groundwater recharge. On the other hand, natural vegetation regrowth or active reforestation can lead to a renewed accumulation of soil organic matter, macropore development and increased infiltration rates. As part of the P4GES project (Can Paying 4 Global Ecosystem Services values reduce poverty?; www.p4ges.org), we study the effects of land use change and reforestation on water resources in the Corridor Ankeniheny-Zahamena (CAZ) in eastern Madagascar. In this poster, we present the results of infiltration and preferential flow measurements in four different land uses in the southern part of the CAZ: (i) closed canopy forest, (ii) 3-14 year-old regrowth on fallow land (savokas), (iii) exhausted and severely degraded land (tany maty), and (iv) recently reforested sites (6-8 years old). The results show that infiltrability increases significantly after several years of forest regrowth after land abandonment, but it remains unclear whether active replanting decreases the time required for restoration of soil hydrological functioning. Preferential flow pathways differed strikingly between the respective land cover types: infiltration in mature forests was predominantly characterized by macropore flow (preferential flow pathways), whereas infiltration in exhausted agricultural land was dominated by matrix flow (few preferential flow pathways). Occurrence of preferential flow pathways in reforestation and fallow sites varied considerably. These results suggest that land cover significantly affects hydrological flow pathways and that natural regeneration and active reforestation of degraded land can result in increased infiltration and a reduced likelihood for surface runoff.

New metabolic pathway for degradation of 2-nitrobenzoate by Arthrobacter sp. SPG

PubMed Central

Arora, Pankaj K.; Sharma, Ashutosh

2015-01-01

Arthrobacter sp. SPG utilized 2-nitrobenzoate as its sole source of carbon and energy and degraded it with accumulation of stoichiometric amounts of nitrite ions. Salicylate and catechol were detected as metabolites of the 2-nitrobenzoate degradation using high performance liquid chromatography and gas chromatography–mass spectrometry. Enzyme activities for 2-nitrobenzoate-2-monooxygenase, salicylate hydroxylase, and catechol-1,2-dioxygenase were detected in the crude extracts of the 2-nitrobenzoate-induced cells of strain SPG. The 2-nitrobenzoate-monooxygenase activity resulted in formation of salicylate and nitrite from 2-nitrobenzoate, whereas salicylate hydroxylase catalyzed the conversion of salicylate to catechol. The ring-cleaving enzyme, catechol-1,2-dioxygenase cleaved catechol to cis,cis-muconic acid. Cells of strain SPG were able to degrade 2-nitrobenzoate in sterile as well as non-sterile soil microcosms. The results of microcosm studies showed that strain SPG degraded more than 90% of 2-nitrobenzoate within 10–12 days. This study clearly shows that Arthrobacter sp. SPG degraded 2-nitrobenzoate via a new pathway with formation of salicylate and catechol as metabolites. Arthrobacter sp. SPG may be used for bioremediation of 2-nitrobenzoate-contaminated sites due to its ability to degrade 2-nitrobenzoate in soil. PMID:26082768

Food-derived immunomodulatory peptides.

PubMed

Santiago-López, Lourdes; Hernández-Mendoza, Adrián; Vallejo-Cordoba, Belinda; Mata-Haro, Verónica; González-Córdova, Aarón F

2016-08-01

Food proteins contain specific amino acid sequences within their structures that may positively impact bodily functions and have multiple immunomodulatory effects. The functional properties of these specific sequences, also referred to as bioactive peptides, are revealed only after the degradation of native proteins during digestion processes. Currently, milk proteins have been the most explored source of bioactive peptides, which presents an interesting opportunity for the dairy industry. However, plant- and animal-derived proteins have also been shown to be important sources of bioactive peptides. This review summarizes the in vitro and in vivo evidence of the role of various food proteins as sources of immunomodulatory peptides and discusses the possible pathways involving these properties. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Ubiquitin-dependent trafficking and turnover of ionotropic glutamate receptors

PubMed Central

Goo, Marisa S.; Scudder, Samantha L.; Patrick, Gentry N.

2015-01-01

Changes in synaptic strength underlie the basis of learning and memory and are controlled, in part, by the insertion or removal of AMPA-type glutamate receptors at the postsynaptic membrane of excitatory synapses. Once internalized, these receptors may be recycled back to the plasma membrane by subunit-specific interactions with other proteins or by post-translational modifications such as phosphorylation. Alternatively, these receptors may be targeted for destruction by multiple degradation pathways in the cell. Ubiquitination, another post-translational modification, has recently emerged as a key signal that regulates the recycling and trafficking of glutamate receptors. In this review, we will discuss recent findings on the role of ubiquitination in the trafficking and turnover of ionotropic glutamate receptors and plasticity of excitatory synapses. PMID:26528125

Ubiquitin-like and ubiquitin-associated domain proteins: significance in proteasomal degradation

PubMed Central

Lau, Alan F.

2009-01-01

The ubiquitin–proteasome pathway of protein degradation is one of the major mechanisms that are involved in the maintenance of the proper levels of cellular proteins. The regulation of proteasomal degradation thus ensures proper cell functions. The family of proteins containing ubiquitin-like (UbL) and ubiquitin-associated (UBA) domains has been implicated in proteasomal degradation. UbL–UBA domain containing proteins associate with substrates destined for degradation as well as with subunits of the proteasome, thus regulating the proper turnover of proteins. PMID:19468686

Genetic and Hormonal Regulation of Chlorophyll Degradation during Maturation of Seeds with Green Embryos.

PubMed

Smolikova, Galina; Dolgikh, Elena; Vikhnina, Maria; Frolov, Andrej; Medvedev, Sergei

2017-09-16

The embryos of some angiosperms (usually referred to as chloroembryos) contain chlorophylls during the whole period of embryogenesis. Developing embryos have photochemically active chloroplasts and are able to produce assimilates, further converted in reserve biopolymers, whereas at the late steps of embryogenesis, seeds undergo dehydration, degradation of chlorophylls, transformation of chloroplast in storage plastids, and enter the dormancy period. However, in some seeds, the process of chlorophyll degradation remains incomplete. These residual chlorophylls compromise the quality of seed material in terms of viability, nutritional value, and shelf life, and represent a serious challenge for breeders and farmers. The mechanisms of chlorophyll degradation during seed maturation are still not completely understood, and only during the recent decades the main pathways and corresponding enzymes could be characterized. Among the identified players, the enzymes of pheophorbide a oxygenase pathway and the proteins encoded by STAY GREEN ( SGR ) genes are the principle ones. On the biochemical level, abscisic acid (ABA) is the main regulator of seed chlorophyll degradation, mediating activity of corresponding catabolic enzymes on the transcriptional level. In general, a deep insight in the mechanisms of chlorophyll degradation is required to develop the approaches for production of chlorophyll-free high quality seeds.

Sulfate radical degradation of acetaminophen by novel iron-copper bimetallic oxidation catalyzed by persulfate: Mechanism and degradation pathways

NASA Astrophysics Data System (ADS)

Zhang, Yuanchun; Zhang, Qian; Hong, Junming

2017-11-01

A novel iron coupled copper oxidate (Fe2O3@Cu2O) catalyst was synthesized to activate persulfate (PS) for acetaminophen (APAP) degradation. The catalysts were characterized via field-emission scanning electron microscopy and energy-dispersive X-ray spectrometry. The effects of the catalyst, PS concentration, catalyst dosage, initial pH, dissolved oxygen were analyzed for treatment optimization. Results indicated that Fe2O3@Cu2O achieved higher efficiency in APAP degradation than Fe2O3/PS and Cu2O/PS systems. The optimal removal efficiency of APAP (90%) was achieved within 40 min with 0.6 g/L PS and 0.3 g/L catalyst. To clarify the mechanism for APAP degradation, intermediates were analyzed with gas chromatography-mass spectrometry. Three possible degradation pathways were identified. During reaction, Cu(I) was found to react with Fe(III) to generate Fe(II), which is the most active phase for PS activation. Through the use of methanol and tert-butyl alcohol (TBA) as radical trappers, SO4rad - was identified as the main radical species that is generated during oxidation.

