Biotransformation of the high-molecular weight polycyclic aromatic hydrocarbon (PAH) benzo[k]fluoranthene by Sphingobium sp. strain KK22 and identification of new products of non-alternant PAH biodegradation by liquid chromatography electrospray ionization tandem mass spectrometry.

PubMed

Maeda, Allyn H; Nishi, Shinro; Hatada, Yuji; Ozeki, Yasuhiro; Kanaly, Robert A

2014-03-01

A pathway for the biotransformation of the environmental pollutant and high-molecular weight polycyclic aromatic hydrocarbon (PAH) benzo[k]fluoranthene by a soil bacterium was constructed through analyses of results from liquid chromatography negative electrospray ionization tandem mass spectrometry (LC/ESI(-)-MS/MS). Exposure of Sphingobium sp. strain KK22 to benzo[k]fluoranthene resulted in transformation to four-, three- and two-aromatic ring products. The structurally similar four- and three-ring non-alternant PAHs fluoranthene and acenaphthylene were also biotransformed by strain KK22, and LC/ESI(-)-MS/MS analyses of these products confirmed the lower biotransformation pathway proposed for benzo[k]fluoranthene. In all, seven products from benzo[k]fluoranthene and seven products from fluoranthene were revealed and included previously unreported products from both PAHs. Benzo[k]fluoranthene biotransformation proceeded through ortho-cleavage of 8,9-dihydroxy-benzo[k]fluoranthene to 8-carboxyfluoranthenyl-9-propenic acid and 9-hydroxy-fluoranthene-8-carboxylic acid, and was followed by meta-cleavage to produce 3-(2-formylacenaphthylen-1-yl)-2-hydroxy-prop-2-enoic acid. The fluoranthene pathway converged with the benzo[k]fluoranthene pathway through detection of the three-ring product, 2-formylacenaphthylene-1-carboxylic acid. Production of key downstream metabolites, 1,8-naphthalic anhydride and 1-naphthoic acid from benzo[k]fluoranthene, fluoranthene and acenaphthylene biotransformations provided evidence for a common pathway by strain KK22 for all three PAHs through acenaphthoquinone. Quantitative analysis of benzo[k]fluoranthene biotransformation by strain KK22 confirmed biodegradation. This is the first pathway proposed for the biotransformation of benzo[k]fluoranthene by a bacterium. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Fluoranthene metabolism and associated proteins in Mycobacterium sp. JS14.

PubMed

Lee, Sung-Eun; Seo, Jong-Su; Keum, Young-Soo; Lee, Kwang-Jun; Li, Qing X

2007-06-01

Fluoranthene is a polycyclic aromatic hydrocarbon (PAH) commonly present in PAH-contaminated soils. We studied fluoranthene catabolism and associated proteins in Mycobacterium sp. JS14, a bacterium isolated from a PAH-contaminated soil in Hilo (HI, USA). Fluoranthene degrades in at least three separated pathways via 1-indanone, 2',3'-dihydroxybiphenyl-2,3,-dicarboxylic acid, and naphthalene-1,8-dicarboxylic acid. Part of the diverse catabolism is converged into phthalate catabolism. An increased expression of 25 proteins related to fluoranthene catabolism is found with 1-D PAGE or 2-DE and nano-LC-MS/MS. Detection of fluoranthene catabolism associated proteins coincides well with its multiple degradation pathways that are mapped via metabolites identified. Among the up-regulated proteins, PAH ring-hydroxylating dioxygenase alpha-subunit and beta-subunit and 2,3-dihydroxybiphenyl 1,2-dioxygenase are notably induced. The up-regulation of trans-2-carboxybenzalpyruvate hydratase suggests that some of fluoranthene metabolites may be further degraded through aromatic dicarboxylic acid pathways. Catalase and superoxide dismutase were up-regulated to control unexpected oxidative stress during the fluoranthene catabolism. The up-regulation of chorismate synthase and nicotine-nucleotide phosphorylase may be necessary for sustaining shikimate pathway and pyrimidine biosynthesis, respectively. A fluoranthene degradation pathway for Mycobacterium sp. JS14 was proposed and confirmed by proteomic study by identifying almost all the enzymes required during the initial steps of fluoranthene degradation.

Bacterial fermentation platform for producing artificial aromatic amines

PubMed Central

Masuo, Shunsuke; Zhou, Shengmin; Kaneko, Tatsuo; Takaya, Naoki

2016-01-01

Aromatic amines containing an aminobenzene or an aniline moiety comprise versatile natural and artificial compounds including bioactive molecules and resources for advanced materials. However, a bio-production platform has not been implemented. Here we constructed a bacterial platform for para-substituted aminobenzene relatives of aromatic amines via enzymes in an alternate shikimate pathway predicted in a Pseudomonad bacterium. Optimization of the metabolic pathway in Escherichia coli cells converted biomass glucose to 4-aminophenylalanine with high efficiency (4.4 g L−1 in fed-batch cultivation). We designed and produced artificial pathways that mimicked the fungal Ehrlich pathway in E. coli and converted 4-aminophenylalanine into 4-aminophenylethanol and 4-aminophenylacetate at 90% molar yields. Combining these conversion systems or fungal phenylalanine decarboxylases, the 4-aminophenylalanine-producing platform fermented glucose to 4-aminophenylethanol, 4-aminophenylacetate, and 4-phenylethylamine. This original bacterial platform for producing artificial aromatic amines highlights their potential as heteroatoms containing bio-based materials that can replace those derived from petroleum. PMID:27167511

FORMATION OF POLYCYCLIC AROMATIC HYDROCARBONS AND THEIR GROWTH TO SOOT -A REVIEW OF CHEMICAL REACTION PATHWAYS. (R824970)

EPA Science Inventory

The generation by combustion processes of airborne species of current health concern such as polycyclic aromatic hydrocarbons (PAH) and soot particles necessitates a detailed understanding of chemical reaction pathways responsible for their formation. The present review discus...

Metabolic engineering of the shikimate pathway

DOEpatents

Juminaga, Darmawi; Keasling, Jay D.

2017-01-10

The present disclosure relates to engineered microorganisms that produce amino acids and amino acid intermediates. In particular, the disclosure relates to recombinant nucleic acids encoding operons that increase production of aromatic amino acids and the aromatic amino acid intermediate shikimate; microorganisms with increased production of aromatic amino acids and the aromatic amino acid intermediate shikimate; and methods related to the production of aromatic amino acids, the aromatic amino acid intermediate shikimate, and commodity chemicals derived therefrom.

AROMATIC AND POLYCYCLIC AROMATIC HYDROCARBON FORMATION IN A LAMINAR PREMIXED N-BUTANE FLAME. (R825412)

EPA Science Inventory

Abstract

Experimental and detailed chemical kinetic modeling work has been performed to investigate aromatic and polycyclic aromatic hydrocarbon (PAH) formation pathways in a premixed, rich, sooting, n-butane_¯oxygen_¯argon burner s...

Rise of inhaled toluene, ethyl benzene, m-xylene, or mesitylene in rat blood after treatment with ethanol

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

Roemer, K.G.; Federsel, R.J.; Freundt, K.J.

Toluene, ethyl benzene, m-xylene, and mesitylene (1,3,5-methyl benzene) are widespread as solvents in industries and laboratories or in the manufacture and application of glues, paints, printing inks etc. These aromatics may be absorbed by employees during exposure at the workplace. Alcoholic beverages may be consumed during occupational inhalation or after shift's end at times. Toxicokinetic interactions between the aromatics and ethanol must be assumed because of the common pathway of biotransformation. The blood levels of toluene and m-xylene after inhalation increased significantly in volunteers dosed simultaneously with ethanol. In this view the present experiments in rats should elucidate whether themore » blood concentrations of inhaled ethyl benzene and mesitylene (both structurally related to toluene and m-xylene) can rise under the influence of ethanol, and whether quantitative differences of this effect due to the structure of these aromatics can occur. From the results informations important for the assessment of occupational health risk are to be expected.« less

(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

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

Structure of aryl O -demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

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

Kohler, Amanda C.; Mills, Matthew J. L.; Adams, Paul D.

Some strains of soil and marine bacteria have evolved intricate metabolic pathways for using environmentally derived aromatics as a carbon source. Many of these metabolic pathways go through intermediates such as vanillate, 3-O-methylgallate, and syringate. Demethylation of these compounds is essential for downstream aryl modification, ring opening, and subsequent assimilation of these compounds into the tricarboxylic acid (TCA) cycle, and, correspondingly, there are a variety of associated aryl demethylase systems that vary in complexity. Intriguingly, only a basic understanding of the least complex system, the tetrahydrofolate-dependent aryl demethylase LigM from Sphingomonas paucimobilis, a bacterial strain that metabolizes lignin-derived aromatics, wasmore » previously available. LigM-catalyzed demethylation enables further modification and rin g opening of the single-ring aromatics vanillate and 3-Omethylgallate, which are common byproducts of biofuel production. We characterize aryl O-demethylation by LigM and report its 1.81-Å crystal structure, revealing a unique demethylase fold and a canonical folate-binding domain. Structural homology and geometry optimization calculations enabled the identification of LigM's tetrahydrofolate-binding site and protein-folate interactions. Computationally guided mutagenesis and kinetic analyses allowed the identification of the enzyme's aryl-binding site location and determination of its unique, catalytic tyrosine-dependent reaction mechanism. This work defines LigM as a distinct demethylase, both structurally and functionally, and provides insight into demethylation and its reaction requirements. Our results afford the mechanistic details required for efficient utilization of LigM as a tool for aryl O-demethylation and as a component of synthetic biology efforts to valorize previously underused aromatic compounds.« less

Structure of aryl O -demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

DOE PAGES

Kohler, Amanda C.; Mills, Matthew J. L.; Adams, Paul D.; ...

2017-04-03

Some strains of soil and marine bacteria have evolved intricate metabolic pathways for using environmentally derived aromatics as a carbon source. Many of these metabolic pathways go through intermediates such as vanillate, 3-O-methylgallate, and syringate. Demethylation of these compounds is essential for downstream aryl modification, ring opening, and subsequent assimilation of these compounds into the tricarboxylic acid (TCA) cycle, and, correspondingly, there are a variety of associated aryl demethylase systems that vary in complexity. Intriguingly, only a basic understanding of the least complex system, the tetrahydrofolate-dependent aryl demethylase LigM from Sphingomonas paucimobilis, a bacterial strain that metabolizes lignin-derived aromatics, wasmore » previously available. LigM-catalyzed demethylation enables further modification and rin g opening of the single-ring aromatics vanillate and 3-Omethylgallate, which are common byproducts of biofuel production. We characterize aryl O-demethylation by LigM and report its 1.81-Å crystal structure, revealing a unique demethylase fold and a canonical folate-binding domain. Structural homology and geometry optimization calculations enabled the identification of LigM's tetrahydrofolate-binding site and protein-folate interactions. Computationally guided mutagenesis and kinetic analyses allowed the identification of the enzyme's aryl-binding site location and determination of its unique, catalytic tyrosine-dependent reaction mechanism. This work defines LigM as a distinct demethylase, both structurally and functionally, and provides insight into demethylation and its reaction requirements. Our results afford the mechanistic details required for efficient utilization of LigM as a tool for aryl O-demethylation and as a component of synthetic biology efforts to valorize previously underused aromatic compounds.« less

The shikimate pathway: review of amino acid sequence, function and three-dimensional structures of the enzymes.

PubMed

Mir, Rafia; Jallu, Shais; Singh, T P

2015-06-01

The aromatic compounds such as aromatic amino acids, vitamin K and ubiquinone are important prerequisites for the metabolism of an organism. All organisms can synthesize these aromatic metabolites through shikimate pathway, except for mammals which are dependent on their diet for these compounds. The pathway converts phosphoenolpyruvate and erythrose 4-phosphate to chorismate through seven enzymatically catalyzed steps and chorismate serves as a precursor for the synthesis of variety of aromatic compounds. These enzymes have shown to play a vital role for the viability of microorganisms and thus are suggested to present attractive molecular targets for the design of novel antimicrobial drugs. This review focuses on the seven enzymes of the shikimate pathway, highlighting their primary sequences, functions and three-dimensional structures. The understanding of their active site amino acid maps, functions and three-dimensional structures will provide a framework on which the rational design of antimicrobial drugs would be based. Comparing the full length amino acid sequences and the X-ray crystal structures of these enzymes from bacteria, fungi and plant sources would contribute in designing a specific drug and/or in developing broad-spectrum compounds with efficacy against a variety of pathogens.

Proteomic Characterization of Plasmid pLA1 for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Marine Bacterium, Novosphingobium pentaromativorans US6-1

PubMed Central

Yun, Sung Ho; Choi, Chi-Won; Lee, Sang-Yeop; Lee, Yeol Gyun; Kwon, Joseph; Leem, Sun Hee; Chung, Young Ho; Kahng, Hyung-Yeel; Kim, Sang Jin; Kwon, Kae Kyoung; Kim, Seung Il

2014-01-01

Novosphingobium pentaromativorans US6-1 is a halophilic marine bacterium able to degrade polycyclic aromatic hydrocarbons (PAHs). Genome sequence analysis revealed that the large plasmid pLA1 present in N. pentaromativorans US6-1 consists of 199 ORFs and possess putative biodegradation genes that may be involved in PAH degradation. 1-DE/LC-MS/MS analysis of N. pentaromativorans US6-1 cultured in the presence of different PAHs and monocyclic aromatic hydrocarbons (MAHs) identified approximately 1,000 and 1,400 proteins, respectively. Up-regulated biodegradation enzymes, including those belonging to pLA1, were quantitatively compared. Among the PAHs, phenanthrene induced the strongest up-regulation of extradiol cleavage pathway enzymes such as ring-hydroxylating dioxygenase, putative biphenyl-2,3-diol 1,2-dioxygenase, and catechol 2,3-dioxygenase in pLA1. These enzymes lead the initial step of the lower catabolic pathway of aromatic hydrocarbons through the extradiol cleavage pathway and participate in the attack of PAH ring cleavage, respectively. However, N. pentaromativorans US6-1 cultured with p-hydroxybenzoate induced activation of another extradiol cleavage pathway, the protocatechuate 4,5-dioxygenase pathway, that originated from chromosomal genes. These results suggest that N. pentaromativorans US6-1 utilizes two different extradiol pathways and plasmid pLA1 might play a key role in the biodegradation of PAH in N. pentaromativorans US6-1. PMID:24608660

Mis-Regulation of 3-Deoxy-d-Arabino-Heptulosonate 7-Phosphate Synthetase Does Not Account for Growth Inhibition by Phenylalanine in Agmenellum quadruplicatum

PubMed Central

Jensen, Roy A.; Stenmark-Cox, S.; Ingram, Lonnie O.

1974-01-01

The growth of the blue-green bacterium, Agmenellum quadruplicatum, is inhibited in the presence of l-phenylalanine. This species has a single, constitutively synthesized 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAHP) synthetase. l-Phenylalanine inhibits DAHP synthetase non-competitively with respect to both substrate reactants. Other aromatic amino acids do not inhibit the activity of DAHP synthetase. A common expectation for branch-point enzymes such as DAHP synthetase is a balanced pattern of feedback control by all of the ultimate end products. It seemed likely that growth inhibition might equate with defective regulation within the branched aromatic pathway. Accordingly, the possibility was examined that mis-regulation of DAHP synthetase by l-phenylalanine in wild-type cells causes starvation for precursors of the other aromatic end products. However, the molecular basis for growth inhibition cannot be attributed to l-phenylalanine inhibition of DAHP synthetase for the following reasons: (i) DAHP synthetase enzymes from l-phenylalanine-resistant mutants are more, rather than less, sensitive to feedback inhibition by l-phenylalanine. (ii) Shikimate not only fails to antagonize inhibition, but is itself inhibitory. (iii) Neither the sensitivity nor the completeness of l-phenylalanine inhibition of the wild-type enzyme in vitro appears sufficient to account for the potent inhibition of growth in vivo by l-phenylalanine. The dominating effect of l-phenylalanine in the control of DAHP synthetase appears to reflect a mechanism that prevents rather than causes growth inhibition by l-phenylalanine. The alteration of the control of DAHP synthetase in mutants selected for resistance to growth inhibition by l-phenylalanine did indicate that the cause for this metabolite vulnerability can be localized within the aromatic amino acid pathway. Apparently, an aromatic intermediate (between shikimate and the end products) accumulates in the presence of l-phenylalanine, causing toxicity by some unknown mechanism. It is concluded that phenylpyruvate, potentially formed by transamination of l-phenylalanine, is an unlikely cause of growth inhibition. Although several significant questions remain unanswered, our results suggest that single-effector control of DAHP synthetase, the first regulatory enzyme activity of a branched pathway, may be more appropriate than it would seem a priori. PMID:4215792

Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View

PubMed Central

Carmona, Manuel; Zamarro, María Teresa; Blázquez, Blas; Durante-Rodríguez, Gonzalo; Juárez, Javier F.; Valderrama, J. Andrés; Barragán, María J. L.; García, José Luis; Díaz, Eduardo

2009-01-01

Summary: Aromatic compounds belong to one of the most widely distributed classes of organic compounds in nature, and a significant number of xenobiotics belong to this family of compounds. Since many habitats containing large amounts of aromatic compounds are often anoxic, the anaerobic catabolism of aromatic compounds by microorganisms becomes crucial in biogeochemical cycles and in the sustainable development of the biosphere. The mineralization of aromatic compounds by facultative or obligate anaerobic bacteria can be coupled to anaerobic respiration with a variety of electron acceptors as well as to fermentation and anoxygenic photosynthesis. Since the redox potential of the electron-accepting system dictates the degradative strategy, there is wide biochemical diversity among anaerobic aromatic degraders. However, the genetic determinants of all these processes and the mechanisms involved in their regulation are much less studied. This review focuses on the recent findings that standard molecular biology approaches together with new high-throughput technologies (e.g., genome sequencing, transcriptomics, proteomics, and metagenomics) have provided regarding the genetics, regulation, ecophysiology, and evolution of anaerobic aromatic degradation pathways. These studies revealed that the anaerobic catabolism of aromatic compounds is more diverse and widespread than previously thought, and the complex metabolic and stress programs associated with the use of aromatic compounds under anaerobic conditions are starting to be unraveled. Anaerobic biotransformation processes based on unprecedented enzymes and pathways with novel metabolic capabilities, as well as the design of novel regulatory circuits and catabolic networks of great biotechnological potential in synthetic biology, are now feasible to approach. PMID:19258534

Cyclic terpenoids of contemporary resinous plant detritus and of fossil woods, ambers and coals

USGS Publications Warehouse

Simoneit, B.R.T.; Grimalt, J.O.; Wang, T.-G.; Cox, R.E.; Hatcher, P.G.; Nissenbaum, A.

1986-01-01

Cyclic terpenoids present in the solvent extractable material of fossil woods, ambers and brown coals have been analyzed. The sample series chosen consisted of wood remains preserved in Holocene to Jurassic sediments and a set of of ambers from the Philippines (copalite), Israel, Canada and Dominican Republic. The brown coals selected were from the Fortuna Garsdorf Mine and Miocene formations on Fiji. The fossil wood extracts contained dominant diterpenoid or sesquiterpenoid skeletons, and aromatized species were present at high concentrations, with a major amount of two-ring aromatic compounds. Tricyclic diterpenoids were the predominant compounds in the ambers. Aromatized derivatives were the major components, consisting of one or two aromatic ring species with the abietane and occasionally pimarane skeletons. The saturated structures were comprised primarily of the abietane and pimarane skeletons having from three to five carbon (C1, C2, etc.) substituents. Kaurane and phyllocladane isomers were present in only minor amounts. Bicyclic sesquiterpenoids as saturated and partial or fully aromatized forms were also common in these samples, but only traces of sesterterpenoids and triterpenoid derivatives were found. The brown coal extracts were composed of major amounts of one- and two-ring aromatized terpenoids, with a greater proportion of triterpenoid derivatives than in the case of the woods and ambers. This was especially noticeable for the German coal, where the triterpenoids were predominant. Open C-ring aromatized structures were also present in this coal. Steroid compounds were not detectable, but some hopanes were found as minor components in the German brown coal. An overview of the skeletal structure classes identified in each sample, as well as the general mass spectrometric characteristics of the unknown compounds are included in the present paper. It can be concluded from these structural distributions that aromatization is the main process for the transformation of terrestrial cyclic terpenoids during diagenesis, constituting a general pathway for all terpenoids. ?? 1986 Pergamon Journals Ltd.

MOLECULAR BASIS OF BIODEGRADATION OF CHLOROAROMATIC COMPOUNDS

EPA Science Inventory

Chlorinated aromatic hydrocarbons are widely used in industry and agriculture, and comprise the bulk of environmental pollutants. Although simple aromatic compounds are biodegradable by a variety of degradative pathways, their halogenated counterparts are more resistant to bacter...

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

Biochemical-Pathway Diversity in Archaebacteria

DTIC Science & Technology

1990-08-30

Classification) (U) Biochemical-pathway diversity in Archaebacteria 12 PERSONAL AUTHOR(S) I Jensen, Roy-A. i3o. TYPE OF REN" RT 12b. Tki~ 0’E D-30-9 4...by block numtb.sj FIEL I ROU I SIGRLJP Archaebacteria , biochemical diversity, prephenate 06 03. 1 dehydratase, aromatic amino acid biosynthesis t...1988 RE10SE: lo assess the extent to which the archaebacteria possess unique biochemical features of aromatic amino acid biosynthesis and regulation and

The old 3-oxoadipate pathway revisited: new insights in the catabolism of aromatics in the saprophytic fungus Aspergillus nidulans.

PubMed

Martins, Tiago M; Hartmann, Diego O; Planchon, Sébastien; Martins, Isabel; Renaut, Jenny; Silva Pereira, Cristina

2015-01-01

Aspergilli play major roles in the natural turnover of elements, especially through the decomposition of plant litter, but the end catabolism of lignin aromatic hydrocarbons remains largely unresolved. The 3-oxoadipate pathway of their degradation combines the catechol and the protocatechuate branches, each using a set of specific genes. However, annotation for most of these genes is lacking or attributed to poorly- or un-characterised families. Aspergillus nidulans can utilise as sole carbon/energy source either benzoate or salicylate (upstream aromatic metabolites of the protocatechuate and the catechol branches, respectively). Using this cultivation strategy and combined analyses of comparative proteomics, gene mining, gene expression and characterisation of particular gene-replacement mutants, we precisely assigned most of the steps of the 3-oxoadipate pathway to specific genes in this fungus. Our findings disclose the genetically encoded potential of saprophytic Ascomycota fungi to utilise this pathway and provide means to untie associated regulatory networks, which are vital to heightening their ecological significance. Copyright © 2014 Elsevier Inc. All rights reserved.

Sediment-Associated Reactions of Aromatic Amines

EPA Science Inventory

Sorption of aromatic amines to sediments and soils can occur by both reversible physical processes and irreversible chemical processes. To elucidate the significance of these sorption pathways, the sorption kinetics of aniline and pyridine were studied in resaturated pond sedimen...

[Recent advances in Sphingobium sp. SYK-6 for lignin aromatic compounds degradation--a review].

PubMed

Zhang, Xiaoyan; Peng, Xue; Masai, Eiji

2014-08-04

Lignin is complex heteropolymer produced from hydroxycinnamyl alcohols through radical coupling. In nature, white-rot fungi are assumed initially to attack native lignin and release lignin-derived-low-molecular-weight compounds, and soil bacteria play an importent role for completely degradation of these compounds. Study on the soil bacteria degrading lignin-derived-low-molecular-weight compounds will give way to understand how aromatic compounds recycle in nature, and to utilize lignin compounds as the renewable materials for valuable materials production. Sphingobium sp. SYK-6 that grows on lignin biphenyl (5,5'-dehydrodivanillate) had been isolated from pulp effluent in 1987. We have researched this bacterium more than 25 years, a serious aromatic metabolic pathway has been determined, and related genes have been isolated. As the complete genome sequence of SYK-6 has been opened to the public in 2012, the entire aromatic compounds degradation mechanisms become more clear. Main contents in our review cover: (1) genome information; (2) aryl metabolism; (3) biphenyl metabolism; (4) ferulate metabolism; (5) tetrahydrofolate-dependent O-demethylation system for lignin compound degrdation; (6) protocatechuate 4,5-cleavage pathway; (7) multiple pathways for 3-O-methylgallate metabolism.

Engineering Escherichia coli to overproduce aromatic amino acids and derived compounds.

PubMed

Rodriguez, Alberto; Martínez, Juan A; Flores, Noemí; Escalante, Adelfo; Gosset, Guillermo; Bolivar, Francisco

2014-09-09

The production of aromatic amino acids using fermentation processes with recombinant microorganisms can be an advantageous approach to reach their global demands. In addition, a large array of compounds with alimentary and pharmaceutical applications can potentially be synthesized from intermediates of this metabolic pathway. However, contrary to other amino acids and primary metabolites, the artificial channelling of building blocks from central metabolism towards the aromatic amino acid pathway is complicated to achieve in an efficient manner. The length and complex regulation of this pathway have progressively called for the employment of more integral approaches, promoting the merge of complementary tools and techniques in order to surpass metabolic and regulatory bottlenecks. As a result, relevant insights on the subject have been obtained during the last years, especially with genetically modified strains of Escherichia coli. By combining metabolic engineering strategies with developments in synthetic biology, systems biology and bioprocess engineering, notable advances were achieved regarding the generation, characterization and optimization of E. coli strains for the overproduction of aromatic amino acids, some of their precursors and related compounds. In this paper we review and compare recent successful reports dealing with the modification of metabolic traits to attain these objectives.

Inverse kinetic solvent isotope effect in TiO2 photocatalytic dehalogenation of non-adsorbable aromatic halides: a proton-induced pathway.

PubMed

Chang, Wei; Sun, Chunyan; Pang, Xibin; Sheng, Hua; Li, Yue; Ji, Hongwei; Song, Wenjing; Chen, Chuncheng; Ma, Wanhong; Zhao, Jincai

2015-02-09

An efficient redox reaction between organic substrates in solution and photoinduced h(+) vb /e(-) cb on the surface of photocatalysts requires the substrates or solvent to be adsorbed onto the surface, and is consequentially marked by a normal kinetic solvent isotope effect (KSIE ≥ 1). Reported herein is a universal inverse KSIE (0.6-0.8 at 298 K) for the reductive dehalogenation of aromatic halides which cannot adsorb onto TiO2 in a [D0 ]methanol/[D4 ]methanol solution. Combined with in situ ATR-FTIR spectroscopy investigations, a previously unknown pathway for the transformation of these aromatic halides in TiO2 photocatalysis was identified: a proton adduct intermediate, induced by released H(+) /D(+) from solvent oxidation, accompanies a change in hybridization from sp(2) to sp(3) at a carbon atom of the aromatic halides. The protonation event leads these aromatic halides to adsorb onto the TiO2 surface and an ET reaction to form dehalogenated products follows. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Forming a Two-Ring Polycyclic Aromatic Hydrocarbon without a Benzene Intermediate: the Reaction of Propargyl with Acetylene

NASA Astrophysics Data System (ADS)

Osborn, David; Savee, John; Selby, Talitha; Welz, Oliver; Taatjes, Craig

The reaction of acetylene (HCCH) with a resonance-stabilized free radical is a commonly invoked mechanism for the generation of polycyclic aromatic hydrocarbons (PAH), which are likely precursors of soot particles in combustion. In this work, we examine the sequential addition of acetylene to the propargyl radical (H2CCCH) at temperatures of 800 and 1000 K. Using time-resolved multiplexed photoionization mass spectrometry with tunable ionizing radiation, we identified the isomeric forms of the C5H5 and C7H7 intermediates in this reaction sequence, and confirmed that the final C9H8 product is the two-ring aromatic compound indene. We identified two different resonance-stabilized C5H5 intermediates, with different temperature dependencies. Furthermore, the C7H7 intermediate is the tropyl radical (c-C7H7) , not the benzyl radical (C6H5CH2) , as is usually assumed in combustion environments. These experimental results are in general agreement with the latest electronic structure / master equation results of da Silva et al. This work shows a pathway for PAH formation that bypasses benzene / benzyl intermediates.

The pattern of shikimate pathway and phenylpropanoids after inhibition by glyphosate or quinate feeding in pea roots.

PubMed

Zabalza, Ana; Orcaray, Luis; Fernández-Escalada, Manuel; Zulet-González, Ainhoa; Royuela, Mercedes

2017-09-01

The shikimate pathway is a metabolic route for the biosynthesis of aromatic amino acids (AAAs) (i.e. phenylalanine, tyrosine, and tryptophan). A key enzyme of shikimate pathway (5-enolpyruvylshikimate-3-phosphate synthase, EPSPS) is the target of the widely used herbicide glyphosate. Quinate is a compound synthesized in plants through a side branch of the shikimate pathway. Glyphosate provokes quinate accumulation and exogenous quinate application to plants shows a potential role of quinate in the toxicity of the herbicide glyphosate. Based on this, we hypothesized that the role of quinate accumulation in the toxicity of the glyphosate would be mediated by a deregulation of the shikimate pathway. In this study the effect of the glyphosate and of the exogenous quinate was evaluated in roots of pea plants by analyzing the time course of a full metabolic map of several metabolites of shikimate and phenylpropanoid pathways. Glyphosate application induced an increase of the 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS, first enzyme of the shikimate pathway) protein and accumulation of metabolites upstream of the enzyme EPSPS. No common effects on the metabolites and regulation of shikimate pathway were detected between quinate and glyphosate treatments, supporting that the importance of quinate in the mode of action of glyphosate is not mediated by a common alteration of the regulation of the shikimate pathway. Contrary to glyphosate, the exogenous quinate supplied was probably incorporated into the main trunk from the branch pathway and accumulated in the final products, such as lignin, concomitant with a decrease in the amount of DAHPS protein. Copyright © 2016 Elsevier B.V. All rights reserved.

New Findings on Aromatic Compounds' Degradation and Their Metabolic Pathways, the Biosurfactant Production and Motility of the Halophilic Bacterium Halomonas sp. KHS3.

PubMed

Corti Monzón, Georgina; Nisenbaum, Melina; Herrera Seitz, M Karina; Murialdo, Silvia E

2018-04-24

The study of the aromatic compounds' degrading ability by halophilic bacteria became an interesting research topic, because of the increasing use of halophiles in bioremediation of saline habitats and effluents. In this work, we focused on the study of aromatic compounds' degradation potential of Halomonas sp. KHS3, a moderately halophilic bacterium isolated from hydrocarbon-contaminated seawater of the Mar del Plata harbour. We demonstrated that H. sp. KHS3 is able to grow using different monoaromatic (salicylic acid, benzoic acid, 4-hydroxybenzoic acid, phthalate) and polyaromatic (naphthalene, fluorene, and phenanthrene) substrates. The ability to degrade benzoic acid and 4-hydroxybenzoic acid was analytically corroborated, and Monod kinetic parameters and yield coefficients for degradation were estimated. Strategies that may enhance substrate bioavailability such as surfactant production and chemotactic responses toward aromatic compounds were confirmed. Genomic sequence analysis of this strain allowed us to identify several genes putatively related to the metabolism of aromatic compounds, being the catechol and protocatechuate branches of β-ketoadipate pathway completely represented. These features suggest that the broad-spectrum xenobiotic degrader H. sp. KHS3 could be employed as a useful biotechnological tool for the cleanup of aromatic compounds-polluted saline habitats or effluents.

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

Mutant characterization and in vivo conditional repression identify aromatic amino acid biosynthesis to be essential for Aspergillus fumigatus virulence

PubMed Central

Sasse, Anna; Hamer, Stefanie N; Amich, Jorge; Binder, Jasmin; Krappmann, Sven

2016-01-01

Pathogenicity of the saprobe Aspergillus fumigatus strictly depends on nutrient acquisition during infection, as fungal growth determines colonisation and invasion of a susceptible host. Primary metabolism has to be considered as a valid target for antimycotic therapy, based on the fact that several fungal anabolic pathways are not conserved in higher eukaryotes. To test whether fungal proliferation during invasive aspergillosis relies on endogenous biosynthesis of aromatic amino acids, defined auxotrophic mutants of A. fumigatus were generated and assessed for their infectious capacities in neutropenic mice and found to be strongly attenuated in virulence. Moreover, essentiality of the complete biosynthetic pathway could be demonstrated, corroborated by conditional gene expression in infected animals and inhibitor studies. This brief report not only validates the aromatic amino acid biosynthesis pathway of A. fumigatus to be a promising antifungal target but furthermore demonstrates feasibility of conditional gene expression in a murine infection model of aspergillosis. PMID:26605426

Toward engineering E. coli with an autoregulatory system for lignin valorization.

PubMed

Wu, Weihua; Liu, Fang; Singh, Seema

2018-03-20

Efficient lignin valorization could add more than 10-fold the value gained from burning it for energy and is critical for economic viability of future biorefineries. However, lignin-derived aromatics from biomass pretreatment are known to be potent fermentation inhibitors in microbial production of fuels and other value-added chemicals. In addition, isopropyl-β-d-1-thiogalactopyranoside and other inducers are routinely added into fermentation broth to induce the expression of pathway enzymes, which further adds to the overall process cost. An autoregulatory system that can diminish the aromatics' toxicity as well as be substrate-inducible can be the key for successful integration of lignin valorization into future lignocellulosic biorefineries. Toward that goal, in this study an autoregulatory system is demonstrated that alleviates the toxicity issue and eliminates the cost of an external inducer. Specifically, this system is composed of a catechol biosynthesis pathway coexpressed with an active aromatic transporter CouP under induction by a vanillin self-inducible promoter, ADH7, to effectively convert the lignin-derived aromatics into value-added chemicals using Escherichia coli as a host. The constructed autoregulatory system can efficiently transport vanillin across the cell membrane and convert it to catechol. Compared with the system without CouP expression, the expression of catechol biosynthesis pathway with transporter CouP significantly improved the catechol yields about 30% and 40% under promoter pTrc and ADH7, respectively. This study demonstrated an aromatic-induced autoregulatory system that enabled conversion of lignin-derived aromatics into catechol without the addition of any costly, external inducers, providing a promising and economically viable route for lignin valorization. Copyright © 2018 the Author(s). Published by PNAS.

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.

Enhancement of anti-inflammatory activity of Aloe vera adventitious root extracts through the alteration of primary and secondary metabolites via salicylic acid elicitation.

PubMed

Lee, Yun Sun; Ju, Hyun Kyoung; Kim, Yeon Jeong; Lim, Tae-Gyu; Uddin, Md Romij; Kim, Yeon Bok; Baek, Jin Hong; Kwon, Sung Won; Lee, Ki Won; Seo, Hak Soo; Park, Sang Un; Yang, Tae-Jin

2013-01-01

Aloe vera (Asphodeloideae) is a medicinal plant in which useful secondary metabolites are plentiful. Among the representative secondary metabolites of Aloe vera are the anthraquinones including aloe emodin and chrysophanol, which are tricyclic aromatic quinones synthesized via a plant-specific type III polyketide biosynthesis pathway. However, it is not yet clear which cellular responses can induce the pathway, leading to production of tricyclic aromatic quinones. In this study, we examined the effect of endogenous elicitors on the type III polyketide biosynthesis pathway and identified the metabolic changes induced in elicitor-treated Aloe vera adventitious roots. Salicylic acid, methyl jasmonate, and ethephon were used to treat Aloe vera adventitious roots cultured on MS liquid media with 0.3 mg/L IBA for 35 days. Aloe emodin and chrysophanol were remarkably increased by the SA treatment, more than 10-11 and 5-13 fold as compared with untreated control, respectively. Ultra-performance liquid chromatography-electrospray ionization mass spectrometry analysis identified a total of 37 SA-induced compounds, including aloe emodin and chrysophanol, and 3 of the compounds were tentatively identified as tricyclic aromatic quinones. Transcript accumulation analysis of polyketide synthase genes and gas chromatography mass spectrometry showed that these secondary metabolic changes resulted from increased expression of octaketide synthase genes and decreases in malonyl-CoA, which is the precursor for the tricyclic aromatic quinone biosynthesis pathway. In addition, anti-inflammatory activity was enhanced in extracts of SA-treated adventitious roots. Our results suggest that SA has an important role in activation of the plant specific-type III polyketide biosynthetic pathway, and therefore that the efficacy of Aloe vera as medicinal agent can be improved through SA treatment.

Enhancement of Anti-Inflammatory Activity of Aloe vera Adventitious Root Extracts through the Alteration of Primary and Secondary Metabolites via Salicylic Acid Elicitation

PubMed Central

Lee, Yun Sun; Ju, Hyun Kyoung; Kim, Yeon Jeong; Lim, Tae-Gyu; Uddin, Md Romij; Kim, Yeon Bok; Baek, Jin Hong; Kwon, Sung Won; Lee, Ki Won; Seo, Hak Soo; Park, Sang Un; Yang, Tae-Jin

2013-01-01

Aloe vera (Asphodeloideae) is a medicinal plant in which useful secondary metabolites are plentiful. Among the representative secondary metabolites of Aloe vera are the anthraquinones including aloe emodin and chrysophanol, which are tricyclic aromatic quinones synthesized via a plant-specific type III polyketide biosynthesis pathway. However, it is not yet clear which cellular responses can induce the pathway, leading to production of tricyclic aromatic quinones. In this study, we examined the effect of endogenous elicitors on the type III polyketide biosynthesis pathway and identified the metabolic changes induced in elicitor-treated Aloe vera adventitious roots. Salicylic acid, methyl jasmonate, and ethephon were used to treat Aloe vera adventitious roots cultured on MS liquid media with 0.3 mg/L IBA for 35 days. Aloe emodin and chrysophanol were remarkably increased by the SA treatment, more than 10–11 and 5–13 fold as compared with untreated control, respectively. Ultra-performance liquid chromatography-electrospray ionization mass spectrometry analysis identified a total of 37 SA-induced compounds, including aloe emodin and chrysophanol, and 3 of the compounds were tentatively identified as tricyclic aromatic quinones. Transcript accumulation analysis of polyketide synthase genes and gas chromatography mass spectrometry showed that these secondary metabolic changes resulted from increased expression of octaketide synthase genes and decreases in malonyl-CoA, which is the precursor for the tricyclic aromatic quinone biosynthesis pathway. In addition, anti-inflammatory activity was enhanced in extracts of SA-treated adventitious roots. Our results suggest that SA has an important role in activation of the plant specific-type III polyketide biosynthetic pathway, and therefore that the efficacy of Aloe vera as medicinal agent can be improved through SA treatment. PMID:24358188

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.