Genetic and Hormonal Regulation of Chlorophyll Degradation during Maturation of Seeds with Green Embryos

PubMed Central

Dolgikh, Elena; Vikhnina, Maria; Frolov, Andrej

2017-01-01

The embryos of some angiosperms (usually referred to as chloroembryos) contain chlorophylls during the whole period of embryogenesis. Developing embryos have photochemically active chloroplasts and are able to produce assimilates, further converted in reserve biopolymers, whereas at the late steps of embryogenesis, seeds undergo dehydration, degradation of chlorophylls, transformation of chloroplast in storage plastids, and enter the dormancy period. However, in some seeds, the process of chlorophyll degradation remains incomplete. These residual chlorophylls compromise the quality of seed material in terms of viability, nutritional value, and shelf life, and represent a serious challenge for breeders and farmers. The mechanisms of chlorophyll degradation during seed maturation are still not completely understood, and only during the recent decades the main pathways and corresponding enzymes could be characterized. Among the identified players, the enzymes of pheophorbide a oxygenase pathway and the proteins encoded by STAY GREEN (SGR) genes are the principle ones. On the biochemical level, abscisic acid (ABA) is the main regulator of seed chlorophyll degradation, mediating activity of corresponding catabolic enzymes on the transcriptional level. In general, a deep insight in the mechanisms of chlorophyll degradation is required to develop the approaches for production of chlorophyll-free high quality seeds. PMID:28926960

Development of a pressurized liquid extraction-solid-phase extraction followed by liquid chromatography-electrospray ionization tandem mass spectrometry method for the quantitative determination of benzoxazolinones and their degradation products in agricultural soil.

PubMed

Villagrasa, M; Guillamón, M; Navarro, A; Eljarrat, E; Barceló, D

2008-02-01

A new analytical method for the quantitative determination of benzoxazolinones and their degradation products in agricultural soils based on the use of pressurized liquid extraction (PLE) followed by solid-phase extraction (SPE) and then instrumental determination using liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS-MS) is described. Using this method, the characterization, separation and quantitative detection of a mixture of two benzoxazolinones, benzoxazolin-2-one (BOA) and 6-methoxybenzoxazolin-2-one (MBOA) and their degradation products, 2-aminophenol (APH), N-(2-hydroxyphenyl)malonamic acid (HMPMA), 2-amino-3-H-phenoxazin-3-one (APO), 9-methoxy-2-amino-3-H-phenoxazin-3-one (AMPO), 2-acetylamino-3-H-phenoxazin-3-one (AAPO) and 2-acetylamino-9-methoxy-2-amino-3-H-phenoxazin-3-one (AAMPO) was achieved. The complete LC-ESI-MS-MS precursor-product ion fragmentation pathways for the degradation products of benzoxazolinones are described for the first time. Quantitative analysis was done in the multiple reaction mode using two specific combinations of precursor-product ion transitions for each compound. The optimized method was quality assessed by the measure of parameter as recovery, linearity, sensitivity, repeatability and reproducibility. Recoveries of the analytes ranged from 53 to 123%. The developed method offered improvements to the sensitivity as compared with our previously LC-MS method, with detection limits down to 2.4-21 ng/g of dry weight. This achievement allows us to identify and quantify for the first time degradation products of benzoxazolinones in real agricultural soil samples. Analytes were found in the range of 20.6-149 ng/g dry weight.

Chlorophyll Degradation: The Tocopherol Biosynthesis-Related Phytol Hydrolase in Arabidopsis Seeds Is Still Missing1[C][W][OPEN

PubMed Central

Zhang, Wei; Liu, Tianqi; Ren, Guodong; Hörtensteiner, Stefan; Zhou, Yongming; Cahoon, Edgar B.; Zhang, Chunyu

2014-01-01

Phytyl diphosphate (PDP) is the prenyl precursor for tocopherol biosynthesis. Based on recent genetic evidence, PDP is supplied to the tocopherol biosynthetic pathway primarily by chlorophyll degradation and sequential phytol phosphorylation. Three enzymes of Arabidopsis (Arabidopsis thaliana) are known to be capable of removing the phytol chain from chlorophyll in vitro: chlorophyllase1 (CLH1), CLH2, and pheophytin pheophorbide hydrolase (PPH), which specifically hydrolyzes pheophytin. While PPH, but not chlorophyllases, is required for in vivo chlorophyll breakdown during Arabidopsis leaf senescence, little is known about the involvement of these phytol-releasing enzymes in tocopherol biosynthesis. To explore the origin of PDP for tocopherol synthesis, seed tocopherol concentrations were determined in Arabidopsis lines engineered for seed-specific overexpression of PPH and in single and multiple mutants in the three genes encoding known dephytylating enzymes. Except for modestly increasing tocopherol content observed in the PPH overexpressor, none of the remaining lines exhibited significantly reduced tocopherol concentrations, suggesting that the known chlorophyll-derived phytol-releasing enzymes do not play major roles in tocopherol biosynthesis. Tocopherol content of seeds from double mutants in NONYELLOWING1 (NYE1) and NYE2, regulators of chlorophyll degradation, had modest reduction compared with wild-type seeds, although mature seeds of the double mutant retained significantly higher chlorophyll levels. These findings suggest that NYEs may play limited roles in regulating an unknown tocopherol biosynthesis-related phytol hydrolase. Meanwhile, seeds of wild-type over-expressing NYE1 had lower tocopherol levels, suggesting that phytol derived from NYE1-dependent chlorophyll degradation probably doesn’t enter tocopherol biosynthesis. Potential routes of chlorophyll degradation are discussed in relation to tocopherol biosynthesis. PMID:25059706

Sonochemical degradation of endocrine-disrupting organochlorine pesticide Dicofol: Investigations on the transformation pathways of dechlorination and the influencing operating parameters.

PubMed

Debabrata, Panda; Sivakumar, Manickam

2018-08-01

Dicofol, an extensively used organochlorine pesticide and a recommended Stockholm convention persistent organic pollutant (POP) candidate is well known for its endocrine disruptive properties. The sonochemical degradation of Dicofol in aqueous media has been investigated using a 20-kHz probe type sonicator with power inputs from 150 to 450 W. The degradation rate was determined as a function of concentration of Dicofol, solution pH, bulk phase temperature, ultrasonic power density and H 2 O 2 addition. At optimum operating conditions, the pseudo-first-order degradation rate constant (k) was determined to be 0.032 min -1 and the extent of degradation was found to be 86% within 60 min of ultrasound treatment. High performance liquid chromatography (HPLC) and Gas chromatography coupled with mass spectroscopy (GC-MS) analysis indicated the presence of degraded products. The obtained results of Dicofol degradation and control experiments in the presence of H 2 O 2 and radical scavenger test suggest thermal decomposition along with radical attack at bubble-vapor interface to be the dominant degradation pathway. Sonochemical treatment is effective and promising for successful removal of harmful pesticides such as Dicofol and superior removal efficiency for other POPs is expected in the near future with the successful implementation of ultrasound-based wastewater treatment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effect of various gases and chemical catalysts on phenol degradation pathways by pulsed electrical discharges.

PubMed

Shen, Yongjun; Lei, Lecheng; Zhang, Xingwang; Zhou, Minghua; Zhang, Yi

2008-02-11

The processes of phenol degradation by pulsed electrical discharges were investigated under several kinds of discharge atmospheres (oxygen, argon, nitrogen and ozone) and chemical catalysts (ferrous ion and hydrogen peroxide). The temporal variations of the concentrations of phenol and the intermediate products were monitored by HPLC and GC-MS, respectively. It has been found that the effect of various gases bubbling on phenol degradation rate ranked in the following order: oxygen-containing ozone>oxygen>argon>nitrogen. The high gas bubbling flow rate was beneficial to the removal of phenol. It was found that the degradation proceeded differently when in the presence and absence of catalysts. The phenol removal rate was increased when ferrous ion was added. This considerable enhancement may be due to the Fenton's reaction. What's more, putting the chemical additives hydrogen peroxide into the reactor led to a dramatic increase in phenol degradation rate. The mechanism was due to the direct or indirect photolysis and pyrolysis destruction in plasma channel. Furthermore, the intermediate products were monitored by GC-MS under three degradation conditions. More THBs were generated under degradation conditions without gases bubbling or adding any catalyst, and more DHBs under the condition of adding ferrous ion, and more carboxylic acids under the condition of oxygen-containing ozone gas bubbling. Consequently, three distinct degradation pathways based on different conditions were proposed.

Combatting Inherent Vulnerabilities of CFAR Algorithms and a New Robust CFAR Design

DTIC Science & Technology

1993-09-01

elements of any automatic radar system. Unfortunately, CFAR systems are inherently vulnerable to degradation caused by large clutter edges, multiple ...edges, multiple targets, and electronic countermeasures (ECM) environments. 20 Distribution, Availability of Abstract 21 Abstract Security...inherently vulnerable to degradation caused by large clutter edges, multiple targets and jamming environments. This thesis presents eight popular and studied

Recovering of images degraded by atmosphere

NASA Astrophysics Data System (ADS)

Lin, Guang; Feng, Huajun; Xu, Zhihai; Li, Qi; Chen, Yueting

2017-08-01

Remote sensing images are seriously degraded by multiple scattering and bad weather. Through the analysis of the radiative transfer procedure in atmosphere, an image atmospheric degradation model considering the influence of atmospheric absorption multiple scattering and non-uniform distribution is proposed in this paper. Based on the proposed model, a novel recovering method is presented to eliminate atmospheric degradation. Mean-shift image segmentation and block-wise deconvolution are used to reduce time cost, retaining a good result. The recovering results indicate that the proposed method can significantly remove atmospheric degradation and effectively improve contrast compared with other removal methods. The results also illustrate that our method is suitable for various degraded remote sensing, including images with large field of view (FOV), images taken in side-glance situations, image degraded by atmospheric non-uniform distribution and images with various forms of clouds.

Cystathionine beta-synthase deficiency alters hepatic phospholipid and choline metabolism: Post-translational repression of phosphatidylethanolamine N-methyltransferase is a consequence rather than a cause of liver injury in homocystinuria.

PubMed

Jacobs, René L; Jiang, Hua; Kennelly, John P; Orlicky, David J; Allen, Robert H; Stabler, Sally P; Maclean, Kenneth N

2017-04-01

Classical homocystinuria (HCU) due to inactivating mutation of cystathionine β-synthase (CBS) is a poorly understood life-threatening inborn error of sulfur metabolism. A previously described cbs-/- mouse model exhibits a semi-lethal phenotype due to neonatal liver failure. The transgenic HO mouse model of HCU exhibits only mild liver injury and recapitulates multiple aspects of the disease as it occurs in humans. Disruption of the methionine cycle in HCU has the potential to impact multiple aspect of phospholipid (PL) metabolism by disruption of both the Kennedy pathway and phosphatidylethanolamine N-methyltransferase (PEMT) mediated synthesis of phosphatidylcholine (PC). Comparative metabolomic analysis of HO mouse liver revealed decreased levels of choline, and choline phosphate indicating disruption of the Kennedy pathway. Alterations in the relative levels of multiple species of PL included significant increases in PL degradation products consistent with enhanced membrane PL turnover. A significant decrease in PC containing 20:4n6 which primarily formed by the methylation of phosphatidylethanolamine to PC was consistent with decreased flux through PEMT. Hepatic expression of PEMT in both the cbs-/- and HO models is post-translationally repressed with decreased levels of PEMT protein and activity that inversely-correlates with the scale of liver injury. Failure to induce further repression of PEMT in HO mice by increased homocysteine, methionine and S-adenosylhomocysteine or depletion of glutathione combined with examination of multiple homocysteine-independent models of liver injury indicated that repression of PEMT in HCU is a consequence rather than a cause of liver injury. Collectively, our data show significant alteration of a broad range of hepatic PL and choline metabolism in HCU with the potential to contribute to multiple aspects of pathogenesis in this disease. Copyright © 2017 Elsevier Inc. All rights reserved.

Indoleamine 2,3 Dioxygenase as a Potential Therapeutic Target in Huntington's Disease.

PubMed

Mazarei, Gelareh; Leavitt, Blair R

2015-01-01

Within the past decade, there has been increasing interest in the role of tryptophan (Trp) metabolites and the kynurenine pathway (KP) in diseases of the brain such as Huntington's disease (HD). Evidence is accumulating to suggest that this pathway is imbalanced in neurologic disease states. The KP diverges into two branches that can lead to production of either neuroprotective or neurotoxic metabolites. In one branch, kynurenine (Kyn) produced as a result of tryptophan (Trp) catabolism is further metabolized to neurotoxic metabolites such as 3-hydroxykunurenine (3-HK) and quinolinic acid (QA). In the other branch, Kyn is converted to the neuroprotective metabolite kynurenic acid (KA). The enzyme Indoleamine 2,3 dioxygenase (IDO1) catalyzes the conversion of Trp into Kyn, the first and rate-limiting enzymatic step of the KP. This reaction takes place throughout the body in multiple cell types as a required step in the degradation of the essential amino acid Trp. Studies of IDO1 in brain have focused primarily on a potential role in depression, immune tolerance associated with brain tumours, and multiple sclerosis; however the role of this enzyme in neurodegenerative disease has garnered significant attention in recent years. This review will provide a summary of the current understanding of the role of IDO1 in Huntington's disease and will assess this enzyme as a potential therapeutic target for HD.

Ubiquitin C-Terminal Hydrolase L1 (UCH-L1) Promotes Hippocampus-Dependent Memory via Its Deubiquitinating Effect on TrkB.

PubMed

Guo, Yun-Yun; Lu, Yi; Zheng, Yuan; Chen, Xiao-Rong; Dong, Jun-Lu; Yuan, Rong-Rong; Huang, Shu-Hong; Yu, Hui; Wang, Yue; Chen, Zhe-Yu; Su, Bo