In Vitro Enzymatic Depolymerization of Lignin with Release of Syringyl, Guaiacyl, and Tricin Units

PubMed Central

Gall, Daniel L.; Kontur, Wayne S.; Lan, Wu; Kim, Hoon; Li, Yanding; Ralph, John

2017-01-01

ABSTRACT New environmentally sound technologies are needed to derive valuable compounds from renewable resources. Lignin, an abundant polymer in terrestrial plants comprised predominantly of guaiacyl and syringyl monoaromatic phenylpropanoid units, is a potential natural source of aromatic compounds. In addition, the plant secondary metabolite tricin is a recently discovered and moderately abundant flavonoid in grasses. The most prevalent interunit linkage between guaiacyl, syringyl, and tricin units is the β-ether linkage. Previous studies have shown that bacterial β-etherase pathway enzymes catalyze glutathione-dependent cleavage of β-ether bonds in dimeric β-ether lignin model compounds. To date, however, it remains unclear whether the known β-etherase enzymes are active on lignin polymers. Here we report on enzymes that catalyze β-ether cleavage from bona fide lignin, under conditions that recycle the cosubstrates NAD+ and glutathione. Guaiacyl, syringyl, and tricin derivatives were identified as reaction products when different model compounds or lignin fractions were used as substrates. These results demonstrate an in vitro enzymatic system that can recycle cosubstrates while releasing aromatic monomers from model compounds as well as natural and engineered lignin oligomers. These findings can improve the ability to produce valuable aromatic compounds from a renewable resource like lignin. IMPORTANCE Many bacteria are predicted to contain enzymes that could convert renewable carbon sources into substitutes for compounds that are derived from petroleum. The β-etherase pathway present in sphingomonad bacteria could cleave the abundant β–O–4-aryl ether bonds in plant lignin, releasing a biobased source of aromatic compounds for the chemical industry. However, the activity of these enzymes on the complex aromatic oligomers found in plant lignin is unknown. Here we demonstrate biodegradation of lignin polymers using a minimal set of β-etherase pathway enzymes, the ability to recycle needed cofactors (glutathione and NAD+) in vitro, and the release of guaiacyl, syringyl, and tricin as depolymerized products from lignin. These observations provide critical evidence for the use and future optimization of these bacterial β-etherase pathway enzymes for industrial-level biotechnological applications designed to derive high-value monomeric aromatic compounds from lignin. PMID:29180366

Identification of Genes and Pathways Related to Phenol Degradation in Metagenomic Libraries from Petroleum Refinery Wastewater

PubMed Central

Silva, Cynthia C.; Hayden, Helen; Sawbridge, Tim; Mele, Pauline; De Paula, Sérgio O.; Silva, Lívia C. F.; Vidigal, Pedro M. P.; Vicentini, Renato; Sousa, Maíra P.; Torres, Ana Paula R.; Santiago, Vânia M. J.; Oliveira, Valéria M.

2013-01-01

Two fosmid libraries, totaling 13,200 clones, were obtained from bioreactor sludge of petroleum refinery wastewater treatment system. The library screening based on PCR and biological activity assays revealed more than 400 positive clones for phenol degradation. From these, 100 clones were randomly selected for pyrosequencing in order to evaluate the genetic potential of the microorganisms present in wastewater treatment plant for biodegradation, focusing mainly on novel genes and pathways of phenol and aromatic compound degradation. The sequence analysis of selected clones yielded 129,635 reads at an estimated 17-fold coverage. The phylogenetic analysis showed Burkholderiales and Rhodocyclales as the most abundant orders among the selected fosmid clones. The MG-RAST analysis revealed a broad metabolic profile with important functions for wastewater treatment, including metabolism of aromatic compounds, nitrogen, sulphur and phosphorus. The predicted 2,276 proteins included phenol hydroxylases and cathecol 2,3- dioxygenases, involved in the catabolism of aromatic compounds, such as phenol, byphenol, benzoate and phenylpropanoid. The sequencing of one fosmid insert of 33 kb unraveled the gene that permitted the host, Escherichia coli EPI300, to grow in the presence of aromatic compounds. Additionally, the comparison of the whole fosmid sequence against bacterial genomes deposited in GenBank showed that about 90% of sequence showed no identity to known sequences of Proteobacteria deposited in the NCBI database. This study surveyed the functional potential of fosmid clones for aromatic compound degradation and contributed to our knowledge of the biodegradative capacity and pathways of microbial assemblages present in refinery wastewater treatment system. PMID:23637911

Toward engineering E. coli with an autoregulatory system for lignin valorization

PubMed Central

Wu, Weihua; Liu, Fang; Singh, Seema

2018-01-01

Efficient lignin valorization could add more than 10-fold the value gained from burning it for energy and is critical for economic viability of future biorefineries. However, lignin-derived aromatics from biomass pretreatment are known to be potent fermentation inhibitors in microbial production of fuels and other value-added chemicals. In addition, isopropyl-β-d-1-thiogalactopyranoside and other inducers are routinely added into fermentation broth to induce the expression of pathway enzymes, which further adds to the overall process cost. An autoregulatory system that can diminish the aromatics’ toxicity as well as be substrate-inducible can be the key for successful integration of lignin valorization into future lignocellulosic biorefineries. Toward that goal, in this study an autoregulatory system is demonstrated that alleviates the toxicity issue and eliminates the cost of an external inducer. Specifically, this system is composed of a catechol biosynthesis pathway coexpressed with an active aromatic transporter CouP under induction by a vanillin self-inducible promoter, ADH7, to effectively convert the lignin-derived aromatics into value-added chemicals using Escherichia coli as a host. The constructed autoregulatory system can efficiently transport vanillin across the cell membrane and convert it to catechol. Compared with the system without CouP expression, the expression of catechol biosynthesis pathway with transporter CouP significantly improved the catechol yields about 30% and 40% under promoter pTrc and ADH7, respectively. This study demonstrated an aromatic-induced autoregulatory system that enabled conversion of lignin-derived aromatics into catechol without the addition of any costly, external inducers, providing a promising and economically viable route for lignin valorization. PMID:29500185

Lasiodiplodia sp. ME4-2, an endophytic fungus from the floral parts of Viscum coloratum, produces indole-3-carboxylic acid and other aromatic metabolites.

PubMed

Qian, Chao-Dong; Fu, Yu-Hang; Jiang, Fu-Sheng; Xu, Zheng-Hong; Cheng, Dong-Qing; Ding, Bin; Gao, Cheng-Xian; Ding, Zhi-Shan

2014-11-30

Studies on endophytes, a relatively under-explored group of microorganisms, are currently popular amongst biologists and natural product researchers. A fungal strain (ME4-2) was isolated from flower samples of mistletoe (Viscum coloratum) during a screening program for endophytes. As limited information on floral endophytes is available, the aim of the present study is to characterise fungal endophytes using their secondary metabolites. ME4-2 grew well in both natural and basic synthetic media but produced no conidia. Sequence analysis of its internal transcribed spacer rDNA demonstrated that ME4-2 forms a distinct branch within the genus Lasiodiplodia and is closely related to L. pseudotheobromae. This floral endophyte was thus identified as Lasiodiplodia sp. based on its molecular biological characteristics. Five aromatic compounds, including cyclo-(Trp-Ala), indole-3-carboxylic acid (ICA), indole-3-carbaldehyde, mellein and 2-phenylethanol, were found in the culture. The structures of these compounds were determined using spectroscopic methods combined with gas chromatography. To the best of our knowledge, our work is the first to report isolation of these aromatic metabolites from a floral endophyte. Interestingly, ICA, a major secondary metabolite produced by ME4-2, seemed to be biosynthesized via an unusual pathway. Furthermore, our results indicate that the fungus ME4-2 is a potent producer of 2-phenylethanol, which is a common component of floral essential oils. This study introduces a fungal strain producing several important aromatic metabolites with pharmaceutical or food applications and suggests that endophytic fungi isolated from plant flowers are promising natural sources of aromatic compounds.

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.

The antitumor effects of geraniol: Modulation of cancer hallmark pathways (Review).

PubMed

Cho, Minsoo; So, Insuk; Chun, Jung Nyeo; Jeon, Ju-Hong

2016-05-01

Geraniol is a dietary monoterpene alcohol that is found in the essential oils of aromatic plants. To date, experimental evidence supports the therapeutic or preventive effects of geraniol on different types of cancer, such as breast, lung, colon, prostate, pancreatic, and hepatic cancer, and has revealed the mechanistic basis for its pharmacological actions. In addition, geraniol sensitizes tumor cells to commonly used chemotherapy agents. Geraniol controls a variety of signaling molecules and pathways that represent tumor hallmarks; these actions of geraniol constrain the ability of tumor cells to acquire adaptive resistance against anticancer drugs. In the present review, we emphasize that geraniol is a promising compound or chemical moiety for the development of a safe and effective multi-targeted anticancer agent. We summarize the current knowledge of the effects of geraniol on target molecules and pathways in cancer cells. Our review provides novel insight into the challenges and perspectives with regard to geraniol research and to its application in future clinical investigation.

The antitumor effects of geraniol: Modulation of cancer hallmark pathways (Review)

PubMed Central

CHO, MINSOO; SO, INSUK; CHUN, JUNG NYEO; JEON, JU-HONG

2016-01-01

Geraniol is a dietary monoterpene alcohol that is found in the essential oils of aromatic plants. To date, experimental evidence supports the therapeutic or preventive effects of geraniol on different types of cancer, such as breast, lung, colon, prostate, pancreatic, and hepatic cancer, and has revealed the mechanistic basis for its pharmacological actions. In addition, geraniol sensitizes tumor cells to commonly used chemotherapy agents. Geraniol controls a variety of signaling molecules and pathways that represent tumor hallmarks; these actions of geraniol constrain the ability of tumor cells to acquire adaptive resistance against anticancer drugs. In the present review, we emphasize that geraniol is a promising compound or chemical moiety for the development of a safe and effective multi-targeted anticancer agent. We summarize the current knowledge of the effects of geraniol on target molecules and pathways in cancer cells. Our review provides novel insight into the challenges and perspectives with regard to geraniol research and to its application in future clinical investigation. PMID:26983575

The production of aromatic alcohols in non-Saccharomyces wine yeast is modulated by nutrient availability.

PubMed

González, Beatriz; Vázquez, Jennifer; Morcillo-Parra, M Ángeles; Mas, Albert; Torija, María Jesús; Beltran, Gemma

2018-09-01

Aromatic alcohols (tryptophol, phenylethanol, tyrosol) positively contribute to organoleptic characteristics of wines, and are also described as bioactive compounds and quorum sensing molecules. These alcohols are produced by yeast during alcoholic fermentation via the Erhlich pathway, although in non-Saccharomyces this production has been poorly studied. We studied how different wine yeast species modulate the synthesis patterns of aromatic alcohol production depending on glucose, nitrogen and aromatic amino acid availability. Nitrogen limitation strongly promoted the production of aromatic alcohols in all strains, whereas low glucose generally inhibited it. Increased aromatic amino acid concentrations stimulated the production of aromatic alcohols in all of the strains and conditions tested. Thus, there was a clear association between the nutrient conditions and production of aromatic alcohols in most of the wine yeast species analysed. Additionally, the synthesis pattern of these alcohols has been evaluated for the first time in Torulaspora delbrueckii, Metschnikowia pulcherrima and Starmellera bacillaris. Copyright © 2018 Elsevier Ltd. All rights reserved.

Aromatic sulfonation with sulfur trioxide: mechanism and kinetic model.

PubMed

Moors, Samuel L C; Deraet, Xavier; Van Assche, Guy; Geerlings, Paul; De Proft, Frank

2017-01-01

Electrophilic aromatic sulfonation of benzene with sulfur trioxide is studied with ab initio molecular dynamics simulations in gas phase, and in explicit noncomplexing (CCl 3 F) and complexing (CH 3 NO 2 ) solvent models. We investigate different possible reaction pathways, the number of SO 3 molecules participating in the reaction, and the influence of the solvent. Our simulations confirm the existence of a low-energy concerted pathway with formation of a cyclic transition state with two SO 3 molecules. Based on the simulation results, we propose a sequence of elementary reaction steps and a kinetic model compatible with experimental data. Furthermore, a new alternative reaction pathway is proposed in complexing solvent, involving two SO 3 and one CH 3 NO 2 .

IMPACTS OF AGING ON IN VIVO AND IN VITRO MEASUREMENTS OF SOIL-BOUND POLYCYCLIC AROMATIC HYDROCARBON AVAILABILITY

EPA Science Inventory

Ingestion of contaminated soil is an exposure pathway at approximately one-half of the Superfund sites in the United States. This study was designed to evaluate the impacts of aging in soil on the availability of polycyclic aromatic hydrocarbons (PAHs). Two coal tar (CT)-amended ...

Aerobic Heterotrophic Bacterial Populations of Sewage and Activated Sludge

PubMed Central

Prakasam, T. B. S.; Dondero, N. C.

1970-01-01

An activated sludge from a sewage treatment plant and a laboratory activated sludge developed on an artificial waste were compared for their ability to utilize 11 aromatic compounds. There were several significant differences between them. The laboratory sludge contained higher numbers of organisms and metabolized the aromatics to a greater extent. Laboratory activated sludges acclimated to utilization of the aromatics differed from each other in population structure and the pattern of oxygen consumption with aromatic substrates. The oxidative patterns of uncontrolled mixed populations were unreliable for investigating metabolic pathways. Extracts of the various sludges elevated the plate counts of the sludges. PMID:5418946

Functional analysis of aromatic biosynthetic pathways in Pseudomonas putida KT2440

PubMed Central

Molina‐Henares, M. Antonia; García‐Salamanca, Adela; Molina‐Henares, A. Jesús; De La Torre, Jesús; Herrera, M. Carmen; Ramos, Juan L.; Duque, Estrella

2009-01-01

Summary Pseudomonas putida KT2440 is a non‐pathogenic prototrophic bacterium with high potential for biotechnological applications. Despite all that is known about this strain, the biosynthesis of essential chemicals has not been fully analysed and auxotroph mutants are scarce. We carried out massive mini‐Tn5 random mutagenesis and screened for auxotrophs that require aromatic amino acids. The biosynthesis of aromatic amino acids was analysed in detail including physical and transcriptional organization of genes, complementation assays and feeding experiments to establish pathway intermediates. There is a single pathway from chorismate leading to the biosynthesis of tryptophan, whereas the biosynthesis of phenylalanine and tyrosine is achieved through multiple convergent pathways. Genes for tryptophan biosynthesis are grouped in unlinked regions with the trpBA and trpGDE genes organized as operons and the trpI, trpE and trpF genes organized as single transcriptional units. The pheA and tyrA gene‐encoding multifunctional enzymes for phenylalanine and tyrosine biosynthesis are linked in the chromosome and form an operon with the serC gene involved in serine biosynthesis. The last step in the biosynthesis of these two amino acids requires an amino transferase activity for which multiple tyrB‐like genes are present in the host chromosome. PMID:21261884

THE PHOTOTOXICITY OF POLYCYCLIC AROMATIC HYDROCARBONS

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) continues to be interested in developing methods for the detection of polycyclic aromatic hydrocarbons (PAHS) in the environment. Polycyclic aromatic hydrocarbons (PAHS) are common contaminants in our environment. Being major product...

Amino Acids, Aromatic Compounds, and Carboxylic Acids: How Did They Get Their Common Names?

ERIC Educational Resources Information Center

Leung, Sam H.

2000-01-01

Surveys the roots of the common names of organic compounds most likely to be encountered by undergraduate organic chemistry students. Includes information for 19 amino acids, 17 aromatic compounds, and 21 carboxylic acids. (WRM)

Proteolytic Pathways Induced by Herbicides That Inhibit Amino Acid Biosynthesis

PubMed Central

Zulet, Amaia; Gil-Monreal, Miriam; Villamor, Joji Grace; Zabalza, Ana; van der Hoorn, Renier A. L.; Royuela, Mercedes

2013-01-01

Background The herbicides glyphosate (Gly) and imazamox (Imx) inhibit the biosynthesis of aromatic and branched-chain amino acids, respectively. Although these herbicides inhibit different pathways, they have been reported to show several common physiological effects in their modes of action, such as increasing free amino acid contents and decreasing soluble protein contents. To investigate proteolytic activities upon treatment with Gly and Imx, pea plants grown in hydroponic culture were treated with Imx or Gly, and the proteolytic profile of the roots was evaluated through fluorogenic kinetic assays and activity-based protein profiling. Results Several common changes in proteolytic activity were detected following Gly and Imx treatment. Both herbicides induced the ubiquitin-26 S proteasome system and papain-like cysteine proteases. In contrast, the activities of vacuolar processing enzymes, cysteine proteases and metacaspase 9 were reduced following treatment with both herbicides. Moreover, the activities of several putative serine protease were similarly increased or decreased following treatment with both herbicides. In contrast, an increase in YVADase activity was observed under Imx treatment versus a decrease under Gly treatment. Conclusion These results suggest that several proteolytic pathways are responsible for protein degradation upon herbicide treatment, although the specific role of each proteolytic activity remains to be determined. PMID:24040092

SEDIMENT-ASSOCIATED REACTIONS OF AROMATIC AMINES: QSAR DEVELOPMENT

EPA Science Inventory

Despite the common occurrence of the aromatic amine functional group in environmental contaminants, few quantitative structure-activity relationships (QSARs) have been developed to predict sorption kinetics for aromatic amines in natural soils and sediments. Towards the goal of d...

Precise through-space control of an abiotic electrophilic aromatic substitution reaction

NASA Astrophysics Data System (ADS)

Murphy, Kyle E.; Bocanegra, Jessica L.; Liu, Xiaoxi; Chau, H.-Y. Katharine; Lee, Patrick C.; Li, Jianing; Schneebeli, Severin T.

2017-04-01

Nature has evolved selective enzymes for the efficient biosynthesis of complex products. This exceptional ability stems from adapted enzymatic pockets, which geometrically constrain reactants and stabilize specific reactive intermediates by placing electron-donating/accepting residues nearby. Here we perform an abiotic electrophilic aromatic substitution reaction, which is directed precisely through space. Ester arms--positioned above the planes of aromatic rings--enable it to distinguish between nearly identical, neighbouring reactive positions. Quantum mechanical calculations show that, in two competing reaction pathways, both [C-H...O]-hydrogen bonding and electrophile preorganization by coordination to a carbonyl group likely play a role in controlling the reaction. These through-space-directed mechanisms are inspired by dimethylallyl tryptophan synthases, which direct biological electrophilic aromatic substitutions by preorganizing dimethylallyl cations and by stabilizing reactive intermediates with [C-H...N]-hydrogen bonding. Our results demonstrate how the third dimension above and underneath aromatic rings can be exploited to precisely control electrophilic aromatic substitutions.

Model compound study of the pathways for aromatic hydrocarbon formation in soot.

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

Tomczyk, N. A.; Hunt, J. E.; Winans, R. E.

2002-04-29

To explore the mechanisms for formation of aromatic hydrocarbons as precursors to soot, a model system using combustion of biphenyl in a fuel rich flame is studied. The soots acquired at three different temperatures are solvent extracted and the extract characterized by both GCMS and high resolution mass spectrometry. A description of the NMR results for the whole soots has been published (1). The production of most products could be rationalized from the coupling of biphenyls and subsequent aromatic species and the addition of acetylenes to existing aromatic molecules. Early work by Badger on pyrolysis of hydrocarbons is used inmore » developing these schemes (2). The reaction schemes to produce larger aromatic hydrocarbons will be discussed. Richter and Howard have discussed in detail potential reaction mechanisms in the formation of aromatics as precursors to soot (3).« less

The aromatic amino acid hydroxylase genes AAH1 and AAH2 in Toxoplasma gondii contribute to transmission in the cat

USDA-ARS?s Scientific Manuscript database

The Toxoplasma gondii genome contains two aromatic amino acid hydroxylase genes, AAH1 and AAH2, which encode proteins that produce L-DOPA, which can serve as a precursor of catecholamine neurotransmitters. It has been suggested that this pathway elevates host dopamine levels thus making infected rod...

SEDIMENT-ASSOCIATED REACTIONS OF AROMATIC AMINES. 2. QSAR DEVELOPMENT

EPA Science Inventory

The fate of aromatic amines in soils and sediments is dominated by irreversible binding through nucleophilic addition and oxidative radical coupling. Despite the common occurrence of the aromatic amine functional group in organic chemicals, the molecular properties useful for pr...

Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer.

PubMed

Denby, Charles M; Li, Rachel A; Vu, Van T; Costello, Zak; Lin, Weiyin; Chan, Leanne Jade G; Williams, Joseph; Donaldson, Bryan; Bamforth, Charles W; Petzold, Christopher J; Scheller, Henrik V; Martin, Hector Garcia; Keasling, Jay D

2018-03-20

Flowers of the hop plant provide both bitterness and "hoppy" flavor to beer. Hops are, however, both a water and energy intensive crop and vary considerably in essential oil content, making it challenging to achieve a consistent hoppy taste in beer. Here, we report that brewer's yeast can be engineered to biosynthesize aromatic monoterpene molecules that impart hoppy flavor to beer by incorporating recombinant DNA derived from yeast, mint, and basil. Whereas metabolic engineering of biosynthetic pathways is commonly enlisted to maximize product titers, tuning expression of pathway enzymes to affect target production levels of multiple commercially important metabolites without major collateral metabolic changes represents a unique challenge. By applying state-of-the-art engineering techniques and a framework to guide iterative improvement, strains are generated with target performance characteristics. Beers produced using these strains are perceived as hoppier than traditionally hopped beers by a sensory panel in a double-blind tasting.

The Anxiolytic and Antidepressant-like Effects of Testosterone and Estrogen in Gonadectomized Male Rats

PubMed Central

Carrier, Nicole; Saland, Samantha K.; Duclot, Florian; He, Huan; Mercer, Roger; Kabbaj, Mohamed

2015-01-01

Background While the influence of testosterone levels on vulnerability to affective disorders is not straightforward, research suggests this hormone may confer some degree of resiliency in men. We recently demonstrated a role for the dentate gyrus in mediating testosterone’s protective effects on depressive-like behavior in gonadectomized male rats. Here, testosterone may exert its effects through androgen receptor-mediated mechanisms or via local aromatization to estradiol. Methods Gonadectomized male rats were implanted with a placebo, testosterone, or estradiol pellet, and subsequent protective anxiolytic- and antidepressant-like effects of testosterone and its aromatized metabolite, estradiol, were then investigated in the open field and sucrose preference tests, respectively. Moreover, their influence on gene expression in the hippocampus was analyzed by genome-wide cDNA microarray analysis. Finally, the contribution of testosterone’s aromatization within the dentate gyrus was assessed by local infusion of the aromatase inhibitor, fadrozole, whose efficacy was confirmed by LC-MS/MS. Results Both hormones had antidepressant-like effects associated with a substantial overlap in transcriptional regulation, particularly in synaptic plasticity- and mitogen-activated protein kinase pathway-related genes. Further, chronic aromatase inhibition within the dentate gyrus blocked the protective effects of testosterone. Conclusions Both testosterone and estradiol exhibit anxiolytic- and antidepressant-like effects in gonadectomized male rats, while similarly regulating critical mediators of these behaviors, suggesting common underlying mechanisms. Accordingly, we demonstrated that testosterone’s protective effects are mediated, in part, by its aromatization in the dentate gyrus. These findings thus provide further insight into a role for estradiol in mediating the protective anxiolytic- and antidepressant-like effects of testosterone. PMID:25683735

An ethnopharmacological study of aromatic Uyghur medicinal plants in Xinjiang, China.

PubMed

Zhao, Lu; Tian, Shuge; Wen, E; Upur, Halmuart

2017-12-01

An ethnobotanical survey was completed in a remote village and surrounding country of Xinjiang, where most Uyghur medicinal plants could be collected. This work clarifies and increases ethnobotanical data. We surveyed and organized aromatic medicinal plants that are commonly used in clinical settings to provide a significant reference for studying new medical activities. In the survey, informants who have traditional knowledge on aromatic Uyghur medicinal plants were interviewed between March 2014 and September 2014. Aromatic medicinal plant species and pertinent information were collected. Some therapeutic methods and modes of preparation of traditional aromatic medicinal plants were found. A total of 86 aromatic medicinal plant species belonging to 36 families were included in our study. We identified 34 plant species introduced from different regions such as Europe, India and Mediterranean areas. Fruits and whole plants were the most commonly used parts of plant, and most aromatic medicinal plants could be applied as medicine and food. We assigned the medicinal plants a use value (UV). Knowing the UV of species is useful in determining the use reliability and pharmacological features of related plants. Xinjiang is an area in which indigenous aromatic medicinal plants are diversely used and has therefore established a sound dimensional medical healthcare treatment system. Some aromatic Uyghur medicinal plants are on the verge of extinction. Hence, further strategies for the conservation of these aromatic medicinal plants should be prioritized.

The evolution of floral scent and insect chemical communication.

PubMed

Schiestl, Florian P

2010-05-01

Plants have evolved a range of strategies to manipulate the behaviour of their insect partners. One powerful strategy is to produce signals that already have a role in the animals' own communication systems. To investigate to what extent the evolution of floral scents is correlated with chemical communication in insects, I analyse the occurrence, commonness, and evolutionary patterns of the 71 most common 'floral' volatile organic compounds (VOCs) in 96 plant families and 87 insect families. I found an overlap of 87% in VOCs produced by plants and insects. 'Floral' monoterpenes showed strong positive correlation in commonness between plants (both gymnosperms and angiosperms) and herbivores, whereas the commonness of 'floral' aromatics was positively correlated between angiosperms and both pollinators and herbivores. According to a multivariate regression analysis the commonness of 'floral' aromatics was best explained by their commonness in pollinators, whereas monoterpenes were best explained by herbivores. Among pollinator orders, aromatics were significantly more common in Lepidoptera than in Hymenoptera, whereas monoterpenes showed no difference among the two orders. Collectively, these patterns suggest that plants and insects converge in overall patterns of volatile production, both for attraction and defence. Monoterpenes seem to have evolved primarily for defence under selection by herbivores, whereas aromatics evolved signalling functions in angiosperms, primarily for pollinator attraction.

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.

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.

Aerobic Biodegradation of Trichloroethylene.

DTIC Science & Technology

1987-07-01

into C02 and unidentified nonvolatile products. Phenol, 41 toiin- andq- cresol were found to replace the site water requirement for TCE metabolism...identified as phenol. Other aromatic compounds that could support TCE degradation were toluene, o- cresol , and m- cresol . The degradation could be...Production...... .. .. .. . 17 4. Test for the Catechol Ortho °Ring-Fission Pathway . 18 5. Oxidation of Aromatic Compounds ............. .18 6

Aromatic metabolism of filamentous fungi in relation to the presence of aromatic compounds in plant biomass.

PubMed

Mäkelä, Miia R; Marinović, Mila; Nousiainen, Paula; Liwanag, April J M; Benoit, Isabelle; Sipilä, Jussi; Hatakka, Annele; de Vries, Ronald P; Hildén, Kristiina S

2015-01-01

The biological conversion of plant lignocellulose plays an essential role not only in carbon cycling in terrestrial ecosystems but also is an important part of the production of second generation biofuels and biochemicals. The presence of the recalcitrant aromatic polymer lignin is one of the major obstacles in the biofuel/biochemical production process and therefore microbial degradation of lignin is receiving a great deal of attention. Fungi are the main degraders of plant biomass, and in particular the basidiomycete white rot fungi are of major importance in converting plant aromatics due to their ability to degrade lignin. However, the aromatic monomers that are released from lignin and other aromatic compounds of plant biomass are toxic for most fungi already at low levels, and therefore conversion of these compounds to less toxic metabolites is essential for fungi. Although the release of aromatic compounds from plant biomass by fungi has been studied extensively, relatively little attention has been given to the metabolic pathways that convert the resulting aromatic monomers. In this review we provide an overview of the aromatic components of plant biomass, and their release and conversion by fungi. Finally, we will summarize the applications of fungal systems related to plant aromatics. Copyright © 2015 Elsevier Inc. All rights reserved.

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.

PubMed

Tan, Kemin; Chang, Changsoo; Cuff, Marianne; Osipiuk, Jerzy; Landorf, Elizabeth; Mack, Jamey C; Zerbs, Sarah; Joachimiak, Andrzej; Collart, Frank R

2013-10-01

Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. Copyright © 2013 Wiley Periodicals, Inc.

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids

PubMed Central

Tan, Kemin; Chang, Changsoo; Cuff, Marianne; Osipiuk, Jerzy; Landorf, Elizabeth; Mack, Jamey C.; Zerbs, Sarah; Joachimiak, Andrzej; Collart, Frank R.

2013-01-01

Lignin comprises 15.25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP.binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute.binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. PMID:23606130

Metabolic Response of Strawberry (Fragaria x ananassa) Leaves Exposed to the Angular Leaf Spot Bacterium (Xanthomonas fragariae).

PubMed

Kim, Min-Sun; Jin, Jong Sung; Kwak, Youn-Sig; Hwang, Geum-Sook

2016-03-09

Plants have evolved various defense mechanisms against biotic stress. The most common mechanism involves the production of metabolites that act as defense compounds. Bacterial angular leaf spot disease (Xanthomonas fragariae) of the strawberry (Fragaria x ananassa) has become increasingly destructive to strawberry leaves and plant production. In this study, we examined metabolic changes associated with the establishment of long-term bacterial disease stress using UPLC-QTOF mass spectrometry. Infected leaves showed decreased levels of gallic acid derivatives and ellagitannins, which are related to the plant defense system. The levels of phenylalanine, tryptophan, and salicylic acid as precursors of aromatic secondary metabolites were increased in inoculated leaves, whereas levels of coumaric acid, quinic acid, and flavonoids were decreased in infected plants, which are involved in the phenylpropanoid pathway. In addition, phenylalanine ammonia-lyase (PAL) activity, a key enzyme in the phenylpropanoid pathway, was decreased following infection. These results suggest that long-term bacterial disease stress may lead to down-regulation of select molecules of the phenylpropanoid metabolic pathway in strawberry leaves. This approach could be applied to explore the metabolic pathway associated with plant protection/breeding in strawberry leaves.

Frog volatile compounds: application of in vivo SPME for the characterization of the odorous secretions from two species of Hypsiboas treefrogs.

PubMed

Brunetti, Andrés E; Merib, Josias; Carasek, Eduardo; Caramão, Elina B; Barbará, Janaina; Zini, Claudia A; Faivovich, Julián

2015-04-01

A novel in vivo design was used in combination with solid-phase microextraction (SPME) and gas chromatography/mass spectrometry (GC/MS) to characterize the volatile compounds from the skin secretion of two species of tree frogs. Conventional SPME-GC/MS also was used for the analysis of volatiles present in skin samples and for the analysis of volatiles present in the diet and terraria. In total, 40 and 37 compounds were identified in the secretion of Hypsiboas pulchellus and H. riojanus, respectively, of which, 35 were common to both species. Aliphatic aldehydes, a low molecular weight alkadiene, an aromatic alcohol, and other aromatics, ketones, a methoxy pyrazine, sulfur containing compounds, and hemiterpenes are reported here for the first time in anurans. Most of the aliphatic compounds seem to be biosynthesized by the frogs following different metabolic pathways, whereas aromatics and monoterpenes are most likely sequestered from environmental sources. The characteristic smell of the secretion of H. pulchellus described by herpetologists as skunk-like or herbaceous is explained by a complex blend of different odoriferous components. The possible role of the volatiles found in H. pulchellus and H. riojanus is discussed in the context of previous hypotheses about the biological function of volatile secretions in frogs (e.g., sex pheromones, defense secretions against predators, mosquito repellents).

Unveiling the Mechanism of Arginine Transport through AdiC with Molecular Dynamics Simulations: The Guiding Role of Aromatic Residues

PubMed Central

Krammer, Eva-Maria; Ghaddar, Kassem; André, Bruno

2016-01-01

Commensal and pathogenic enteric bacteria have developed several systems to adapt to proton leakage into the cytoplasm resulting from extreme acidic conditions. One such system involves arginine uptake followed by export of the decarboxylated product agmatine, carried out by the arginine/agmatine antiporter (AdiC), which thus works as a virtual proton pump. Here, using classical and targeted molecular dynamics, we investigated at the atomic level the mechanism of arginine transport through AdiC of E. coli. Overall, our MD simulation data clearly demonstrate that global rearrangements of several transmembrane segments are necessary but not sufficient for achieving transitions between structural states along the arginine translocation pathway. In particular, local structural changes, namely rotameric conversions of two aromatic residues, are needed to regulate access to both the outward- and inward-facing states. Our simulations have also enabled identification of a few residues, overwhelmingly aromatic, which are essential to guiding arginine in the course of its translocation. Most of them belong to gating elements whose coordinated motions contribute to the alternating access mechanism. Their conservation in all known E. coli acid resistance antiporters suggests that the transport mechanisms of these systems share common features. Last but not least, knowledge of the functional properties of AdiC can advance our understanding of the members of the amino acid-carbocation-polyamine superfamily, notably in eukaryotic cells. PMID:27482712

Anomalous length dependence of conductance of aromatic nanoribbons with amine anchoring groups

NASA Astrophysics Data System (ADS)

Bilić, Ante; Sanvito, Stefano

2012-09-01

Two sets of aromatic nanoribbons, based around a common hexagonal scaffolding, with single and dual terminal amine groups have been considered as potential molecular wires in a junction formed by gold leads. Charge transport through the two-terminal device has been modeled using density functional theory (with and without self-interaction correction) and the nonequilibrium Green's function method. The effects of wire length, multiple terminal contacts, and pathways across the junction have been investigated. For nanoribbons with the oligopyrene motif and conventional single amine terminal groups, an increase in the wire length causes an exponential drop in the conductance. In contrast, for the nanoribbons with the oligoperylene motif and dual amine anchoring groups the predicted conductance rises with the wire length over the whole range of investigated lengths. Only when the effects of self-interaction correction are taken into account, the conductance of the oligoperylene ribbons exhibits saturation for longer members of the series. The oligoperylene nanoribbons, with dual amine groups at both terminals, show the potential to fully harness the highly conjugated system of π molecular orbitals across the junction.

METABOLIC ENGINEERING TO DEVELOP A PATHWAY FOR THE SELECTIVE CLEAVAGE OF CARBON-NITROGEN BONDS

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

John J. Kilbane II

The objective of the project is to develop biochemical pathways for the selective cleavage of C-N bonds in molecules found in petroleum. The initial phase of the project was focused on the isolation or development of an enzyme capable of cleaving the C-N bond in aromatic amides, specifically 2-aminobiphenyl. The objective of the second phase of the research will be to construct a biochemical pathway for the selective removal of nitrogen from carbazole by combining the carA genes from Sphingomonas sp. GTIN11 with the gene(s) encoding an appropriate deaminase. The objective of the final phase of the project will bemore » to develop derivative C-N bond cleaving enzymes that have broader substrate ranges and to demonstrate the use of such strains to selectively remove nitrogen from petroleum. During the first year of the project (October, 2002-September, 2003) enrichment culture experiments resulted in the isolation of microbial cultures that utilize aromatic amides as sole nitrogen sources, several amidase genes were cloned and were included in directed evolution experiments to obtain derivatives that can cleave C-N bonds in aromatic amides, and the carA genes from Sphingomonas sp. GTIN11, and Pseudomonas resinovorans CA10 were cloned in vectors capable of replicating in Escherichia coli. During the second year of the project (October, 2003-September, 2004) enrichment culture experiments succeeded in isolating a mixed bacterial culture that can utilize 2-aminobiphenyl as a sole nitrogen source, directed evolution experiments were focused on the aniline dioxygenase enzyme that is capable of deaminating aniline, and expression vectors were constructed to enable the expression of genes encoding C-N bond cleaving enzymes in Rhodococcus hosts. The construction of a new metabolic pathway to selectively remove nitrogen from carbazole and other molecules typically found in petroleum should lead to the development of a process to improve oil refinery efficiency by reducing the poisoning, by nitrogen, of catalysts used in the hydrotreating and catalytic cracking of petroleum. Aromatic compounds such as carbazole are representative of the difficult-to-treat organonitrogen compounds most commonly encountered in petroleum. There are two C-N bonds in carbazole and the construction of a metabolic pathway for the removal of nitrogen from carbazole will require enzymes capable cleaving both C-N bonds. A multi-component enzyme, carbazole dioxygenase, which can selectively cleave the first C-N bond has been identified and the genes that encode this enzyme have been cloned, sequenced, and are being expressed in Rhodococcus erythropolis, a bacterial culture that tolerates exposure to petroleum. An enzyme capable of selectively cleaving the second C-N bond in carbazole has not yet been identified, but enrichment culture experiments have recently succeeded in isolating a bacterial culture that is a likely candidate and may possess a suitable enzyme. Research in the near future will verify if a suitable enzyme for the cleavage of the second C-N bond in carbazole has indeed been found, then the genes encoding a suitable enzyme will be identified, cloned, and sequenced. Ultimately genes encoding enzymes for selective cleavage of both C-N bonds in carbazole will be assembled into a new metabolic pathway and the ability of the resulting bacterial culture to remove nitrogen from petroleum will be determined.« less

Volatile profiles of aromatic and non-aromatic rice

USDA-ARS?s Scientific Manuscript database

Rice is enjoyed by many people as a staple food because of its flavor and texture. Some scented varieties command a premium in the marketplace because of their distinctive aroma and flavor. The compound most commonly associated with the popcorn or nutty scent of aromatic rice is 2-acetyl-1-pyrroline...

Catalytic conversion of isophorone to jet-fuel range aromatic hydrocarbons over a MoO(x)/SiO2 catalyst.

PubMed

Chen, Fang; Li, Ning; Wang, Wentao; Wang, Aiqin; Cong, Yu; Wang, Xiaodong; Zhang, Tao

2015-07-28

For the first time, jet fuel range C8-C9 aromatic hydrocarbons were synthesized in high carbon yield (∼80%) by the catalytic conversion of isophorone over MoO(x)/SiO2 at atmospheric pressure. A possible reaction pathway was proposed according to the control experiments and the intermediates generated during the reaction.

Simultaneous metabolism of chloro- and methyl-aromatic compounds by selected bacterial strains. Final report, 20 August 1991-19 August 1992

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

Focht, D.D.

Microorganisms are frequently able to degrade anthropogenic materials using pathways that evolved for the assimilation of related naturally-occurring compounds. Complications can arise, however, during the metabolism of mixtures when incompatible intermediates are formed from different components. The breakdown of chloro- and methyl-aromatics, for example, produces catechols which are oxidized differently: chlorocatechols are normally cleaved by ortho fission and methylcatechols by meta fission. If both systems act simultaneously, suicide substrates or dead-end metabolites are usually formed. Nevertheless, bacteria differ in their, ability to cope with such mixtures. A unique bacterium, Pseudomonas cepacia MB2 was isolated by selective enrichment on 2-methylbenzoate, yetmore » was also able to fortuitously utilize 3-chloro-2-methylbenzoate as a sole carbon source. This strain is unique in its ability to utilize an aromatic acid containing both a methyl and chloro substituent via the metafission pathway without the production of suicidal products.« less

Directional synthesis of ethylbenzene through catalytic transformation of lignin.

PubMed

Fan, Minghui; Jiang, Peiwen; Bi, Peiyan; Deng, Shumei; Yan, Lifeng; Zhai, Qi; Wang, Tiejun; Li, Quanxin

2013-09-01

Transformation of lignin to ethylbenzene can provide an important bulk raw material for the petrochemical industry. This work explored the production of ethylbenzene from lignin through the directional catalytic depolymerization of lignin into the aromatic monomers followed by the selective alkylation of the aromatic monomers. For the first step, the aromatics selectivity of benzene derived from the catalytic depolymerization of lignin reached about 90.2 C-mol% over the composite catalyst of Re-Y/HZSM-5 (25). For the alkylation of the aromatic monomers in the second step, the highest selectivity of ethylbenzene was about 72.3 C-mol% over the HZSM-5 (25) catalyst. The reaction pathway for the transformation of lignin to ethylbenzene was also addressed. Present transformation potentially provides a useful approach for the production of the basic petrochemical material and development of high-end chemicals utilizing lignin as the abundant natural aromatic resource. Copyright © 2013 Elsevier Ltd. All rights reserved.

Metabolic Engineering of Saccharomyces cerevisiae for High-Level Production of Salidroside from Glucose.

PubMed

Jiang, Jingjie; Yin, Hua; Wang, Shuai; Zhuang, Yibin; Liu, Shaowei; Liu, Tao; Ma, Yanhe

2018-05-02

Salidroside is an important plant-derived aromatic compound with diverse biological properties. Because of inadequate natural resources, the supply of salidroside is currently limited. In this work, we engineered the production of salidroside in yeast. First, the aromatic aldehyde synthase (AAS) from Petroselinum crispum was overexpressed in Saccharomyces cerevisiae when combined with endogenous Ehrlich pathway to produce tyrosol from tyrosine. Glucosyltransferases from different resources were tested for ideal production of salidroside in the yeast. Metabolic flux was enhanced toward tyrosine biosynthesis by overexpressing pathway genes and eliminating feedback inhibition. The pathway genes were integrated into yeast chromosome, leading to a recombinant strain that produced 239.5 mg/L salidroside and 965.4 mg/L tyrosol. The production of salidroside and tyrosol reached up to 732.5 and 1394.6 mg/L, respectively, by fed-batch fermentation. Our work provides an alternative way for industrial large-scale production of salidroside and tyrosol from S. cerevisiae.

Peculiarities of the photoinitiator-free photopolymerization of pentabrominated and pentafluorinated aromatic acrylates and methacrylates.

PubMed

Daikos, Olesya; Naumov, Sergej; Knolle, Wolfgang; Heymann, Katja; Scherzer, Tom

2016-11-30

Pentabrominated and fluorinated aromatic (meth)acrylates as well as their non-halogenated counterparts have been studied with the aim to avoid conventional photoinitiators and to overcome some negative consequences related to their use. Therefore, RTIR spectroscopy, laser flash photolysis and GC/MS were utilized. Even low concentrations (1 to 5 wt%) of brominated (meth)acrylates in the model varnish lead to initiation of a photopolymerization reaction under exposure to UV light with λ > 300 nm. This is due to the fact that excitation of the aryl moiety leads to the homolysis of bromine-phenyl bonds with a high quantum yield of ∼0.15-0.3. Both, bromine radicals released from either ortho, meta or para position as well as the corresponding tetrabromoaryl radicals, may initiate the polymerization of brominated aromatic (meth)acrylates. In contrast, fluorinated aromatic (meth)acrylates undergo α-cleavage of the carboxyl group (as in the case of non-halogenated aromatic (meth)acrylates), if excitation of the acrylic double bonds is done with UV-C light (λ < 280 nm). Radical formation occurs with a comparable quantum yield of 0.1-0.22 (fluorinated) and 0.16-0.36 (non-halogenated compounds), despite the different pathway of fragmentation. Thus, in all cases the efficiency of initiation is comparable to conventional photoinitiators. Quantum chemical calculations of orbitals involved and of the Gibbs free energy of transients and products support the suggested reaction pathway.

Transformation among Aromatic Iodinated Disinfection Byproducts in the Presence of Monochloramine: From Monoiodophenol to Triiodophenol and Diiodonitrophenol.

PubMed

Gong, Tingting; Tao, Yuxian; Zhang, Xiangru; Hu, Shaoyang; Yin, Jinbao; Xian, Qiming; Ma, Jian; Xu, Bin

2017-09-19

Aromatic iodinated disinfection byproducts (DBPs) are a newly identified category of highly toxic DBPs. Among the identified aromatic iodinated DBPs, 2,4,6-triiodophenol and 2,6-diiodo-4-nitrophenol have shown relatively widespread occurrence and high toxicity. In this study, we found that 4-iodophenol underwent transformation to form 2,4,6-triiodophenol and 2,6-diiodo-4-nitrophenol in the presence of monochloramine. The transformation pathways were investigated, the decomposition kinetics of 4-iodophenol and the formation of 2,4,6-triiodophenol and 2,6-diiodo-4-nitrophenol were studied, the factors affecting the transformation were examined, the toxicity change during the transformation was evaluated, and the occurrence of the proposed transformation pathways during chloramination of source water was verified. The results revealed that 2,4,6-triiodophenol and 2,6-diiodo-4-nitrophenol, which could account for 71.0% of iodine in the transformed 4-iodophenol, were important iodinated transformation products of 4-iodophenol in the presence of monochloramine. The transformation pathways of 4-iodophenol in the presence of monochloramine were proposed and verified. The decomposition of 4-iodophenol in the presence of monochloramine followed a pseudo-second-order decay. Various factors including monochloramine dose, pH, temperature, nitrite concentration, and free chlorine contact time (before chloramination) affected the transformation. The cytotoxicity of the chloraminated 4-iodophenol samples increased continuously with contact time. The proposed transformation pathways occurred during chloramination of source water.

Catalytic conversion of lignin pyrolysis model compound- guaiacol and its kinetic model including coke formation.

PubMed

Zhang, Huiyan; Wang, Yun; Shao, Shanshan; Xiao, Rui

2016-11-21

Lignin is the most difficult to be converted and most easy coking component in biomass catalytic pyrolysis to high-value liquid fuels and chemicals. Catalytic conversion of guaiacol as a lignin model compound was conducted in a fixed-bed reactor over ZSM-5 to investigate its conversion and coking behaviors. The effects of temperature, weight hourly space velocity (WHSV) and partial pressure on product distribution were studied. The results show the maximum aromatic carbon yield of 28.55% was obtained at temperature of 650 °C, WHSV of 8 h -1 and partial pressure of 2.38 kPa, while the coke carbon yield was 19.55%. The reaction pathway was speculated to be removing methoxy group to form phenols with further aromatization to form aromatics. The amount of coke increased with increasing reaction time. The surface area and acidity of catalysts declined as coke formed on the acid sites and blocked the pore channels, which led to the decrease of aromatic yields. Finally, a kinetic model of guaiacol catalytic conversion considering coke deposition was built based on the above reaction pathway to properly predict product distribution. The experimental and model predicting data agreed well. The correlation coefficient of all equations were all higher than 0.90.

Catalytic conversion of lignin pyrolysis model compound- guaiacol and its kinetic model including coke formation

PubMed Central

Zhang, Huiyan; Wang, Yun; Shao, Shanshan; Xiao, Rui

2016-01-01

Lignin is the most difficult to be converted and most easy coking component in biomass catalytic pyrolysis to high-value liquid fuels and chemicals. Catalytic conversion of guaiacol as a lignin model compound was conducted in a fixed-bed reactor over ZSM-5 to investigate its conversion and coking behaviors. The effects of temperature, weight hourly space velocity (WHSV) and partial pressure on product distribution were studied. The results show the maximum aromatic carbon yield of 28.55% was obtained at temperature of 650 °C, WHSV of 8 h−1 and partial pressure of 2.38 kPa, while the coke carbon yield was 19.55%. The reaction pathway was speculated to be removing methoxy group to form phenols with further aromatization to form aromatics. The amount of coke increased with increasing reaction time. The surface area and acidity of catalysts declined as coke formed on the acid sites and blocked the pore channels, which led to the decrease of aromatic yields. Finally, a kinetic model of guaiacol catalytic conversion considering coke deposition was built based on the above reaction pathway to properly predict product distribution. The experimental and model predicting data agreed well. The correlation coefficient of all equations were all higher than 0.90. PMID:27869228

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

Glyphosate has limited short-term effects on commensal bacterial community composition in the gut environment due to sufficient aromatic amino acid levels.

PubMed

Nielsen, Lene Nørby; Roager, Henrik M; Casas, Mònica Escolà; Frandsen, Henrik L; Gosewinkel, Ulrich; Bester, Kai; Licht, Tine Rask; Hendriksen, Niels Bohse; Bahl, Martin Iain

2018-02-01

Recently, concerns have been raised that residues of glyphosate-based herbicides may interfere with the homeostasis of the intestinal bacterial community and thereby affect the health of humans or animals. The biochemical pathway for aromatic amino acid synthesis (Shikimate pathway), which is specifically inhibited by glyphosate, is shared by plants and numerous bacterial species. Several in vitro studies have shown that various groups of intestinal bacteria may be differently affected by glyphosate. Here, we present results from an animal exposure trial combining deep 16S rRNA gene sequencing of the bacterial community with liquid chromatography mass spectrometry (LC-MS) based metabolic profiling of aromatic amino acids and their downstream metabolites. We found that glyphosate as well as the commercial formulation Glyfonova ® 450 PLUS administered at up to fifty times the established European Acceptable Daily Intake (ADI = 0.5 mg/kg body weight) had very limited effects on bacterial community composition in Sprague Dawley rats during a two-week exposure trial. The effect of glyphosate on prototrophic bacterial growth was highly dependent on the availability of aromatic amino acids, suggesting that the observed limited effect on bacterial composition was due to the presence of sufficient amounts of aromatic amino acids in the intestinal environment. A strong correlation was observed between intestinal concentrations of glyphosate and intestinal pH, which may partly be explained by an observed reduction in acetic acid produced by the gut bacteria. We conclude that sufficient intestinal levels of aromatic amino acids provided by the diet alleviates the need for bacterial synthesis of aromatic amino acids and thus prevents an antimicrobial effect of glyphosate in vivo. It is however possible that the situation is different in cases of human malnutrition or in production animals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Phenyl radical + propene: a prototypical reaction surface for aromatic-catalyzed 1,2-hydrogen-migration and subsequent resonance-stabilized radical formation.

PubMed

Buras, Zachary J; Chu, Te-Chun; Jamal, Adeel; Yee, Nathan W; Middaugh, Joshua E; Green, William H

2018-05-16

The C9H11 potential energy surface (PES) was experimentally and theoretically explored because it is a relatively simple, prototypical alkylaromatic radical system. Although the C9H11 PES has already been extensively studied both experimentally (under single-collision and thermal conditions) and theoretically, new insights were made in this work by taking a new experimental approach: flash photolysis combined with time-resolved molecular beam mass spectrometry (MBMS) and visible laser absorbance. The C9H11 PES was experimentally accessed by photolytic generation of the phenyl radical and subsequent reaction with excess propene (C6H5 + C3H6). The overall kinetics of C6H5 + C3H6 was measured using laser absorbance with high time-resolution from 300 to 700 K and was found to be in agreement with earlier measurements over a lower temperature range. Five major product channels of C6H5 + C3H6 were observed with MBMS at 600 and 700 K, four of which were expected: hydrogen (H)-abstraction (measured by the stable benzene, C6H6, product), methyl radical (CH3)-loss (styrene detected), H-loss (phenylpropene isomers detected) and radical adduct stabilization. The fifth, unexpected product observed was the benzyl radical, which was rationalized by the inclusion of a previously unreported pathway on the C9H11 PES: aromatic-catalysed 1,2-H-migration and subsequent resonance stabilized radical (RSR, benzyl radical in this case) formation. The current theoretical understanding of the C9H11 PES was supported (including the aromatic-catalyzed pathway) by quantitative comparisons between modelled and experimental MBMS results. At 700 K, the branching to styrene + CH3 was 2-4 times greater than that of any other product channel, while benzyl radical + C2H4 from the aromatic-catalyzed pathway accounted for ∼10% of the branching. Single-collision conditions were also simulated on the updated PES to explain why previous crossed molecular beam experiments did not see evidence of the aromatic-catalyzed pathway. This experimentally validated knowledge of the C9H11 PES was added to the database of the open-source Reaction Mechanism Generator (RMG), which was then used to generalize the findings on the C9H11 PES to a slightly more complicated alkylaromatic system.

Low-temperature, mineral-catalyzed air oxidation: a possible new pathway for PAH stabilization in sediments and soils.

PubMed

Ghislain, Thierry; Faure, Pierre; Biache, Coralie; Michels, Raymond

2010-11-15

Reactivity of polycyclic aromatic hydrocarbons (PAHs) in the subsurface is of importance to environmental assessment, as they constitute a highly toxic hazard. Understanding their reactivity in the long term in natural recovering systems is thus a key issue. This article describes an experimental investigation on the air oxidation of fluoranthene (a PAH abundant in natural systems polluted by industrial coal use) at 100°C on different mineral substrates commonly found in soils and sediments (quartz sand, limestone, and clay). Results demonstrate that fluoranthene is readily oxidized in the presence of limestone and clay, leading to the formation of high molecular weight compounds and a carbonaceous residue as end product especially for clay experiments. As demonstrated elsewhere, the experimental conditions used permitted the reproduction of the geochemical pathway of organic matter observed under natural conditions. It is therefore suggested that low-temperature, mineral-catalyzed air oxidation is a mechanism relevant to the stabilization of PAHs in sediments and soils.

Multifaceted plant responses to circumvent Phe hyperaccumulation by downregulation of flux through the shikimate pathway and by vacuolar Phe sequestration.

PubMed

Lynch, Joseph H; Orlova, Irina; Zhao, Chengsong; Guo, Longyun; Jaini, Rohit; Maeda, Hiroshi; Akhtar, Tariq; Cruz-Lebron, Junellie; Rhodes, David; Morgan, John; Pilot, Guillaume; Pichersky, Eran; Dudareva, Natalia

2017-12-01

Detrimental effects of hyperaccumulation of the aromatic amino acid phenylalanine (Phe) in animals, known as phenylketonuria, are mitigated by excretion of Phe derivatives; however, how plants endure Phe accumulating conditions in the absence of an excretion system is currently unknown. To achieve Phe hyperaccumulation in a plant system, we simultaneously decreased in petunia flowers expression of all three Phe ammonia lyase (PAL) isoforms that catalyze the non-oxidative deamination of Phe to trans-cinnamic acid, the committed step for the major pathway of Phe metabolism. A total decrease in PAL activity by 81-94% led to an 18-fold expansion of the internal Phe pool. Phe accumulation had multifaceted intercompartmental effects on aromatic amino acid metabolism. It resulted in a decrease in the overall flux through the shikimate pathway, and a redirection of carbon flux toward the shikimate-derived aromatic amino acids tyrosine and tryptophan. Accumulation of Phe did not lead to an increase in flux toward phenylacetaldehyde, for which Phe is a direct precursor. Metabolic flux analysis revealed this to be due to the presence of a distinct metabolically inactive pool of Phe, likely localized in the vacuole. We have identified a vacuolar cationic amino acid transporter (PhCAT2) that contributes to sequestering excess of Phe in the vacuole. In vitro assays confirmed PhCAT2 can transport Phe, and decreased PhCAT2 expression in PAL-RNAi transgenic plants resulted in 1.6-fold increase in phenylacetaldehyde emission. These results demonstrate mechanisms by which plants maintain intercompartmental aromatic amino acid homeostasis, and provide critical insight for future phenylpropanoid metabolic engineering strategies. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Cation-π Interactions: Computational Analyses of the Aromatic Box Motif and the Fluorination Strategy for Experimental Evaluation

PubMed Central

Davis, Matthew R.; Dougherty, Dennis A.

2015-01-01

Cation-π interactions are common in biological systems, and many structural studies have revealed the aromatic box as a common motif. With the aim of understanding the nature of the aromatic box, several computational methods were evaluated for their ability to reproduce experimental cation-π binding energies. We find the DFT method M06 with the 6-31G(d,p) basis set performs best of several methods tested. The binding of benzene to a number of different cations (sodium, potassium, ammonium, tetramethylammonium, and guanidinium) was studied. In addition, the binding of the organic cations NH4+ and NMe4+ to ab initio generated aromatic boxes as well as examples of aromatic boxes from protein crystal structures were investigated. These data, along with a study of the distance dependence of the cation-π interaction, indicate that multiple aromatic residues can meaningfully contribute to cation binding, even with displacements of more than an angstrom from the optimal cation-π interaction. Progressive fluorination of benzene and indole was studied as well, and binding energies obtained were used to reaffirm the validity of the “fluorination strategy” to study cation-π interactions in vivo. PMID:26467787

Cation-π interactions: computational analyses of the aromatic box motif and the fluorination strategy for experimental evaluation.

PubMed

Davis, Matthew R; Dougherty, Dennis A

2015-11-21

Cation-π interactions are common in biological systems, and many structural studies have revealed the aromatic box as a common motif. With the aim of understanding the nature of the aromatic box, several computational methods were evaluated for their ability to reproduce experimental cation-π binding energies. We find the DFT method M06 with the 6-31G(d,p) basis set performs best of several methods tested. The binding of benzene to a number of different cations (sodium, potassium, ammonium, tetramethylammonium, and guanidinium) was studied. In addition, the binding of the organic cations NH4(+) and NMe4(+) to ab initio generated aromatic boxes as well as examples of aromatic boxes from protein crystal structures were investigated. These data, along with a study of the distance dependence of the cation-π interaction, indicate that multiple aromatic residues can meaningfully contribute to cation binding, even with displacements of more than an angstrom from the optimal cation-π interaction. Progressive fluorination of benzene and indole was studied as well, and binding energies obtained were used to reaffirm the validity of the "fluorination strategy" to study cation-π interactions in vivo.

Comparison of carbon-sulfur and carbon-amine bond in therapeutic drug: 4β-S-aromatic heterocyclic podophyllum derivatives display antitumor activity

PubMed Central

Li, Jian-Long; Zhao, Wei; Zhou, Chen; Zhang, Ya-Xuan; Li, Hong-Mei; Tang, Ya-Ling; Liang, Xin-Hua; Chen, Tao; Tang, Ya-Jie

2015-01-01

Herein is a first effort to systematically study the significance of carbon-sulfur (C-S) and carbon-amine (C-NH) bonds on the antitumor proliferation activity of podophyllum derivatives and their precise mechanism of apoptosis. Compared with the derivative modified by a C-NH bond, the derivative modified by a C-S bond exhibited superior antitumor activity, the inhibition activity of target proteins tubulin or Topo II, cell cycle arrest, and apoptosis induction. Antitumor mechanistic studies showed that the death receptor and the mitochondrial apoptotic pathways were simultaneously activated by the C-S bond modified aromatic heterocyclic podophyllum derivatives with a higher cellular uptake percentage of 60–90% and induction of a higher level of reactive oxygen species (ROS). Only the mitochondrial apoptotic pathway was activated by the C-NH bond modified aromatic heterocyclic podophyllum derivatives, with a lower cellular uptake percentage of 40–50%. This study provided insight into effects of the C-S and C-NH bond modification on the improvement of the antitumor activity of Podophyllum derivatives. PMID:26443888

Linking secondary metabolites to biosynthesis genes in the fungal endophyte Cyanodermella asteris: The anti-cancer bisanthraquinone skyrin.

PubMed

Jahn, Linda; Schafhauser, Thomas; Wibberg, Daniel; Rückert, Christian; Winkler, Anika; Kulik, Andreas; Weber, Tilmann; Flor, Liane; van Pée, Karl-Heinz; Kalinowski, Jörn; Ludwig-Müller, Jutta; Wohlleben, Wolfgang

2017-09-10

Fungal aromatic polyketides display a very diverse and widespread group of natural products. Due to their excellent light absorption properties and widely studied biological activities, they offer numerous application for food, textile and pharmaceutical industry. The biosynthetic pathways of fungal aromatic polyketides usually involve a set of successive enzymes, in which a non-reductive polyketide synthase iteratively catalyzes the essential assembly of simple building blocks into (often polycyclic) aromatic compounds. However, only a limited number of such pathways have been described so far and further elucidation of the individual biosynthetic steps is needed to fully exploit the biotechnological and medicinal potential of these compounds. Here, we identified the bisanthraquinone skyrin as the main pigment of the fungus Cyanodermella asteris, an endophyte that has recently been isolated from the traditional Chinese medicinal plant Aster tataricus. The genome of C. asteris was sequenced, assembled and annotated, which enables first insights into a genome from a non-lichenized member of the class Lecanoromycetes. Genetic and in silico analyses led to the identification of a gene cluster of five genes suggested to encode the enzymatic pathway for skyrin. Our study is a starting point for rational pathway engineering in order to drive the production towards higher yields or more active derivatives. Moreover, our investigations revealed a large potential of secondary metabolite production in C. asteris as well as in all Lecanoromycetes of which genomes were available. These findings convincingly emphasize that Lecanoromycetes are prolific producers of secondary metabolites. Copyright © 2017 Elsevier B.V. All rights reserved.

Furan production from glycoaldehyde over HZSM-5

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

Kim, Seonah; Evans, Tabitha J.; Mukarakate, Calvin

Catalytic fast pyrolysis of biomass over zeolite catalysts results primarily in aromatic (e.g. benzene, toluene, xylene) and olefin products. However, furans are a higher value intermediate for their ability to be readily transformed into gasoline, diesel, and chemicals. Here we investigate possible mechanisms for the coupling of glycoaldehyde, a common product of cellulose pyrolysis, over HZSM-5 for the formation of furans. Experimental measurements of neat glycoaldehyde over a fixed bed of HZSM-5 confirm furans (e.g. furanone) are products of this reaction at temperatures below 300 degrees C with several aldol condensation products as co-products (e.g. benzoquinone). However, under typical catalyticmore » fast pyrolysis conditions (>400 degrees C), further reactions occur that lead to the usual aromatic product slate. ONIOM calculations were utilized to identify the pathway for glycoaldehyde coupling toward furanone and hydroxyfuranone products with dehydration reactions serving as the rate determining steps with typical intrinsic reaction barriers of 40 kcal mol-1. The reaction mechanisms for glycoaldehyde will likely be similar to that of other small oxygenates such as acetaldehyde, lactaldehyde, and hydroxyacetone and this study provides a generalizable mechanism of oxygenate coupling and furan formation over zeolite catalysts.« less

Kinetics of acetaminophen degradation by Fenton oxidation in a fluidized-bed reactor.

PubMed

de Luna, Mark Daniel G; Briones, Rowena M; Su, Chia-Chi; Lu, Ming-Chun

2013-01-01

Acetaminophen (ACT), an analgesic and antipyretic substance, is one of the most commonly detected pharmaceutical compound in surface waters and wastewaters. In this study, fluidized-bed Fenton (FB-Fenton) was used to decompose ACT into its final degradation products. The 1.45-L cylindrical glass reactor had inlet, outlet and recirculating sections. SiO(2) carrier particles were supported by glass beads with 2-4 mm in diameter. ACT concentration was determined by high performance liquid chromatography (HPLC). During the first 40 min of reaction, a fast initial ACT removal was observed and the "two-stage" ACT degradation conformed to a pseudo reaction kinetics. The effects of ferrous ion dosage and [Fe(2+)]/[H(2)O(2)] (FH ratio) were integrated into the derived pseudo second-order kinetic model. A reaction pathway was proposed based on the intermediates detected through SPME/GC-MS. The aromatic intermediates identified were hydroquinone, benzaldehydes and benzoic acids while the non-aromatic substances include alcohols, ketones, aldehydes and carboxylic acids. Rapid initial ACT degradation rate can be accomplished by high initial ferrous ion concentration and/or low FH ratio. Copyright © 2012 Elsevier Ltd. All rights reserved.

Furan production from glycoaldehyde over HZSM-5

DOE PAGES

Kim, Seonah; Evans, Tabitha J.; Mukarakate, Calvin; ...

2016-04-03

Catalytic fast pyrolysis of biomass over zeolite catalysts results primarily in aromatic (e.g. benzene, toluene, xylene) and olefin products. However, furans are a higher value intermediate for their ability to be readily transformed into gasoline, diesel, and chemicals. Here we investigate possible mechanisms for the coupling of glycoaldehyde, a common product of cellulose pyrolysis, over HZSM-5 for the formation of furans. Experimental measurements of neat glycoaldehyde over a fixed bed of HZSM-5 confirm furans (e.g. furanone) are products of this reaction at temperatures below 300 degrees C with several aldol condensation products as co-products (e.g. benzoquinone). However, under typical catalyticmore » fast pyrolysis conditions (>400 degrees C), further reactions occur that lead to the usual aromatic product slate. ONIOM calculations were utilized to identify the pathway for glycoaldehyde coupling toward furanone and hydroxyfuranone products with dehydration reactions serving as the rate determining steps with typical intrinsic reaction barriers of 40 kcal mol-1. The reaction mechanisms for glycoaldehyde will likely be similar to that of other small oxygenates such as acetaldehyde, lactaldehyde, and hydroxyacetone and this study provides a generalizable mechanism of oxygenate coupling and furan formation over zeolite catalysts.« less

Utilization of aromatic compounds by the Penicillium strain Bi 7/2.

PubMed

Hofrichter, M; Scheibner, K

1993-01-01

The Penicillium strain Bi 7/2 utilized phenol, catechol, resorcinol, hydroquinone, pyrogallol, hydroxyhydroquinone, phloroglucinol, m- and p-cresol, orcinol, 4-methylcatechol, 4-methoxyphenol, 4-aminophenol, benzyl alcohol, benzoic acid, 2-, 3- and 4-hydroxybenzoic acid, anthranilic acid, protocatechuic acid and gallic acid as sole sources of carbon and energy. The central metabolites catechol, protocatechuic acid and hydroxyquinone could be determined by HPLC with diode-array detection. Pathways for the degradation of aromatic substances were proposed.

Uncovering the formation and selection of benzylmalonyl-CoA from the biosynthesis of splenocin and enterocin reveals a versatile way to introduce amino acids into polyketide carbon scaffolds.

PubMed

Chang, Chenchen; Huang, Rong; Yan, Yan; Ma, Hongmin; Dai, Zheng; Zhang, Benying; Deng, Zixin; Liu, Wen; Qu, Xudong

2015-04-01

Selective modification of carbon scaffolds via biosynthetic engineering is important for polyketide structural diversification. Yet, this scope is currently restricted to simple aliphatic groups due to (1) limited variety of CoA-linked extender units, which lack aromatic structures and chemical reactivity, and (2) narrow acyltransferase (AT) specificity, which is limited to aliphatic CoA-linked extender units. In this report, we uncovered and characterized the first aromatic CoA-linked extender unit benzylmalonyl-CoA from the biosynthetic pathways of splenocin and enterocin in Streptomyces sp. CNQ431. Its synthesis employs a deamination/reductive carboxylation strategy to convert phenylalanine into benzylmalonyl-CoA, providing a link between amino acid and CoA-linked extender unit synthesis. By characterization of its selection, we further validated that AT domains of splenocin, and antimycin polyketide synthases are able to select this extender unit to introduce the phenyl group into their dilactone scaffolds. The biosynthetic machinery involved in the formation of this extender unit is highly versatile and can be potentially tailored for tyrosine, histidine and aspartic acid. The disclosed aromatic extender unit, amino acid-oriented synthetic pathway, and aromatic-selective AT domains provides a systematic breakthrough toward current knowledge of polyketide extender unit formation and selection, and also opens a route for further engineering of polyketide carbon scaffolds using amino acids.

Aerobic biodegradation process of petroleum and pathway of main compounds in water flooding well of Dagang oil field.

PubMed

Cai, Minmin; Yao, Jun; Yang, Huaijun; Wang, Ruixia; Masakorala, Kanaji

2013-09-01

Aerobic biodegradation of crude oil and its pathways were investigated via in vitro culture and GC-MS analysis in water flooding wells of Dagang oil field. The in vitro aerobic culture lasted 90 days when 99.0% of n-alkanes and 43.03-99.9% of PAHs were degraded and the biomarkers and their ratios were changed. The spectra of components in the residual oil showed the similar biodegradation between aerobic process of 90 days and degradation in reservoir which may last for some millions years, and the potential of serious aerobic biodegradation of petroleum in reservoir. 24 Metabolites compounds were separated and identified from aerobic culture, including fatty acid, naphthenic acid, aromatic carboxylic acid, unsaturated acid, alcohols, ketones and aldehydes. The pathways of alkanes and aromatics were proposed, which suggests that oxidation of hydrocarbon to organic acid is an important process in the aerobic biodegradation of petroleum. Copyright © 2013 Elsevier Ltd. All rights reserved.

Genetic analysis of chromosomal operons involved in degradation of aromatic hydrocarbons in Pseudomonas putida TMB

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

Polissi, A.; Bestetti, G.; Bertoni, G.

1990-11-01

The catabolic pathway for the degradation of aromatic hydrocarbons encoded by Pseudomonas putida TMB differs from the TOL plasmid-encoded pathway as far as regulation of the upper pathway is concerned. We found, by analyzing Tn5-induced mutants and by Southern blot hybridization with appropriate probes derived from the TOL plasmid pWWO, that the catabolic genes of strain TMB were located on the bacterial chromosome and not on the 84-kb plasmid harbored by this strain. The catabolic genes of TMB and pWWO had sequence homology, as shown by Southern blot hybridization, but different significantly in their restriction patterns. The analysis of themore » mutants suggests that a regulatory mechanism similar to that present in pWWO coexists in TMB with a second mode of regulation which is epistatic on the former and that the chromosomal region carrying the catabolic genes is prone to rearrangements and deletions.« less

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.

Selective Oxidation of Lignin Model Compounds.

PubMed

Gao, Ruili; Li, Yanding; Kim, Hoon; Mobley, Justin K; Ralph, John

2018-05-02

Lignin, the planet's most abundant renewable source of aromatic compounds, is difficult to degrade efficiently to welldefined aromatics. We developed a microwave-assisted catalytic Swern oxidation system using an easily prepared catalyst, MoO 2 Cl 2 (DMSO) 2 , and DMSO as the solvent and oxidant. It demonstrated high efficiency in transforming lignin model compounds containing the units and functional groups found in native lignins. The aromatic ring substituents strongly influenced the selectivity of β-ether phenolic dimer cleavage to generate sinapaldehyde and coniferaldehyde, monomers not usually produced by oxidative methods. Time-course studies on two key intermediates provided insight into the reaction pathway. Owing to the broad scope of this oxidation system and the insight gleaned with regard to its mechanism, this strategy could be adapted and applied in a general sense to the production of useful aromatic chemicals from phenolics and lignin. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

METABOLIC ENGINEERING TO DEVELOP A PATHWAY FOR THE SELECTIVE CLEAVAGE OF CARBON-NITROGEN BONDS

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

John J. Kilbane III

The objective of the project is to develop biochemical pathways for the selective cleavage of C-N bonds in molecules found in petroleum. The initial phase of the project will focus on the isolation or development of an enzyme capable of cleaving the C-N bond in aromatic amides, specifically 2-aminobiphenyl. The objective of the second phase of the research will be to construct a biochemical pathway for the selective removal of nitrogen from carbazole by combining the carA genes from Sphingomonas sp. GTIN11 with the gene(s) encoding an appropriate amidase. The objective of the final phase of the project will bemore » to develop derivative CN bond cleaving enzymes that have broader substrate ranges and to demonstrate the use of such strains to selectively remove nitrogen from petroleum. The project is on schedule and no major difficulties have been encountered. During the first year of the project (October, 2002-September, 2003) enrichment culture experiments have resulted in the isolation of promising cultures that may be capable of cleaving C-N bonds in aromatic amides, several amidase genes have been cloned and are currently undergoing directed evolution to obtain derivatives that can cleave C-N bonds in aromatic amides, and the carA genes from Sphingomonas sp. GTIN11, and Pseudomonas resinovorans CA10 were cloned in vectors capable of replicating in Escherichia coli. Future research will address expression of these genes in Rhodococcus erythropolis. Enrichment culture experiments and directed evolution experiments continue to be a main focus of research activity and further work is required to obtain an appropriate amidase that will selectively cleave C-N bonds in aromatic substrates. Once an appropriate amidase gene is obtained it must be combined with genes encoding an enzyme capable of converting carbazole to 2'aminobiphenyl-2,3-diol: specifically carA genes. The carA genes from two sources have been cloned and are ready for construction of C-N bond cleavage pathway. The construction of a new metabolic pathway to selectively remove nitrogen from carbazole and other molecules typically found in petroleum should lead to the development of a process to improve oil refinery efficiency by reducing the poisoning, by nitrogen, of catalysts used in the hydrotreating and catalytic cracking of petroleum.« less

Antioxidant effect of aromatic volatiles emitted by Lavandula dentata, Mentha spicata, and M. piperita on mouse subjected to low oxygen condition.

PubMed

Hu, Zenghui; Wang, Chunling; Shen, Hong; Zhang, Kezhong; Leng, Pingsheng

2017-12-01

This study aims to investigate the antioxidant effect of aromatic volatiles of three common aromatic plants, Lavandula dentata, Mentha spicata, and M. piperita. In this study, kunming mice subjected to low oxygen condition were treated with the volatiles emitted from these aromatic plants through inhalation administration. Then the blood cell counts, and the activities and gene expressions of antioxidant enzymes in different tissues were tested. The results showed that low oxygen increased the counts of red blood cells, white blood cells, and blood platelets of mice, and aromatic volatiles decreased their counts. Exposure to aromatic volatiles resulted in decreases in the malonaldehyde contents, and increases in the activities and gene expressions of superoxide dismutase, glutathione peroxidase, and catalase in different tissues under low oxygen. In addition, as the main component of aromatic volatiles, eucalyptol was the potential source that imparted positive antioxidant effect.

Δg: The new aromaticity index based on g-factor calculation applied for polycyclic benzene rings

NASA Astrophysics Data System (ADS)

Ucun, Fatih; Tokatlı, Ahmet

2015-02-01

In this work, the aromaticity of polycyclic benzene rings was evaluated by the calculation of g-factor for a hydrogen placed perpendicularly at geometrical center of related ring plane at a distance of 1.2 Å. The results have compared with the other commonly used aromatic indices, such as HOMA, NICSs, PDI, FLU, MCI, CTED and, generally been found to be in agreement with them. So, it was proposed that the calculation of the average g-factor as Δg could be applied to study the aromaticity of polycyclic benzene rings without any restriction in the number of benzene rings as a new magnetic-based aromaticity index.

Iodinated contrast media electro-degradation: process performance and degradation pathways.

PubMed

Del Moro, Guido; Pastore, Carlo; Di Iaconi, Claudio; Mascolo, Giuseppe

2015-02-15

The electrochemical degradation of six of the most widely used iodinated contrast media was investigated. Batch experiments were performed under constant current conditions using two DSA® electrodes (titanium coated with a proprietary and patented mixed metal oxide solution of precious metals such as iridium, ruthenium, platinum, rhodium and tantalum). The degradation removal never fell below 85% (at a current density of 64 mA/cm(2) with a reaction time of 150 min) when perchlorate was used as the supporting electrolyte; however, when sulphate was used, the degradation performance was above 80% (at a current density of 64 mA/cm(2) with a reaction time of 150 min) for all of the compounds studied. Three main degradation pathways were identified, namely, the reductive de-iodination of the aromatic ring, the reduction of alkyl aromatic amides to simple amides and the de-acylation of N-aromatic amides to produce aromatic amines. However, as amidotrizoate is an aromatic carboxylate, this is added via the decarboxylation reaction. The investigation did not reveal toxicity except for the lower current density used, which has shown a modest toxicity, most likely for some reaction intermediates that are not further degraded. In order to obtain total removal of the contrast media, it was necessary to employ a current intensity between 118 and 182 mA/cm(2) with energy consumption higher than 370 kWh/m(3). Overall, the electrochemical degradation was revealed to be a reliable process for the treatment of iodinated contrast media that can be found in contaminated waters such as hospital wastewater or pharmaceutical waste-contaminated streams. Copyright © 2014 Elsevier B.V. All rights reserved.

ADSORPTION OF POLYCYCLIC AROMATIC HYDROCARBONS IN AGED HARBOR SEDIMENTS

EPA Science Inventory

Polycyclic aromatic hydrocarbons (PAHs) are a group of hydrophobic organic contaminants which have low aqueous solubilities and are common pollutants in harbor sediments. Adsorption and desorption isotherms for PAHs are conducted to study the abiotic sorption of PAHs in uncontami...

MUTAGENICITY IN SALMONELLA OF SULFUR-CONTAINING POLYCYCLIC AROMATIC HETEROCYCLES AND THEIR DIHYDRODIOL DERIVATIVES

EPA Science Inventory

Polycyclic aromatic sulfur heterocycles (PASH) are common constituents of cigarette smoke, fossil fuel-derived materials, and their combustion byproducts. Many PASH are known mutagens and carcinogens. However, unlike their nonsulfur-containing counterparts, relatively little is k...

BIOCHEMICAL AND GENETIC CHARACTERIZATION OF AN EARLY STEP IN A NOVEL PATHWAY FOR THE BIOSYNTHESIS OF AROMATIC AMINO ACIDS AND P-AMINOBENZOIC ACID IN THE ARCHAEON METHANOCOCCUS MARIPALUDIS

EPA Science Inventory

Methanococcus maripaludis is a strictly anaerobic, methane-producing archaeon and facultative autotroph capable of biosynthesizing all the amino acids and vitamins required for growth. In this work, the novel 6-deoxy-5-ketofructose-1-phosphate (DKFP) pathway for the biosynthesis ...

Induction of c-Jun by air particulate matter (PM₁₀) of Mexico city: Participation of polycyclic aromatic hydrocarbons.

PubMed

Salcido-Neyoy, Martha Estela; Sánchez-Pérez, Yesennia; Osornio-Vargas, Alvaro Román; Gonsebatt, María Eugenia; Meléndez-Zajgla, Jorge; Morales-Bárcenas, Rocío; Petrosyan, Pavel; Molina-Servin, Edith Danny; Vega, Elizabeth; Manzano-León, Natalia; García-Cuellar, Claudia M

2015-08-01

The carcinogenic potential of urban particulate matter (PM) has been partly attributed to polycyclic aromatic hydrocarbons (PAHs) content, which activates the aryl hydrocarbon receptor (AhR). Here we report the effect of PM with an aerodynamic size of 10 μm (PM10) on the induction of AhR pathway in A549 cells, evaluating its downstream targets CYP1B1, IL-6, IL-8 and c-Jun. Significant increases in CYP1B1 protein and enzyme activity; IL-6 and IL-8 secretion and c-Jun protein were found in response to PM10. The formation of PAH-DNA adducts was also detected. The involvement of AhR pathway was confirmed with Resveratrol as AhR antagonist, which reversed CYP1B1 and c-Jun induction. Nevertheless, in IL-6 and IL-8 secretion, the Resveratrol was ineffective, suggesting an effect independent of this pathway. Considering the role of c-Jun in oncogenesis, its induction by PM may be contributing to its carcinogenic potential through induction of AhR pathway by PAHs present in PM10. Copyright © 2015 Elsevier Ltd. All rights reserved.

The translational repressor Crc controls the Pseudomonas putida benzoate and alkane catabolic pathways using a multi-tier regulation strategy.

PubMed

Hernández-Arranz, Sofía; Moreno, Renata; Rojo, Fernando

2013-01-01

Metabolically versatile bacteria usually perceive aromatic compounds and hydrocarbons as non-preferred carbon sources, and their assimilation is inhibited if more preferable substrates are available. This is achieved via catabolite repression. In Pseudomonas putida, the expression of the genes allowing the assimilation of benzoate and n-alkanes is strongly inhibited by catabolite repression, a process controlled by the translational repressor Crc. Crc binds to and inhibits the translation of benR and alkS mRNAs, which encode the transcriptional activators that induce the expression of the benzoate and alkane degradation genes respectively. However, sequences similar to those recognized by Crc in benR and alkS mRNAs exist as well in the translation initiation regions of the mRNA of several structural genes of the benzoate and alkane pathways, which suggests that Crc may also regulate their translation. The present results show that some of these sites are functional, and that Crc inhibits the induction of both pathways by limiting not only the translation of their transcriptional activators, but also that of genes coding for the first enzyme in each pathway. Crc may also inhibit the translation of a gene involved in benzoate uptake. This multi-tier approach probably ensures the rapid regulation of pathway genes, minimizing the assimilation of non-preferred substrates when better options are available. A survey of possible Crc sites in the mRNAs of genes associated with other catabolic pathways suggested that targeting substrate uptake, pathway induction and/or pathway enzymes may be a common strategy to control the assimilation of non-preferred compounds. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Biodegradation of organic pollutants in saline wastewater by halophilic microorganisms: a review.

PubMed

Castillo-Carvajal, Laura C; Sanz-Martín, José Luis; Barragán-Huerta, Blanca E

2014-01-01

Agro-food, petroleum, textile, and leather industries generate saline wastewater with a high content of organic pollutants such as aromatic hydrocarbons, phenols, nitroaromatics, and azo dyes. Halophilic microorganisms are of increasing interest in industrial waste treatment, due to their ability to degrade hazardous substances efficiently under high salt conditions. However, their full potential remains unexplored. The isolation and identification of halophilic and halotolerant microorganisms from geographically unrelated and geologically diverse hypersaline sites supports their application in bioremediation processes. Past investigations in this field have mainly focused on the elimination of polycyclic aromatic hydrocarbons and phenols, whereas few studies have investigated N-aromatic compounds, such as nitro-substituted compounds, amines, and azo dyes, in saline wastewater. Information regarding the growth conditions and degradation mechanisms of halophilic microorganisms is also limited. In this review, we discuss recent research on the removal of organic pollutants such as organic matter, in terms of chemical oxygen demand (COD), dyes, hydrocarbons, N-aliphatic and N-aromatic compounds, and phenols, in conditions of high salinity. In addition, some proposal pathways for the degradation of aromatic compounds are presented.