2017-06-21

Multiple studies have established that brain-derived neurotrophic factor (BDNF) plays a critical role in the regulation of synaptic plasticity via its receptor, TrkB. In addition to being phosphorylated, TrkB has also been demonstrated to be ubiquitinated. However, the mechanisms of TrkB ubiquitination and its biological functions remain poorly understood. In this study, we demonstrate that ubiquitin C-terminal hydrolase L1 (UCH-L1) promotes contextual fear conditioning learning and memory via the regulation of ubiquitination of TrkB. We provide evidence that UCH-L1 can deubiquitinate TrkB directly. K460 in the juxtamembane domain of TrkB is the primary ubiquitination site and is regulated by UCH-L1. By using a peptide that competitively inhibits the association between UCH-L1 and TrkB, we show that the blockade of UCH-L1-regulated TrkB deubiquitination leads to increased BDNF-induced TrkB internalization and consequently directs the internalized TrkB to the degradation pathway, resulting in increased degradation of surface TrkB and attenuation of TrkB activation and its downstream signaling pathways. Moreover, injection of the peptide into the DG region of mice impairs hippocampus-dependent memory. Together, our results suggest that the ubiquitination of TrkB is a mechanism that controls its downstream signaling pathways via the regulation of its endocytosis and postendocytic trafficking and that UCH-L1 mediates the deubiquitination of TrkB and could be a potential target for the modulation of hippocampus-dependent memory. SIGNIFICANCE STATEMENT Ubiquitin C-terminal hydrolase L1 (UCH-L1) has been demonstrated to play important roles in the regulation of synaptic plasticity and learning and memory. TrkB, the receptor for brain-derived neurotrophic factor, has also been shown to be a potent regulator of synaptic plasticity. In this study, we demonstrate that UCH-L1 functions as a deubiquitinase for TrkB. The blockage of UCH-L1-regulated deubiquitination of TrkB eventually results in the increased degradation of surface TrkB and decreased activation of TrkB and its downstream signaling pathways. In vivo , UCH-L1-regulated TrkB deubiquitination is necessary for hippocampus-dependent memory. Overall, our study provides novel insights into the mechanisms of UCH-L1-mediated neurobiological functions and suggests that ubiquitination is an important regulatory signal for TrkB functions. Copyright © 2017 the authors 0270-6474/17/375978-18$15.00/0.

Cyclophilin C Participates in the US2-Mediated Degradation of Major Histocompatibility Complex Class I Molecules.

PubMed

Chapman, Daniel C; Stocki, Pawel; Williams, David B

2015-01-01

Human cytomegalovirus uses a variety of mechanisms to evade immune recognition through major histocompatibility complex class I molecules. One mechanism mediated by the immunoevasin protein US2 causes rapid disposal of newly synthesized class I molecules by the endoplasmic reticulum-associated degradation pathway. Although several components of this degradation pathway have been identified, there are still questions concerning how US2 targets class I molecules for degradation. In this study we identify cyclophilin C, a peptidyl prolyl isomerase of the endoplasmic reticulum, as a component of US2-mediated immune evasion. Cyclophilin C could be co-isolated with US2 and with the class I molecule HLA-A2. Furthermore, it was required at a particular expression level since depletion or overexpression of cyclophilin C impaired the degradation of class I molecules. To better characterize the involvement of cyclophilin C in class I degradation, we used LC-MS/MS to detect US2-interacting proteins that were influenced by cyclophilin C expression levels. We identified malectin, PDIA6, and TMEM33 as proteins that increased in association with US2 upon cyclophilin C knockdown. In subsequent validation all were shown to play a functional role in US2 degradation of class I molecules. This was specific to US2 rather than general ER-associated degradation since depletion of these proteins did not impede the degradation of a misfolded substrate, the null Hong Kong variant of α1-antitrypsin.

Cyclophilin C Participates in the US2-Mediated Degradation of Major Histocompatibility Complex Class I Molecules

PubMed Central

Chapman, Daniel C.; Stocki, Pawel; Williams, David B.

2015-01-01

Human cytomegalovirus uses a variety of mechanisms to evade immune recognition through major histocompatibility complex class I molecules. One mechanism mediated by the immunoevasin protein US2 causes rapid disposal of newly synthesized class I molecules by the endoplasmic reticulum-associated degradation pathway. Although several components of this degradation pathway have been identified, there are still questions concerning how US2 targets class I molecules for degradation. In this study we identify cyclophilin C, a peptidyl prolyl isomerase of the endoplasmic reticulum, as a component of US2-mediated immune evasion. Cyclophilin C could be co-isolated with US2 and with the class I molecule HLA-A2. Furthermore, it was required at a particular expression level since depletion or overexpression of cyclophilin C impaired the degradation of class I molecules. To better characterize the involvement of cyclophilin C in class I degradation, we used LC-MS/MS to detect US2-interacting proteins that were influenced by cyclophilin C expression levels. We identified malectin, PDIA6, and TMEM33 as proteins that increased in association with US2 upon cyclophilin C knockdown. In subsequent validation all were shown to play a functional role in US2 degradation of class I molecules. This was specific to US2 rather than general ER-associated degradation since depletion of these proteins did not impede the degradation of a misfolded substrate, the null Hong Kong variant of α1-antitrypsin. PMID:26691022

Lewy Body-like α-Synuclein Aggregates Resist Degradation and Impair Macroautophagy*♦

PubMed Central

Tanik, Selcuk A.; Schultheiss, Christine E.; Volpicelli-Daley, Laura A.; Brunden, Kurt R.; Lee, Virginia M. Y.

2013-01-01

Cytoplasmic α-synuclein (α-syn) aggregates, referred to as Lewy bodies, are pathological hallmarks of a number of neurodegenerative diseases, most notably Parkinson disease. Activation of macroautophagy is suggested to facilitate degradation of certain proteinaceous inclusions, but it is unclear if this pathway is capable of degrading α-syn aggregates. Here, we examined this issue by utilizing cellular models in which intracellular Lewy body-like α-syn inclusions accumulate after internalization of pre-formed α-syn fibrils into α-syn-expressing HEK293 cells or cultured primary neurons. We demonstrate that α-syn inclusions cannot be effectively degraded, even though they co-localize with essential components of both the autophagic and proteasomal protein degradation pathways. The α-syn aggregates persist even after soluble α-syn levels have been substantially reduced, suggesting that once formed, the α-syn inclusions are refractory to clearance. Importantly, we also find that α-syn aggregates impair overall macroautophagy by reducing autophagosome clearance, which may contribute to the increased cell death that is observed in aggregate-bearing cells. PMID:23532841

Endoplasmic reticulum stress and proteasomal system in amyotrophic lateral sclerosis.

PubMed

Karademir, Betul; Corek, Ceyda; Ozer, Nesrin Kartal

2015-11-01

Protein processing including folding, unfolding and degradation is involved in the mechanisms of many diseases. Unfolded protein response and/or endoplasmic reticulum stress are accepted to be the first steps which should be completed via protein degradation. In this direction, proteasomal system and autophagy play important role as the degradation pathways and controlled via complex mechanisms. Amyotrophic lateral sclerosis is a multifactorial neurodegenerative disease which is also known as the most catastrophic one. Mutation of many different genes are involved in the pathogenesis such as superoxide dismutase 1, chromosome 9 open reading frame 72 and ubiquilin 2. These genes are mainly related to the antioxidant defense systems, endoplasmic reticulum stress related proteins and also protein aggregation, degradation pathways and therefore mutation of these genes cause related disorders.This review focused on the role of protein processing via endoplasmic reticulum and proteasomal system in amyotrophic lateral sclerosis which are the main players in the pathology. In this direction, dysfunction of endoplasmic reticulum associated degradation and related cell death mechanisms that are autophagy/apoptosis have been detailed. Copyright © 2015 Elsevier Inc. All rights reserved.

Cometabolic degradation of chloramphenicol via a meta-cleavage pathway in a microbial fuel cell and its microbial community.

PubMed

Zhang, Qinghua; Zhang, Yanyan; Li, Daping

2017-04-01

The performance of a microbial fuel cell (MFC) in terms of degradation of chloramphenicol (CAP) was investigated. Approximately 84% of 50mg/L CAP was degraded within 12h in the MFC. A significant interaction of pH, temperature, and initial CAP concentration was found on removal of CAP, and a maximum degradation rate of 96.53% could theoretically be achieved at 31.48°C, a pH of 7.12, and an initial CAP concentration of 106.37mg/L. Moreover, CAP was further degraded through a ring-cleavage pathway. The antibacterial activity of CAP towards Escherichia coli ATCC 25922 and Shewanella oneidensis MR-1 was largely eliminated by MFC treatment. High-throughput sequencing analysis indicated that Azonexus, Comamonas, Nitrososphaera, Chryseobacterium, Azoarcus, Rhodococcus, and Dysgonomonas were the predominant genera in the MFC anode biofilm. In conclusion, the MFC shows potential for the treatment of antibiotic residue-containing wastewater due to its high rates of CAP removal and energy recovery. Copyright © 2017 Elsevier Ltd. All rights reserved.

Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases

PubMed Central

Devkota, Sushil; Jeong, Hyobin; Kim, Yunmi; Ali, Muhammad; Roh, Jae-il; Hwang, Daehee; Lee, Han-Woong

2016-01-01

ABSTRACT Historically, the ubiquitin-proteasome system (UPS) and autophagy pathways were believed to be independent; however, recent data indicate that these pathways engage in crosstalk. To date, the players mediating this crosstalk have been elusive. Here, we show experimentally that EI24 (EI24, autophagy associated transmembrane protein), a key component of basal macroautophagy/autophagy, degrades 14 physiologically important E3 ligases with a RING (really interesting new gene) domain, whereas 5 other ligases were not degraded. Based on the degradation results, we built a statistical model that predicts the RING E3 ligases targeted by EI24 using partial least squares discriminant analysis. Of 381 RING E3 ligases examined computationally, our model predicted 161 EI24 targets. Those targets are primarily involved in transcription, proteolysis, cellular bioenergetics, and apoptosis and regulated by TP53 and MTOR signaling. Collectively, our work demonstrates that EI24 is an essential player in UPS-autophagy crosstalk via degradation of RING E3 ligases. These results indicate a paradigm shift regarding the fate of E3 ligases. PMID:27541728

Defective downregulation of receptor tyrosine kinases in cancer

PubMed Central

Bache, Kristi G; Slagsvold, Thomas; Stenmark, Harald

2004-01-01

Most growth factors control cellular functions by activating specific receptor tyrosine kinases (RTKs). While overactivation of RTK signalling pathways is strongly associated with carcinogenesis, it is becoming increasingly clear that impaired deactivation of RTKs may also be a mechanism in cancer. A major deactivation pathway, receptor downregulation, involves ligand-induced endocytosis of the RTK and subsequent degradation in lysosomes. A complex molecular machinery that uses the small protein ubiquitin as a key regulator assures proper endocytosis and degradation of RTKs. Here we discuss evidence that implicates deregulation of this machinery in cancer. PMID:15229652

Design and optimization of an energy degrader with a multi-wedge scheme based on Geant4

NASA Astrophysics Data System (ADS)

Liang, Zhikai; Liu, Kaifeng; Qin, Bin; Chen, Wei; Liu, Xu; Li, Dong; Xiong, Yongqian

2018-05-01

A proton therapy facility based on an isochronous superconducting cyclotron is under construction in Huazhong University of Science and Technology (HUST). To meet the clinical requirements, an energy degrader is essential in the beamline to modulate the fixed beam energy extracted from the cyclotron. Because of the multiple Coulomb scattering in the degrader, the beam emittance and the energy spread will be considerably increased during the energy degradation process. Therefore, a set of collimators is designed to restrict the increase in beam emittance after the energy degradation. The energy spread will be reduced in the following beam line which is not discussed in this paper. In this paper, the design considerations of an energy degrader and collimators are introduced, and the properties of the degrader material, degrader structure and the initial beam parameters are discussed using the Geant4 Monte-Carlo toolkit, with the main purpose of improving the overall performance of the degrader by multiple parameter optimization.

APC Inhibits Ligand-Independent Wnt Signaling by the Clathrin Endocytic Pathway.

PubMed

Saito-Diaz, Kenyi; Benchabane, Hassina; Tiwari, Ajit; Tian, Ai; Li, Bin; Thompson, Joshua J; Hyde, Annastasia S; Sawyer, Leah M; Jodoin, Jeanne N; Santos, Eduardo; Lee, Laura A; Coffey, Robert J; Beauchamp, R Daniel; Williams, Christopher S; Kenworthy, Anne K; Robbins, David J; Ahmed, Yashi; Lee, Ethan

2018-03-12

Adenomatous polyposis coli (APC) mutations cause Wnt pathway activation in human cancers. Current models for APC action emphasize its role in promoting β-catenin degradation downstream of Wnt receptors. Unexpectedly, we find that blocking Wnt receptor activity in APC-deficient cells inhibits Wnt signaling independently of Wnt ligand. We also show that inducible loss of APC is rapidly followed by Wnt receptor activation and increased β-catenin levels. In contrast, APC2 loss does not promote receptor activation. We show that APC exists in a complex with clathrin and that Wnt pathway activation in APC-deficient cells requires clathrin-mediated endocytosis. Finally, we demonstrate conservation of this mechanism in Drosophila intestinal stem cells. We propose a model in which APC and APC2 function to promote β-catenin degradation, and APC also acts as a molecular "gatekeeper" to block receptor activation via the clathrin pathway. Copyright © 2018 Elsevier Inc. All rights reserved.

Interaction between Wnt/β-catenin and RAS-ERK pathways and an anti-cancer strategy via degradations of β-catenin and RAS by targeting the Wnt/β-catenin pathway.

PubMed

Jeong, Woo-Jeong; Ro, Eun Ji; Choi, Kang-Yell

2018-01-01

Aberrant activation of the Wnt/β-catenin and RAS-extracellular signal-regulated kinase (ERK) pathways play important roles in the tumorigenesis of many different types of cancer, most notably colorectal cancer (CRC). Genes for these two pathways, such as adenomatous polyposis coli ( APC ) and KRAS are frequently mutated in human CRC, and involved in the initiation and progression of the tumorigenesis, respectively. Moreover, recent studies revealed interaction of APC and KRAS mutations in the various stages of colorectal tumorigenesis and even in metastasis accompanying activation of the cancer stem cells (CSCs). A key event in the synergistic cooperation between Wnt/β-catenin and RAS-ERK pathways is a stabilization of both β-catenin and RAS especially mutant KRAS by APC loss, and pathological significance of this was indicated by correlation of increased β-catenin and RAS levels in human CRC where APC mutations occur as high as 90% of CRC patients. Together with the notion of the protein activity reduction by lowering its level, inhibition of both β-catenin and RAS especially by degradation could be a new ideal strategy for development of anti-cancer drugs for CRC. In this review, we will discuss interaction between the Wnt/β-catenin and RAS-ERK pathways in the colorectal tumorigenesis by providing the mechanism of RAS stabilization by aberrant activation of Wnt/β-catenin. We will also discuss our small molecular anti-cancer approach controlling CRC by induction of specific degradations of both β-catenin and RAS via targeting Wnt/β-catenin pathway especially for the KYA1797K, a small molecule specifically binding at the regulator of G-protein signaling (RGS)-domain of Axin.

Central insulin signaling is attenuated by long-term insulin exposure via insulin receptor substrate-1 serine phosphorylation, proteasomal degradation, and lysosomal insulin receptor degradation.

PubMed

Mayer, Christopher M; Belsham, Denise D

2010-01-01

Central insulin signaling is critical for the prevention of insulin resistance. Hyperinsulinemia contributes to insulin resistance, but it is not yet clear whether neurons are subject to cellular insulin resistance. We used an immortalized, hypothalamic, clonal cell line, mHypoE-46, which exemplifies neuronal function and expresses the components of the insulin signaling pathway, to determine how hyperinsulinemia modifies neuronal function. Western blot analysis indicated that prolonged insulin treatment of mHypoE-46 cells attenuated insulin signaling through phospho-Akt. To understand the mechanisms involved, time-course analysis was performed. Insulin exposure for 4 and 8 h phosphorylated Akt and p70-S6 kinase (S6K1), whereas 8 and 24 h treatment decreased insulin receptor (IR) and IR substrate 1 (IRS-1) protein levels. Insulin phosphorylation of S6K1 correlated with IRS-1 ser1101 phosphorylation and the mTOR-S6K1 pathway inhibitor rapamycin prevented IRS-1 serine phosphorylation. The proteasomal inhibitor epoxomicin and the lysosomal pathway inhibitor 3-methyladenine prevented the degradation of IRS-1 and IR by insulin, respectively, and pretreatment with rapamycin, epoxomicin, or 3-methyladenine prevented attenuation of insulin signaling by long-term insulin exposure. Thus, a sustained elevation of insulin levels diminishes neuronal insulin signaling through mTOR-S6K1-mediated IRS-1 serine phosphorylation, proteasomal degradation of IRS-1 and lysosomal degradation of the IR.

Mendel's green cotyledon gene encodes a positive regulator of the chlorophyll-degrading pathway

PubMed Central

Sato, Yutaka; Morita, Ryouhei; Nishimura, Minoru; Yamaguchi, Hiroyasu; Kusaba, Makoto

2007-01-01

Mutants that retain greenness of leaves during senescence are known as “stay-green” mutants. The most famous stay-green mutant is Mendel's green cotyledon pea, one of the mutants used in determining the law of genetics. Pea plants homozygous for this recessive mutation (known as i at present) retain greenness of the cotyledon during seed maturation and of leaves during senescence. We found tight linkage between the I locus and stay-green gene originally found in rice, SGR. Molecular analysis of three i alleles including one with no SGR expression confirmed that the I gene encodes SGR in pea. Functional analysis of sgr mutants in pea and rice further revealed that leaf functionality is lowered despite a high chlorophyll a (Chl a) and chlorophyll b (Chl b) content in the late stage of senescence, suggesting that SGR is primarily involved in Chl degradation. Consistent with this observation, a wide range of Chl–protein complexes, but not the ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunit, were shown to be more stable in sgr than wild-type plants. The expression of OsCHL and NYC1, which encode the first enzymes in the degrading pathways of Chl a and Chl b, respectively, was not affected by sgr in rice. The results suggest that SGR might be involved in activation of the Chl-degrading pathway during leaf senescence through translational or posttranslational regulation of Chl-degrading enzymes. PMID:17709752

Mendel's green cotyledon gene encodes a positive regulator of the chlorophyll-degrading pathway.

PubMed

Sato, Yutaka; Morita, Ryouhei; Nishimura, Minoru; Yamaguchi, Hiroyasu; Kusaba, Makoto

2007-08-28

Mutants that retain greenness of leaves during senescence are known as "stay-green" mutants. The most famous stay-green mutant is Mendel's green cotyledon pea, one of the mutants used in determining the law of genetics. Pea plants homozygous for this recessive mutation (known as i at present) retain greenness of the cotyledon during seed maturation and of leaves during senescence. We found tight linkage between the I locus and stay-green gene originally found in rice, SGR. Molecular analysis of three i alleles including one with no SGR expression confirmed that the I gene encodes SGR in pea. Functional analysis of sgr mutants in pea and rice further revealed that leaf functionality is lowered despite a high chlorophyll a (Chl a) and chlorophyll b (Chl b) content in the late stage of senescence, suggesting that SGR is primarily involved in Chl degradation. Consistent with this observation, a wide range of Chl-protein complexes, but not the ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunit, were shown to be more stable in sgr than wild-type plants. The expression of OsCHL and NYC1, which encode the first enzymes in the degrading pathways of Chl a and Chl b, respectively, was not affected by sgr in rice. The results suggest that SGR might be involved in activation of the Chl-degrading pathway during leaf senescence through translational or posttranslational regulation of Chl-degrading enzymes.

Mechanism and toxicity research of benzalkonium chloride oxidation in aqueous solution by H2O2/Fe(2+) process.

PubMed

Zhang, Qian; Xia, Yu-Feng; Hong, Jun-Ming

2016-09-01

As widely used disinfectants, the pollution caused by benzalkonium chloride (BAC) has attracted a lot of attention in recent years. Since it is not suitable for biodegradation, BAC was degraded firstly by Fenton advanced oxidation technologies (AOTs) in this research to enhance the biodegradability of the pollutions. The result revealed that the optimal molar ratio of H2O2/Fe(2+) for BAC degradation was 10:1, and the COD removal rate was 32 %. To clarify the pathway of degradation, the technique of GC-MS was implemented herein to identify intermediates and the toxicity of those BAC intermediates were also novelty tested through microbial fuel cells (MFC). The findings indicated that ten transformation products including benzyl dimethyl amine and dodecane were formed during the H2O2/Fe(2+) processes, which means the degradation pathway of BAC was initiated both on the hydrophobic (alkyl chain) and hydrophilic (benzyl and ammonium moiety) region of the surfactant. The toxicity of BAC before and after treated by Fenton process was monitored through MFC system. The electricity generation was improved 337 % after BAC was treated by H2O2/Fe(2+) oxidation processes which indicated that the toxicity of those intermediates were much lower than BAC. The mechanism and toxicity research in this paper could provide the in-depth understanding to the pathway of BAC degradation and proved the possibility of AOTs for the pretreatment of a biodegradation process.

Azo dye degradation pathway and bacterial community structure in biofilm electrode reactors.

PubMed

Cao, Xian; Wang, Hui; Zhang, Shuai; Nishimura, Osamu; Li, Xianning

2018-05-31

In this study, the degradation pathway of the azo dye X-3B was explored in biofilm electrode reactors (BERs). The X-3B and chemical oxygen demand (COD) removal efficiencies were evaluated under different voltages, salinities, and temperatures. The removal efficiencies increased with increasing voltage. Additionally, the BER achieved maximum X-3B removal efficiencies of 66.26% and 75.27% at a NaCl concentration of 0.33 g L -1 and temperature of 32 °C, respectively; it achieved a COD removal efficiency of 75.64% at a NaCl concentration of 0.330 g L -1 . Fourier transform infrared spectrometry and gas chromatography-mass spectrometry analysis indicated that the X-3B biodegradation process first involved the interruption of the conjugated double-bond, resulting in aniline, benzodiazepine substance, triazine, and naphthalene ring formation. These compounds were further degraded into lower-molecular-weight products. From this, the degradation pathway of the azo dye X-3B was proposed in BERs. The relative abundances of the microbial community at the phylum and genus levels were affected by temperature, the presence of electrons, and an anaerobic environment in the BERs. To achieve better removal efficiencies, further studies on the functions of the microorganisms are needed. Copyright © 2018. Published by Elsevier Ltd.