The high-temperature oxidation of aromatic hydrocarbons

NASA Technical Reports Server (NTRS)

Brezinsky, K.

1986-01-01

Chemical mechanisms of the atmospheric pressure, high-temperature (875-1500 K) gas-phase oxidation of benzene, toluene, ethylbenzene, and propylbenzene are described and discussed. Oxidation trends evident from turbulent flow reactor experiments serve as the basis for the mechanisms of the oxidation of benzene and alkylated aromatics. The potential effects of very high temperatures and pressures on the chemistry of oxidation of aromatics are described. The oxidation of benzene and phenyl radical has been found to proceed in a stepwise C6-C5-C4 sequence. Species profiles obtained from flow-reactor experiments suggest that the oxidation of benzene and phenyl radical follows the generalized route via phenoxy, cyclopentadienyl and butadienyl radical. The oxidation of the C4 species branches into multiple pathways that yield copious amounts of ethylene and acetylene. Certain major trends are evident: the alkylated aromatics on initial attack either form styrene, benzyl radical or benzene. The styrene reacts further to produce a benzyl radical or benzene. The oxidation of an alkylated aromatic hydrocarbon appears eventually to reduce to the oxidation of either phenyl radical or benzene.

Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons under anaerobic conditions: Overview of studies, proposed pathways and future perspectives.

PubMed

Nzila, Alexis

2018-05-07

The biodegradation of low- and high-molecular-weight polycyclic aromatic hydrocarbons (PAHs) (LWM-PAHs and HMW-PAHs, respectively) has been studied extensively under aerobic conditions. Molecular O 2 plays 2 critical roles in this biodegradation process. O 2 activates the aromatic rings through hydroxylation prior to ring opening and serves as a terminal electron acceptor (TEA). However, several microorganisms have devised ways of activating aromatic rings, leading to ring opening (and thus biodegradation) when TEAs other than O 2 are used (under anoxic conditions). These microorganisms belong to the sulfate-, nitrate-, and metal-ion-reducing bacteria and the methanogens. Although the anaerobic biodegradation of monocyclic aromatic hydrocarbons and LWM-PAH naphthalene have been studied, little information is available about the biodegradation of HMW-PAHs. This manuscript reviews studies of the anaerobic biodegradation of HMW-PAHs and identifies gaps that limit both our understanding and the efficiency of this biodegradation process. Strategies that can be employed to overcome these limitations are also discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Carbon molecules in space: from astrochemistry to astrobiology.

PubMed

Ehrenfreund, Pascale; Sephton, Mark A

2006-01-01

How complex carbonaceous molecules in space are, what their abundance is and on what timescales they form are crucial questions within cosmochemistry. Despite the large heterogeneity of galactic and interstellar regions the organic chemistry in the universe seems to follow common pathways. The largest fraction of carbon in the universe is incorporated into aromatic molecules (gaseous polycyclic aromatic hydrocarbon as well as solid macromolecular aromatic structures). Macromolecular carbon constitutes more than half of the interstellar carbon, approximately 80% of the carbon in meteorites, and is likely to be present in comets. Molecules of high astrobiological relevance such as N-heterocycles, amino acids and pre-sugars have all been identified in trace quantities (ppb) in extracts of carbonaceous meteorites. Their presence in inter- and circumstellar regions is either unknown or contentious. In any event such fragile species are easily destroyed by UV radiation, shocks and thermal processing and are unlikely to survive incorporation into Solar System material without some degradation. The more refractory material, in particular macromolecular carbon may retain an interstellar heritage more faithfully. We present laboratory measurements on the photostability of organic compounds and discuss their survival in regions with elevated UV radiation. We also show recent observations of diffuse interstellar bands indicating the presence of fullerenes. We investigate the link between the carbon chemistry in interstellar space and in the Solar System by analyzing the carbonaceous fraction of meteorites and by reviewing stable isotopic data. It also seems evident that both volatile and refractory material from carbonaceous meteoritic has been substantially altered owing to thermal and aqueous processing within the Solar System.

Mild Aromatic Palladium-Catalyzed Protodecarboxylation: Kinetic Assessment of the Decarboxylative Palladation and the Protodepalladation Steps

PubMed Central

Dickstein, Joshua S.; Curto, John M.; Gutierrez, Osvaldo; Mulrooney, Carol A.; Kozlowski, Marisa C.

2013-01-01

Mechanism studies of a mild palladium catalyzed decarboxylation of aromatic carboxylic acids are described. In particular, reaction orders and activation parameters for the two stages of the transformation were determined. These studies guided development of a catalytic system capable of turnover. Further evidence reinforces that the second stage, protonation of the aryl palladium intermediate, is the rate-determining step of the reaction. The first step, decarboxylative palladation is proposed to occur through an intramolecular electrophilic palladation pathway, which is supported by computational and mechansim studies. In contrast to the reverse reaction (C-H insertion), the data support an electrophilic aromatic substitution mechanism involving a stepwise intramolecular protonation sequence for the protodepalladation portion of the reaction. PMID:23590518

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

Major contribution of the Ehrlich pathway for 2-phenylethanol/rose flavor production in Ashbya gossypii.

PubMed

Ravasio, Davide; Wendland, Jürgen; Walther, Andrea

2014-09-01

Aroma alcohols of fermented food and beverages are derived from fungal amino acids catabolism via the Ehrlich pathway. This linear pathway consists of three enzymatic reactions to form fusel alcohols. Regulation of some of the enzymes occurs on the transcriptional level via Aro80. The riboflavin overproducer Ashbya gossypii produces strong fruity flavours in contrast to its much less aromatic relative Eremothecium cymbalariae. Genome comparisons indicated that A. gossypii harbors genes for aromatic amino acid catabolism (ARO8a, ARO8b, ARO10, and ARO80) while E. cymbalariae only encodes ARO8a and thus lacks major components of aromatic amino acid catabolism. Volatile compound (VOC) analysis showed that both Eremothecium species produce large amounts of isoamyl alcohol while A. gossypii also produces high levels of 2-phenylethanol. Deletion of the A. gossypii ARO-genes did not confer any growth deficiencies. However, A. gossypii ARO-mutants (except Agaro8a) were strongly impaired in aroma production, particularly in the production of the rose flavour 2-phenylethanol. Conversely, overexpression of ARO80 via the AgTEF1 promoter resulted in 50% increase in VOC production. Together these data indicate that A. gossypii is a very potent flavour producer and that amongst the non-Saccharomyces biodiversity strains can be identified that could provide positive sensory properties to fermented beverages. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Magnolia officinalis (Hou Po) bark extract stimulates the Nrf2-pathway in hepatocytes and protects against oxidative stress.

PubMed

Rajgopal, Arun; Missler, Stephen R; Scholten, Jeffery D

2016-12-04

The highly aromatic bark of Magnolia officinalis Rehder and EH Wilson, (magnolia bark) has been widely used in traditional Chinese medicine where it is known as Hou Po. Historically the bark of the tree has been used for treating variety of disorders the most common use of magnolia bark in traditional prescription has been to treat stress and anxiety disorders. Till date it is not clear regarding the fundamental cellular pathway it modulates. NRF2 signaling has emerged as the central pathway that protects cells from variety of stressors this led us to hypothesize that basis for magnolia bark's effects could be via activating NRF2 pathway. We utilized variety of biochemical procedures like luciferase reporter assay, enzyme induction, gene expression to determine NRF2 inducing activity by magnolia bark extract and its significance. Further we identified the phytochemicals inducing this activity using bio-directed fractionation procedure. In this study, we demonstrate that magnolia bark extract activates Nrf2-dependent gene expression and protects against hydrogen peroxide mediated oxidative stress in hepatocytes. We further identified through HPLC fractionation and mass spectroscopy that magnolol, 4-methoxy honokiol and honokiol are the active phytochemicals inducing the Nrf2-mediated activity. This could be the molecular basis for its numerous beneficial activity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Proposal of an in silico profiler for categorisation of repeat dose toxicity data of hair dyes.

PubMed

Nelms, M D; Ates, G; Madden, J C; Vinken, M; Cronin, M T D; Rogiers, V; Enoch, S J

2015-05-01

This study outlines the analysis of 94 chemicals with repeat dose toxicity data taken from Scientific Committee on Consumer Safety opinions for commonly used hair dyes in the European Union. Structural similarity was applied to group these chemicals into categories. Subsequent mechanistic analysis suggested that toxicity to mitochondria is potentially a key driver of repeat dose toxicity for chemicals within each of the categories. The mechanistic hypothesis allowed for an in silico profiler consisting of four mechanism-based structural alerts to be proposed. These structural alerts related to a number of important chemical classes such as quinones, anthraquinones, substituted nitrobenzenes and aromatic azos. This in silico profiler is intended for grouping chemicals into mechanism-based categories within the adverse outcome pathway paradigm.

A framework for the use of single-chemical transcriptomics data in predicting the hazards associated with complex mixtures of polycyclic aromatic hydrocarbons.

PubMed

Labib, Sarah; Williams, Andrew; Kuo, Byron; Yauk, Carole L; White, Paul A; Halappanavar, Sabina

2017-07-01

The assumption of additivity applied in the risk assessment of environmental mixtures containing carcinogenic polycyclic aromatic hydrocarbons (PAHs) was investigated using transcriptomics. MutaTMMouse were gavaged for 28 days with three doses of eight individual PAHs, two defined mixtures of PAHs, or coal tar, an environmentally ubiquitous complex mixture of PAHs. Microarrays were used to identify differentially expressed genes (DEGs) in lung tissue collected 3 days post-exposure. Cancer-related pathways perturbed by the individual or mixtures of PAHs were identified, and dose-response modeling of the DEGs was conducted to calculate gene/pathway benchmark doses (BMDs). Individual PAH-induced pathway perturbations (the median gene expression changes for all genes in a pathway relative to controls) and pathway BMDs were applied to models of additivity [i.e., concentration addition (CA), generalized concentration addition (GCA), and independent action (IA)] to generate predicted pathway-specific dose-response curves for each PAH mixture. The predicted and observed pathway dose-response curves were compared to assess the sensitivity of different additivity models. Transcriptomics-based additivity calculation showed that IA accurately predicted the pathway perturbations induced by all mixtures of PAHs. CA did not support the additivity assumption for the defined mixtures; however, GCA improved the CA predictions. Moreover, pathway BMDs derived for coal tar were comparable to BMDs derived from previously published coal tar-induced mouse lung tumor incidence data. These results suggest that in the absence of tumor incidence data, individual chemical-induced transcriptomics changes associated with cancer can be used to investigate the assumption of additivity and to predict the carcinogenic potential of a mixture.

Polybenzoxazole via aromatic nucleophilic displacement

NASA Technical Reports Server (NTRS)

Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor); Smith, Joseph G., Jr. (Inventor)

1993-01-01

Polybenzoxazoles (PBO) are heterocyclic macromolecules which were first synthesized in a two-step process by the initial formation of aromatic diacid chlorides with bis(o-aminophenol)s through solution condensation of aromatic diacid chlorides with bis(o-aminophenol)s followed by thermal cyclodehydration. Since then several methods were utilized in their synthesis. The most common synthetic method for PBO involves a polycondensation of bis(o-aminophenol)s with aromatic diacid diphenyl esters. Another preparative route involves the solution polycondensation of the hydrochloride salts of bis(o-amino phenol)s with aromatic diacids in polyphosphoric acid. Another synthetic method involves the initial formation of poly(o-hydroxy amide)s from silylated bis(o-aminophenol)s with aromatic diacid chlorides followed by thermal cyclodehydration to PBO. A recent preparative route involves the reaction of aromatic bisphenols with bis(fluorophenyl) benzoxazoles by the displacement reaction to form PBO. The novelty of the present invention is that high molecular weight PBO of new chemical structures are prepared that exhibit a favorable combination of physical and mechanical properties.

Formation of highly oxygenated organic molecules from aromatic compounds

NASA Astrophysics Data System (ADS)

Molteni, Ugo; Bianchi, Federico; Klein, Felix; El Haddad, Imad; Frege, Carla; Rossi, Michel J.; Dommen, Josef; Baltensperger, Urs

2018-02-01

Anthropogenic volatile organic compounds (AVOCs) often dominate the urban atmosphere and consist to a large degree of aromatic hydrocarbons (ArHCs), such as benzene, toluene, xylenes, and trimethylbenzenes, e.g., from the handling and combustion of fuels. These compounds are important precursors for the formation of secondary organic aerosol. Here we show that the oxidation of aromatics with OH leads to a subsequent autoxidation chain reaction forming highly oxygenated molecules (HOMs) with an O : C ratio of up to 1.09. This is exemplified for five single-ring ArHCs (benzene, toluene, o-/m-/p-xylene, mesitylene (1,3,5-trimethylbenzene) and ethylbenzene), as well as two conjugated polycyclic ArHCs (naphthalene and biphenyl). We report the elemental composition of the HOMs and show the differences in the oxidation patterns of these ArHCs. A potential pathway for the formation of these HOMs from aromatics is presented and discussed. We hypothesize that AVOCs may contribute substantially to new particle formation events that have been detected in urban areas.

Electronic coupling through natural amino acids.

PubMed

Berstis, Laura; Beckham, Gregg T; Crowley, Michael F

2015-12-14

Myriad scientific domains concern themselves with biological electron transfer (ET) events that span across vast scales of rate and efficiency through a remarkably fine-tuned integration of amino acid (AA) sequences, electronic structure, dynamics, and environment interactions. Within this intricate scheme, many questions persist as to how proteins modulate electron-tunneling properties. To help elucidate these principles, we develop a model set of peptides representing the common α-helix and β-strand motifs including all natural AAs within implicit protein-environment solvation. Using an effective Hamiltonian strategy with density functional theory, we characterize the electronic coupling through these peptides, furthermore considering side-chain dynamics. For both motifs, predictions consistently show that backbone-mediated electronic coupling is distinctly sensitive to AA type (aliphatic, polar, aromatic, negatively charged and positively charged), and to side-chain orientation. The unique properties of these residues may be employed to design activated, deactivated, or switch-like superexchange pathways. Electronic structure calculations and Green's function analyses indicate that localized shifts in the electron density along the peptide play a role in modulating these pathways, and further substantiate the experimentally observed behavior of proline residues as superbridges. The distinct sensitivities of tunneling pathways to sequence and conformation revealed in this electronic coupling database help improve our fundamental understanding of the broad diversity of ET reactivity and provide guiding principles for peptide design.

Heterocyclic Aromatics in Petroleum Coke, Snow, Lake Sediments, and Air Samples from the Athabasca Oil Sands Region.

PubMed

Manzano, Carlos A; Marvin, Chris; Muir, Derek; Harner, Tom; Martin, Jonathan; Zhang, Yifeng

2017-05-16

The aromatic fractions of snow, lake sediment, and air samples collected during 2011-2014 in the Athabasca oil sands region were analyzed using two-dimensional gas chromatography following a nontargeted approach. Commonly monitored aromatics (parent and alkylated-polycyclic aromatic hydrocarbons and dibenzothiophenes) were excluded from the analysis, focusing mainly on other heterocyclic aromatics. The unknowns detected were classified into isomeric groups and tentatively identified using mass spectral libraries. Relative concentrations of heterocyclic aromatics were estimated and were found to decrease with distance from a reference site near the center of the developments and with increasing depth of sediments. The same heterocyclic aromatics identified in snow, lake sediments, and air were observed in extracts of delayed petroleum coke, with similar distributions. This suggests that petroleum coke particles are a potential source of heterocyclic aromatics to the local environment, but other oil sands sources must also be considered. Although the signals of these heterocyclic aromatics diminished with distance, some were detected at large distances (>100 km) in snow and surface lake sediments, suggesting that the impact of industry can extend >50 km. The list of heterocyclic aromatics and the mass spectral library generated in this study can be used for future source apportionment studies.

ortho- and meta-substituted aromatic thiols are efficient redox buffers that increase the folding rate of a disulfide-containing protein.

PubMed

Gough, Jonathan D; Barrett, Elvis J; Silva, Yenia; Lees, Watson J

2006-08-20

Thiol based redox buffers are used to enhance the folding rates of disulfide-containing proteins in vitro. Traditionally, small molecule aliphatic thiols such as glutathione are employed. Recently, we have demonstrated that aromatic thiols can further enhance protein-folding rates. In the presence of para-substituted aromatic thiols the folding rate of a disulfide-containing protein was increased by 4-23 times over that measured for glutathione. However, several important practical issues remain to be addressed. Aromatic thiols have never been tested in the presence of denaturants such as guanidine hydrochloride. Only two of the para-substituted aromatic thiols previously examined are commercially available. To expand the number of aromatic thiols for protein folding, several commercially available meta- and ortho-substituted aromatic thiols were studied. Furthermore, an ortho-substituted aromatic thiol, easily obtained from inexpensive starting materials, was investigated. Folding rates of scrambled ribonuclease A at pH 6.0, 7.0 and 7.7, with ortho- and meta-substituted aromatic thiols, were up to 10 times greater than those with glutathione. In the presence of the common denaturant guanidine hydrochloride (0.5M) aromatic thiols provided 100% yield of active protein while maintaining equivalent folding rates.

A Free-Radical Pathway to Hydrogenated Phenanthrene in Molecular Clouds-Low Temperature Growth of Polycyclic Aromatic Hydrocarbons.

PubMed

Thomas, Aaron M; Lucas, Michael; Yang, Tao; Kaiser, Ralf I; Fuentes, Luis; Belisario-Lara, Daniel; Mebel, Alexander M

2017-08-05

The hydrogen-abstraction/acetylene-addition mechanism has been fundamental to unravelling the synthesis of polycyclic aromatic hydrocarbons (PAHs) detected in combustion flames and carbonaceous meteorites like Orgueil and Murchison. However, the fundamental reaction pathways accounting for the synthesis of complex PAHs, such as the tricyclic anthracene and phenanthrene along with their dihydrogenated counterparts, remain elusive to date. By investigating the hitherto unknown chemistry of the 1-naphthyl radical with 1,3-butadiene, we reveal a facile barrierless synthesis of dihydrophenanthrene adaptable to low temperatures. These aryl-type radical additions to conjugated hydrocarbons via resonantly stabilized free-radical intermediates defy conventional wisdom that PAH growth is predominantly a high-temperature phenomenon and thus may represent an overlooked path to PAHs as complex as coronene and corannulene in cold regions of the interstellar medium like in the Taurus Molecular Cloud. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Indole-3-acetic acid biosynthetic pathway and aromatic amino acid aminotransferase activities in Pantoea dispersa strain GPK.

PubMed

Kulkarni, G B; Nayak, A S; Sajjan, S S; Oblesha, A; Karegoudar, T B

2013-05-01

This investigation deals with the production of IAA by a bacterial isolate Pantoea dispersa strain GPK (PDG) identified by 16S rRNA gene sequence analysis. HPLC and Mass spectral analysis of metabolites from bacterial spent medium revealed that, IAA production by PDG is Trp-dependent and follows indole-3-pyruvic acid (IPyA) pathway. Substrate specificity study of aromatic amino acid aminotransferase (AAT) showed high activities, only when tryptophan (Trp) and α-ketoglutarate (α-kg) were used as substrates. AAT is highly specific for Trp and α-kg as amino group donor and acceptor, respectively. The effect of exogenous IAA on bacterial growth was established. Low concentration of exogenous IAA induced the growth, whereas high concentration decreased the growth of bacterium. PDG treatment significantly increased the root length, shoot length and dry mass of the chickpea and pigeon pea plants. © 2013 The Society for Applied Microbiology.

Production of Cinnamic and p-Hydroxycinnamic Acids in Engineered Microbes.

PubMed

Vargas-Tah, Alejandra; Gosset, Guillermo

2015-01-01

The aromatic compounds cinnamic and p-hydroxycinnamic acids (pHCAs) are phenylpropanoids having applications as precursors for the synthesis of thermoplastics, flavoring, cosmetic, and health products. These two aromatic acids can be obtained by chemical synthesis or extraction from plant tissues. However, both manufacturing processes have shortcomings, such as the generation of toxic subproducts or a low concentration in plant material. Alternative production methods are being developed to enable the biotechnological production of cinnamic and (pHCAs) by genetically engineering various microbial hosts, including Escherichia coli, Saccharomyces cerevisiae, Pseudomonas putida, and Streptomyces lividans. The natural capacity to synthesize these aromatic acids is not existent in these microbial species. Therefore, genetic modification have been performed that include the heterologous expression of genes encoding phenylalanine ammonia-lyase and tyrosine ammonia-lyase activities, which catalyze the conversion of l-phenylalanine (l-Phe) and l-tyrosine (l-Tyr) to cinnamic acid and (pHCA), respectively. Additional host modifications include the metabolic engineering to increase carbon flow from central metabolism to the l-Phe or l-Tyr biosynthetic pathways. These strategies include the expression of feedback insensitive mutant versions of enzymes from the aromatic pathways, as well as genetic modifications to central carbon metabolism to increase biosynthetic availability of precursors phosphoenolpyruvate and erythrose-4-phosphate. These efforts have been complemented with strain optimization for the utilization of raw material, including various simple carbon sources, as well as sugar polymers and sugar mixtures derived from plant biomass. A systems biology approach to production strains characterization has been limited so far and should yield important data for future strain improvement.

Production of Cinnamic and p-Hydroxycinnamic Acids in Engineered Microbes

PubMed Central

Vargas-Tah, Alejandra; Gosset, Guillermo

2015-01-01

The aromatic compounds cinnamic and p-hydroxycinnamic acids (pHCAs) are phenylpropanoids having applications as precursors for the synthesis of thermoplastics, flavoring, cosmetic, and health products. These two aromatic acids can be obtained by chemical synthesis or extraction from plant tissues. However, both manufacturing processes have shortcomings, such as the generation of toxic subproducts or a low concentration in plant material. Alternative production methods are being developed to enable the biotechnological production of cinnamic and (pHCAs) by genetically engineering various microbial hosts, including Escherichia coli, Saccharomyces cerevisiae, Pseudomonas putida, and Streptomyces lividans. The natural capacity to synthesize these aromatic acids is not existent in these microbial species. Therefore, genetic modification have been performed that include the heterologous expression of genes encoding phenylalanine ammonia-lyase and tyrosine ammonia-lyase activities, which catalyze the conversion of l-phenylalanine (l-Phe) and l-tyrosine (l-Tyr) to cinnamic acid and (pHCA), respectively. Additional host modifications include the metabolic engineering to increase carbon flow from central metabolism to the l-Phe or l-Tyr biosynthetic pathways. These strategies include the expression of feedback insensitive mutant versions of enzymes from the aromatic pathways, as well as genetic modifications to central carbon metabolism to increase biosynthetic availability of precursors phosphoenolpyruvate and erythrose-4-phosphate. These efforts have been complemented with strain optimization for the utilization of raw material, including various simple carbon sources, as well as sugar polymers and sugar mixtures derived from plant biomass. A systems biology approach to production strains characterization has been limited so far and should yield important data for future strain improvement. PMID:26347861

Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data

PubMed Central

Bargiela, Rafael; Gertler, Christoph; Magagnini, Mirko; Mapelli, Francesca; Chen, Jianwei; Daffonchio, Daniele; Golyshin, Peter N.; Ferrer, Manuel

2015-01-01

Biostimulation with different nitrogen sources is often regarded as a strategy of choice in combating oil spills in marine environments. Such environments are typically depleted in nitrogen, therefore limiting the balanced microbial utilization of carbon-rich petroleum constituents. It is fundamental, yet only scarcely accounted for, to analyze the catabolic consequences of application of biostimulants. Here, we examined such alterations in enrichment microcosms using sediments from chronically crude oil-contaminated marine sediment at Ancona harbor (Italy) amended with natural fertilizer, uric acid (UA), or ammonium (AMM). We applied the web-based AromaDeg resource using as query Illumina HiSeq meta-sequences (UA: 27,893 open reading frames; AMM: 32,180) to identify potential catabolic differences. A total of 45 (for UA) and 65 (AMM) gene sequences encoding key catabolic enzymes matched AromaDeg, and their participation in aromatic degradation reactions could be unambiguously suggested. Genomic signatures for the degradation of aromatics such as 2-chlorobenzoate, indole-3-acetate, biphenyl, gentisate, quinoline and phenanthrene were common for both microcosms. However, those for the degradation of orcinol, ibuprofen, phenylpropionate, homoprotocatechuate and benzene (in UA) and 4-aminobenzene-sulfonate, p-cumate, dibenzofuran and phthalate (in AMM), were selectively enriched. Experimental validation was conducted and good agreement with predictions was observed. This suggests certain discrepancies in action of these biostimulants on the genomic content of the initial microbial community for the catabolism of petroleum constituents or aromatics pollutants. In both cases, the emerging microbial communities were phylogenetically highly similar and were composed by very same proteobacterial families. However, examination of taxonomic assignments further revealed different catabolic pathway organization at the organismal level, which should be considered for designing oil spill mitigation strategies in the sea. PMID:26635742

RELATING DAILY SOLAR ULTRAVIOLET RADIATION DOSE IN SALT MARSH-ASSOCIATED ESTUARINE SYSTEMS TO LABORATORY ASSESSMENTS OF PHOTOACTIVATED POLYCYCLIC AROMATIC HYDROCARBON TOXICITY

EPA Science Inventory

Estuaries of the southeastern United States not only serve an important nursery function but also are common repositories of polycyclic aromatic hydrocarbons (PAHs) derived from upland activities. Thus, these habitats may be at risk for PAHphototoxicity. To better characterize ...

Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a novel functional role for a buried arginine

PubMed Central

Winn, Peter J.; Lüdemann, Susanna K.; Gauges, Ralph; Lounnas, Valère; Wade, Rebecca C.

2002-01-01

Understanding the mechanism and specificity of substrate binding in the cytochrome P450 (P450) superfamily is an important step toward explaining its key role in drug metabolism, toxicity, xenobiotic degradation, and several biosynthetic pathways. Here we investigate the ligand exit pathways and mechanisms of P450cam (CYP101), P450BM-3 (CYP102), and P450eryF (CYP107A1) by using random expulsion molecular dynamics and classical molecular dynamics simulations. Although several different pathways are found for each protein, one pathway is common to all three. The mechanism of ligand exit along this pathway is, however, quite different in the three different proteins. For P450cam, small backbone conformational changes, in combination with aromatic side chain rotation, allow for the passage of the rather rigid, compact, and hydrophobic substrate, camphor. In P450BM-3, larger transient backbone changes are observed on ligand exit. R47, situated at the entrance to the channel, appears important in guiding negatively charged fatty acid substrates in and out of the active site. In P450eryF, an isolated buried arginine, R185, stabilized by four hydrogen bonds to backbone carbonyl oxygen atoms, is located in the exit channel and is identified as having a particularly unusual functionality, dynamically gating channel opening. The results for these three P450s suggest that the channel opening mechanisms are adjusted to the physico-chemical properties of the substrate and can kinetically modulate protein-substrate specificity. PMID:11959989

Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System.

PubMed

McCloskey, Douglas; Xu, Sibei; Sandberg, Troy E; Brunk, Elizabeth; Hefner, Ying; Szubin, Richard; Feist, Adam M; Palsson, Bernhard O

2018-06-15

Aromatic metabolites provide the backbone for numerous industrial and pharmaceutical compounds of high value. The Phosphotransferase System (PTS) is common to many bacteria, and is the primary mechanism for glucose uptake by Escherichia coli. The PTS was removed to conserve phosphoenolpyruvate (pep), which is a precursor for aromatic metabolites and consumed by the PTS, for aromatic metabolite production. Replicate adaptive laboratory evolution (ALE) of PTS and detailed omics data sets collected revealed that the PTS bridged the gap between respiration and fermentation, leading to distinct high fermentative and high respiratory rate phenotypes. It was also found that while all strains retained high levels of aromatic amino acid (AAA) biosynthetic precursors, only one replicate from the high glycolytic clade retained high levels of intracellular AAAs. The fast growth and high AAA precursor phenotypes could provide a starting host for cell factories targeting the overproduction aromatic metabolites. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Metabolic engineering of a tyrosine-overproducing yeast platform using targeted metabolomics.

PubMed

Gold, Nicholas D; Gowen, Christopher M; Lussier, Francois-Xavier; Cautha, Sarat C; Mahadevan, Radhakrishnan; Martin, Vincent J J

2015-05-28

L-tyrosine is a common precursor for a wide range of valuable secondary metabolites, including benzylisoquinoline alkaloids (BIAs) and many polyketides. An industrially tractable yeast strain optimized for production of L-tyrosine could serve as a platform for the development of BIA and polyketide cell factories. This study applied a targeted metabolomics approach to evaluate metabolic engineering strategies to increase the availability of intracellular L-tyrosine in the yeast Saccharomyces cerevisiae CEN.PK. Our engineering strategies combined localized pathway engineering with global engineering of central metabolism, facilitated by genome-scale steady-state modelling. Addition of a tyrosine feedback resistant version of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase Aro4 from S. cerevisiae was combined with overexpression of either a tyrosine feedback resistant yeast chorismate mutase Aro7, the native pentafunctional arom protein Aro1, native prephenate dehydrogenase Tyr1 or cyclohexadienyl dehydrogenase TyrC from Zymomonas mobilis. Loss of aromatic carbon was limited by eliminating phenylpyruvate decarboxylase Aro10. The TAL gene from Rhodobacter sphaeroides was used to produce coumarate as a simple test case of a heterologous by-product of tyrosine. Additionally, multiple strategies for engineering global metabolism to promote tyrosine production were evaluated using metabolic modelling. The T21E mutant of pyruvate kinase Cdc19 was hypothesized to slow the conversion of phosphoenolpyruvate to pyruvate and accumulate the former as precursor to the shikimate pathway. The ZWF1 gene coding for glucose-6-phosphate dehydrogenase was deleted to create an NADPH deficiency designed to force the cell to couple its growth to tyrosine production via overexpressed NADP(+)-dependent prephenate dehydrogenase Tyr1. Our engineered Zwf1(-) strain expressing TYRC ARO4(FBR) and grown in the presence of methionine achieved an intracellular L-tyrosine accumulation up to 520 μmol/g DCW or 192 mM in the cytosol, but sustained flux through this pathway was found to depend on the complete elimination of feedback inhibition and degradation pathways. Our targeted metabolomics approach confirmed a likely regulatory site at DAHP synthase and identified another possible cofactor limitation at prephenate dehydrogenase. Additionally, the genome-scale metabolic model identified design strategies that have the potential to improve availability of erythrose 4-phosphate for DAHP synthase and cofactor availability for prephenate dehydrogenase. We evaluated these strategies and provide recommendations for further improvement of aromatic amino acid biosynthesis in S. cerevisiae.

Molecular evolution of the endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L.

PubMed

Yu, Guoqin; Olsen, Kenneth M; Schaal, Barbara A

2011-01-01

The evolution of metabolic pathways is a fundamental but poorly understood aspect of evolutionary change. One approach for understanding the complexity of pathway evolution is to examine the molecular evolution of genes that together comprise an integrated metabolic pathway. The rice endosperm starch biosynthetic pathway is one of the most thoroughly characterized metabolic pathways in plants, and starch is a trait that has evolved in response to strong selection during rice domestication. In this study, we have examined six key genes (AGPL2, AGPS2b, SSIIa, SBEIIb, GBSSI, ISA1) in the rice endosperm starch biosynthesis pathway to investigate the evolution of these genes before and after rice domestication. Genome-wide sequence tagged sites data were used as a neutral reference to overcome the problems of detecting selection in species with complex demographic histories such as rice. Five variety groups of Oryza sativa (aus, indica, tropical japonica, temperate japonica, aromatic) and its wild ancestor (O. rufipogon) were sampled. Our results showed evidence of purifying selection at AGPL2 in O. rufipogon and strong evidence of positive selection at GBSSI in temperate japonica and tropical japonica varieties and at GBSSI and SBEIIb in aromatic varieties. All the other genes showed a pattern consistent with neutral evolution in both cultivated rice and its wild ancestor. These results indicate the important role of positive selection in the evolution of starch genes during rice domestication. We discuss the role of SBEIIb and GBSSI in the evolution of starch quality during rice domestication and the power and limitation of detecting selection using genome-wide data as a neutral reference.

Production of Eight Different Hydride Complexes and Nitrite Release from 2,4,6-Trinitrotoluene by Yarrowia lipolytica▿ †

PubMed Central

Ziganshin, Ayrat M.; Gerlach, Robin; Borch, Thomas; Naumov, Anatoly V.; Naumova, Rimma P.

2007-01-01

2,4,6-Trinitrotoluene (TNT) transformation by the yeast strain Yarrowia lipolytica AN-L15 was shown to occur via two different pathways. Direct aromatic ring reduction was the predominant mechanism of TNT transformation, while nitro group reduction was observed to be a minor pathway. Although growth of Y. lipolytica AN-L15 was inhibited initially in the presence of TNT, TNT transformation was observed, indicating that the enzymes necessary for TNT reduction were present initially. Aromatic ring reduction resulted in the transient accumulation of eight different TNT-hydride complexes, which were characterized using high-performance liquid chromatography, UV-visible diode array detection, and negative-mode atmospheric pressure chemical ionization mass spectrometry (APCI-MS). APCI-MS analysis revealed three different groups of TNT-hydride complexes with molecular ions at m/z 227, 228, and 230, which correspond to TNT-mono- and dihydride complexes and protonated dihydride isomers, respectively. One of the three protonated dihydride complex isomers detected appears to release nitrite in the presence of strain AN-L15. This release of nitrite is of particular interest since it can provide a pathway towards complete degradation and detoxification of TNT. PMID:17933928

Tough, soluble, aromatic, thermoplastic copolyimides

NASA Technical Reports Server (NTRS)

Bryant, Robert G. (Inventor)

1994-01-01

Tough, soluble, aromatic, thermoplastic copolyimides were prepared by reacting 4,4'-oxydiphthalic anhydride, 3,4,3',4'-biphenyltetracarboxylic dianhydride and 3,4'-oxydianiline. These copolyimides were found to be soluble in common amide solvents such as acetamide, Nmethylpyrrolidinone, and dimethylformamide allowing them to be applied as the fully imidized copolymer and to be used to prepare a wide range of articles.

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

Polycyclic Aromatic Hydrocarbons: A Critical Review of Environmental Occurrence and Bioremediation.

PubMed

Alegbeleye, Oluwadara Oluwaseun; Opeolu, Beatrice Oluwatoyin; Jackson, Vanessa Angela

2017-10-01

The degree of polycyclic aromatic hydrocarbon contamination of environmental matrices has increased over the last several years due to increase in industrial activities. Interest has surrounded the occurrence and distribution of polycyclic aromatic hydrocarbons for many decades because they pose a serious threat to the health of humans and ecosystems. The importance of the need for sustainable abatement strategies to alleviate contamination therefore cannot be overemphasised, as daily human activities continue to create pollution from polycyclic aromatic hydrocarbons and impact the natural environment. Globally, attempts have been made to design treatment schemes for the remediation and restoration of contaminated sites. Several techniques and technologies have been proposed and tested over time, the majority of which have significant limitations. This has necessitated research into environmentally friendly and cost-effective clean-up techniques. Bioremediation is an appealing option that has been extensively researched and adopted as it has been proven to be relatively cost-effective, environmentally friendly and is publicly accepted. In this review, the physicochemical properties of some priority polycyclic aromatic hydrocarbons, as well as the pathways and mechanisms through which they enter the soil, river systems, drinking water, groundwater and food are succinctly examined. Their effects on human health, other living organisms, the aquatic ecosystem, as well as soil microbiota are also elucidated. The persistence and bioavailability of polycyclic aromatic hydrocarbons are discussed as well, as they are important factors that influence the rate, efficiency and overall success of remediation. Bioremediation (aerobic and anaerobic), use of biosurfactants and bioreactors, as well as the roles of biofilms in the biological treatment of polycyclic aromatic hydrocarbons are also explored.

Polycyclic Aromatic Hydrocarbons: A Critical Review of Environmental Occurrence and Bioremediation

NASA Astrophysics Data System (ADS)

Alegbeleye, Oluwadara Oluwaseun; Opeolu, Beatrice Oluwatoyin; Jackson, Vanessa Angela

2017-10-01

The degree of polycyclic aromatic hydrocarbon contamination of environmental matrices has increased over the last several years due to increase in industrial activities. Interest has surrounded the occurrence and distribution of polycyclic aromatic hydrocarbons for many decades because they pose a serious threat to the health of humans and ecosystems. The importance of the need for sustainable abatement strategies to alleviate contamination therefore cannot be overemphasised, as daily human activities continue to create pollution from polycyclic aromatic hydrocarbons and impact the natural environment. Globally, attempts have been made to design treatment schemes for the remediation and restoration of contaminated sites. Several techniques and technologies have been proposed and tested over time, the majority of which have significant limitations. This has necessitated research into environmentally friendly and cost-effective clean-up techniques. Bioremediation is an appealing option that has been extensively researched and adopted as it has been proven to be relatively cost-effective, environmentally friendly and is publicly accepted. In this review, the physicochemical properties of some priority polycyclic aromatic hydrocarbons, as well as the pathways and mechanisms through which they enter the soil, river systems, drinking water, groundwater and food are succinctly examined. Their effects on human health, other living organisms, the aquatic ecosystem, as well as soil microbiota are also elucidated. The persistence and bioavailability of polycyclic aromatic hydrocarbons are discussed as well, as they are important factors that influence the rate, efficiency and overall success of remediation. Bioremediation (aerobic and anaerobic), use of biosurfactants and bioreactors, as well as the roles of biofilms in the biological treatment of polycyclic aromatic hydrocarbons are also explored.

TDAE strategy in the benzoxazolone series: synthesis and reactivity of a new benzoxazolinonic anion.

PubMed

Nadji-Boukrouche, Aïda R; Khoumeri, Omar; Terme, Thierry; Liacha, Messaoud; Vanelle, Patrice

2015-01-14

We describe an original pathway to produce new 5-substituted 3-methyl-6-nitro-benzoxazolones by the reaction of aromatic carbonyl and α-carbonyl ester derivatives with a benzoxazolinonic anion formed exclusively via the TDAE strategy.

Changes in the aromatic profile of espresso coffee as a function of the grinding grade and extraction time: a study by the electronic nose system.

PubMed

Severini, C; Ricci, I; Marone, M; Derossi, A; De Pilli, T

2015-03-04

The changes in chemical attributes and aromatic profile of espresso coffee (EC) were studied taking into account the extraction time and grinding level as independent variables. Particularly, using an electronic nose system, the changes of the global aromatic profile of EC were highlighted. The results shown as the major amounts of organic acids, solids, and caffeine were extracted in the first 8 s of percolation. The grinding grade significantly affected the quality of EC probably as an effect of the particle size distribution and the percolation pathways of water through the coffee cake. The use of an electronic nose system allowed us to discriminate the fractions of the brew as a function of the percolation time and also the regular coffee obtained from different grinding grades. Particularly, the aromatic profile of a regular coffee (25 mL) was significantly affected by the grinding level of the coffee grounds and percolation time, which are two variables under the control of the bar operator.

Optimizing catalysis conditions to decrease aromatic hydrocarbons and increase alkanes for improving jet biofuel quality.

PubMed

Cheng, Jun; Li, Tao; Huang, Rui; Zhou, Junhu; Cen, Kefa

2014-04-01

To produce quality jet biofuel with high amount of alkanes and low amount of aromatic hydrocarbons, two zeolites of HY and HZSM-5 supporting Ni and Mo were used as catalysts to convert soybean oil into jet fuel. Zeolite HY exhibited higher jet range alkane selectivity (40.3%) and lower jet range aromatic hydrocarbon selectivity (23.8%) than zeolite HZSM-5 (13.8% and 58.9%). When reaction temperature increased from 330 to 390°C, yield of jet fuel over Ni-Mo/HY catalyst at 4 MPa hydrogen pressure increased from 0% to 49.1% due to the shift of reaction pathway from oligomerization to cracking reaction. Further increase of reaction temperature from 390 to 410°C resulted in increased yield of jet range aromatic hydrocarbons from 18.7% to 30%, which decreased jet fuel quality. A high yield of jet fuel (48.2%) was obtained at 1 MPa low hydrogen pressure over Ni (8 wt.%)-Mo (12 wt.%)/HY catalyst. Copyright © 2014 Elsevier Ltd. All rights reserved.