Tumor suppressor activity of the ERK/MAPK pathway by promoting selective protein degradation

PubMed Central

Deschênes-Simard, Xavier; Gaumont-Leclerc, Marie-France; Bourdeau, Véronique; Lessard, Frédéric; Moiseeva, Olga; Forest, Valérie; Igelmann, Sebastian; Mallette, Frédérick A.; Saba-El-Leil, Marc K.; Meloche, Sylvain; Saad, Fred; Mes-Masson, Anne-Marie; Ferbeyre, Gerardo

2013-01-01

Constitutive activation of growth factor signaling pathways paradoxically triggers a cell cycle arrest known as cellular senescence. In primary cells expressing oncogenic ras, this mechanism effectively prevents cell transformation. Surprisingly, attenuation of ERK/MAP kinase signaling by genetic inactivation of Erk2, RNAi-mediated knockdown of ERK1 or ERK2, or MEK inhibitors prevented the activation of the senescence mechanism, allowing oncogenic ras to transform primary cells. Mechanistically, ERK-mediated senescence involved the proteasome-dependent degradation of proteins required for cell cycle progression, mitochondrial functions, cell migration, RNA metabolism, and cell signaling. This senescence-associated protein degradation (SAPD) was observed not only in cells expressing ectopic ras, but also in cells that senesced due to short telomeres. Individual RNAi-mediated inactivation of SAPD targets was sufficient to restore senescence in cells transformed by oncogenic ras or trigger senescence in normal cells. Conversely, the anti-senescence viral oncoproteins E1A, E6, and E7 prevented SAPD. In human prostate neoplasms, high levels of phosphorylated ERK were found in benign lesions, correlating with other senescence markers and low levels of STAT3, one of the SAPD targets. We thus identified a mechanism that links aberrant activation of growth signaling pathways and short telomeres to protein degradation and cellular senescence. PMID:23599344

H₃PW₁₂O₄₀/TiO₂ catalyst-induced photodegradation of bisphenol A (BPA): kinetics, toxicity and degradation pathways.

PubMed

Lu, Nan; Lu, Ying; Liu, Fangyuan; Zhao, Kun; Yuan, Xing; Zhao, Yahui; Li, Yuan; Qin, Hongwei; Zhu, Jia

2013-05-01

A series of experiments were conducted to investigate the kinetics of bisphenol A (2,2-bis(4-hydroxyphenyl)propane, BPA) degradation using H₃PW₁₂O₄₀/TiO₂ (PW₁₂/TiO₂) composite catalyst, toxicity of BPA intermediate products and degradation pathways. The results showed that the BPA photodegradation using PW₁₂/TiO₂ catalyst followed the first-order kinetics, and under the optimal experimental conditions at H₃PW₁₂O₄₀ loading amount of 6.3%, BPA initial concentration of 5 mg L(-1), and the solution pH of 8.2, the kinetic constant was 3.7-fold larger than that of pristine TiO₂. The hydroxyl radicals derived from the electroreduction of dissolved oxygen with electrons via chain reactions was the main reactive oxygen species. According to the identified intermediates, 4-isopropanolphenol, hydroquinone, 4-hydroxybenzoic acid, and phenol, the possible BPA photodegradation pathways were proposed. Upon 12h irradiation, 77% BPA (20 mg L(-1)) was mineralized and the toxicity to Daphnia magna (D. magna) was almost disappeared, implying the strong oxidation ability of PW₁₂/TiO₂ catalyst. The studies provide important information about the BPA degradation and promote the technical development for BPA removal. Copyright © 2013 Elsevier Ltd. All rights reserved.

Transposon mutagenesis and cloning analysis of the pathways for degradation of 2,4-dichlorophenoxyacetic acid and 3-chlorobenzoate in Alcaligenes eutrophus JMP134(pJP4).

PubMed Central

Don, R H; Weightman, A J; Knackmuss, H J; Timmis, K N

1985-01-01

Plasmid pJP4 permits its host bacterium, strain JMP134, to degrade and utilize as sole sources of carbon and energy 3-chlorobenzoate and 2,4-dichlorophenoxyacetic acid (R. H. Don and J. M. Pemberton, J. Bacteriol. 145:681-686, 1981). Mutagenesis of pJP4 by transposons Tn5 and Tn1771 enabled localization of five genes for enzymes involved in these catabolic pathways. Four of the genes, tfdB, tfdC, tfdD, and tfdE, encoded 2,4-dichlorophenol hydroxylase, dichlorocatechol 1,2-dioxygenase, chloromuconate cycloisomerase, and chlorodienelactone hydrolase, respectively. No function has been assigned to the fifth gene, tfdF, although it may encode a trans-chlorodiene-lactone isomerase. Inactivation of genes tfdC, tfdD, and tfdE, which encode the transformation of dichlorocatechol to chloromaleylacetic acid, prevented host strain JMP134 from degrading both 3-chlorobenzoate and 2,4-dichlorophenoxyacetic acid, which indicates that the pathways for these two substrates utilize common enzymes for the dissimilation of chlorocatechols. Studies with cloned catabolic genes from pJP4 indicated that whereas all essential steps in the degradation of 2,4-dichlorophenoxyacetic acid are plasmid encoded, the conversion of 3-chlorobenzoate to chlorocatechol is specified by chromosomal genes. PMID:2981813

It's all about talking: two-way communication between proteasomal and lysosomal degradation pathways via ubiquitin.

PubMed

Liebl, Martina P; Hoppe, Thorsten

2016-08-01

Selective degradation of proteins requires a fine-tuned coordination of the two major proteolytic pathways, the ubiquitin-proteasome system (UPS) and autophagy. Substrate selection and proteolytic activity are defined by a plethora of regulatory cofactors influencing each other. Both proteolytic pathways are initiated by ubiquitylation to mark substrate proteins for degradation, although the size and/or topology of the modification are different. In this context E3 ubiquitin ligases, ensuring the covalent attachment of activated ubiquitin to the substrate, are of special importance. The regulation of E3 ligase activity, competition between different E3 ligases for binding E2 conjugation enzymes and substrates, as well as their interplay with deubiquitylating enzymes (DUBs) represent key events in the cross talk between the UPS and autophagy. The coordination between both degradation routes is further influenced by heat shock factors and ubiquitin-binding proteins (UBPs) such as p97, p62, or optineurin. Mutations in enzymes and ubiquitin-binding proteins or a general decline of both proteolytic systems during aging result in accumulation of damaged and aggregated proteins. Thus further mechanistic understanding of how UPS and autophagy communicate might allow therapeutic intervention especially against age-related diseases. Copyright © 2016 the American Physiological Society.

Intracellular degradation of functionalized carbon nanotube/iron oxide hybrids is modulated by iron via Nrf2 pathway

PubMed Central

Elgrabli, Dan; Dachraoui, Walid; Marmier, Hélène de; Ménard-Moyon, Cécilia; Bégin, Dominique; Bégin-Colin, Sylvie; Bianco, Alberto; Alloyeau, Damien; Gazeau, Florence

2017-01-01

The in vivo fate and biodegradability of carbon nanotubes is still a matter of debate despite tremendous applications. In this paper we describe a molecular pathway by which macrophages degrade functionalized multi-walled carbon nanotubes (CNTs) designed for biomedical applications and containing, or not, iron oxide nanoparticles in their inner cavity. Electron microscopy and Raman spectroscopy show that intracellularly-induced structural damages appear more rapidly for iron-free CNTs in comparison to iron-loaded ones, suggesting a role of iron in the degradation mechanism. By comparing the molecular responses of macrophages derived from THP1 monocytes to both types of CNTs, we highlight a molecular mechanism regulated by Nrf2/Bach1 signaling pathways to induce CNT degradation via NOX2 complex activation and O2•−, H2O2 and OH• production. CNT exposure activates an oxidative stress-dependent production of iron via Nrf2 nuclear translocation, Ferritin H and Heme oxygenase 1 translation. Conversely, Bach1 was translocated to the nucleus of cells exposed to iron-loaded CNTs to recycle embedded iron. Our results provide new information on the role of oxidative stress, iron metabolism and Nrf2-mediated host defence for regulating CNT fate in macrophages. PMID:28120861

Aerobic Degradation of N-Methyl-4-Nitroaniline (MNA) by Pseudomonas sp. Strain FK357 Isolated from Soil

PubMed Central

Khan, Fazlurrahman; Vyas, Bhawna; Pal, Deepika; Cameotra, Swaranjit Singh

2013-01-01

N-Methyl-4-nitroaniline (MNA) is used as an additive to lower the melting temperature of energetic materials in the synthesis of insensitive explosives. Although the biotransformation of MNA under anaerobic condition has been reported, its aerobic microbial degradation has not been documented yet. A soil microcosms study showed the efficient aerobic degradation of MNA by the inhabitant soil microorganisms. An aerobic bacterium, Pseudomonas sp. strain FK357, able to utilize MNA as the sole carbon, nitrogen, and energy source, was isolated from soil microcosms. HPLC and GC-MS analysis of the samples obtained from growth and resting cell studies showed the formation of 4-nitroaniline (4-NA), 4-aminophenol (4-AP), and 1, 2, 4-benzenetriol (BT) as major metabolic intermediates in the MNA degradation pathway. Enzymatic assay carried out on cell-free lysates of MNA grown cells confirmed N-demethylation reaction is the first step of MNA degradation with the formation of 4-NA and formaldehyde products. Flavin-dependent transformation of 4-NA to 4-AP in cell extracts demonstrated that the second step of MNA degradation is a monooxygenation. Furthermore, conversion of 4-AP to BT by MNA grown cells indicates the involvement of oxidative deamination (release of NH2 substituent) reaction in third step of MNA degradation. Subsequent degradation of BT occurs by the action of benzenetriol 1, 2-dioxygenase as reported for the degradation of 4-nitrophenol. This is the first report on aerobic degradation of MNA by a single bacterium along with elucidation of metabolic pathway. PMID:24116023

Aerobic degradation of N-methyl-4-nitroaniline (MNA) by Pseudomonas sp. strain FK357 isolated from soil.

PubMed

Khan, Fazlurrahman; Vyas, Bhawna; Pal, Deepika; Cameotra, Swaranjit Singh

2013-01-01

N-Methyl-4-nitroaniline (MNA) is used as an additive to lower the melting temperature of energetic materials in the synthesis of insensitive explosives. Although the biotransformation of MNA under anaerobic condition has been reported, its aerobic microbial degradation has not been documented yet. A soil microcosms study showed the efficient aerobic degradation of MNA by the inhabitant soil microorganisms. An aerobic bacterium, Pseudomonas sp. strain FK357, able to utilize MNA as the sole carbon, nitrogen, and energy source, was isolated from soil microcosms. HPLC and GC-MS analysis of the samples obtained from growth and resting cell studies showed the formation of 4-nitroaniline (4-NA), 4-aminophenol (4-AP), and 1, 2, 4-benzenetriol (BT) as major metabolic intermediates in the MNA degradation pathway. Enzymatic assay carried out on cell-free lysates of MNA grown cells confirmed N-demethylation reaction is the first step of MNA degradation with the formation of 4-NA and formaldehyde products. Flavin-dependent transformation of 4-NA to 4-AP in cell extracts demonstrated that the second step of MNA degradation is a monooxygenation. Furthermore, conversion of 4-AP to BT by MNA grown cells indicates the involvement of oxidative deamination (release of NH2 substituent) reaction in third step of MNA degradation. Subsequent degradation of BT occurs by the action of benzenetriol 1, 2-dioxygenase as reported for the degradation of 4-nitrophenol. This is the first report on aerobic degradation of MNA by a single bacterium along with elucidation of metabolic pathway.

Efficient degradation of TCE in groundwater using Pd and electro-generated H2 and O2: a shift in pathway from hydrodechlorination to oxidation in the presence of ferrous ions.

PubMed

Yuan, Songhu; Mao, Xuhui; Alshawabkeh, Akram N

2012-03-20

Degradation of trichloroethylene (TCE) in simulated groundwater by Pd and electro-generated H(2) and O(2) is investigated in the absence and presence of Fe(II). In the absence of Fe(II), hydrodechlorination dominates TCE degradation, with accumulation of H(2)O(2) up to 17 mg/L. Under weak acidity, low concentrations of oxidizing •OH radicals are detected due to decomposition of H(2)O(2), slightly contributing to TCE degradation via oxidation. In the presence of Fe(II), the degradation efficiency of TCE at 396 μM improves to 94.9% within 80 min. The product distribution proves that the degradation pathway shifts from 79% hydrodechlorination in the absence of Fe(II) to 84% •OH oxidation in the presence of Fe(II). TCE degradation follows zeroth-order kinetics with rate constants increasing from 2.0 to 4.6 μM/min with increasing initial Fe(II) concentration from 0 to 27.3 mg/L at pH 4. A good correlation between TCE degradation rate constants and •OH generation rate constants confirms that •OH is the predominant reactive species for TCE oxidation. Presence of 10 mM Na(2)SO(4), NaCl, NaNO(3), NaHCO(3), K(2)SO(4), CaSO(4), and MgSO(4) does not significantly influence degradation, but sulfite and sulfide greatly enhance and slightly suppress degradation, respectively. A novel Pd-based electrochemical process is proposed for groundwater remediation.

Efficient Degradation of TCE in Groundwater Using Pd and Electro-generated H2 and O2: A Shift in Pathway from Hydrodechlorination to Oxidation in the Presence of Ferrous Ions

PubMed Central

Yuan, Songhu; Mao, Xuhui; Alshawabkeh, Akram N.

2012-01-01

Degradation of trichloroethylene (TCE) in simulated groundwater by Pd and electro-generated H2 and O2 is investigated in the absence and presence of Fe(II). In the absence of Fe(II), hydrodechlorination dominates TCE degradation, with accumulation of H2O2 up to 17 mg/L. Under weak acidity, low concentrations of oxidizing •OH radical are detected due to decomposition of H2O2, slightly contributing to TCE degradation via oxidation. In the presence of Fe(II), the degradation efficiency of TCE at 396 μM improves to 94.9% within 80 min. The product distribution proves that the degradation pathway shifts from 79% hydrodechlorination in the absence of Fe(II) to 84% •OH oxidation in the presence of Fe(II). TCE degradation follows zeroth-order kinetics with rate constants increasing from 2.0 to 4.6 μM/min with increasing initial Fe(II) concentration from 0 to 27.3 mg/L at pH 4. A good correlation between TCE degradation rate constants and •OH generation rate constants confirms that •OH is the predominant reactive species for TCE oxidation. Presence of 10 mM Na2SO4, NaCl, NaNO3, NaHCO3, K2SO4, CaSO4 and MgSO4 does not significantly influence degradation, but sulfite and sulfide greatly enhance and slightly suppresses degradation, respectively. A novel Pd-based electrochemical process is proposed for groundwater remediation. PMID:22315993

Sorption of triazine and organophosphorus pesticides on soil and biochar

USDA-ARS?s Scientific Manuscript database

Although a large number of reports are available on sorption and degradation of triazine and organophosphorus pesticides in soils, systematic studies are lacking to directly compare and predict the fate of agrochemicals having different susceptibilities for hydrolysis and other degradation pathways....

Naringenin degradation by the endophytic diazotroph Herbaspirillum seropedicae SmR1.

PubMed

Marin, A M; Souza, E M; Pedrosa, F O; Souza, L M; Sassaki, G L; Baura, V A; Yates, M G; Wassem, R; Monteiro, R A

2013-01-01

Several bacteria are able to degrade flavonoids either to use them as carbon sources or as a detoxification mechanism. Degradation pathways have been proposed for several bacteria, but the genes responsible are not known. We identified in the genome of the endophyte Herbaspirillum seropedicae SmR1 an operon potentially associated with the degradation of aromatic compounds. We show that this operon is involved in naringenin degradation and that its expression is induced by naringenin and chrysin, two closely related flavonoids. Mutation of fdeA, the first gene of the operon, and fdeR, its transcriptional activator, abolished the ability of H. seropedicae to degrade naringenin.