Factors affecting elimination of polycyclic aromatic hydrocarbons from traditional smoked common carp meat

NASA Astrophysics Data System (ADS)

Babić, J.; Vidaković, S.; Škaljac, S.; Kartalović, B.; Ljubojević, D.; Ćirković, M.; Teodorović, V.

2017-09-01

Smoking techniques have been progressively improved and different procedures have been developed in different regions for treating fish. In these times, the technology is mainly used for enrichment of fish with specific taste and odour, to extend the shelf-life of these perishable products and appearance required widely on the market. A lot of chemical contaminants such as polycyclic aromatic hydrocarbons (PAHs) are formed during the combustion of fuel in the smoking process. PAHs are a group of compounds that have been the subject of great concern in the recent years due to their toxic, mutagenic and/or carcinogenic potentials to humans. These fact can have a significant impact on the acceptance of these products by consumers. In this review article, the objective is to describe factors affecting elimination of polycyclic aromatic hydrocarbons from traditional smoked common carp meat.

Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill.

PubMed

Mason, Olivia U; Han, James; Woyke, Tanja; Jansson, Janet K

2014-01-01

During the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico a deep-sea hydrocarbon plume developed resulting in a rapid succession of bacteria. Colwellia eventually supplanted Oceanospirillales, which dominated the plume early in the spill. These successional changes may have resulted, in part, from the changing composition and abundance of hydrocarbons over time. Colwellia abundance peaked when gaseous and simple aromatic hydrocarbons increased, yet the metabolic pathway used by Colwellia in hydrocarbon disposition is unknown. Here we used single-cell genomics to gain insights into the genome properties of a Colwellia enriched during the DWH deep-sea plume. A single amplified genome (SAG) of a Colwellia cell isolated from a DWH plume, closely related (avg. 98% 16S rRNA gene similarity) to other plume Colwellia, was sequenced and annotated. The SAG was similar to the sequenced isolate Colwellia psychrerythraea 34H (84% avg. nucleotide identity). Both had genes for denitrification, chemotaxis, and motility, adaptations to cold environments and a suite of nutrient acquisition genes. The Colwellia SAG may be capable of gaseous and aromatic hydrocarbon degradation, which contrasts with a DWH plume Oceanospirillales SAG which encoded non-gaseous n-alkane and cycloalkane degradation pathways. The disparate hydrocarbon degradation pathways are consistent with hydrocarbons that were abundant at different times in the deep-sea plume; first, non-gaseous n-alkanes and cycloalkanes that could be degraded by Oceanospirillales, followed by gaseous, and simple aromatic hydrocarbons that may have been degraded by Colwellia. These insights into the genomic properties of a Colwellia species, which were supported by existing metagenomic sequence data from the plume and DWH contaminated sediments, help further our understanding of the successional changes in the dominant microbial players in the plume over the course of the DWH spill.

Varietal Dependence of GLVs Accumulation and LOX-HPL Pathway Gene Expression in Four Vitis vinifera Wine Grapes

PubMed Central

Qian, Xu; Xu, Xiao-Qing; Yu, Ke-Ji; Zhu, Bao-Qing; Lan, Yi-Bin; Duan, Chang-Qing; Pan, Qiu-Hong

2016-01-01

Variety is one of the major factors influencing grape and wine aromatic characteristics. Green leaf volatiles (GLVs), derived from lipoxygenase-hydroperoxides lyase (LOX-HPL) pathway, are important components for the aromatic quality of grapes and wines. However, the varietal difference regarding GLVs accumulation and related gene expression are poorly studied. This work exhibited that the accumulation of various GLVs and the expression of LOX-HPL pathway genes in four Vitis vinifera wine grape cultivars: Syrah, Muscat Tchervine, Gewürztraminer and Chardonnay. The results showed a variety dependence of GLVs profile. Muscat Tchervine harvested grapes contained less C6 aldehydes and the most abundant esters, which corresponded to very low VvLOXA and VvHPL1 expression abundance as well as high VvAAT transcript in this variety. High expression level of both VvLOXA and VvHPL1 paralleled with higher level of C6 aldehydes together with higher alcohols in Syrah grape. Gewürztraminer and Chardonnay grapes had high aldehydes and alcohols as well as low esters, which were resulted from their higher expression level of VvLOXA or VvHPL1 and lower VvAAT. From these above corresponding relations, it is concluded that VvLOXA, VvHPL1 and VvAAT in the LOX-HPL pathway are targets for altering GLVs composition in the grape varieties. PMID:27886056

Remnants of an ancient pathway to L-phenylalanine and L-tyrosine in enteric bacteria: Evolutionary implications and biotechnological impact. [Escherichia coli; Salmonella typhimurium; Neurospora crassa

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

Bonner, C.A.; Fischer, R.S.; Ahmad, S.

The pathway construction for biosynthesis of aromatic amino acids in Escherichia coli is atypical of the phylogenetic subdivision of gram-negative bacteria to which it belongs. Related organisms possess second pathways to phenylalanine and tyrosine which depend upon the expression of a monofunctional chorismate mutase (CM-F) and cyclohexadienyl dehydratase (CDT). Some enteric bacteria, unlike E. coli, possess either CM-F or CDT. These essentially cryptic remnants of an ancestral pathway can be a latent source of biochemical potential under certain conditions. As one example of advantageous biochemical potential, the presence of CM-F in Salmonella typhimurium increases the capacity for prephenate accumulation inmore » a tyrA auxotroph. We report the finding that a significant fraction of the latter prephenate is transaminated to L-arogenate. The tyrA19 mutant is now the organism of choice for isolation of L-arogenate, uncomplicated by the presence of other cyclohexadienyl products coaccumulated by a Neurospora crassa mutant that had previously served as the prime biological source of L-arogenate. Prephenate aminotransferase activity was not conferred by a discrete enzyme, but rather was found to be synonymous with the combined activities of aspartate aminotransferase (aspC), aromatic aminotransferase (tyrB), and branched-chain aminotransferase (ilvE).« less

Two shikimate dehydrogenases, VvSDH3 and VvSDH4, are involved in gallic acid biosynthesis in grapevine

PubMed Central

Bontpart, Thibaut; Marlin, Thérèse; Vialet, Sandrine; Guiraud, Jean-Luc; Pinasseau, Lucie; Meudec, Emmanuelle; Sommerer, Nicolas; Cheynier, Véronique; Terrier, Nancy

2016-01-01

In plants, the shikimate pathway provides aromatic amino acids that are used to generate numerous secondary metabolites, including phenolic compounds. In this pathway, shikimate dehydrogenases (SDH) ‘classically’ catalyse the reversible dehydrogenation of 3-dehydroshikimate to shikimate. The capacity of SDH to produce gallic acid from shikimate pathway metabolites has not been studied in depth. In grapevine berries, gallic acid mainly accumulates as galloylated flavan-3-ols. The four grapevine SDH proteins have been produced in Escherichia coli. In vitro, VvSDH1 exhibited the highest ‘classical’ SDH activity. Two genes, VvSDH3 and VvSDH4, mainly expressed in immature berry tissues in which galloylated flavan-3-ols are accumulated, encoded enzymes with lower ‘classical’ activity but were able to produce gallic acid in vitro. The over-expression of VvSDH3 in hairy-roots increased the content of aromatic amino acids and hydroxycinnamates, but had little or no effect on molecules more distant from the shikimate pathway (stilbenoids and flavan-3-ols). In parallel, the contents of gallic acid, β-glucogallin, and galloylated flavan-3-ols were increased, attesting to the influence of this gene on gallic acid metabolism. Phylogenetic analysis from dicotyledon SDHs opens the way for the examination of genes from other plants which accumulate gallic acid-based metabolites. PMID:27241494

Quantitation of chlorophylls and 22 of their colored degradation products in culinary aromatic herbs by HPLC-DAD-MS and correlation with color changes during the dehydration process.

PubMed

Lafeuille, Jean-Louis; Lefèvre, Stéphane; Lebuhotel, Julie

2014-02-26

Chlorophylls and their green and olive-brown derivatives were successfully separated from culinary herb extracts by HPLC with photodiode-array and mass spectrometry detection. The method involved a ternary gradient elution and reverse-phase separation conditions capable of resolving 24 different pigments (2 chlorophylls and 22 of their derivatives) of different polarities within 28 min. The method was applied to monitor color changes in 50 samples of culinary aromatic herbs subjected to five different drying treatments. Of the 24 pigments, 14 were key to understanding the differences between the primary degradation pathways of chlorophyll a and chlorophyll b in culinary herbs during drying processes. A color degradation ladder based on the total molar percentage of all the remaining green pigments was also proposed as a tool to measure the impact of drying treatments on aromatic herb visual aspects.

Aromatics and phenols from catalytic pyrolysis of Douglas fir pellets in microwave with ZSM-5 as a catalyst

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

Wang, Lu; Lei, Hanwu; Ren, Shoujie

Microwave assisted catalytic pyrolysis was investigated to convert Douglas fir pellets to bio-oils by a ZSM-5 Zeolite catalyst. A central composite experimental design (CCD) was used to optimize the catalytic pyrolysis process. The effects of reaction time, temperature and catalyst to biomass ratio on the bio-oil, syngas, and biochar yields were determined. GC/MS analysis results showed that the bio-oil contained a series of important and useful chemical compounds. Phenols, guaiacols, and aromatic hydrocarbons were the most abundant compounds which were about 50-82 % in bio-oil depending on the pyrolysis conditions. Comparison between the bio-oils from microwave pyrolysis with and withoutmore » catalyst showed that the catalyst increased the content of aromatic hydrocarbons and phenols. A reaction pathway was proposed for microwave assisted catalyst pyrolysis of Douglas fir pellets.« less

Development of Chemical and Metabolite Sensors for Rhodococcus opacus PD630.

PubMed

DeLorenzo, Drew M; Henson, William R; Moon, Tae Seok

2017-10-20

Rhodococcus opacus PD630 is a nonmodel, Gram-positive bacterium that possesses desirable traits for biomass conversion, including consumption capabilities for lignocellulose-based sugars and toxic lignin-derived aromatic compounds, significant triacylglycerol accumulation, relatively rapid growth rate, and genetic tractability. However, few genetic elements have been directly characterized in R. opacus, limiting its application for lignocellulose bioconversion. Here, we report the characterization and development of genetic tools for tunable gene expression in R. opacus, including: (1) six fluorescent reporters for quantifying promoter output, (2) three chemically inducible promoters for variable gene expression, and (3) two classes of metabolite sensors derived from native R. opacus promoters that detect nitrogen levels or aromatic compounds. Using these tools, we also provide insights into native aromatic consumption pathways in R. opacus. Overall, this work expands the ability to control and characterize gene expression in R. opacus for future lignocellulose-based fuel and chemical production.

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

Sadjadi, Seyedabdolreza; Zhang, Yong; Kwok, Sun, E-mail: sunkwok@hku.hk

The 3.3 μ m unidentified infrared emission feature is commonly attributed to the C–H stretching band of aromatic molecules. Astronomical observations have shown that this feature is composed of two separate bands at 3.28 and 3.30 μ m, and the origin of these two bands is unclear. In this paper, we perform vibrational analyses based on quantum mechanical calculations of 153 organic molecules, including both pure aromatic molecules and molecules with mixed aromatic/olefinic/aliphatic hydridizations. We find that many of the C–H stretching vibrational modes in polycyclic aromatic hydrocarbon (PAH) molecules are coupled. Even considering the uncoupled modes only, the correlationmore » between the band intensity ratios and the structure of the PAH molecule is not observed, and the 3.28 and 3.30 μ m features cannot be directly interpreted in the PAH model. Based on these results, the possible aromatic, olefinic, and aliphatic origins of the 3.3 μ m feature are discussed. We suggest that the 3.28 μ m feature is assigned to aromatic C–H stretch whereas the 3.30 μ m feature is olefinic. From the ratio of these two features, the relative olefinic to aromatic content of the carrier can be determined.« less

Electronic coupling through natural amino acids

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

Berstis, Laura; Beckham, Gregg T., E-mail: michael.crowley@nrel.gov, E-mail: gregg.beckham@nrel.gov; Crowley, Michael F., E-mail: michael.crowley@nrel.gov, E-mail: gregg.beckham@nrel.gov

2015-12-14

Myriad scientific domains concern themselves with biological electron transfer (ET) events that span across vast scales of rate and efficiency through a remarkably fine-tuned integration of amino acid (AA) sequences, electronic structure, dynamics, and environment interactions. Within this intricate scheme, many questions persist as to how proteins modulate electron-tunneling properties. To help elucidate these principles, we develop a model set of peptides representing the common α-helix and β-strand motifs including all natural AAs within implicit protein-environment solvation. Using an effective Hamiltonian strategy with density functional theory, we characterize the electronic coupling through these peptides, furthermore considering side-chain dynamics. For bothmore » motifs, predictions consistently show that backbone-mediated electronic coupling is distinctly sensitive to AA type (aliphatic, polar, aromatic, negatively charged and positively charged), and to side-chain orientation. The unique properties of these residues may be employed to design activated, deactivated, or switch-like superexchange pathways. Electronic structure calculations and Green’s function analyses indicate that localized shifts in the electron density along the peptide play a role in modulating these pathways, and further substantiate the experimentally observed behavior of proline residues as superbridges. The distinct sensitivities of tunneling pathways to sequence and conformation revealed in this electronic coupling database help improve our fundamental understanding of the broad diversity of ET reactivity and provide guiding principles for peptide design.« less

Fermentation Products of Solvent Tolerant Marine Bacterium Moraxella spp. MB1 and Its Biotechnological Applications in Salicylic Acid Bioconversion

PubMed Central

Wahidullah, Solimabi; Naik, Deepak N.; Devi, Prabha

2013-01-01

As part of a proactive approach to environmental protection, emerging issues with potential impact on the environment is the subject of ongoing investigation. One emerging area of environmental research concerns pharmaceuticals like salicylic acid, which is the main metabolite of various analgesics including aspirin. It is a common component of sewage effluent and also an intermediate in the degradation pathway of various aromatic compounds which are introduced in the marine environment as pollutants. In this study, biotransformation products of salicylic acid by seaweed, Bryopsis plumosa, associated marine bacterium, Moraxella spp. MB1, have been investigated. Phenol, conjugates of phenol and hydroxy cinnamic acid derivatives (coumaroyl, caffeoyl, feruloyl and trihydroxy cinnamyl) with salicylic acid (3–8) were identified as the bioconversion products by electrospray ionization mass spectrometry. These results show that the microorganism do not degrade phenolic acid but catalyses oxygen dependent transformations without ring cleavage. The degradation of salicylic acid is known to proceed either via gentisic acid pathway or catechol pathway but this is the first report of biotransformation of salicylic acid into cinnamates, without ring cleavage. Besides cinnamic acid derivatives (9–12), metabolites produced by the bacterium include antimicrobial indole (13) and β-carbolines, norharman (14), harman (15) and methyl derivative (16), which are beneficial to the host and the environment. PMID:24391802

Biotransformation and Detoxification of Xylidine Orange Dye Using Immobilized Cells of Marine-Derived Lysinibacillus sphaericus D3

PubMed Central

Devi, Prabha; Wahidullah, Solimabi; Sheikh, Farhan; Pereira, Rochelle; Narkhede, Niteen; Amonkar, Divya; Tilvi, Supriya; Meena, Ram Murthy

2017-01-01

Lysinibacillus sphaericus D3 cell-immobilized beads in natural gel sodium alginate decolorized the xylidine orange dye 1-(dimethylphenylazo)-2-naphthol-6-sulfonic acid sodium salt in the laboratory. Optimal conditions were selected for decolorization and the products formed were evaluated for toxicity by disc diffusion assay against common marine bacteria which revealed the non-toxic nature of the dye-degraded products. Decolorization of the brightly colored dye to colorless products was measured on an Ultra Violet-Vis spectrophotometer and its biodegradation products monitored on Thin Layer Chromatographic plate and High Performance Liquid Chromatography (HPLC). Finally, the metabolites formed in the decolorized medium were characterized by mass spectrometry. This analysis confirms the conversion of the parent molecule into lower molecular weight aromatic phenols and sulfonic acids as the final products of biotransformation. Based on the results, the probable degradation products of xylidine orange were naphthol, naphthylamine-6-sulfonic acid, 2-6-dihydroxynaphthalene, and bis-dinaphthylether. Thus, it may be concluded that the degradation pathway of the dye involved (a) reduction of its azo group by azoreductase enzyme (b) dimerization of the hydrazo compound followed by (c) degradation of monohydrazo as well as dimeric metabolites into low molecular weight aromatics. Finally, it may be worth exploring the possibility of commercially utilizing L. sphaericus D3 for industrial applications for treating large-scale dye waste water. PMID:28208715

Treatability of phenol-production wastewater: Rate constant and pathway of dimethyl phenyl carbinol oxidation by hydroxyl radicals.

PubMed

Boonrattanakij, Nonglak; Joysampao, Atsawin; Pobsuktanasub, Tuksinaiya; Anotai, Jin; Ruangchainikom, Chalermchai

2017-12-15

Phenol-production wastewater is difficult to treat biologically by aerobic processes to meet the effluent standard COD of 120 mg L -1 because it contains several highly refractory aromatic pollutants, particularly dimethyl phenyl carbinol. Pretreatment revealed that dimethyl phenyl carbinol was slowly oxidized by molecular ozone; however, it readily reacted with hydroxyl radicals to yield acetophenone as a primary product. Acetophenone was further oxidized, first through five different pathways to form benzoic acid, phenyl glyoxalic acid, 4-4'-diacetyl biphenyl, and several hydroxylated aromatic compounds, and later to aliphatic carboxylic acids via ring cleavage. Regardless of system configuration (homogeneous vs heterogeneous), operating mode (batch vs continuous), and chemical concentration, the average intrinsic rate constants were 1.05 × 10 10 and 9.29 × 10 9  M -1  s -1 for dimethyl phenyl carbinol and acetophenone, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

FORMATION OF POLYCYCLIC AROMATIC HYDROCARBONS AND CARBONACEOUS SOLIDS IN GAS-PHASE CONDENSATION EXPERIMENTS

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

Jaeger, C.; Huisken, F.; Henning, Th.

2009-05-01

Carbonaceous grains represent a major component of cosmic dust. In order to understand their formation pathways, they have been prepared in the laboratory by gas-phase condensation reactions such as laser pyrolysis and laser ablation. Our studies demonstrate that the temperature in the condensation zone determines the formation pathway of carbonaceous particles. At temperatures lower than 1700 K, the condensation by-products are mainly polycyclic aromatic hydrocarbons (PAHs) that are also the precursors or building blocks for the condensing soot grains. The low-temperature condensates contain PAH mixtures that are mainly composed of volatile three to five ring systems. At condensation temperatures highermore » than 3500 K, fullerene-like carbon grains and fullerene compounds are formed. Fullerene fragments or complete fullerenes equip the nucleating particles. Fullerenes can be identified as soluble components. Consequently, condensation products in cool and hot astrophysical environments such as cool and hot asymptotic giant branch stars or Wolf-Rayet stars should be different and should have distinct spectral properties.« less

Reassessing the atmospheric oxidation mechanism of toluene

NASA Astrophysics Data System (ADS)

Ji, Yuemeng; Zhao, Jun; Terazono, Hajime; Misawa, Kentaro; Levitt, Nicholas P.; Li, Yixin; Lin, Yun; Peng, Jianfei; Wang, Yuan; Duan, Lian; Pan, Bowen; Zhang, Fang; Feng, Xidan; An, Taicheng; Marrero-Ortiz, Wilmarie; Secrest, Jeremiah; Zhang, Annie L.; Shibuya, Kazuhiko; Molina, Mario J.; Zhang, Renyi

2017-08-01

Photochemical oxidation of aromatic hydrocarbons leads to tropospheric ozone and secondary organic aerosol (SOA) formation, with profound implications for air quality, human health, and climate. Toluene is the most abundant aromatic compound under urban environments, but its detailed chemical oxidation mechanism remains uncertain. From combined laboratory experiments and quantum chemical calculations, we show a toluene oxidation mechanism that is different from the one adopted in current atmospheric models. Our experimental work indicates a larger-than-expected branching ratio for cresols, but a negligible formation of ring-opening products (e.g., methylglyoxal). Quantum chemical calculations also demonstrate that cresols are much more stable than their corresponding peroxy radicals, and, for the most favorable OH (ortho) addition, the pathway of H extraction by O2 to form the cresol proceeds with a smaller barrier than O2 addition to form the peroxy radical. Our results reveal that phenolic (rather than peroxy radical) formation represents the dominant pathway for toluene oxidation, highlighting the necessity to reassess its role in ozone and SOA formation in the atmosphere.

Investigation of the Reactions and Distribution of Polycyclic Aromatic Hydrocarbons and Fullerenes in Extraterrestrial Material

NASA Technical Reports Server (NTRS)

Zare, Richard N.

2005-01-01

The work funded by this research grant includes four specific projects: (1) Mapping the spatial distribution of polycyclic aromatic hydrocarbons (PAHs) in a variety of meteoritic samples and comparing this distribution with mineralogical features of the meteorite to determine whether a correlation exists between the two. (2) Developing a method for detection of fullerenes in extraterrestrial samples using microprobe laser-desorption laser-ionization mass spectrometry ( pL2MS) and utilizing this technique to investigate fullerene presence, while exploring the possibility of spatially mapping the fullerene distribution in these samples through in situ detection. (3) Investigating a possible formation pathway for meteoritic and ancient terrestrial kerogen involving the photochemical reactions of PAHs with alkanes under prebiotic and astrophysically relevant conditions. (4) Studying reaction pathways and identifying the photoproducts generated during the photochemical evolution of PAH-containing interstellar ice analogs as part of an ongoing collaboration with researchers at the Astrochemistry Lab at NASA Ames.

Tough, Soluble, Aromatic, Thermoplastic Copolyimides

NASA Technical Reports Server (NTRS)

Bryant, Robert G. (Inventor)

1998-01-01

Tough, soluble, aromatic, thermoplastic copolyimides were prepared by reacting 4,4'-oxydiphthalic anhydride, 3,4,3',4'-biphenyltetracarboxylic dianhydride and 3,4'-oxydianiline. These copolyimides were found to be soluble in common amide solvents such as N,N'-dimethyl acetamide, N-methylpyrrolidinone, and dimethylformamide allowing them to be applied as the fully imidized copolymer and to be used to prepare a wide range of articles.

Influence of extraction methodologies on the analysis of five major volatile aromatic compounds of citronella grass (Cymbopogon nardus) and lemongrass (Cymbopogon citratus) grown in Thailand

USDA-ARS?s Scientific Manuscript database

Infusions of citronella grass (Cymbopogon nardus) and lemongrass (Cymbopogon citratus) have been commonly used in folk medicine in Thailand and other Asian countries. This study focuses on a systematic comparison of two extraction methods for major volatile aromatic compounds (VACs) of citronella g...

Fish Reproduction Is Disrupted upon Lifelong Exposure to Environmental PAHs Fractions Revealing Different Modes of Action

PubMed Central

Vignet, Caroline; Larcher, Thibaut; Davail, Blandine; Joassard, Lucette; Le Menach, Karyn; Guionnet, Tiphaine; Lyphout, Laura; Ledevin, Mireille; Goubeau, Manon; Budzinski, Hélène; Bégout, Marie-Laure; Cousin, Xavier

2016-01-01

Polycyclic aromatic hydrocarbons (PAHs) constitute a large family of organic pollutants emitted in the environment as complex mixtures, the compositions of which depend on origin. Among a wide range of physiological defects, PAHs are suspected to be involved in disruption of reproduction. In an aquatic environment, the trophic route is an important source of chronic exposure to PAHs. Here, we performed trophic exposure of zebrafish to three fractions of different origin, one pyrolytic and two petrogenic. Produced diets contained PAHs at environmental concentrations. Reproductive traits were analyzed at individual, tissue and molecular levels. Reproductive success and cumulative eggs number were disrupted after exposure to all three fractions, albeit to various extents depending on the fraction and concentrations. Histological analyses revealed ovary maturation defects after exposure to all three fractions as well as degeneration after exposure to a pyrolytic fraction. In testis, hypoplasia was observed after exposure to petrogenic fractions. Genes expression analysis in gonads has allowed us to establish common pathways such as endocrine disruption or differentiation/maturation defects. Taken altogether, these results indicate that PAHs can indeed disrupt fish reproduction and that different fractions trigger different pathways resulting in different effects. PMID:29051429

Detecting concentration differences in aromatic oils.

PubMed

Morris, Neil

2002-12-01

200 University of Wolverhampton undergraduates rank-ordered samples of aromatic oils commonly used in complementary medicine in terms of their concentration in the air above an oil-soaked cotton ball. Each participant was assigned the task of discriminating between 5 microl, 10 microl, and 20 microl of oil absorbed onto cotton balls. 25 participants assessed each oil, and 8 oils were used. Cardamom, Rosemary, and Ylang Ylang were highly discriminable; however, discrimination of different concentrations of Chamomile, Cyprus, Geranium, Jasmine, and Lavender did not significantly differ from chance. These data provide useful indices for choosing aromatic oils for research purposes.

Molecular cloning and expression of gene encoding aromatic amino acid decarboxylase in 'Vidal blanc' grape berries.

PubMed

Pan, Qiu-Hong; Chen, Fang; Zhu, Bao-Qing; Ma, Li-Yan; Li, Li; Li, Jing-Ming

2012-04-01

The pleasantly fruity and floral 2-phenylethanol are a dominant aroma compound in post-ripening 'Vidal blanc' grapes. However, to date little has been reported about its synthetic pathway in grapevine. In the present study, a full-length cDNA of VvAADC (encoding aromatic amino acid decarboxylase) was firstly cloned from the berries of 'Vidal blanc', an interspecific hybrid variety of Vitis vinifera × Vitis riparia. This sequence encodes a complete open reading frame of 482 amino acids with a calculated molecular mass of 54 kDa and isoelectric point value (pI) of 5.73. The amino acid sequence deduced shared about 79% identity with that of aromatic L: -amino acid decarboxylases (AADCs) from tomato. Real-time PCR analysis indicated that VvAADC transcript abundance presented a small peak at 110 days after full bloom and then a continuous increase at the berry post-ripening stage, which was consistent with the accumulation of 2-phenylethanol, but did not correspond to the trends of two potential intermediates, phenethylamine and 2-phenylacetaldehyde. Furthermore, phenylalanine still exhibited a continuous increase even in post-ripening period. It is thus suggested that 2-phenylethanol biosynthetic pathway mediated by AADC exists in grape berries, but it has possibly little contribution to a considerable accumulation of 2-phenylethanol in post-ripening 'Vidal blanc' grapes.

Formation Mechanism of NDMA from Ranitidine, Trimethylamine, and Other Tertiary Amines during Chloramination: A Computational Study

PubMed Central

2015-01-01

Chloramination of drinking waters has been associated with N-nitrosodimethylamine (NDMA) formation as a disinfection byproduct. NDMA is classified as a probable carcinogen and thus its formation during chloramination has recently become the focus of considerable research interest. In this study, the formation mechanisms of NDMA from ranitidine and trimethylamine (TMA), as models of tertiary amines, during chloramination were investigated by using density functional theory (DFT). A new four-step formation pathway of NDMA was proposed involving nucleophilic substitution by chloramine, oxidation, and dehydration followed by nitrosation. The results suggested that nitrosation reaction is the rate-limiting step and determines the NDMA yield for tertiary amines. When 45 other tertiary amines were examined, the proposed mechanism was found to be more applicable to aromatic tertiary amines, and there may be still some additional factors or pathways that need to be considered for aliphatic tertiary amines. The heterolytic ONN(Me)2–R+ bond dissociation energy to release NDMA and carbocation R+ was found to be a criterion for evaluating the reactivity of aromatic tertiary amines. A structure–activity study indicates that tertiary amines with benzyl, aromatic heterocyclic ring, and diene-substituted methenyl adjacent to the DMA moiety are potentially significant NDMA precursors. The findings of this study are helpful for understanding NDMA formation mechanism and predicting NDMA yield of a precursor. PMID:24968236

Formation mechanism of NDMA from ranitidine, trimethylamine, and other tertiary amines during chloramination: a computational study.

PubMed

Liu, Yong Dong; Selbes, Meric; Zeng, Chengchu; Zhong, Rugang; Karanfil, Tanju

2014-01-01

Chloramination of drinking waters has been associated with N-nitrosodimethylamine (NDMA) formation as a disinfection byproduct. NDMA is classified as a probable carcinogen and thus its formation during chloramination has recently become the focus of considerable research interest. In this study, the formation mechanisms of NDMA from ranitidine and trimethylamine (TMA), as models of tertiary amines, during chloramination were investigated by using density functional theory (DFT). A new four-step formation pathway of NDMA was proposed involving nucleophilic substitution by chloramine, oxidation, and dehydration followed by nitrosation. The results suggested that nitrosation reaction is the rate-limiting step and determines the NDMA yield for tertiary amines. When 45 other tertiary amines were examined, the proposed mechanism was found to be more applicable to aromatic tertiary amines, and there may be still some additional factors or pathways that need to be considered for aliphatic tertiary amines. The heterolytic ONN(Me)2-R(+) bond dissociation energy to release NDMA and carbocation R(+) was found to be a criterion for evaluating the reactivity of aromatic tertiary amines. A structure-activity study indicates that tertiary amines with benzyl, aromatic heterocyclic ring, and diene-substituted methenyl adjacent to the DMA moiety are potentially significant NDMA precursors. The findings of this study are helpful for understanding NDMA formation mechanism and predicting NDMA yield of a precursor.

Complete Sequence of a 184-Kilobase Catabolic Plasmid from Sphingomonas aromaticivorans F199†

PubMed Central

Romine, Margaret F.; Stillwell, Lisa C.; Wong, Kwong-Kwok; Thurston, Sarah J.; Sisk, Ellen C.; Sensen, Christoph; Gaasterland, Terry; Fredrickson, Jim K.; Saffer, Jeffrey D.

1999-01-01

The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1, from Sphingomonas aromaticivorans F199 has been determined. A total of 186 open reading frames (ORFs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. Genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. The unusual coclustering of genes associated with different pathways appears to have evolved in response to similarities in biochemical mechanisms required for the degradation of intermediates in different pathways. A putative efflux pump and several hypothetical membrane-associated proteins were identified and predicted to be involved in the transport of aromatic compounds and/or intermediates in catabolism across the cell wall. Several genes associated with integration and recombination, including two group II intron-associated maturases, were identified in the replication region, suggesting that pNL1 is able to undergo integration and excision events with the chromosome and/or other portions of the plasmid. Conjugative transfer of pNL1 to another Sphingomonas sp. was demonstrated, and genes associated with this function were found in two large clusters. Approximately one-third of the ORFs (59 of them) have no obvious homology to known genes. PMID:10049392

Dechlorination of chlorinated phenols by subnanoscale Pd 0 /Fe 0 intercalated in smectite: pathway, reactivity, and selectivity.

PubMed

Jia, Hanzhong; Wang, Chuanyi

2015-12-30

Smectite clay was employed as templated matrix to prepare subnanoscale Pd(0)/Fe(0) particles, and their components as well as intercalated architectures were well characterized by X-ray energy dispersive spectroscopy (X-EDS) and X-ray diffraction (XRD). Furthermore, as-prepared Pd(0)/Fe(0) subnanoscale nanoparticles were evaluated for their dechlorination effect using chlorinated phenols as model molecules. As a result, pentachlorophenol (PCP) is selectively transformed to phenol in a stepwise dechlorination pathway within 6h, and the dechlorination rate constants show linearly relationship with contents of Pd as its loadings <0.065%. Comparing with PCP, other chlorinated phenols display similar degradation pattern but within much shorter time frame. The dechlorination rate of chlorinated phenols increases with decreasing in number of -Cl attached to aromatic ring, which can be predicted by the total charge of the aromatic ring, exhibiting an inversely linear relationship with the dechlorination rates. While the selectivity of dechlorination depends on the charges associated with the individual aromatic carbon. Chloro-functional groups at the ortho-position are easier to be dechlorinated than that at meta- and para- positions yielding primarily 3,4,5-TCP as intermediate from PCP, further to phenol. The effective dechlorination warrants their potential utilizations in development of in-situ remediation technologies for organic pollutants in contaminated water. Copyright © 2015 Elsevier B.V. All rights reserved.

The Homogentisate Pathway: a Central Catabolic Pathway Involved in the Degradation of l-Phenylalanine, l-Tyrosine, and 3-Hydroxyphenylacetate in Pseudomonas putida

PubMed Central

Arias-Barrau, Elsa; Olivera, Elías R.; Luengo, José M.; Fernández, Cristina; Galán, Beatriz; García, José L.; Díaz, Eduardo; Miñambres, Baltasar

2004-01-01

Pseudomonas putida metabolizes Phe and Tyr through a peripheral pathway involving hydroxylation of Phe to Tyr (PhhAB), conversion of Tyr into 4-hydroxyphenylpyruvate (TyrB), and formation of homogentisate (Hpd) as the central intermediate. Homogentisate is then catabolized by a central catabolic pathway that involves three enzymes, homogentisate dioxygenase (HmgA), fumarylacetoacetate hydrolase (HmgB), and maleylacetoacetate isomerase (HmgC), finally yielding fumarate and acetoacetate. Whereas the phh, tyr, and hpd genes are not linked in the P. putida genome, the hmgABC genes appear to form a single transcriptional unit. Gel retardation assays and lacZ translational fusion experiments have shown that hmgR encodes a specific repressor that controls the inducible expression of the divergently transcribed hmgABC catabolic genes, and homogentisate is the inducer molecule. Footprinting analysis revealed that HmgR protects a region in the Phmg promoter that spans a 17-bp palindromic motif and an external direct repetition from position −16 to position 29 with respect to the transcription start site. The HmgR protein is thus the first IclR-type regulator that acts as a repressor of an aromatic catabolic pathway. We engineered a broad-host-range mobilizable catabolic cassette harboring the hmgABC, hpd, and tyrB genes that allows heterologous bacteria to use Tyr as a unique carbon and energy source. Remarkably, we show here that the catabolism of 3-hydroxyphenylacetate in P. putida U funnels also into the homogentisate central pathway, revealing that the hmg cluster is a key catabolic trait for biodegradation of a small number of aromatic compounds. PMID:15262943

The homogentisate pathway: a central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida.

PubMed

Arias-Barrau, Elsa; Olivera, Elías R; Luengo, José M; Fernández, Cristina; Galán, Beatriz; García, José L; Díaz, Eduardo; Miñambres, Baltasar

2004-08-01

Pseudomonas putida metabolizes Phe and Tyr through a peripheral pathway involving hydroxylation of Phe to Tyr (PhhAB), conversion of Tyr into 4-hydroxyphenylpyruvate (TyrB), and formation of homogentisate (Hpd) as the central intermediate. Homogentisate is then catabolized by a central catabolic pathway that involves three enzymes, homogentisate dioxygenase (HmgA), fumarylacetoacetate hydrolase (HmgB), and maleylacetoacetate isomerase (HmgC), finally yielding fumarate and acetoacetate. Whereas the phh, tyr, and hpd genes are not linked in the P. putida genome, the hmgABC genes appear to form a single transcriptional unit. Gel retardation assays and lacZ translational fusion experiments have shown that hmgR encodes a specific repressor that controls the inducible expression of the divergently transcribed hmgABC catabolic genes, and homogentisate is the inducer molecule. Footprinting analysis revealed that HmgR protects a region in the Phmg promoter that spans a 17-bp palindromic motif and an external direct repetition from position -16 to position 29 with respect to the transcription start site. The HmgR protein is thus the first IclR-type regulator that acts as a repressor of an aromatic catabolic pathway. We engineered a broad-host-range mobilizable catabolic cassette harboring the hmgABC, hpd, and tyrB genes that allows heterologous bacteria to use Tyr as a unique carbon and energy source. Remarkably, we show here that the catabolism of 3-hydroxyphenylacetate in P. putida U funnels also into the homogentisate central pathway, revealing that the hmg cluster is a key catabolic trait for biodegradation of a small number of aromatic compounds.

Hidden overflow pathway to L-phenylalanine in Pseudomonas aeruginosa.

PubMed Central

Fiske, M J; Whitaker, R J; Jensen, R A

1983-01-01

Pseudomonas aeruginosa is representative of a large group of pseudomonad bacteria that possess coexisting alternative pathways to L-phenylalanine (as well as to L-tyrosine). These multiple flow routes to aromatic end products apparently account for the inordinate resistance of P. aeruginosa to end product analogs. Manipulation of carbon source nutrition produced a physiological state of sensitivity to p-fluorophenylalanine and m-fluorophenylalanine, each a specific antimetabolite of L-phenylalanine. Analog-resistant mutants obtained fell into two classes. One type lacked feedback sensitivity of prephenate dehydratase and was the most dramatic excretor of L-phenylalanine. The presence of L-tyrosine curbed phenylalanine excretion to one-third, a finding explained by potent early-pathway regulation of 3-deoxy-D-arabinoheptulosonate 7-phosphate (DAHP) synthase-Tyr (a DAHP synthase subject to allosteric inhibition by L-tyrosine). The second class of regulatory mutants possessed a completely feedback-resistant DAHP synthase-Tyr, the major species (greater than 90%) of two isozymes. Deregulation of DAHP synthase-Tyr resulted in the escape of most chorismate molecules produced into an unregulated overflow route consisting of chorismate mutase (monofunctional), prephenate aminotransferase, and arogenate dehydratase. In the wild type the operation of the overflow pathway is restrained by factors that restrict early-pathway flux. These factors include the highly potent feedback control of DAHP synthase isozymes by end products as well as the strikingly variable abilities of different carbon source nutrients to supply the aromatic pathway with beginning substrates. Even in the wild type, where all allosteric regulation in intact, some phenylalanine overflow was found on glucose-based medium, but not on fructose-based medium. This carbon source-dependent difference was much more exaggerated in each class of regulatory mutants. PMID:6132913

Unbiased plasma metabolomics reveal the correlation of metabolic pathways and Prakritis of humans.

PubMed

Shirolkar, Amey; Chakraborty, Sutapa; Mandal, Tusharkanti; Dabur, Rajesh

2017-11-25

Ayurveda, an ancient Indian medicinal system, has categorized human body constitutions in three broad constitutional types (prakritis) i.e. Vata, Pitta and Kapha. Analysis of plasma metabolites and related pathways to classify Prakriti specific dominant marker metabolites and metabolic pathways. 38 healthy male individuals were assessed for dominant Prakritis and their fasting blood samples were collected. The processed plasma samples were subjected to rapid resolution liquid chromatography-electrospray ionization-quadrupole time of flight mass spectrometry (RRLC-ESI-QTOFMS). Mass profiles were aligned and subjected to multivariate analysis. Partial least square discriminant analysis (PLS-DA) model showed 97.87% recognition capability. List of PLS-DA metabolites was subjected to permutative Benjamini-Hochberg false discovery rate (FDR) correction and final list of 76 metabolites with p < 0.05 and fold-change > 2.0 was identified. Pathway analysis using metascape and JEPETTO plugins in Cytoscape revealed that steroidal hormone biosynthesis, amino acid, and arachidonic acid metabolism are major pathways varying with different constitution. Biological Go processes analysis showed that aromatic amino acids, sphingolipids, and pyrimidine nucleotides metabolic processes were dominant in kapha type of body constitution. Fat soluble vitamins, cellular amino acid, and androgen biosynthesis process along with branched chain amino acid and glycerolipid catabolic processes were dominant in pitta type individuals. Vata Prakriti was found to have dominant catecholamine, arachidonic acid and hydrogen peroxide metabolomics processes. The neurotransmission and oxidative stress in vata, BCAA catabolic, androgen, xenobiotics metabolic processes in pitta, and aromatic amino acids, sphingolipid, and pyrimidine metabolic process in kaphaPrakriti were the dominant marker pathways. Copyright © 2017 Transdisciplinary University, Bangalore and World Ayurveda Foundation. Published by Elsevier B.V. All rights reserved.

A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals.

PubMed

Parthasarathy, Anutthaman; Cross, Penelope J; Dobson, Renwick C J; Adams, Lily E; Savka, Michael A; Hudson, André O

2018-01-01

Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids (AAA) involved in protein synthesis. These amino acids and their metabolism are linked to the synthesis of a variety of secondary metabolites, a subset of which are involved in numerous anabolic pathways responsible for the synthesis of pigment compounds, plant hormones and biological polymers, to name a few. In addition, these metabolites derived from the AAA pathways mediate the transmission of nervous signals, quench reactive oxygen species in the brain, and are involved in the vast palette of animal coloration among others pathways. The AAA and metabolites derived from them also have integral roles in the health of both plants and animals. This review delineates the de novo biosynthesis of the AAA by microbes and plants, and the branching out of AAA metabolism into major secondary metabolic pathways in plants such as the phenylpropanoid pathway. Organisms that do not possess the enzymatic machinery for the de novo synthesis of AAA must obtain these primary metabolites from their diet. Therefore, the metabolism of AAA by the host animal and the resident microflora are important for the health of all animals. In addition, the AAA metabolite-mediated host-pathogen interactions in general, as well as potential beneficial and harmful AAA-derived compounds produced by gut bacteria are discussed. Apart from the AAA biosynthetic pathways in plants and microbes such as the shikimate pathway and the tryptophan pathway, this review also deals with AAA catabolism in plants, AAA degradation via the monoamine and kynurenine pathways in animals, and AAA catabolism via the 3-aryllactate and kynurenine pathways in animal-associated microbes. Emphasis will be placed on structural and functional aspects of several key AAA-related enzymes, such as shikimate synthase, chorismate mutase, anthranilate synthase, tryptophan synthase, tyrosine aminotransferase, dopachrome tautomerase, radical dehydratase, and type III CoA-transferase. The past development and current potential for interventions including the development of herbicides and antibiotics that target key enzymes in AAA-related pathways, as well as AAA-linked secondary metabolism leading to antimicrobials are also discussed.

A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals

PubMed Central

Parthasarathy, Anutthaman; Cross, Penelope J.; Dobson, Renwick C. J.; Adams, Lily E.; Savka, Michael A.; Hudson, André O.

2018-01-01

Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids (AAA) involved in protein synthesis. These amino acids and their metabolism are linked to the synthesis of a variety of secondary metabolites, a subset of which are involved in numerous anabolic pathways responsible for the synthesis of pigment compounds, plant hormones and biological polymers, to name a few. In addition, these metabolites derived from the AAA pathways mediate the transmission of nervous signals, quench reactive oxygen species in the brain, and are involved in the vast palette of animal coloration among others pathways. The AAA and metabolites derived from them also have integral roles in the health of both plants and animals. This review delineates the de novo biosynthesis of the AAA by microbes and plants, and the branching out of AAA metabolism into major secondary metabolic pathways in plants such as the phenylpropanoid pathway. Organisms that do not possess the enzymatic machinery for the de novo synthesis of AAA must obtain these primary metabolites from their diet. Therefore, the metabolism of AAA by the host animal and the resident microflora are important for the health of all animals. In addition, the AAA metabolite-mediated host-pathogen interactions in general, as well as potential beneficial and harmful AAA-derived compounds produced by gut bacteria are discussed. Apart from the AAA biosynthetic pathways in plants and microbes such as the shikimate pathway and the tryptophan pathway, this review also deals with AAA catabolism in plants, AAA degradation via the monoamine and kynurenine pathways in animals, and AAA catabolism via the 3-aryllactate and kynurenine pathways in animal-associated microbes. Emphasis will be placed on structural and functional aspects of several key AAA-related enzymes, such as shikimate synthase, chorismate mutase, anthranilate synthase, tryptophan synthase, tyrosine aminotransferase, dopachrome tautomerase, radical dehydratase, and type III CoA-transferase. The past development and current potential for interventions including the development of herbicides and antibiotics that target key enzymes in AAA-related pathways, as well as AAA-linked secondary metabolism leading to antimicrobials are also discussed. PMID:29682508

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

DISTRIBUTIONS, ASSOCIATIONS, AND PARTIAL AGGREGATE EXPOSURE OF PESTICIDES AND POLYNUCLEAR AROMATIC HYDROCARBONS IN THE MINNESOTA CHILDREN'S PESTICIDE EXPOSURE STUDY (MNCPES)

EPA Science Inventory

The Minnesota Children's Pesticide Exposure Study (MNCPES) provides exposure, environmental, and biologic data relating to multi-pathway exposures of children for four primary pesticides (chlorpyrifos, malathion, diazinon, and atrazine), 14 secondary pesticides, and 13 polynucl...

Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity

DOE PAGES

Johnson, Christopher W.; Salvachua, Davinia; Khanna, Payal; ...

2016-04-22

The conversion of biomass-derived sugars and aromatic molecules to cis,cis-muconic acid (referred to hereafter as muconic acid or muconate) has been of recent interest owing to its facile conversion to adipic acid, an important commodity chemical. Metabolic routes to produce muconate from both sugars and many lignin-derived aromatic compounds require the use of a decarboxylase to convert protocatechuate (PCA, 3,4-dihydroxybenzoate) to catechol (1,2-dihydroxybenzene), two central aromatic intermediates in this pathway. Several studies have identified the PCA decarboxylase as a metabolic bottleneck, causing an accumulation of PCA that subsequently reduces muconate production. A recent study showed that activity of the PCAmore » decarboxylase is enhanced by co-expression of two genetically associated proteins, one of which likely produces a flavin-derived cofactor utilized by the decarboxylase. Using entirely genome-integrated gene expression, we have engineered Pseudomonas putida KT2440-derived strains to produce muconate from either aromatic molecules or sugars and demonstrate in both cases that co-expression of these decarboxylase associated proteins reduces PCA accumulation and enhances muconate production relative to strains expressing the PCA decarboxylase alone. In bioreactor experiments, co-expression increased the specific productivity (mg/g cells/h) of muconate from the aromatic lignin monomer p-coumarate by 50% and resulted in a titer of >15 g/L. In strains engineered to produce muconate from glucose, co-expression more than tripled the titer, yield, productivity, and specific productivity, with the best strain producing 4.92+/-0.48 g/L muconate. Furthermore, this study demonstrates that overcoming the PCA decarboxylase bottleneck can increase muconate yields from biomass-derived sugars and aromatic molecules in industrially relevant strains and cultivation conditions.« less

Increasing Prion Propensity by Hydrophobic Insertion

PubMed Central

Petri, Michelina; Flores, Noe; Rogge, Ryan A.; Cascarina, Sean M.; Ross, Eric D.

2014-01-01

Prion formation involves the conversion of proteins from a soluble form into an infectious amyloid form. Most yeast prion proteins contain glutamine/asparagine-rich regions that are responsible for prion aggregation. Prion formation by these domains is driven primarily by amino acid composition, not primary sequence, yet there is a surprising disconnect between the amino acids thought to have the highest aggregation propensity and those that are actually found in yeast prion domains. Specifically, a recent mutagenic screen suggested that both aromatic and non-aromatic hydrophobic residues strongly promote prion formation. However, while aromatic residues are common in yeast prion domains, non-aromatic hydrophobic residues are strongly under-represented. Here, we directly test the effects of hydrophobic and aromatic residues on prion formation. Remarkably, we found that insertion of as few as two hydrophobic residues resulted in a multiple orders-of-magnitude increase in prion formation, and significant acceleration of in vitro amyloid formation. Thus, insertion or deletion of hydrophobic residues provides a simple tool to control the prion activity of a protein. These data, combined with bioinformatics analysis, suggest a limit on the number of strongly prion-promoting residues tolerated in glutamine/asparagine-rich domains. This limit may explain the under-representation of non-aromatic hydrophobic residues in yeast prion domains. Prion activity requires not only that a protein be able to form prion fibers, but also that these fibers be cleaved to generate new independently-segregating aggregates to offset dilution by cell division. Recent studies suggest that aromatic residues, but not non-aromatic hydrophobic residues, support the fiber cleavage step. Therefore, we propose that while both aromatic and non-aromatic hydrophobic residues promote prion formation, aromatic residues are favored in yeast prion domains because they serve a dual function, promoting both prion formation and chaperone-dependent prion propagation. PMID:24586661

Stimulated anoxic biodegradation of aromatic hydrocarbons using Fe(III) ligands

USGS Publications Warehouse

Lovley, D.R.; Woodward, J.C.; Chapelle, F.H.

1994-01-01

Contamination of ground waters with water-soluble aromatic hydrocarbons, common components of petroleum pollution, often produces anoxic conditions under which microbial degradation of the aromatics is slow. Oxygen is often added to contaminated ground water to stimulate biodegradation, but this can be technically difficult and expensive. Insoluble Fe(III) oxides, which are generally abundant in shallow aquifers, are alternative potential oxidants, but are difficult for microorganisms to access. Here we report that adding organic ligands that bind to Fe(III) dramatically increases its bioavailability, and that in the presence of these ligands, rates of degradation of aromatic hydrocarbons in anoxic aquifer sediments are comparable to those in oxic sediments. We find that even benzene, which is notoriously refractory in the absence of oxygen, can be rapidly degraded. Our results suggest that increasing the bioavailability of Fe(III) by adding suitable ligands provides a potential alternative to oxygen addition for the bioremediation of petroleum-contaminated aquifers.Contamination of ground waters with water-soluble aromatic hydrocarbons, common components of petroleum pollution, often produces anoxic conditions under which microbial degradation of the aromatics is slow. Oxygen is often added to contaminated ground water to stimulate biodegradation, but this can be technically difficult and expensive. Insoluble Fe(III) oxides, which are generally abundant in shallow aquifers, are alternative potential oxidants, but are difficult for microorganisms to access. Here we report that adding organic ligands that bind to Fe(III) dramatically increases its bioavailability, and that in the presence of these ligands, rates of degradation of aromatic hydrocarbons in anoxic aquifer sediments are comparable to those in oxic sediments. We find that even benzene, which is notoriously refractory in the absence of oxygen, can be rapidly degraded. Our results suggest that increasing the bioavailability of Fe(III) by adding suitable ligands provides a potential alternative to oxygen addition for the bioremediation of petroleum-contamined aquifers.

Aromatic and heterocyclic perfluoroalkyl sulfides. Methods of preparation

PubMed Central

2010-01-01

Summary This review covers all of the common methods for the syntheses of aromatic and heterocyclic perfluoroalkyl sulfides, a class of compounds which is finding increasing application as starting materials for the preparation of agrochemicals, pharmaceutical products and, more generally, fine chemicals. A systematic approach is taken depending on the mode of incorporation of the SRF groups and also on the type of reagents used. PMID:20978611

POLYCYCLIC AROMATIC HYDROCARBONS DISRUPT AXIAL DEVELOPMENT IN SEA URCHIN EMBRYOS THROUGH A S-CATENIN DEPENDENT PATHWAY. (R828676C002)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Quantitative High-Throughput Screening and Confirmation Studies for Identification of Compounds that Activate the Aryl Hydrocarbon Receptor Pathway (SETAC)

EPA Science Inventory

The aryl hydrocarbon receptor (AhR) is a transcription factor that mediates adaptive responses to known environmental pollutants, such as aromatic hydrocarbons, through regulation of Phase I and II xenobiotic metabolizing enzymes as well as important growth and differentiation pa...

Comparative genomic analysis of 26 Sphingomonas and Sphingobium strains: Dissemination of bioremediation capabilities, biodegradation potential and horizontal gene transfer.

PubMed

Zhao, Qiang; Yue, Shengjie; Bilal, Muhammad; Hu, Hongbo; Wang, Wei; Zhang, Xuehong

2017-12-31

Bacteria belonging to the genera Sphingomonas and Sphingobium are known for their ability to catabolize aromatic compounds. In this study, we analyzed the whole genome sequences of 26 strains in the genera Sphingomonas and Sphingobium to gain insight into dissemination of bioremediation capabilities, biodegradation potential, central pathways and genome plasticity. Phylogenetic analysis revealed that both Sphingomonas sp. strain BHC-A and Sphingomonas paucimobilis EPA505 should be placed in the genus Sphingobium. The bph and xyl gene cluster was found in 6 polycyclic aromatic hydrocarbons-degrading strains. Transposase and IS coding genes were found in the 6 gene clusters, suggesting the mobility of bph and xyl gene clusters. β-ketoadipate and homogentisate pathways were the main central pathways in Sphingomonas and Sphingobium strains. A large number of oxygenase coding genes were predicted in the 26 genomes, indicating a huge biodegradation potential of the Sphingomonas and Sphingobium strains. Horizontal gene transfer related genes and prophages were predicted in the analyzed strains, suggesting the ongoing evolution and shaping of the genomes. Analysis of the 26 genomes in this work contributes to the understanding of dispersion of bioremediation capabilities, bioremediation potential and genome plasticity in strains belonging to the genera Sphingomonas and Sphingobium. Copyright © 2017 Elsevier B.V. All rights reserved.

Investigation on the light alkanes aromatization over Zn and Ga modified HZSM-5 catalysts in the presence of methane

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

Li, Qingyin; Zhang, Fengqi; Jarvis, Jack

The catalytic co-aromatization of methane and paraffin-rich raffinate oil was investigated along with hexane, heptane and octane as its model compounds over zinc and gallium modified ZSM-5 zeolite catalysts. The benzene, toluene and xylene (BTX) components derived from light alkane aromatization were highly promoted with the assistance of methane. The co-existence of Zn and Ga metal species has a positive effect on the formation of BTX components, whereas the individual metal loaded catalyst resulted in the production of heavy aromatics, suggesting that zinc and gallium have a synergistic effect on the formation of BTX under the methane environment. When concernedmore » with gaseous analysis, the introduced methane might interact with smaller intermediates and then transform into larger hydrocarbons. From the DRIFT observation, it was witnessed that the interaction between light alkane and methane occurred on the surface of the charged Zn-Ga/ZSM-5 catalyst. According to the comprehensive catalyst characterizations, the excellent catalytic performance may be closely associated with greatly dispersed metal species on the zeolite support, improved microporous characteristic, moderate Bronsted and increased Lewis acidic sites during the paraffin-rich liquid feedstock aromatization under methane environment. This research provides a promising pathway for the highly effective and profitable utilization of petrochemical resources and natural gas.« less

Investigation on the light alkanes aromatization over Zn and Ga modified HZSM-5 catalysts in the presence of methane

DOE PAGES

Li, Qingyin; Zhang, Fengqi; Jarvis, Jack; ...

2018-03-16

The catalytic co-aromatization of methane and paraffin-rich raffinate oil was investigated along with hexane, heptane and octane as its model compounds over zinc and gallium modified ZSM-5 zeolite catalysts. The benzene, toluene and xylene (BTX) components derived from light alkane aromatization were highly promoted with the assistance of methane. The co-existence of Zn and Ga metal species has a positive effect on the formation of BTX components, whereas the individual metal loaded catalyst resulted in the production of heavy aromatics, suggesting that zinc and gallium have a synergistic effect on the formation of BTX under the methane environment. When concernedmore » with gaseous analysis, the introduced methane might interact with smaller intermediates and then transform into larger hydrocarbons. From the DRIFT observation, it was witnessed that the interaction between light alkane and methane occurred on the surface of the charged Zn-Ga/ZSM-5 catalyst. According to the comprehensive catalyst characterizations, the excellent catalytic performance may be closely associated with greatly dispersed metal species on the zeolite support, improved microporous characteristic, moderate Bronsted and increased Lewis acidic sites during the paraffin-rich liquid feedstock aromatization under methane environment. This research provides a promising pathway for the highly effective and profitable utilization of petrochemical resources and natural gas.« less

Environmental Temperature Effect on the Far-Infrared Absorption Features of Aromatic-Based Titan's Aerosol Analogs

NASA Technical Reports Server (NTRS)

Gautier, Thomas; Trainer, Melissa G.; Loeffler, Mark J.; Sebree, Joshua A.; Anderson, Carrie M.

2016-01-01

Benzene detection has been reported in Titans atmosphere both in the stratosphere at ppb levels by remote sensing and in the thermosphere at ppm levels by the Cassini's Ion and Neutral Mass Spectrometer. This detection supports the idea that aromatic and heteroaromatic reaction pathways may play an important role in Titans atmospheric chemistry, especially in the formation of aerosols. Indeed, aromatic molecules are easily dissociated by ultraviolet radiation and can therefore contribute significantly to aerosol formation. It has been shown recently that aerosol analogs produced from a gas mixture containing a low concentration of aromatic and/or heteroaromatic molecules (benzene, naphthalene, pyridine, quinoline and isoquinoline) have spectral signatures below 500/cm, a first step towards reproducing the aerosol spectral features observed by Cassini's Composite InfraRed Spectrometer (CIRS) in the far infrared. In this work we investigate the influence of environmental temperature on the absorption spectra of such aerosol samples, simulating the temperature range to which aerosols, once formed, are exposed during their transport through Titans stratosphere. Our results show that environmental temperature does not have any major effect on the spectral shape of these aerosol analogs in the far-infrared, which is consistent with the CIRS observations.

Tailoring ZSM-5 Zeolites for the Fast Pyrolysis of Biomass to Aromatic Hydrocarbons.

PubMed

Hoff, Thomas C; Gardner, David W; Thilakaratne, Rajeeva; Wang, Kaige; Hansen, Thomas W; Brown, Robert C; Tessonnier, Jean-Philippe

2016-06-22

The production of aromatic hydrocarbons from cellulose by zeolite-catalyzed fast pyrolysis involves a complex reaction network sensitive to the zeolite structure, crystallinity, elemental composition, porosity, and acidity. The interplay of these parameters under the reaction conditions represents a major roadblock that has hampered significant improvement in catalyst design for over a decade. Here, we studied commercial and laboratory-synthesized ZSM-5 zeolites and combined data from 10 complementary characterization techniques in an attempt to identify parameters common to high-performance catalysts. Crystallinity and framework aluminum site accessibility were found to be critical to achieve high aromatic yields. These findings enabled us to synthesize a ZSM-5 catalyst with enhanced activity, which offers the highest aromatic hydrocarbon yield reported to date. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Two shikimate dehydrogenases, VvSDH3 and VvSDH4, are involved in gallic acid biosynthesis in grapevine.

PubMed

Bontpart, Thibaut; Marlin, Thérèse; Vialet, Sandrine; Guiraud, Jean-Luc; Pinasseau, Lucie; Meudec, Emmanuelle; Sommerer, Nicolas; Cheynier, Véronique; Terrier, Nancy

2016-05-01

In plants, the shikimate pathway provides aromatic amino acids that are used to generate numerous secondary metabolites, including phenolic compounds. In this pathway, shikimate dehydrogenases (SDH) 'classically' catalyse the reversible dehydrogenation of 3-dehydroshikimate to shikimate. The capacity of SDH to produce gallic acid from shikimate pathway metabolites has not been studied in depth. In grapevine berries, gallic acid mainly accumulates as galloylated flavan-3-ols. The four grapevine SDH proteins have been produced in Escherichia coli In vitro, VvSDH1 exhibited the highest 'classical' SDH activity. Two genes, VvSDH3 and VvSDH4, mainly expressed in immature berry tissues in which galloylated flavan-3-ols are accumulated, encoded enzymes with lower 'classical' activity but were able to produce gallic acid in vitro The over-expression of VvSDH3 in hairy-roots increased the content of aromatic amino acids and hydroxycinnamates, but had little or no effect on molecules more distant from the shikimate pathway (stilbenoids and flavan-3-ols). In parallel, the contents of gallic acid, β-glucogallin, and galloylated flavan-3-ols were increased, attesting to the influence of this gene on gallic acid metabolism. Phylogenetic analysis from dicotyledon SDHs opens the way for the examination of genes from other plants which accumulate gallic acid-based metabolites. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Dermal exposure to jet fuel suppresses delayed-type hypersensitivity: a critical role for aromatic hydrocarbons.

PubMed

Ramos, Gerardo; Limon-Flores, Alberto Yairh; Ullrich, Stephen E

2007-12-01

Dermal exposure to military (JP-8) and/or commercial (Jet-A) jet fuel suppresses cell-mediated immune reactions. Immune regulatory cytokines and biological modifiers, including platelet activating factor (PAF), prostaglandin E(2), and interleukin-10, have been implicated in the pathway of events leading to immune suppression. It is estimated that approximately 260 different hydrocarbons are found in jet fuel, and the exact identity of the active immunotoxic agent(s) is unknown. The recent availability of synthetic jet fuel (S-8), which is refined from natural gas, and is devoid of aromatic hydrocarbons, made it feasible to design experiments to address this problem. Here we tested the hypothesis that the aromatic hydrocarbons present in jet fuel are responsible for immune suppression. We report that applying S-8 to the skin of mice does not upregulate the expression of epidermal cyclooxygenase-2 (COX-2) nor does it induce immune suppression. Adding back a cocktail of seven of the most prevalent aromatic hydrocarbons found in jet fuel (benzene, toluene, ethylbenzene, xylene, 1,2,4-trimethlybenzene, cyclohexylbenzene, and dimethylnaphthalene) to S-8 upregulated epidermal COX-2 expression and suppressed a delayed-type hypersensitivity (DTH) reaction. Injecting PAF receptor antagonists, or a selective cycloozygenase-2 inhibitor into mice treated with S-8 supplemented with the aromatic cocktail, blocked suppression of DTH, similar to data previously reported using JP-8. These findings identify the aromatic hydrocarbons found in jet fuel as the agents responsible for suppressing DTH, in part by the upregulation of COX-2, and the production of immune regulatory factors and cytokines.

Effects of EPSPS Copy Number Variation (CNV) and Glyphosate Application on the Aromatic and Branched Chain Amino Acid Synthesis Pathways in Amaranthus palmeri

PubMed Central

Fernández-Escalada, Manuel; Zulet-González, Ainhoa; Gil-Monreal, Miriam; Zabalza, Ana; Ravet, Karl; Gaines, Todd; Royuela, Mercedes

2017-01-01

A key enzyme of the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19), is the known target of the widely used herbicide glyphosate. Glyphosate resistance in Amaranthus palmeri, one of the most troublesome weeds in agriculture, has evolved through increased EPSPS gene copy number. The aim of this work was to study the pleiotropic effects of (i) EPSPS increased transcript abundance due to gene copy number variation (CNV) and of (ii) glyphosate application on the aromatic amino acid (AAA) and branched chain amino acid (BCAA) synthesis pathways. Hydroponically grown glyphosate sensitive (GS) and glyphosate resistant (GR) plants were treated with glyphosate 3 days after treatment. In absence of glyphosate treatment, high EPSPS gene copy number had only a subtle effect on transcriptional regulation of AAA and BCAA pathway genes. In contrast, glyphosate treatment provoked a general accumulation of the transcripts corresponding to genes of the AAA pathway leading to synthesis of chorismate in both GS and GR. After chorismate, anthranilate synthase transcript abundance was higher while chorismate mutase transcription showed a small decrease in GR and remained stable in GS, suggesting a regulatory branch point in the pathway that favors synthesis toward tryptophan over phenylalanine and tyrosine after glyphosate treatment. This was confirmed by studying enzyme activities in vitro and amino acid analysis. Importantly, this upregulation was glyphosate dose dependent and was observed similarly in both GS and GR populations. Glyphosate treatment also had a slight effect on the expression of BCAA genes but no general effect on the pathway could be observed. Taken together, our observations suggest that the high CNV of EPSPS in A. palmeri GR populations has no major pleiotropic effect on the expression of AAA biosynthetic genes, even in response to glyphosate treatment. This finding supports the idea that the fitness cost associated with EPSPS CNV in A. palmeri may be limited. PMID:29201035

Procedure for and results of simultaneous determination of aromatic hydrocarbons and fatty acid methyl esters in diesel fuels by high performance liquid chromatography.

PubMed

Kamiński, M; Gilgenast, E; Przyjazny, A; Romanik, G

2006-07-28

The content of aromatic hydrocarbons in diesel fuels is regulated by appropriate standards, and a further reduction in the allowed concentration of these hazardous substances in these fuels is expected. The content of aromatic hydrocarbons in diesel fuels is most often determined using standard methods EN-12916 or ASTM D-6591. The content of polycyclic aromatic hydrocarbons (PAHs) is determined from a single peak obtained using normal phase high-performance liquid chromatography (NP-HPLC), a column of the NH2 type, n-heptane as the eluent, refractive index detector (RID) and backflushing of the eluent. However, the methods mentioned above cannot be applied when the fuel contains fatty acid methyl esters (FAME), which lately has become more common. The content of FAME in diesel oils is determined using mid-IR spectrophotometry based on the absorption of carbonyl group. However, no standard procedure for the determination of classes of aromatic hydrocarbons in diesel fuels containing FAME is yet available. The present work describes such a modification of methods EN-12916/ASTM D-6591 that provides a simultaneous determination of individual groups of aromatic hydrocarbons, total content of polycyclic aromatic hydrocarbons and the FAME content in diesel fuels. The refractive index detector (RID) and n-heptane as the mobile phase are still used, but backflushing of the eluent is applied after the elution of all polycyclic aromatic hydrocarbons. Additionally, ultraviolet diode array detection is used for the exact determination of low contents of polycyclic aromatic hydrocarbons and to confirm the presence of FAME in the analyzed fuel.

Phthalocyanines as Molecular Scaffolds to Block Disease-Associated Protein Aggregation.

PubMed

Valiente-Gabioud, Ariel A; Miotto, Marco C; Chesta, María E; Lombardo, Verónica; Binolfi, Andres; Fernández, Claudio O

2016-05-17

The aggregation of proteins into toxic conformations plays a critical role in the development of different neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and Creutzfled-Jakob's disease (CJD). These disorders share a common pathological mechanism that involves the formation of aggregated protein species including toxic oligomers and amyloid fibrils. The aggregation of alpha-synuclein (αS) in PD and the amyloid beta peptide (Aβ) and tau protein in AD results in neuronal death and disease onset. In the case of CJD, the misfolding of the physiological prion protein (PrP) induces a chain reaction that results in accumulation of particles that elicit brain damage. Currently, there is no preventive therapy for these diseases and the available therapeutic approaches are based on the treatment of the symptoms rather than the underlying causes of the disease. Accordingly, the aggregation pathway of these proteins represents a useful target for therapeutic intervention. Therefore, understanding the mechanism of amyloid formation and its inhibition is of high clinical importance. The design of small molecules that efficiently inhibit the aggregation process and/or neutralize its associated toxicity constitutes a promising tool for the development of therapeutic strategies against these disorders. In this accounts, we discuss current knowledge on the anti-amyloid activity of phthalocyanines and their potential use as drug candidates in neurodegeneration. These tetrapyrrolic compounds modulate the amyloid assembly of αS, tau, Aβ, and the PrP in vitro, and protect cells from the toxic effects of amyloid aggregates. In addition, in scrapie-infected mice, these compounds showed important prophylactic antiscrapie properties. The structural basis for the inhibitory effect of phthalocyanines on amyloid filament assembly relies on specific π-π interactions between the aromatic ring system of these molecules and aromatic residues in the amyloidogenic proteins. Analysis of the structure-activity relationship in phthalocyanines revealed that their anti-amyloid activity is highly dependent on the type of metal ion coordinated to the tetrapyrrolic system but is not sensitive to the number of peripheral charged substituents. The tendency of phthalocyanines to oligomerize (self-association) via aromatic-aromatic stacking interactions correlates precisely with their binding capabilities to target proteins and, more importantly, determines their efficiency as anti-amyloid agents. The ability to block different types of disease-associated protein aggregation raises the possibility that these cyclic tetrapyrrole compounds have a common mechanism of action to impair the formation of a variety of pathological aggregates. Because the structural and molecular basis for the anti-amyloid effects of these molecules is starting to emerge, combined efforts from the fields of structural, cellular, and animal biology will result critical for the rational design and discovery of new drugs for the treatment of amyloid related neurological disorders.

Quasi-targeted analysis of hydroxylation-related metabolites of polycyclic aromatic hydrocarbons in human urine by liquid chromatography-mass spectrometry.

PubMed

Tang, Caiming; Tan, Jianhua; Fan, Ruifang; Zhao, Bo; Tang, Caixing; Ou, Weihui; Jin, Jiabin; Peng, Xianzhi

2016-08-26

Metabolite identification is crucial for revealing metabolic pathways and comprehensive potential toxicities of polycyclic aromatic hydrocarbons (PAHs) in human body. In this work, a quasi-targeted analysis strategy was proposed for metabolite identification of monohydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) in human urine using liquid chromatography triple quadruple mass spectrometry (LC-QqQ-MS/MS) combined with liquid chromatography high resolution mass spectrometry (LC-HRMS). Potential metabolites of OH-PAHs were preliminarily screened out by LC-QqQ-MS/MS in association with filtering in a self-constructed information list of possible metabolites, followed by further identification and confirmation with LC-HRMS. The developed method can provide more reliable and systematic results compared with traditional untargeted analysis using LC-HRMS. In addition, data processing for LC-HRMS analysis were greatly simplified. This quasi-targeted analysis method was successfully applied to identifying phase I and phase II metabolites of OH-PAHs in human urine. Five metabolites of hydroxynaphthalene, seven of hydroxyfluorene, four of hydroxyphenanthrene, and three of hydroxypyrene were tentatively identified. Metabolic pathways of PAHs in human body were putatively revealed based on the identified metabolites. The experimental results will be valuable for investigating the metabolic processes of PAHs in human body, and the quasi-targeted analysis strategy can be expanded to the metabolite identification and profiling of other compounds in vivo. Copyright © 2016 Elsevier B.V. All rights reserved.

Vapor-Phase Hydrodeoxygenation of Guaiacol to Aromatics over Pt/HBeta: Identification of the Role of Acid Sites and Metal Sites on the Reaction Pathway

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

Nie, Lei; Peng, Bo; Zhu, Xinli

Hydrodeoxygenation of guaiacol, a phenolic compound derived from lignin fraction of biomass, over a Pt/HBeta catalyst at 350 °C and atmospheric pressure produces benzene, toluene, xylenes, and C9+ aromatics with yield of 42%, 29%, 12%, and 5%, respectively. Reaction pathways for conversion of two functional groups (hydroxyl and methoxyl) over the bifunctional catalyst were studied. Both guaiacol and intermediate products (catechol and cyclopentanone) were fed onto zeolite HBeta and Pt/SiO2 to identify the individual role of acid site and metal site. Acid sites (mainly Brønsted acid site, BAS) catalyze transalkylation and dehydroxylation reactions in sequence, producing phenol, cresols and xylenolsmore » as the major products at high conversion. Pt sites catalyze demethylation reaction resulting in catechol as the primary product, which can either be deoxygenated to phenol followed by phenol to benzene, or decarbonylated to cyclopentanone and further to butane. The close proximity of Pt and BAS in bifunctional Pt/HBeta enables both transalkylation and deoxygenation reactions with inhibited demethylation and decarbonylation reactions, producing aromatics as major final products with a total yield > 85%. Both activity and stability of bifunctional Pt/HBeta during hydrodeoxygenation of guaiacol is improved compared to HBeta and Pt/SiO2. The addition of water to the feed further improves the activity and stability via hydrolysis of O-CH3 bond of guaiacol on BAS and removing coke around Pt.« less

Characterization of products from hydrothermal carbonization of pine.

PubMed

Wu, Qiong; Yu, Shitao; Hao, Naijia; Wells, Tyrone; Meng, Xianzhi; Li, Mi; Pu, Yunqiao; Liu, Shouxin; Ragauskas, Arthur J

2017-11-01

This study aims to reveal the structural features and reaction pathways for solid-liquid products from hydrothermal carbonization of Loblolly pine, where the solid products can be used as catalysts, adsorbents and electrode materials while liquid products can be treated yielding fuels and platform chemicals. Results revealed when treated at 240°C, cellulose and hemicellulose were degraded, in part, to 5-hydroxy-methyl furfural and furfural which were further transformed to aromatic structures via ring opening and Diels Alder reactions. Lignin degradation and formation of carbon-carbon bonds, forming aromatic motifs in the presence of furanic compounds connected via aliphatic bridges, ether or condensation reactions. After hydrothermal treatment, condensed aromatic carbon materials with methoxy groups were recovered with high fixed carbon content and HHV. The recovered liquid products are lignin-like value-added chemicals consisting of furfural and polyaromatic structure with alkanes and carboxyl, their total hydroxyl group content decreased when increasing reaction time. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterization of products from hydrothermal carbonization of pine

DOE PAGES

Wu, Qiong; Yu, Shitao; Hao, Naijia; ...

2017-07-27

This study aims to reveal the structural features and reaction pathways for solid–liquid products from hydrothermal carbonization of Loblolly pine, where the solid products can be used as catalysts, adsorbents and electrode materials while liquid products can be treated yielding fuels and platform chemicals. Results revealed when treated at 240 °C, cellulose and hemicellulose were degraded, in part, to 5-hydroxy-methyl furfural and furfural which were further transformed to aromatic structures via ring opening and Diels Alder reactions. Lignin degradation and formation of carbon–carbon bonds, forming aromatic motifs in the presence of furanic compounds connected via aliphatic bridges, ether or condensationmore » reactions. After hydrothermal treatment, condensed aromatic carbon materials with methoxy groups were recovered with high fixed carbon content and HHV. As a result, the recovered liquid products are lignin-like value-added chemicals consisting of furfural and polyaromatic structure with alkanes and carboxyl, their total hydroxyl group content decreased when increasing reaction time.« less

Development of Chemical and Metabolite Sensors for Rhodococcus opacus PD630

DOE PAGES

DeLorenzo, Drew M.; Henson, William R.; Moon, Tae Seok

2017-07-26

Rhodococcus opacus PD630 is a non-model, gram positive bacterium that possesses desirable traits for biomass conversion, including consumption capabilities for lignocellulose-based sugars and toxic lignin-derived aromatic compounds, significant triacylglycerol accumulation, relatively rapid growth rate, and genetic tractability. However, few genetic elements have been directly characterized in R. opacus, limiting its application for lignocellulose bioconversion. Here, we report the characterization and development of genetic tools for tunable gene expression in R. opacus, including: 1) six fluorescent reporters for quantifying promoter output, 2) three chemically inducible promoters for variable gene expression, and 3) two classes of metabolite sensors derived from native R.more » opacus promoters that detect nitrogen levels or aromatic compounds. Using these tools, we also provide insights into native aromatic consumption pathways in R. opacus. Overall, this work expands the ability to control and characterize gene expression in R. opacus for future lignocellulose-based fuel and chemical production.« less

Identification of crude-oil components and microorganisms that cause souring under anaerobic conditions.

PubMed

Hasegawa, R; Toyama, K; Miyanaga, K; Tanji, Y

2014-02-01

Oil souring has important implications with respect to energy resources. Understanding the physiology of the microorganisms that play a role and the biological mechanisms are both important for the maintenance of infrastructure and mitigation of corrosion processes. The objective of this study was to identify crude-oil components and microorganisms in oil-field water that contribute to crude-oil souring. To identify the crude-oil components and microorganisms that are responsible for anaerobic souring in oil reservoirs, biological conversion of crude-oil components under anaerobic conditions was investigated. Microorganisms in oil field water in Akita, Japan degraded alkanes and aromatics to volatile fatty acids (VFAs) under anaerobic conditions, and fermenting bacteria such as Fusibacter sp. were involved in VFA production. Aromatics such as toluene and ethylbenzene were degraded by sulfate-reducing bacteria (Desulfotignum sp.) via the fumarate-addition pathway and not only degradation of VFA but also degradation of aromatics by sulfate-reducing bacteria was the cause of souring. Naphthenic acid and 2,4-xylenol were not converted.

Polycyclic aromatic hydrocarbon degradation by biosurfactant-producing Pseudomonas sp. IR1.

PubMed

Kumara, Manoj; Leon, Vladimir; De Sisto Materano, Angela; Ilzins, Olaf A; Galindo-Castro, Ivan; Fuenmayor, Sergio L

2006-01-01

We characterized a newly isolated bacterium, designated as IR1, with respect to its ability to degrade polycyclic aromatic hydrocarbons (PAHs) and to produce biosurfactants. Isolated IR1 was identified as Pseudomonas putida by analysis of 16S rRNA sequences (99.6% homology). It was capable of utilizing two-, three- and four-ring PAHs but not hexadecane and octadecane as a sole carbon and energy source. PCR and DNA hybridization studies showed that enzymes involved in PAH metabolism were related to the naphthalene dioxygenase pathway. Observation of both tensio-active and emulsifying activities indicated that biosurfactants were produced by IR1 during growth on both water miscible and immiscible substrates. The biosurfactants lowered the surface tension of medium from 54.9 dN cm(-1) to 35.4 dN cm(-1) and formed a stable and compact emulsion with an emulsifying activity of 74% with diesel oil, when grown on dextrose. These findings indicate that this isolate may be useful for bioremediation of sites contaminated with aromatic hydrocarbons.

Aromatic Glucosinolate Biosynthesis Pathway in Barbarea vulgaris and its Response to Plutella xylostella Infestation

PubMed Central

Liu, Tongjin; Zhang, Xiaohui; Yang, Haohui; Agerbirk, Niels; Qiu, Yang; Wang, Haiping; Shen, Di; Song, Jiangping; Li, Xixiang

2016-01-01

The inducibility of the glucosinolate resistance mechanism is an energy-saving strategy for plants, but whether induction would still be triggered by glucosinolate-tolerant Plutella xylostella (diamondback moth, DBM) after a plant had evolved a new resistance mechanism (e.g., saponins in Barbara vulgaris) was unknown. In B. vulgaris, aromatic glucosinolates derived from homo-phenylalanine are the dominant glucosinolates, but their biosynthesis pathway was unclear. In this study, we used G-type (pest-resistant) and P-type (pest-susceptible) B. vulgaris to compare glucosinolate levels and the expression profiles of their biosynthesis genes before and after infestation by DBM larvae. Two different stereoisomers of hydroxylated aromatic glucosinolates are dominant in G- and P-type B. vulgaris, respectively, and are induced by DBM. The transcripts of genes in the glucosinolate biosynthesis pathway and their corresponding transcription factors were identified from an Illumina dataset of G- and P-type B. vulgaris. Many genes involved or potentially involved in glucosinolate biosynthesis were induced in both plant types. The expression patterns of six DBM induced genes were validated by quantitative PCR (qPCR), while six long-fragment genes were validated by molecular cloning. The core structure biosynthetic genes showed high sequence similarities between the two genotypes. In contrast, the sequence identity of two apparent side chain modification genes, the SHO gene in the G-type and the RHO in P-type plants, showed only 77.50% identity in coding DNA sequences and 65.48% identity in deduced amino acid sequences. The homology to GS-OH in Arabidopsis, DBM induction of the transcript and a series of qPCR and glucosinolate analyses of G-type, P-type and F1 plants indicated that these genes control the production of S and R isomers of 2-hydroxy-2-phenylethyl glucosinolate. These glucosinolates were significantly induced by P. xylostella larvae in both the susceptiple P-type and the resistant G-type, even though saponins are the main DBM-resistance causing metabolites in G-type plants. Indol-3-ylmethylglucosinolate was induced in the G-type only. These data will aid our understanding of the biosynthesis and induction of aromatic glucosinolates at the molecular level and also increase our knowledge of the complex mechanisms underpinning defense induction in plants. PMID:26904055

INVESTIGATION OF THE PATHWAYS TO PCDDS/FS FROM AN ETHYLENE DIFFUSION FLAME: FORMATION FROM SOOT AND AROMATICS

EPA Science Inventory

The formation of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDDs/Fs) has been shown to occur from the combustion products of fuels as complex as municipal solid waste and as relatively simple as a methane flame. PCDD/F emissions from flame carbon in th...

Catalytic co-pyrolysis of switchgrass and polyethylene over HZSM-5: catalyst deactivation and coke formation

USDA-ARS?s Scientific Manuscript database

When conducted in the presence of a zeolite catalyst such as HZSM-5, fast pyrolysis of biomass can promote the rejection of oxygen and the formation of aromatic hydrocarbons in the organic liquid products. Unfortunately, this pathway removes hydrogen from the already hydrogen deficient biomass start...

Aromatic hydrocarbon biodegradation activates neutral lipid biosynthesis in oleaginous yeast.

PubMed

Deeba, Farha; Pruthi, Vikas; Negi, Yuvraj S

2018-05-01

In this study, the biodegradation ability of oleaginous yeast Cryptococcus psychrotolerans IITRFD for aromatic hydrocarbons (AHs) was investigated. It was found to completely degrade range of AHs such as 1 g/L phenol, 0.75 g/L naphthalene, 0.50 g/L anthracene and 0.50 g/L pyrene with lipid productivity (g/L/h) of 0.0444, 0.0441, 0.0394 and 0.0383, respectively. This work demonstrated the ring cleavage pathways of AHs by this yeast which follow ortho route for phenol and naphthalene while meta route for anthracene and pyrene degradation. The end products generated during biodegradation of AHs are feed as precursors for de novo triacylglycerols (TAG) biosynthesis pathway of oleaginous yeast. A high quantity of lipid content (46.54%) was observed on phenol as compared to lipid content on naphthalene (46.38%), anthracene (44.97%) and pyrene (44.16%). The lipid profile revealed by GC-MS analysis shows elevated monounsaturated fatty acid (MUFA) content with improved biodiesel quality. Copyright © 2018 Elsevier Ltd. All rights reserved.

Writing with ring currents: selectively hydrogenated polycyclic aromatics as finite models of graphene and graphane

PubMed Central

Fowler, Patrick W.; Gibson, Christopher M.; Bean, David E.

2014-01-01

Alternating partial hydrogenation of the interior region of a polycyclic aromatic hydrocarbon gives a finite model system representing systems on the pathway from graphene to the graphane modification of the graphene sheet. Calculations at the DFT and coupled Hartree–Fock levels confirm that sp2 cycles of bare carbon centres isolated by selective hydrogenation retain the essentially planar geometry and electron delocalization of the annulene that they mimic. Delocalization is diagnosed by the presence of ring currents, as detected by ipsocentric calculation and visualization of the current density induced in the π system by a perpendicular external magnetic field. These induced ‘ring’ currents have essentially the same sense, strength and orbital origin as in the free hydrocarbon. Subjected to the important experimental proviso of the need for atomic-scale control of hydrogenation, this finding predicts the possibility of writing single, multiple and concentric diatropic and/or paratropic ring currents on the graphene/graphane sheet. The implication is that pathways for free flow of ballistic current can be modelled in the same way. PMID:24611026

Isolation, cloning, and characterization of a partial novel aro A gene in common reed (Phragmites australis).

PubMed

Taravat, Elham; Zebarjadi, Alireza; Kahrizi, Danial; Yari, Kheirollah

2015-05-01

Among the essential amino acids, phenylalanine, tryptophan, and tyrosine are aromatic amino acids which are synthesized by the shikimate pathway in plants and bacteria. Herbicide glyphosate can inhibit the biosynthesis of these amino acids. So, identification of the gene tolerant to glyphosate is very important. It has been shown that the common reed or Phragmites australis Cav. (Poaceae) is relatively tolerant to glyphosate. The aim of the current research is identification, cloning, sequencing, and registering of partial aro A gene of the common reed P. australis. The partial aro A gene of common reed (P. australis) was cloned in Escherichia coli and the amino acid sequence was identified/determined for the first time. This is the first report for isolation, cloning, and sequencing of a part of aro A gene from the common reed. A 670 bp fragment including two introns (86 bp and 289 bp) was obtained. The open reading frame (ORF) region in part of gene was encoded for 98 amino acids. Alignment showed high similarity among this region with Zea mays (L.) (Poaceae) (94.6%), Eleusine indica L. Gaertn (Poaceae) (94.2%), and Zoysia japonica Steud. (Poaceae) (94.2%). The alignment of amino acid sequence of the investigated part of the gene showed a homology with aro A from several other plants. This conserved region forms the enzyme active site. The alignment results of nucleotide and amino acid residues with related sequences showed that there are some differences among them. The relative glyphosate tolerance in the common reed may be related to these differences.

Mechanism of sodium channel block by local anesthetics, antiarrhythmics, and anticonvulsants

PubMed Central

Tikhonov, Denis B.

2017-01-01

Local anesthetics, antiarrhythmics, and anticonvulsants include both charged and electroneutral compounds that block voltage-gated sodium channels. Prior studies have revealed a common drug-binding region within the pore, but details about the binding sites and mechanism of block remain unclear. Here, we use the x-ray structure of a prokaryotic sodium channel, NavMs, to model a eukaryotic channel and dock representative ligands. These include lidocaine, QX-314, cocaine, quinidine, lamotrigine, carbamazepine (CMZ), phenytoin, lacosamide, sipatrigine, and bisphenol A. Preliminary calculations demonstrated that a sodium ion near the selectivity filter attracts electroneutral CMZ but repels cationic lidocaine. Therefore, we further docked electroneutral and cationic drugs with and without a sodium ion, respectively. In our models, all the drugs interact with a phenylalanine in helix IVS6. Electroneutral drugs trap a sodium ion in the proximity of the selectivity filter, and this same site attracts the charged group of cationic ligands. At this position, even small drugs can block the permeation pathway by an electrostatic or steric mechanism. Our study proposes a common pharmacophore for these diverse drugs. It includes a cationic moiety and an aromatic moiety, which are usually linked by four bonds. PMID:28258204

Mechanism of sodium channel block by local anesthetics, antiarrhythmics, and anticonvulsants.

PubMed

Tikhonov, Denis B; Zhorov, Boris S

2017-04-03

Local anesthetics, antiarrhythmics, and anticonvulsants include both charged and electroneutral compounds that block voltage-gated sodium channels. Prior studies have revealed a common drug-binding region within the pore, but details about the binding sites and mechanism of block remain unclear. Here, we use the x-ray structure of a prokaryotic sodium channel, NavMs, to model a eukaryotic channel and dock representative ligands. These include lidocaine, QX-314, cocaine, quinidine, lamotrigine, carbamazepine (CMZ), phenytoin, lacosamide, sipatrigine, and bisphenol A. Preliminary calculations demonstrated that a sodium ion near the selectivity filter attracts electroneutral CMZ but repels cationic lidocaine. Therefore, we further docked electroneutral and cationic drugs with and without a sodium ion, respectively. In our models, all the drugs interact with a phenylalanine in helix IVS6. Electroneutral drugs trap a sodium ion in the proximity of the selectivity filter, and this same site attracts the charged group of cationic ligands. At this position, even small drugs can block the permeation pathway by an electrostatic or steric mechanism. Our study proposes a common pharmacophore for these diverse drugs. It includes a cationic moiety and an aromatic moiety, which are usually linked by four bonds. © 2017 Tikhonov and Zhorov.

First evidence of a membrane-bound, tyramine and beta-phenylethylamine producing, tyrosine decarboxylase in Enterococcus faecalis: a two-dimensional electrophoresis proteomic study.

PubMed

Pessione, Enrica; Pessione, Alessandro; Lamberti, Cristina; Coïsson, Daniel Jean; Riedel, Kathrin; Mazzoli, Roberto; Bonetta, Silvia; Eberl, Leo; Giunta, Carlo

2009-05-01

The soluble and membrane proteome of a tyramine producing Enterococcus faecalis, isolated from an Italian goat cheese, was investigated. A detailed analysis revealed that this strain also produces small amounts of beta-phenylethylamine. Kinetics of tyramine and beta-phenylethylamine accumulation, evaluated in tyrosine plus phenylalanine-enriched cultures (stimulated condition), suggest that the same enzyme, the tyrosine decarboxylase (TDC), catalyzes both tyrosine and phenylalanine decarboxylation: tyrosine was recognized as the first substrate and completely converted into tyramine (100% yield) while phenylalanine was decarboxylated to beta-phenylethylamine (10% yield) only when tyrosine was completely depleted. The presence of an aspecific aromatic amino acid decarboxylase is a common feature in eukaryotes, but in bacteria only indirect evidences of a phenylalanine decarboxylating TDC have been presented so far. Comparative proteomic investigations, performed by 2-DE and MALDI-TOF/TOF MS, on bacteria grown in conditions stimulating tyramine and beta-phenylethylamine biosynthesis and in control conditions revealed 49 differentially expressed proteins. Except for aromatic amino acid biosynthetic enzymes, no significant down-regulation of the central metabolic pathways was observed in stimulated conditions, suggesting that tyrosine decarboxylation does not compete with the other energy-supplying routes. The most interesting finding is a membrane-bound TDC highly over-expressed during amine production. This is the first evidence of a true membrane-bound TDC, longly suspected in bacteria on the basis of the gene sequence.

Swit_4259, an acetoacetate decarboxylase-like enzyme from Sphingomonas wittichii RW1

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

Mydy, Lisa S.; Mashhadi, Zahra; Knight, T. William

The Gram-negative bacteriumSphingomonas wittichiiRW1 is notable for its ability to metabolize a variety of aromatic hydrocarbons. Not surprisingly, theS. wittichiigenome contains a number of putative aromatic hydrocarbon-degrading gene clusters. One of these includes an enzyme of unknown function, Swit_4259, which belongs to the acetoacetate decarboxylase-like superfamily (ADCSF). Here, it is reported that Swit_4259 is a small (28.8 kDa) tetrameric ADCSF enzyme that, unlike the prototypical members of the superfamily, does not have acetoacetate decarboxylase activity. Structural characterization shows that the tertiary structure of Swit_4259 is nearly identical to that of the true decarboxylases, but there are important differences in themore » fine structure of the Swit_4259 active site that lead to a divergence in function. In addition, it is shown that while it is a poor substrate, Swit_4259 can catalyze the hydration of 2-oxo-hex-3-enedioate to yield 2-oxo-4-hydroxyhexanedioate. It is also demonstrated that Swit_4259 has pyruvate aldolase-dehydratase activity, a feature that is common to all of the family V ADCSF enzymes studied to date. The enzymatic activity, together with the genomic context, suggests that Swit_4259 may be a hydratase with a role in the metabolism of an as-yet-unknown hydrocarbon. These data have implications for engineering bioremediation pathways to degrade specific pollutants, as well as structure–function relationships within the ADCSF in general.« less

Carbohydrate–Aromatic Interactions in Proteins

PubMed Central

2015-01-01

Protein–carbohydrate interactions play pivotal roles in health and disease. However, defining and manipulating these interactions has been hindered by an incomplete understanding of the underlying fundamental forces. To elucidate common and discriminating features in carbohydrate recognition, we have analyzed quantitatively X-ray crystal structures of proteins with noncovalently bound carbohydrates. Within the carbohydrate-binding pockets, aliphatic hydrophobic residues are disfavored, whereas aromatic side chains are enriched. The greatest preference is for tryptophan with an increased prevalence of 9-fold. Variations in the spatial orientation of amino acids around different monosaccharides indicate specific carbohydrate C–H bonds interact preferentially with aromatic residues. These preferences are consistent with the electronic properties of both the carbohydrate C–H bonds and the aromatic residues. Those carbohydrates that present patches of electropositive saccharide C–H bonds engage more often in CH−π interactions involving electron-rich aromatic partners. These electronic effects are also manifested when carbohydrate–aromatic interactions are monitored in solution: NMR analysis indicates that indole favorably binds to electron-poor C–H bonds of model carbohydrates, and a clear linear free energy relationships with substituted indoles supports the importance of complementary electronic effects in driving protein–carbohydrate interactions. Together, our data indicate that electrostatic and electronic complementarity between carbohydrates and aromatic residues play key roles in driving protein–carbohydrate complexation. Moreover, these weak noncovalent interactions influence which saccharide residues bind to proteins, and how they are positioned within carbohydrate-binding sites. PMID:26561965

Carbohydrate-Aromatic Interactions in Proteins.

PubMed

Hudson, Kieran L; Bartlett, Gail J; Diehl, Roger C; Agirre, Jon; Gallagher, Timothy; Kiessling, Laura L; Woolfson, Derek N

2015-12-09

Protein-carbohydrate interactions play pivotal roles in health and disease. However, defining and manipulating these interactions has been hindered by an incomplete understanding of the underlying fundamental forces. To elucidate common and discriminating features in carbohydrate recognition, we have analyzed quantitatively X-ray crystal structures of proteins with noncovalently bound carbohydrates. Within the carbohydrate-binding pockets, aliphatic hydrophobic residues are disfavored, whereas aromatic side chains are enriched. The greatest preference is for tryptophan with an increased prevalence of 9-fold. Variations in the spatial orientation of amino acids around different monosaccharides indicate specific carbohydrate C-H bonds interact preferentially with aromatic residues. These preferences are consistent with the electronic properties of both the carbohydrate C-H bonds and the aromatic residues. Those carbohydrates that present patches of electropositive saccharide C-H bonds engage more often in CH-π interactions involving electron-rich aromatic partners. These electronic effects are also manifested when carbohydrate-aromatic interactions are monitored in solution: NMR analysis indicates that indole favorably binds to electron-poor C-H bonds of model carbohydrates, and a clear linear free energy relationships with substituted indoles supports the importance of complementary electronic effects in driving protein-carbohydrate interactions. Together, our data indicate that electrostatic and electronic complementarity between carbohydrates and aromatic residues play key roles in driving protein-carbohydrate complexation. Moreover, these weak noncovalent interactions influence which saccharide residues bind to proteins, and how they are positioned within carbohydrate-binding sites.

Linear pi-Acceptor-Templated Dynamic Clipping to Macrobicycles and[2]Rotaxanes

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

Klivansky, Liana M.; Koshkakaryan, Gayane; Cao, Dennis

2009-04-30

Functional rotaxanes are one of the representative nanoscale molecular machines that have found applications in many areas, including molecular electronics, nanoelectromechanical systems (NEMS), photo controllable smart surfaces, and nanovalves. With the advent of molecular recognition and self-assembly, such molecular compounds can now be obtained efficiently through template-directed synthesis. One of the common strategies of making [2]rotaxanes involves the clipping of a macrocycle around a preformed dumbbell-shaped template in a [1+1] or [2+2] manner. While early examples were based on irreversible kinetic pathway through covalent bond formation, recent advances on reversible dynamic covalent chemistry (DCC) has attracted great attention to thismore » field. By virtue of thermodynamically controlled equilibria, DCC has provided highly efficient and versatile synthetic routes in the selection of specific products from a complex system. Among the several reversible reactions in the category of DCC reactions, the imine formation has proven to be very versatile in macrocyclization to give complex interlocked molecular compounds. Cryptands are three dimensional bicyclic hosts with preorganized cavities capable of inclusion of ions and small molecules. Replacing the nitrogen bridgeheads in common cryptands with aromatic ring systems gives cyclophane-based macrobicycles. The introduction of aromatic ring systems into a preorganized cage-like geometry facilitates ion-{pi} interactions and {pi}-{pi} interactions, resulting in novel metal sandwiches, fluoride receptors, and host-guest complexes. In particular, the seminal work by Gibson, Huang and coworkers on cryptand complexation with paraquat and diquat guests have resulted in the efficient synthesis of mechanically interlocked rotaxanes. The synthesis of cyclophane-based macrobicycles, however, was mostly realized through multiple reaction steps and in high-dilution conditions, which often suffered from low yield and tedious workup. Thus, a one-step, five-component [2+3] clipping reaction that can give the desired macrobicycle is highly desirable. We are motivated by a {pi}-guest templating protocol, because not only {pi}-{pi} interactions can contribute to the formation of macrobicycles, but also the resulting host-guest system holds great promise as a forerunner in the construction of interlocked molecules. (Scheme 1c) Very simple precursors, namely 1,3,5-benzenetrialdehyde (1) and 2,2{prime}-(ethylenedioxy)diethylamine (2) were chosen as the components for desired macrobicycle. (Scheme 2) The formation of six imine bonds would connect the five components to give a macrobicycle while extending the conjugation in the C{sub 3}-symmetric aromatic 'ceiling' and 'floor', which is suitable for enhancing the {pi}-{pi} interactions with a complementary aromatic template. Meanwhile, the ethylene glycol 'pillars' can provide sufficient flexibility, proper spacing, and polar binding sites to assist guest encapsulation. Initial screening of ?-templates engaged several C{sub 3} symmetric aromatic compounds in order to match the symmetry of the desired macrobicycle, which only resulted in nonspecific mixtures. It was found instead that linear bipyridinium (BPY) containing guests effectively templated the [2+3] clipping reaction. Based on this protocol, a [2]rotaxane was successfully assembled as the single product from the six-component reaction.« less

Aromatic Amino Acid-Derived Compounds Induce Morphological Changes and Modulate the Cell Growth of Wine Yeast Species

PubMed Central

González, Beatriz; Vázquez, Jennifer; Cullen, Paul J.; Mas, Albert; Beltran, Gemma; Torija, María-Jesús

2018-01-01

Yeasts secrete a large diversity of compounds during alcoholic fermentation, which affect growth rates and developmental processes, like filamentous growth. Several compounds are produced during aromatic amino acid metabolism, including aromatic alcohols, serotonin, melatonin, and tryptamine. We evaluated the effects of these compounds on growth parameters in 16 different wine yeasts, including non-Saccharomyces wine strains, for which the effects of these compounds have not been well-defined. Serotonin, tryptamine, and tryptophol negatively influenced yeast growth, whereas phenylethanol and tyrosol specifically affected non-Saccharomyces strains. The effects of the aromatic alcohols were observed at concentrations commonly found in wines, suggesting a possible role in microbial interaction during wine fermentation. Additionally, we demonstrated that aromatic alcohols and ethanol are able to affect invasive and pseudohyphal growth in a manner dependent on nutrient availability. Some of these compounds showed strain-specific effects. These findings add to the understanding of the fermentation process and illustrate the diversity of metabolic communication that may occur among related species during metabolic processes. PMID:29696002

In silico and experimental methods revealed highly diverse bacteria with quorum sensing and aromatics biodegradation systems--a potential broad application on bioremediation.

PubMed

Huang, Yili; Zeng, Yanhua; Yu, Zhiliang; Zhang, Jing; Feng, Hao; Lin, Xiuchun

2013-11-01

Phylogenetic overlaps between aromatics-degrading bacteria and acyl-homoserine-lactone (AHL) or autoinducer (AI) based quorum-sensing (QS) bacteria were evident in literatures; however, the diversity of bacteria with both activities had never been finely described. In-silico searching in NCBI genome database revealed that more than 11% of investigated population harbored both aromatic ring-hydroxylating-dioxygenase (RHD) gene and AHL/AI-synthetase gene. These bacteria were distributed in 10 orders, 15 families, 42 genus and 78 species. Horizontal transfers of both genes were common among them. Using enrichment and culture dependent method, 6 Sphingomonadales and 4 Rhizobiales with phenanthrene- or pyrene-degrading ability and AHL-production were isolated from marine, wetland and soil samples. Thin-layer-chromatography and gas-chromatography-mass-spectrum revealed that these Sphingomonads produced various AHL molecules. This is the first report of highly diverse bacteria that harbored both aromatics-degrading and QS systems. QS regulation may have broad impacts on aromatics biodegradation, and would be a new angle for developing bioremediation technology. Copyright © 2013 Elsevier Ltd. All rights reserved.

Enzymic aromatization of 6-alkyl-substituted androgens, potent competitive and mechanism-based inhibitors of aromatase.

PubMed Central

Numazawa, M; Yoshimura, A; Oshibe, M

1998-01-01

To gain insight into the relationships between the aromatase inhibitory activity of 6-alkyl-substituted androgens, potent competitive inhibitors, and their ability to serve as a substrate of aromatase, we studied the aromatization of a series of 6alpha- and 6beta-alkyl (methyl, ethyl, n-propyl, n-pentyl and n-heptyl)-substituted androst-4-ene-3,17-diones (ADs) and their androsta-1,4-diene-3,17-dione (ADD) derivatives with human placental aromatase, by gas chromatography-mass spectrometry. Among the inhibitors examined, ADD and its 6alpha-alkyl derivatives with alkyl functions less than three carbons long, together with 6beta-methyl ADD, are suicide substrates of aromatase. All of the steroids, except for 6beta-n-pentyl ADD and its n-heptyl analogue as well as 6beta-n-heptyl AD, were found to be converted into the corresponding 6-alkyl oestrogens. The 6-methyl steroids were aromatized most efficiently in each series, and the aromatization rate essentially decreased in proportion to the length of the 6-alkyl chains in each series, where the 6alpha-alkyl androgens were more efficient substrates than the corresponding 6beta isomers. The Vmax of 6alpha-methyl ADD was approx. 2.5-fold that of the natural substrate AD and approx. 3-fold that of the parent ADD. On the basis of this, along with the facts that the rates of a mechanism-based inactivation of aromatase by ADD and its 6alpha-methyl derivative are similar, it is implied that alignment of 6alpha-methyl ADD in the active site could favour the pathway leading to oestrogen over the inactivation pathway, compared with that of ADD. The relative apparent Km values for the androgens obtained in this study are different from the relative Ki values obtained previously, indicating that there is a difference between the ability to serve as an inhibitor and the ability to serve as a substrate in the 6-alkyl androgen series. PMID:9405288

Computational modeling of soot nucleation

NASA Astrophysics Data System (ADS)

Chung, Seung-Hyun

Recent studies indicate that soot is the second most significant driver of climate change---behind CO2, but ahead of methane---and increased levels of soot particles in the air are linked to health hazards such as heart disease and lung cancer. Within the soot formation process, soot nucleation is the least understood step, and current experimental findings are still limited. This thesis presents computational modeling studies of the major pathways of the soot nucleation process. In this study, two regimes of soot nucleation---chemical growth and physical agglomeration---were evaluated and the results demonstrated that combustion conditions determine the relative importance of these two routes. Also, the dimerization process of polycyclic aromatic hydrocarbons, which has been regarded as one of the most important physical agglomeration processes in soot formation, was carefully examined with a new method for obtaining the nucleation rate using molecular dynamics simulation. The results indicate that the role of pyrene dimerization, which is the commonly accepted model, is expected to be highly dependent on various flame temperature conditions and may not be a key step in the soot nucleation process. An additional pathway, coronene dimerization in this case, needed to be included to improve the match with experimental data. The results of this thesis provide insight on the soot nucleation process and can be utilized to improve current soot formation models.

Aromatic organosulfates in atmospheric aerosols: synthesis, characterization, and abundance.

PubMed

Staudt, Sean; Kundu, Shuvashish; Lehmler, Hans-Joachim; He, Xianran; Cui, Tianqu; Lin, Ying-Hsuan; Kristensen, Kasper; Glasius, Marianne; Zhang, Xiaolu; Weber, Rodney J; Surratt, Jason D; Stone1, Elizabeth A

2014-09-01

Aromatic organosulfates are identified and quantified in fine particulate matter (PM 2.5 ) from Lahore, Pakistan, Godavari, Nepal, and Pasadena, California. To support detection and quantification, authentic standards of phenyl sulfate, benzyl sulfate, 3-and 4-methylphenyl sulfate and 2-, 3-, and 4-methylbenzyl sulfate were synthesized. Authentic standards and aerosol samples were analyzed by ultra-performance liquid chromatography (UPLC) coupled to negative electrospray ionization (ESI) quadrupole time-of-flight (ToF) mass spectrometry. Benzyl sulfate was present in all three locations at concentrations ranging from 4 - 90 pg m -3 . Phenyl sulfate, methylphenyl sulfates and methylbenzyl sulfates were observed intermittently with abundances of 4 pg m -3 , 2-31 pg m -3 , 109 pg m -3 , respectively. Characteristic fragment ions of aromatic organosulfates include the sulfite radical ( • SO 3 - , m/z 80) and the sulfate radical ( • SO 4 - , m/z 96). Instrumental response factors of phenyl and benzyl sulfates varied by a factor of 4.3, indicating that structurally-similar organosulfates may have significantly different instrumental responses and highlighting the need to develop authentic standards for absolute quantitation organosulfates. In an effort to better understand the sources of aromatic organosulfates to the atmosphere, chamber experiments with the precursor toluene were conducted under conditions that form biogenic organosulfates. Aromatic organosulfates were not detected in the chamber samples, suggesting that they form through different pathways, have different precursors (e.g. naphthalene or methylnaphthalene), or are emitted from primary sources.

Can two-dimensional gas chromatography/mass spectrometric identification of bicyclic aromatic acids in petroleum fractions help to reveal further details of aromatic hydrocarbon biotransformation pathways?

PubMed

West, Charles E; Pureveen, Jos; Scarlett, Alan G; Lengger, Sabine K; Wilde, Michael J; Korndorffer, Frans; Tegelaar, Erik W; Rowland, Steven J

2014-05-15

The identification of key acid metabolites ('signature' metabolites) has allowed significant improvements to be made in our understanding of the biodegradation of petroleum hydrocarbons, in reservoir and in contaminated natural systems, such as aquifers and seawater. On this basis, anaerobic oxidation is now more widely accepted as one viable mechanism, for instance. However, identification of metabolites in the complex acid mixtures from petroleum degradation is challenging and would benefit from use of more highly resolving analytical methods. Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry (GCxGC/TOFMS) with both nominal mass and accurate mass measurement was used to study the complex mixtures of aromatic acids (as methyl esters) in petroleum fractions. Numerous mono- and di-aromatic acid isomers were identified in a commercial naphthenic acids fraction from petroleum and in an acids fraction from a biodegraded petroleum. In many instances, compounds were identified by comparison of mass spectral and retention time data with those of authentic compounds. The identification of a variety of alkyl naphthalene carboxylic and alkanoic and alkyl tetralin carboxylic and alkanoic acids, plus identifications of a range of alkyl indane acids, provides further evidence for 'signature' metabolites of biodegradation of aromatic petroleum hydrocarbons. Identifications such as these now offer the prospect of better differentiation of metabolites of bacterial processes (e.g. aerobic, methanogenic, sulphate-reducing) in polar petroleum fractions. Copyright © 2014 John Wiley & Sons, Ltd.

Aromatic organosulfates in atmospheric aerosols: Synthesis, characterization, and abundance

NASA Astrophysics Data System (ADS)

Staudt, Sean; Kundu, Shuvashish; Lehmler, Hans-Joachim; He, Xianran; Cui, Tianqu; Lin, Ying-Hsuan; Kristensen, Kasper; Glasius, Marianne; Zhang, Xiaolu; Weber, Rodney J.; Surratt, Jason D.; Stone, Elizabeth A.

2014-09-01

Aromatic organosulfates are identified and quantified in fine particulate matter (PM2.5) from Lahore, Pakistan, Godavari, Nepal, and Pasadena, California. To support detection and quantification, authentic standards of phenyl sulfate, benzyl sulfate, 3- and 4-methylphenyl sulfate and 2-, 3-, and 4-methylbenzyl sulfate were synthesized. Authentic standards and aerosol samples were analyzed by ultra-performance liquid chromatography (UPLC) coupled to negative electrospray ionization (ESI) quadrupole time-of-flight (ToF) mass spectrometry. Benzyl sulfate was present in all three locations at concentrations ranging from 4 to 90 pg m-3. Phenyl sulfate, methylphenyl sulfates and methylbenzyl sulfates were observed intermittently with abundances of 4 pg m-3, 2-31 pg m-3, 109 pg m-3, respectively. Characteristic fragment ions of aromatic organosulfates include the sulfite radical (rad SO3-, m/z 80) and the sulfate radical (rad SO4-, m/z 96). Instrumental response factors of phenyl and benzyl sulfates varied by a factor of 4.3, indicating that structurally-similar organosulfates have significantly different instrumental responses and highlighting the need to develop authentic standards for absolute quantitation organosulfates. In an effort to better understand the sources of aromatic organosulfates to the atmosphere, chamber experiments with the precursor toluene were conducted under conditions that form biogenic organosulfates. Aromatic organosulfates were not detected in the chamber samples, suggesting that they form through different pathways, have different precursors (e.g. naphthalene or methylnaphthalene), or are emitted from primary sources.

Cancer Risk Assessment of Polycyclic Aromatic Hydrocarbons in the Soils and Sediments of India: A Meta-Analysis.

PubMed

Tarafdar, Abhrajyoti; Sinha, Alok

2017-10-01

A carcinogenic risk assessment of polycyclic aromatic hydrocarbons in soils and sediments was conducted using the probabilistic approach from a national perspective. Published monitoring data of polycyclic aromatic hydrocarbons present in soils and sediments at different study points across India were collected and converted to their corresponding BaP equivalent concentrations. These BaP equivalent concentrations were used to evaluate comprehensive cancer risk for two different age groups. Monte Carlo simulation and sensitivity analysis were applied to quantify uncertainties of risk estimation. The analysis denotes 90% cancer risk value of 1.770E-5 for children and 3.156E-5 for adults at heavily polluted site soils. Overall carcinogenic risks of polycyclic aromatic hydrocarbons in soils of India were mostly in acceptance limits. However, the food ingestion exposure route for sediments leads them to a highly risked zone. The 90% risk values from sediments are 7.863E-05 for children and 3.999E-04 for adults. Sensitivity analysis reveals exposure duration and relative skin adherence factor for soil as the most influential parameter of the assessment, followed by BaP equivalent concentration of polycyclic aromatic hydrocarbons. For sediments, biota to sediment accumulation factor of fish in terms of BaP is most sensitive on the total outcome, followed by BaP equivalent and exposure duration. Individual exposure route analysis showed dermal contact for soils and food ingestion for sediments as the main exposure pathway. Some specific locations such as surrounding areas of Bhavnagar, Raniganj, Sunderban, Raipur, and Delhi demand potential strategies of carcinogenic risk management and reduction. The current study is probably the first attempt to provide information on the carcinogenic risk of polycyclic aromatic hydrocarbons in soil and sediments across India.

Cancer Risk Assessment of Polycyclic Aromatic Hydrocarbons in the Soils and Sediments of India: A Meta-Analysis

NASA Astrophysics Data System (ADS)

Tarafdar, Abhrajyoti; Sinha, Alok

2017-10-01

A carcinogenic risk assessment of polycyclic aromatic hydrocarbons in soils and sediments was conducted using the probabilistic approach from a national perspective. Published monitoring data of polycyclic aromatic hydrocarbons present in soils and sediments at different study points across India were collected and converted to their corresponding BaP equivalent concentrations. These BaP equivalent concentrations were used to evaluate comprehensive cancer risk for two different age groups. Monte Carlo simulation and sensitivity analysis were applied to quantify uncertainties of risk estimation. The analysis denotes 90% cancer risk value of 1.770E-5 for children and 3.156E-5 for adults at heavily polluted site soils. Overall carcinogenic risks of polycyclic aromatic hydrocarbons in soils of India were mostly in acceptance limits. However, the food ingestion exposure route for sediments leads them to a highly risked zone. The 90% risk values from sediments are 7.863E-05 for children and 3.999E-04 for adults. Sensitivity analysis reveals exposure duration and relative skin adherence factor for soil as the most influential parameter of the assessment, followed by BaP equivalent concentration of polycyclic aromatic hydrocarbons. For sediments, biota to sediment accumulation factor of fish in terms of BaP is most sensitive on the total outcome, followed by BaP equivalent and exposure duration. Individual exposure route analysis showed dermal contact for soils and food ingestion for sediments as the main exposure pathway. Some specific locations such as surrounding areas of Bhavnagar, Raniganj, Sunderban, Raipur, and Delhi demand potential strategies of carcinogenic risk management and reduction. The current study is probably the first attempt to provide information on the carcinogenic risk of polycyclic aromatic hydrocarbons in soil and sediments across India.

Evidence and quantitation of aromatic organosulfates in ambient aerosols in Lahore, Pakistan

NASA Astrophysics Data System (ADS)

Kundu, S.; Quraishi, T. A.; Yu, G.; Suarez, C.; Keutsch, F. N.; Stone, E. A.

2013-05-01

Organosulfates are important components of atmospheric organic aerosols, yet their structures, abundances, sources and formation processes are not adequately understood. This study presents the identification and quantitation of benzyl sulfate in atmospheric aerosols, which is the first confirmed atmospheric organosulfate with aromatic carbon backbone. Benzyl sulfate was identified and quantified in fine particulate matter (PM2.5) collected in Lahore, Pakistan, during 2007-2008. An authentic standard of benzyl sulfate was synthesized, standardized, and identified in atmospheric aerosols with quadrupole time-of-flight (Q-ToF) mass spectrometry (MS). Benzyl sulfate was quantified in aerosol samples using ultra performance liquid chromatography (UPLC) coupled to negative electrospray ionization triple quadrupole (TQ) MS. The highest benzyl sulfate concentrations were recorded in November and January 2007 (0.50 ± 0.11 ng m-3) whereas the lowest concentration was observed in July (0.05 ± 0.02 ng m-3). To evaluate matrix effects, benzyl sulfate concentrations were determined using external calibration and the method of standard addition; comparable concentrations were detected by the two methods, which ruled out significant matrix effects in benzyl sulfate quantitation. Three additional organosulfates with m/z 187, 201 and 215 were qualitatively identified as aromatic organosulfates with additional methyl substituents by high-resolution mass measurements and tandem MS. The observed aromatic organosulfates form a homologous series analogous to toluene, xylene, and trimethylbenzene, which are abundant anthropogenic volatile organic compounds (VOC), suggesting that aromatic organosulfates may be formed by secondary reactions. However, stronger statistical correlations of benzyl sulfate with combustion tracers (EC and levoglucosan) than with secondary tracers (SO42- and α-pinene-derived nitrooxy organosulfates) suggest that aromatic organosulfates may be emitted from the combustion sources or their subsequent atmospheric processing. Further studies are needed to elucidate the sources and formation pathways of aromatic organosulfates in the atmosphere.

Role of aromatic interactions in amyloid formation by islet amyloid polypeptide.

PubMed

Tu, Ling-Hsien; Raleigh, Daniel P

2013-01-15

Aromatic-aromatic and aromatic-hydrophobic interactions have been proposed to play a role in amyloid formation by a range of polypeptides, including islet amyloid polypeptide (IAPP or amylin). IAPP is responsible for amyloid formation in patients with type 2 diabetes. The polypeptide is 37 residues long and contains three aromatic residues, Phe-15, Phe-23, and Tyr-37. The ability of all single aromatic to leucine mutants, all double aromatic to leucine mutants, and the triple leucine mutant to form amyloid were examined. Amyloid formation was almost twice as rapid for the F15L mutant as for the wild type but was almost 3-fold slower for the Y37L mutant and almost 2-fold slower for the F23L mutant. Amyloid fibrils formed from each of the single mutants were effective at seeding amyloid formation by wild-type IAPP, implying that the fibril structures are similar. The F15L/F23L double mutant has a larger effect than the F15L/Y37L double mutant on the rate of amyloid formation, even though a Y37L substitution has more drastic consequences in the wild-type background than does the F23L mutation, suggesting nonadditive effects between the different sites. The triple leucine mutant and the F23L/Y37L double mutant are the slowest to form amyloid. F15 has been proposed to make important contacts early in the aggregation pathway, but the data for the F15L mutant indicate that they are not optimal. A set of variants containing natural and unnatural amino acids at position 15, which were designed to conserve hydrophobicity, but alter α-helix and β-sheet propensity, were analyzed to determine the properties of this position that control the rate of amyloid formation. There is no correlation between β-sheet propensity at this position and the rate of amyloid formation, but there is a correlation with α-helical propensity.

One-step hydroprocessing of fatty acids into renewable aromatic hydrocarbons over Ni/HZSM-5: insights into the major reaction pathways.

PubMed

Xing, Shiyou; Lv, Pengmei; Wang, Jiayan; Fu, Junying; Fan, Pei; Yang, Lingmei; Yang, Gaixiu; Yuan, Zhenhong; Chen, Yong

2017-01-25

For high caloricity and stability in bio-aviation fuels, a certain content of aromatic hydrocarbons (AHCs, 8-25 wt%) is crucial. Fatty acids, obtained from waste or inedible oils, are a renewable and economic feedstock for AHC production. Considerable amounts of AHCs, up to 64.61 wt%, were produced through the one-step hydroprocessing of fatty acids over Ni/HZSM-5 catalysts. Hydrogenation, hydrocracking, and aromatization constituted the principal AHC formation processes. At a lower temperature, fatty acids were first hydrosaturated and then hydrodeoxygenated at metal sites to form long-chain hydrocarbons. Alternatively, the unsaturated fatty acids could be directly deoxygenated at acid sites without first being saturated. The long-chain hydrocarbons were cracked into gases such as ethane, propane, and C 6 -C 8 olefins over the catalysts' Brønsted acid sites; these underwent Diels-Alder reactions on the catalysts' Lewis acid sites to form AHCs. C 6 -C 8 olefins were determined as critical intermediates for AHC formation. As the Ni content in the catalyst increased, the Brønsted-acid site density was reduced due to coverage by the metal nanoparticles. Good performance was achieved with a loading of 10 wt% Ni, where the Ni nanoparticles exhibited a polyhedral morphology which exposed more active sites for aromatization.

Identification of microbial carotenoids and isoprenoid quinones from Rhodococcus sp. B7740 and its stability in the presence of iron in model gastric conditions.

PubMed

Chen, Yashu; Xie, Bijun; Yang, Jifang; Chen, Jigang; Sun, Zhida

2018-02-01

Rhodococcus sp. B7740 is a newfound bacterium which was isolated from 25m deep seawater in the arctic. In this paper, Rhodococcus sp. B7740 was firstly discovered to produce abundant natural isoprenoids, including ubiquinone-4(UQ-4), 13 kinds of menaquinones, three rare aromatic carotenoids and more than one common carotenoid. These compounds were identified by UV-Visible, HPLC-APCI-MS/MS and HRMS spectra. Results demonstrated that Rhodococcus sp. B7740 might be a worthy source of natural isoprenoids especially for scarce aromatic carotenoids. Among them, isorenieratene with 528.3762Da (calculated for 528.3756Da, error: 1.1ppm), a carotenoid with aromatic ring, was purified by HSCCC. The stability of isorenieratene under the mimical gastric conditions was measured compared with common dietary carotenoids, β-carotene and lutein. Unlike β-carotene and lutein, isorenieratene exhibited rather stable in the presence of free iron or heme iron. Its high retention rate in gastrointestinal tract after ingestion indicates the benefits for health. Copyright © 2017. Published by Elsevier Ltd.

Bioactive Compounds Derived from the Yeast Metabolism of Aromatic Amino Acids during Alcoholic Fermentation

PubMed Central

Guillamon, Jose Manuel; Torija, Maria Jesus; Beltran, Gemma; Troncoso, Ana M.; Garcia-Parrilla, M. Carmen

2014-01-01

Metabolites resulting from nitrogen metabolism in yeast are currently found in some fermented beverages such as wine and beer. Their study has recently attracted the attention of researchers. Some metabolites derived from aromatic amino acids are bioactive compounds that can behave as hormones or even mimic their role in humans and may also act as regulators in yeast. Although the metabolic pathways for their formation are well known, the physiological significance is still far from being understood. The understanding of this relevance will be a key element in managing the production of these compounds under controlled conditions, to offer fermented food with specific enrichment in these compounds or even to use the yeast as nutritional complements. PMID:24895623

Elucidation of reaction mechanism for m -cresol hydrodeoxygenation over Fe based catalysts: A kinetic study

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

Hong, Yongchun; Wang, Yong

Fe based catalysts are promising for hydrodeoxygenation (HDO) of lignin derived phenolics due to their high selectivity for aromatics. In this work, the reaction mechanism of m-cresol HDO on Fe catalysts and the kinetic consequence with Pd addition were elucidated by examining the effect of H2, H2O and m-cresol pressures on toluene formation rate on Fe and PdFe catalysts. A direct CO bond cleavage mechanism is proposed for HDO catalysis on both Fe and PdFe catalysts, while Pd provides a facilitated reaction pathway at the PdFe interface and therefore promotes the catalysis on Fe without changing the high selectivity towardsmore » aromatics.« less

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

IDENTIFICATION AND QUANTITATION OF BENZO[A]PYRENE DERIVED DNA ADDUCTS FORMED AT LOW ADDUCTION LEVEL IN MICE LUNG TISSUE

EPA Science Inventory

The two major metabolic pathways of benzo[a]pyrene (BP), as well as other polycyclic aromatic hydrocarbons, that allow for the induction of DNA lesions are monooxygenation that results in diol epoxides (BPDE), and one-electron oxidation that yields a BP radical cation. The DNA ad...

Tuning dispersion correction in DFT-D2 for metal-molecule interactions: A tailored reparameterization strategy for the adsorption of aromatic systems on Ag(1 1 1)

NASA Astrophysics Data System (ADS)

Schiavo, Eduardo; Muñoz-García, Ana B.; Barone, Vincenzo; Vittadini, Andrea; Casarin, Maurizio; Forrer, Daniel; Pavone, Michele

2018-02-01

Common local and semi-local density functionals poorly describe the molecular physisorption on metal surfaces due to the lack of dispersion interactions. In the last decade, several correction schemes have been proposed to amend this fundamental flaw of Density Functional Theory. Using the prototypical case of aromatic molecules adsorbed on Ag(1 1 1), we discuss the accuracy of different dispersion-correction methods and present a reparameterization strategy for the simple and effective DFT-D2. For the adsorption of different aromatic systems on the same metallic substrate, good results at feasible computational costs are achieved by means of a fitting procedure against MP2 data.

Investigation of Source of Irritant Gas Produced by PATRIOT Missile System Air Conditioners

DTIC Science & Technology

1986-03-31

is the mass fragment CF3 . It is a common fragment of perfluorinated hydrocarbons, and is found to be present in most of the compounds detected by...used would allow detection of the target par3meters acrolein, aromatics, a broad range of organic compounds ,. formaldehyde, and hydrogen cyanide...organic compounds were observed. Thus, aromatic organic compounds were not produced by or from any of the four new units tested. 4 1CZ 3) With the

New and Improved Methods of Production of Energy Rich Materials

DTIC Science & Technology

1990-11-01

present in its molecular form (with some N2 03 also present). In acid solutions above 60-65% concentration it is present as nitrosonium ions . In an excess...Electrophilic Aromatic Nitration b~y the Nitronium Ion 1.2 Effect of Nitrous Acid 1.3 Nitration of Carbazoic. 1.4 Nitration of Dibenzothiophene -1.5...HLt~ron i un Ion The nitration -of aromatic compounds can he, achieved in a variety of media. Mixed acid nitration is the most common type used in

Development of multi-membrane near-infrared diode mass spectrometer for field analysis of aromatic hydrocarbons.

PubMed

Mach, Phillip M; Wright, Kenneth C; Verbeck, Guido F

2015-02-01

Membrane Inlet Mass Spectrometry (MIMS) is a technique that incorporates a semi-permeable membrane selective for differing organic molecules and chemistries. This eliminates the need for time-consuming sample preparation and facilitates near instantaneous analysis. This study will examine how the front end of MIMS incorporates three dual inlet ports, allowing for differing MIMS materials and selectivity for specific environments. Polydimethylsiloxane (PDMS) membranes have proven to be selective of benzene, toluene, and xylene (BTX) as well as aromatic hydrocarbons that are common in petroleum products while remaining selective against the aliphatic chains. PDMS has proven to be a successful choice of membrane with high permeability in atmospheric environments. In addition, polycyclic aromatic hydrocarbons (PAHs) such as acenaphthene, acenapthylene, naphthalene, and fluorene have recently been detected to the 5 ppb level in a nitrogen atmosphere with our current configuration. This preliminary work provides proof of concept using near-infrared laser diodes that act upon the membrane to increase its permeability and provide higher sensitivity of aromatic samples.

Effectiveness of Liquid-Liquid Extraction, Solid Phase Extraction, and Headspace Technique for Determination of Some Volatile Water-Soluble Compounds of Rose Aromatic Water

PubMed Central

2017-01-01

Steam distillation is used to isolate scent of rose flowers. Rose aromatic water is commonly used in European cuisine and aromatherapy besides its use in cosmetic industry for its lovely scent. In this study, three different sampling techniques, liquid-liquid extraction (LLE), headspace technique (HS), and solid phase extraction (SPE), were compared for the analysis of volatile water-soluble compounds in commercial rose aromatic water. Some volatile water-soluble compounds of rose aromatic water were also analyzed by gas chromatography mass spectrometry (GCMS). In any case, it was concluded that one of the solid phase extraction methods led to higher recoveries for 2-phenylethyl alcohol (PEA) in the rose aromatic water than the liquid-liquid extraction and headspace technique. Liquid-liquid extraction method provided higher recovery ratios for citronellol, nerol, and geraniol than others. Ideal linear correlation coefficient values were observed by GCMS for quantitative analysis of volatile compounds (r2 ≥ 0.999). Optimized methods showed acceptable repeatability (RSDs < 5%) and excellent recovery (>95%). For compounds such as α-pinene, linalool, β-caryophyllene, α-humulene, methyl eugenol, and eugenol, the best recovery values were obtained with LLE and SPE. PMID:28791049

Aromatic Polyketide GTRI-02 is a Previously Unidentified Product of the act Gene Cluster in Streptomyces coelicolor A3(2).

PubMed

Wu, Changsheng; Ichinose, Koji; Choi, Young Hae; van Wezel, Gilles P

2017-07-18

The biosynthesis of aromatic polyketides derived from type II polyketide synthases (PKSs) is complex, and it is not uncommon that highly similar gene clusters give rise to diverse structural architectures. The act biosynthetic gene cluster (BGC) of the model actinomycete Streptomyces coelicolor A3(2) is an archetypal type II PKS. Here we show that the act BGC also specifies the aromatic polyketide GTRI-02 (1) and propose a mechanism for the biogenesis of its 3,4-dihydronaphthalen-1(2H)-one backbone. Polyketide 1 was also produced by Streptomyces sp. MBT76 after activation of the act-like qin gene cluster by overexpression of the pathway-specific activator. Mining of this strain also identified dehydroxy-GTRI-02 (2), which most likely originated from dehydration of 1 during the isolation process. This work shows that even extensively studied model gene clusters such as act of S. coelicolor can still produce new chemistry, offering new perspectives for drug discovery. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Secondary organic aerosol formation through cloud processing of aromatic VOCs

NASA Astrophysics Data System (ADS)

Herckes, P.; Hutchings, J. W.; Ervens, B.

2010-12-01

Field observations have shown substantial concentrations (20-5,500 ng L-1) of aromatic volatile organic compounds (VOC) in cloud droplets. The potential generation of secondary organic aerosol mass through the processing of these anthropogenic VOCs was investigated through laboratory and modeling studies. Under simulated atmospheric laboratory conditions, in idealized solutions, benzene, toluene, ethylbenzene, and xylene (BTEX) degraded quickly in the aqueous phase. The degradation process yielded less volatile products which would contribute to new aerosol mass upon cloud evaporation. However, when realistic cloud solutions containing natural organic matter were used in the experiments, the reaction rates decreased with increasing organic carbon content. Kinetic data derived from these experiments were used as input to a multiphase box model in order to evaluate the secondary organic aerosol (SOA) mass formation potential of cloud processing of BTEX. Model results will be presented that quantify the SOA amounts from these aqueous phase pathways. The efficiency of this multiphase SOA source will be compared to SOA yields from the same aromatics as treated in traditional SOA models that are restricted to gas phase oxidation and subsequent condensation on particles.

Cloning and heterologous expression of two aryl-aldehyde dehydrogenases from the white-rot basidiomycete Phanerochaete chrysosporium

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

Nakamura, Tomofumi; Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu-shi, Fukuoka 818-0135; Ichinose, Hirofumi

2010-04-09

We identified two aryl-aldehyde dehydrogenase proteins (PcALDH1 and PcALDH2) from the white-rot basidiomycete Phanerochaete chrysosporium. Both PcALDHs were translationally up-regulated in response to exogenous addition of vanillin, one of the key aromatic compounds in the pathway of lignin degradation by basidiomycetes. To clarify the catalytic functions of PcALDHs, we isolated full-length cDNAs encoding these proteins and heterologously expressed the recombinant enzymes using a pET/Escherichia coli system. The open reading frames of both PcALDH1 and PcALDH2 consisted of 1503 nucleotides. The deduced amino acid sequences of both proteins showed high homologies with aryl-aldehyde dehydrogenases from other organisms and contained ten conservedmore » domains of ALDHs. Moreover, a novel glycine-rich motif 'GxGxxxG' was located at the NAD{sup +}-binding site. The recombinant PcALDHs catalyzed dehydrogenation reactions of several aryl-aldehyde compounds, including vanillin, to their corresponding aromatic acids. These results strongly suggested that PcALDHs metabolize aryl-aldehyde compounds generated during fungal degradation of lignin and various aromatic xenobiotics.« less

Effect of iodide on transformation of phenolic compounds by nonradical activation of peroxydisulfate in the presence of carbon nanotube: Kinetics, impacting factors, and formation of iodinated aromatic products.

PubMed

Guan, Chaoting; Jiang, Jin; Pang, Suyan; Luo, Congwei; Yang, Yi; Ma, Jun; Yu, Jing; Zhao, Xi

2018-06-04

Our recent study has demonstrated that iodide (I - ) can be easily and almost entirely oxidized to hypoiodous acid (HOI) but not to iodate by nonradical activation of peroxydisulfate (PDS) in the presence of a commercial carbon nanotube (CNT). In this work, the oxidation kinetics of phenolic compounds by the PDS/CNT system in the presence of I - were examined and potential formation of iodinated aromatic products was explored. Experimental results suggested that I - enhanced the transformation of six selected substituted phenols, primarily attributed to the generation of HOI that was considerably reactive toward these phenolic compounds. More significant enhancement was obtained at higher I - concentrations or lower pH values, while the change of PDS or CNT dosages exhibited a slight impact on the enhancing effect of I - . Product analyses with liquid chromatography tandem mass spectrometry clearly revealed the production of iodinated aromatic products when p-hydroxybenzoic acid (p-HBA, a model phenol) was treated by the PDS/CNT/I - system in both synthetic and real waters. Their formation pathways probably involved the substitution of HOI on aromatic ring of p-HBA, as well as the generation of iodinated p-HBA phenoxyl radicals and subsequent coupling of these radicals. Given the considerable toxicity and harmful effects of these iodinated aromatic products, particular attention should be paid when the novel PDS/CNT oxidation technology is applied for treatment of phenolic contaminants in iodide-containing waters. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

Polycyclic aromatic hydrocarbons and cytochrome P450 in HIV pathogenesis

PubMed Central

Rao, P. S. S.; Kumar, Santosh

2015-01-01

High prevalence of cigarette smoking in HIV patients is associated with increased HIV pathogenesis and disease progression. While the effect of smoking on the occurrence of lung cancer has been studied extensively, the association between smoking and HIV pathogenesis is poorly studied. We have recently shown the possible role of cytochrome P450 (CYP) in smoking/nicotine-mediated viral replication. In this review, we focus on the potential role of CYP pathway in polycyclic aromatic hydrocarbons (PAH), important constituents of cigarette smoke, mediated HIV pathogenesis. More specifically, we will discuss the role of CYP1A1 and CYP1B1, which are the major PAH-activating CYP enzymes. Our results have shown that treatment with cigarette smoke condensate (CSC) increases viral replication in HIV-infected macrophages. CSC contains PAH, which are known to be activated by CYP1A1 and CYP1B1 into procarcinogens/toxic metabolites. The expression of these CYPs is regulated by aryl hydrocarbon receptors (AHR), the cellular target of PAH, and an important player in various diseases including cancer. We propose that PAH/AHR-mediated CYP pathway is a novel target to develop new interventions for HIV positive smokers. PMID:26082767

In situ {sup 13}C MAS NMR study of n-hexane conversion on Pt and Pd supported on basic materials

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

Ivanova, I.I.; Pasau-Claerbout, A.; Seivert, M.

n-Hexane conversion was studied in situ on Pt and Pd supported on aluminum-stabilized magnesium oxide and Pt on Zeolite KL catalysts (Pt/Mg(Al)O, Pd/Mg(Al)O and Pt/KL) by means of {sup 13}C MAS NMR spectroscopy. n-Hexane 1-{sup 13}C was used as a labelled reactant. Forty NMR lines corresponding to 14 different products were resolved and identified. The NMR line assignments were confirmed by adsorption of model compounds. The NMR results were further quantified and compared with continuous flow microreactor tests. Four parallel reaction pathways were identified under flow conditions: isomerization, cracking, dehydrocyclization, and dehydrogenation. Aromatization occurs via two reaction routes: (1) n-hexanemore » dehydrogenation towards hexadienes and hexatrienes, followed by dehydrogenation of a cyclic intermediate. The former reaction pathway is prevented under NMR batch conditions. High pressures induced in the NMR cells at high reaction temperatures (573, 653 K) shift the reaction equilibrium towards hydrogenation. NMR experiments showed that on Pt catalysts aromatization occurs via a cyclohexane intermediate, whereas on Pd it takes place via methylcyclopentane ring enlargement. 54 refs., 15 figs., 3 tabs.« less

Roles of Ring-Hydroxylating Dioxygenases in Styrene and Benzene Catabolism in Rhodococcus jostii RHA1▿ †

PubMed Central

Patrauchan, Marianna A.; Florizone, Christine; Eapen, Shawn; Gómez-Gil, Leticia; Sethuraman, Bhanu; Fukuda, Masao; Davies, Julian; Mohn, William W.; Eltis, Lindsay D.

2008-01-01

Proteomics and targeted gene disruption were used to investigate the catabolism of benzene, styrene, biphenyl, and ethylbenzene in Rhodococcus jostii RHA1, a well-studied soil bacterium whose potent polychlorinated biphenyl (PCB)-transforming properties are partly due to the presence of the related Bph and Etb pathways. Of 151 identified proteins, 22 Bph/Etb proteins were among the most abundant in biphenyl-, ethylbenzene-, benzene-, and styrene-grown cells. Cells grown on biphenyl, ethylbenzene, or benzene contained both Bph and Etb enzymes and at least two sets of lower Bph pathway enzymes. By contrast, styrene-grown cells contained no Etb enzymes and only one set of lower Bph pathway enzymes. Gene disruption established that biphenyl dioxygenase (BPDO) was essential for growth of RHA1 on benzene or styrene but that ethylbenzene dioxygenase (EBDO) was not required for growth on any of the tested substrates. Moreover, whole-cell assays of the ΔbphAa and etbAa1::cmrA etbAa2::aphII mutants demonstrated that while both dioxygenases preferentially transformed biphenyl, only BPDO transformed styrene. Deletion of pcaL of the β-ketoadipate pathway disrupted growth on benzene but not other substrates. Thus, styrene and benzene are degraded via meta- and ortho-cleavage, respectively. Finally, catalases were more abundant during growth on nonpolar aromatic compounds than on aromatic acids. This suggests that the relaxed specificities of BPDO and EBDO that enable RHA1 to grow on a range of compounds come at the cost of increased uncoupling during the latter's initial transformation. The stress response may augment RHA1's ability to degrade PCBs and other pollutants that induce similar uncoupling. PMID:17965160

Multifaceted regulations of gateway enzyme phenylalanine ammonia-lyase in the biosynthesis of phenylpropanoids

DOE PAGES

Zhang, Xuebin; Liu, Chang-Jun

2014-12-11

Phenylpropanoid biosynthesis in plants engenders a vast variety of aromatic metabolites critically important for their growth, development, and environmental adaptation. Some of these aromatic compounds have high economic value. Phenylalanine ammonia-lyase (PAL) is the first committed enzyme in the pathway; it diverts the central flux of carbon from primary metabolism to the synthesis of myriad phenolics. Over the decades, many studies have shown that exquisite regulatory mechanisms at multiple levels control the transcription and the enzymatic activity of PALs. In this review, we present a current overview on our understanding of the complicated regulatory mechanisms governing PAL's activity; we particularlymore » highlight recent progresses in unraveling its post-translational modifications, its metabolite feedback regulation, and its enzyme organization.« less

Multifaceted regulations of gateway enzyme phenylalanine ammonia-lyase in the biosynthesis of phenylpropanoids

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

Zhang, Xuebin; Liu, Chang-Jun

Phenylpropanoid biosynthesis in plants engenders a vast variety of aromatic metabolites critically important for their growth, development, and environmental adaptation. Some of these aromatic compounds have high economic value. Phenylalanine ammonia-lyase (PAL) is the first committed enzyme in the pathway; it diverts the central flux of carbon from primary metabolism to the synthesis of myriad phenolics. Over the decades, many studies have shown that exquisite regulatory mechanisms at multiple levels control the transcription and the enzymatic activity of PALs. In this review, we present a current overview on our understanding of the complicated regulatory mechanisms governing PAL's activity; we particularlymore » highlight recent progresses in unraveling its post-translational modifications, its metabolite feedback regulation, and its enzyme organization.« less

Photoionization of Benzene and Small Polycyclic Aromatic Hydrocarbons in Ultraviolet-Processed Astrophysical Ices: A Computational Study

NASA Technical Reports Server (NTRS)

Woon, D. E.; Park, J.-Y.

2004-01-01

We employed density functional theory (DFT) calculations to model the photoionization behavior of benzene and small polycyclic aromatic hydrocarbons when they are embedded in a matrix of water ice in order to investigate issues raised by recent experimental work by Gudipati and Allamandola. The ionization energies of benzene, naphthalene, anthracene, and pyrene were found to be lowered by 1.5-2.1 eV in water ice. Low-lying vertical electronic excitation energies were computed with time-dependent DFT for both neutral and ionized species and are found in both cases to be remarkably unaffected by the ice matrix. Chemical behavior in ultraviolet-photoprocessed ices is also discussed, with a focus on electron recombination and pathways leading to phenol and analogous products.

Bio-based production of monomers and polymers by metabolically engineered microorganisms.

PubMed

Chung, Hannah; Yang, Jung Eun; Ha, Ji Yeon; Chae, Tong Un; Shin, Jae Ho; Gustavsson, Martin; Lee, Sang Yup

2015-12-01

Recent metabolic engineering strategies for bio-based production of monomers and polymers are reviewed. In the case of monomers, we describe strategies for producing polyamide precursors, namely diamines (putrescine, cadaverine, 1,6-diaminohexane), dicarboxylic acids (succinic, glutaric, adipic, and sebacic acids), and ω-amino acids (γ-aminobutyric, 5-aminovaleric, and 6-aminocaproic acids). Also, strategies for producing diols (monoethylene glycol, 1,3-propanediol, and 1,4-butanediol) and hydroxy acids (3-hydroxypropionic and 4-hydroxybutyric acids) used for polyesters are reviewed. Furthermore, we review strategies for producing aromatic monomers, including styrene, p-hydroxystyrene, p-hydroxybenzoic acid, and phenol, and propose pathways to aromatic polyurethane precursors. Finally, in vivo production of polyhydroxyalkanoates and recombinant structural proteins having interesting applications are showcased. Copyright © 2015 Elsevier Ltd. All rights reserved.

Brain aromatase: roles in reproduction and neuroprotection.

PubMed

Roselli, Charles F

2007-01-01

It is well established that aromatization constitutes an essential part of testosterone's signaling pathway in brain and that estrogen metabolites, often together with testosterone, organize and activate masculine neural circuits. This paper summarizes the current understanding regarding the distribution, regulation and function of brain aromatase in mammals. Data from our laboratory are presented that highlight the important function of aromatase in the regulation of androgen feedback sensitivity in non-human primates and the possible role that aromatase plays in determining the brain structure and sexual partner preferences of rams. In addition, new data is presented indicating that the capacity for aromatization in cortical astrocytes is associated with cell survival and may be important for neuroprotection. It is anticipated that a better appreciation of the physiological and pathophysiological functions of aromatase will lead to important clinical insights.

Relationship between chemical composition and oxidative potential of secondary organic aerosol from polycyclic aromatic hydrocarbons

NASA Astrophysics Data System (ADS)

Wang, Shunyao; Ye, Jianhuai; Soong, Ronald; Wu, Bing; Yu, Legeng; Simpson, André J.; Chan, Arthur W. H.

2018-03-01

Owing to the complex nature and dynamic behaviors of secondary organic aerosol (SOA), its ability to cause oxidative stress (known as oxidative potential, or OP) and adverse health outcomes remains poorly understood. In this work, we probed the linkages between the chemical composition of SOA and its OP, and investigated impacts from various SOA evolution pathways, including atmospheric oligomerization, heterogeneous oxidation, and mixing with metal. SOA formed from photooxidation of the two most common polycyclic aromatic hydrocarbons (naphthalene and phenanthrene) were studied as model systems. OP was evaluated using the dithiothreitol (DTT) assay. The oligomer-rich fraction separated by liquid chromatography dominates DTT activity in both SOA systems (52 ± 10 % for naphthalene SOA (NSOA), and 56 ± 5 % for phenanthrene SOA (PSOA)). Heterogeneous ozonolysis of NSOA was found to enhance its OP, which is consistent with the trend observed in selected individual oxidation products. DTT activities from redox-active organic compounds and metals were found to be not additive. When mixing with highly redox-active metal (Cu), OP of the mixture decreased significantly for 1,2-naphthoquinone (42 ± 7 %), 2,3-dihydroxynaphthalene (35 ± 1 %), NSOA (50 ± 6 %), and PSOA (43 ± 4 %). Evidence from proton nuclear magnetic resonance (1H NMR) spectroscopy illustrates that such OP reduction upon mixing can be ascribed to metal-organic binding interactions. Our results highlight the role of aerosol chemical composition under atmospheric aging processes in determining the OP of SOA, which is needed for more accurate and explicit prediction of the toxicological impacts from particulate matter.

Polycyclic Aromatic Hydrocarbons and digestive tract cancers - a perspective

PubMed Central

Diggs, Deacqunita L.; Huderson, Ashley C.; Harris, Kelly L.; Myers, Jeremy N.; Banks, Leah D.; Rekhadevi, Perumalla V.; Niaz, Mohammad S.; Ramesh, Aramandla

2011-01-01

Cancers of the colon are most common in the Western world. In majority of these cases, there is no familial history and sporadic gene damage seems to play an important role in the development of tumors in the colon. Studies have shown that environmental factors, especially diet, play an important role in susceptibility to GI tract cancers. Consequently, environmental chemicals that contaminate food or diet during its preparation becomes important in the development of GI cancers. Polycyclic aromatic hydrocarbons (PAHs) are one such family of ubiquitous environmental toxicants. These pollutants enter the human body through consumption of contaminated food, drinking water, inhalation of cigarette smoke, automobile exhausts, and contaminated air from occupational settings. Among these pathways, dietary intake of PAHs constitutes a major source of exposure in humans. Although many reviews and books on PAHs and their ability to cause toxicity and breast or lung cancer have been published, aspects on contribution of diet, smoking and other factors towards development of digestive tract cancers and strategies to assess risk from exposure to PAHs have received much less attention. This review, therefore, focuses on dietary intake of PAHs in humans, animal models, and cell cultures used for GI cancer studies along with epidemiological findings. Bioavailability and biotransformation processes, which influence the disposition of PAHs in body and the underlying causative mechanisms of GI cancers, are also discussed. The existing data gaps and scope for future studies is also emphasized. This information is expected to stimulate research on mechanisms of sporadic GI cancers caused by exposure to environmental carcinogens. PMID:22107166

Evolution of interstellar organic compounds under asteroidal hydrothermal conditions

NASA Astrophysics Data System (ADS)

Vinogradoff, V.; Bernard, S.; Le Guillou, C.; Remusat, L.

2018-05-01

Carbonaceous chondrites (CC) contain a diversity of organic compounds. No definitive evidence for a genetic relationship between these complex organic molecules and the simple organic molecules detected in the interstellar medium (ISM) has yet been reported. One of the many difficulties arises from the transformations of organic compounds during accretion and hydrothermal alteration on asteroids. Here, we report results of hydrothermal alteration experiments conducted on a common constituent of interstellar ice analogs, Hexamethylenetetramine (HMT - C6H12N4). We submitted HMT to asteroidal hydrothermal conditions at 150 °C, for various durations (up to 31 days) and under alkaline pH. Organic products were characterized by gas chromatography mass spectrometry, infrared spectroscopy and synchrotron-based X-ray absorption near edge structure spectroscopy. Results show that, within a few days, HMT has evolved into (1) a very diverse suite of soluble compounds dominated by N-bearing aromatic compounds (> 150 species after 31 days), including for instance formamide, pyridine, pyrrole and their polymers (2) an aromatic and N-rich insoluble material that forms after only 7 days of experiment and then remains stable through time. The reaction pathways leading to the soluble compounds likely include HMT dissociation, formose and Maillard-type reactions, e.g. reactions of sugar derivatives with amines. The present study demonstrates that, if interstellar organic compounds such as HMT had been accreted by chondrite parent bodies, they would have undergone chemical transformations during hydrothermal alteration, potentially leading to the formation of high molecular weight insoluble organic molecules. Some of the diversity of soluble and insoluble organic compounds found in CC may thus result from asteroidal hydrothermal alteration.

Solubilization of aromatic and hydrophobic moieties by arginine in aqueous solutions

NASA Astrophysics Data System (ADS)

Li, Jianguo; Garg, Manju; Shah, Dhawal; Rajagopalan, Raj

2010-08-01

Experiments hold intriguing, circumstantial clues to the mechanisms behind arginine-mediated solubilization of small organic drugs and suppression of protein aggregation driven by hydrophobic or aromatic associations, but how exactly arginine's molecular structure and interactions contribute to its function remains unclear since attention has focused so far on the thermodynamics of the preferential exclusion or binding of arginine. Here, we examine, through molecular dynamics simulations, how arginine solubilizes nanoscale particles with hydrophobic surfaces or aromatic-ring-type surface interactions. We show that preferential, hydrophobic, and dispersion interactions of arginine's guanidinium group with the particles lead to a surfactant-like behavior of arginine around the particles and to a solvation layer with a protective polar mask creating a hydrophilic shell. Additionally, arginine-arginine association around the solvation layer further prevents aggregative contacts. The results shed some light on the mechanistic basis of arginine's function as a suppressant of protein aggregation, although the complex energy landscapes and kinetic pathways of aggregation are protein-dependent and pose formidable challenges to developing comprehensive mechanistic pictures. Our results suggest arginine's mode of interaction with hydrophobic patches and aromatic residues could reduce aggregation-prone intermediate states of proteins and shield protein-protein aggregative contacts. The approach used here offers a systematic way of exploring implications of other amino acid/excipient interactions by studying interactions of the excipient with particles grafted with amino acids.

Environmental temperature effect on the far-infrared absorption features of aromatic-based Titan's aerosol analogs

NASA Astrophysics Data System (ADS)

Gautier, Thomas; Trainer, Melissa G.; Loeffler, Mark J.; Sebree, Joshua A.; Anderson, Carrie M.

2017-01-01

Benzene detection has been reported in Titan's atmosphere both in the stratosphere at ppb levels by remote sensing (Coustenis et al., 2007; Vinatier et al., 2007) and in the thermosphere at ppm levels by the Cassini's Ion and Neutral Mass Spectrometer (Waite et al., 2007). This detection supports the idea that aromatic and heteroaromatic reaction pathways may play an important role in Titan's atmospheric chemistry, especially in the formation of aerosols. Indeed, aromatic molecules are easily dissociated by ultraviolet radiation and can therefore contribute significantly to aerosol formation. It has been shown recently that aerosol analogs produced from a gas mixture containing a low concentration of aromatic and/or heteroaromatic molecules (benzene, naphthalene, pyridine, quinoline and isoquinoline) have spectral signatures below 500 cm-1, a first step towards reproducing the aerosol spectral features observed by Cassini's Composite InfraRed Spectrometer (CIRS) in the far infrared (Anderson and Samuelson 2011, and references therein). In this work we investigate the influence of environmental temperature on the absorption spectra of such aerosol samples, simulating the temperature range to which aerosols, once formed, are exposed during their transport through Titan's stratosphere. Our results show that environmental temperature does not have any major effect on the spectral shape of these aerosol analogs in the far-infrared, which is consistent with the CIRS observations.

The Impact of Single Amino Acids on Growth and Volatile Aroma Production by Saccharomyces cerevisiae Strains

PubMed Central

Fairbairn, Samantha; McKinnon, Alexander; Musarurwa, Hannibal T.; Ferreira, António C.; Bauer, Florian F.

2017-01-01

Nitrogen availability and utilization by Saccharomyces cerevisiae significantly influence fermentation kinetics and the production of volatile compounds important for wine aroma. Amino acids are the most important nitrogen source and have been classified based on how well they support growth. This study evaluated the effect of single amino acids on growth kinetics and major volatile production of two phenotypically different commercial wine yeast strains in synthetic grape must. Four growth parameters, lag phase, maximum growth rate, total biomass formation and time to complete fermentation were evaluated. In contrast with previous findings, in fermentative conditions, phenylalanine and valine supported growth well and asparagine supported it poorly. The four parameters showed good correlations for most amino acid treatments, with some notable exceptions. Single amino acid treatments resulted in the predictable production of aromatic compounds, with a linear correlation between amino acid concentration and the concentration of aromatic compounds that are directly derived from these amino acids. With the increased complexity of nitrogen sources, linear correlations were lost and aroma production became unpredictable. However, even in complex medium minor changes in amino acid concentration continued to directly impact the formation of aromatic compounds, suggesting that the relative concentration of individual amino acids remains a predictor of aromatic outputs, independently of the complexity of metabolic interactions between carbon and nitrogen metabolism and between amino acid degradation and utilization pathways. PMID:29312237

The Impact of Single Amino Acids on Growth and Volatile Aroma Production by Saccharomyces cerevisiae Strains.

PubMed

Fairbairn, Samantha; McKinnon, Alexander; Musarurwa, Hannibal T; Ferreira, António C; Bauer, Florian F

2017-01-01

Nitrogen availability and utilization by Saccharomyces cerevisiae significantly influence fermentation kinetics and the production of volatile compounds important for wine aroma. Amino acids are the most important nitrogen source and have been classified based on how well they support growth. This study evaluated the effect of single amino acids on growth kinetics and major volatile production of two phenotypically different commercial wine yeast strains in synthetic grape must. Four growth parameters, lag phase, maximum growth rate, total biomass formation and time to complete fermentation were evaluated. In contrast with previous findings, in fermentative conditions, phenylalanine and valine supported growth well and asparagine supported it poorly. The four parameters showed good correlations for most amino acid treatments, with some notable exceptions. Single amino acid treatments resulted in the predictable production of aromatic compounds, with a linear correlation between amino acid concentration and the concentration of aromatic compounds that are directly derived from these amino acids. With the increased complexity of nitrogen sources, linear correlations were lost and aroma production became unpredictable. However, even in complex medium minor changes in amino acid concentration continued to directly impact the formation of aromatic compounds, suggesting that the relative concentration of individual amino acids remains a predictor of aromatic outputs, independently of the complexity of metabolic interactions between carbon and nitrogen metabolism and between amino acid degradation and utilization pathways.

Effects of aromatic amino acids, phenylacetate and phenylpropionate on fermentation of xylan by the rumen anaerobic fungi, Neocallimastix frontalis and Piromyces communis.

PubMed

Guliye, A Y; Wallace, R J

2007-10-01

Anaerobic fungi are important members of the fibrolytic community of the rumen. The aim of this study was to study their requirement for aromatic amino acids (AA) and related phenyl acids (phenylpropionic and phenylacetic acids) for optimal xylan fermentation. Neocallimastix frontalis RE1 and Piromyces communis P were grown in a defined medium containing oat spelts xylan as the sole energy source, plus one of the following N sources: ammonia; ammonia plus a complete mixture of 20 AA commonly found in protein; ammonia plus complete AA mixture minus aromatic AA; ammonia plus phenyl acids; ammonia plus complete AA mixture without aromatic AA plus phenyl acids. Both species grew in all the media, indicating no absolute requirement for AA. The complete AA mixture increased (P<0.05) acetate concentration by 18% and 15%, sugar utilization by 33% and 22% and microbial yield by about 22% and 15% in N. frontalis and P. communis, respectively, in comparison with the treatments that had ammonia as the only N source. Neither the supply of aromatic AA or phenol acids, nor their deletion from the complete AA mixture, affected the fermentation rate, products or yield of either species. AA were not essential for N. frontalis and P. communis, but their growth on xylan was stimulated. The effects could not be explained in terms of aromatic AA alone. Ruminant diets should contain sufficient protein to sustain optimal fibre digestion by ruminal fungi. Aromatic AA or phenyl acids alone cannot replace the complete AA mixture.

Arbuscular mycorrhizal fungi and plant growth-promoting pseudomonads increases anthocyanin concentration in strawberry fruits (Fragaria x ananassa var. Selva) in conditions of reduced fertilization.

PubMed

Lingua, Guido; Bona, Elisa; Manassero, Paola; Marsano, Francesco; Todeschini, Valeria; Cantamessa, Simone; Copetta, Andrea; D'Agostino, Giovanni; Gamalero, Elisa; Berta, Graziella

2013-08-06

Anthocyanins are a group of common phenolic compounds in plants. They are mainly detected in flowers and fruits, are believed to play different important roles such as in the attraction of animals and seed dispersal, and also in the increase of the antioxidant response in tissues directly or indirectly affected by biotic or abiotic stress factors. As a major group of secondary metabolites in plants commonly consumed as food, they are of importance in both the food industry and human nutrition. It is known that arbuscular mycorrhizal (AM) fungi can influence the plant secondary metabolic pathways such as the synthesis of essential oils in aromatic plants, of secondary metabolites in roots, and increase flavonoid concentration. Plant Growth-Promoting Bacteria (PGPB) are able to increase plant growth, improving plant nutrition and supporting plant development under natural or stressed conditions. Various studies confirmed that a number of bacterial species living on and inside the root system are beneficial for plant growth, yield and crop quality. In this work it is shown that inoculation with AM fungi and/or with selected and tested Pseudomonas strains, under conditions of reduced fertilization, increases anthocyanin concentration in the fruits of strawberry.

Arbuscular Mycorrhizal Fungi and Plant Growth-Promoting Pseudomonads Increases Anthocyanin Concentration in Strawberry Fruits (Fragaria x ananassa var. Selva) in Conditions of Reduced Fertilization

PubMed Central

Lingua, Guido; Bona, Elisa; Manassero, Paola; Marsano, Francesco; Todeschini, Valeria; Cantamessa, Simone; Copetta, Andrea; D’Agostino, Giovanni; Gamalero, Elisa; Berta, Graziella

2013-01-01

Anthocyanins are a group of common phenolic compounds in plants. They are mainly detected in flowers and fruits, are believed to play different important roles such as in the attraction of animals and seed dispersal, and also in the increase of the antioxidant response in tissues directly or indirectly affected by biotic or abiotic stress factors. As a major group of secondary metabolites in plants commonly consumed as food, they are of importance in both the food industry and human nutrition. It is known that arbuscular mycorrhizal (AM) fungi can influence the plant secondary metabolic pathways such as the synthesis of essential oils in aromatic plants, of secondary metabolites in roots, and increase flavonoid concentration. Plant Growth-Promoting Bacteria (PGPB) are able to increase plant growth, improving plant nutrition and supporting plant development under natural or stressed conditions. Various studies confirmed that a number of bacterial species living on and inside the root system are beneficial for plant growth, yield and crop quality. In this work it is shown that inoculation with AM fungi and/or with selected and tested Pseudomonas strains, under conditions of reduced fertilization, increases anthocyanin concentration in the fruits of strawberry. PMID:23924942

PAH-Mineral Interactions. A Laboratory Approach to Astrophysical Catalysis

NASA Astrophysics Data System (ADS)

Adolfo Cruz Diaz, Gustavo; Mattioda, Andrew

2017-06-01

Polycyclic Aromatic Hydrocarbon (PAH) molecules carry the infrared emission features which dominate the spectra of most galactic and extragalactic sources. Our study investigates the chemical evolution, chemical properties, physical properties, thermal stability, and photostability of samples produced from the UV-irradiation of simulated mineral dust grains coated with aromatics and astrobiologically relevant ices, using infrared spectroscopy. We investigate the chemical evolution of aromatic organics via anhydrous (no H2O ice) and hydrous (H2O ice) mechanisms. The anhydrous mechanism involves UV-induced catalytic reactions between organics and dense-cloud mineral grains, whereas the hydrous mechanism incorporates H2O-rich ice mixtures with the minerals and organics. These investigations identify the chemical and physical interactions occurring between the organic species, the dust grains and water-rich ices.These laboratory simulations also generate observable IR spectroscopic parameters for future astronomical observations with infrared telescopes such as SOFIA and JWST as well as provide empirical parameters for input into astronomical models of the early stages of planetary formation. These studies give us a deeper understanding of the potential catalytic pathways mineral surfaces provide and a deeper understanding of the role of ice-organic compositions in the chemical reaction pathways and how these processes fit into the formation of new planetary systems.In order to achieve these goals we use the Harrick ‘Praying Mantis’ Diffuse Reflectance Accessory (DRIFTS), which allows FTIR measurements of dust samples under ambient conditions by measuring the light scattered by the dust sample. We have also incorporated a low -temperature reaction chamber permitting the DRIFTS measurements at low temperatures and high-vacuum. This set-up permits the analysis of the solid particles surfaces revealing the chemical species adsorbed as well as their chemical evolution via the introduction of reactant gases, UV irradiation, temperature change, etc.

Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus

PubMed Central

Holmes, Dawn E; Risso, Carla; Smith, Jessica A; Lovley, Derek R

2012-01-01

Insight into the mechanisms for the anaerobic metabolism of aromatic compounds by the hyperthermophilic archaeon Ferroglobus placidus is expected to improve understanding of the degradation of aromatics in hot (>80° C) environments and to identify enzymes that might have biotechnological applications. Analysis of the F. placidus genome revealed genes predicted to encode enzymes homologous to those previously identified as having a role in benzoate and phenol metabolism in mesophilic bacteria. Surprisingly, F. placidus lacks genes for an ATP-independent class II benzoyl-CoA (coenzyme A) reductase (BCR) found in all strictly anaerobic bacteria, but has instead genes coding for a bzd-type ATP-consuming class I BCR, similar to those found in facultative bacteria. The lower portion of the benzoate degradation pathway appears to be more similar to that found in the phototroph Rhodopseudomonas palustris, than the pathway reported for all heterotrophic anaerobic benzoate degraders. Many of the genes predicted to be involved in benzoate metabolism were found in one of two gene clusters. Genes for phenol carboxylation proceeding through a phenylphosphate intermediate were identified in a single gene cluster. Analysis of transcript abundance with a whole-genome microarray and quantitative reverse transcriptase polymerase chain reaction demonstrated that most of the genes predicted to be involved in benzoate or phenol metabolism had higher transcript abundance during growth on those substrates vs growth on acetate. These results suggest that the general strategies for benzoate and phenol metabolism are highly conserved between microorganisms living in moderate and hot environments, and that anaerobic metabolism of aromatic compounds might be analyzed in a wide range of environments with similar molecular targets. PMID:21776029

Risk assessment for the daily intake of polycyclic aromatic hydrocarbons from the ingestion of cockle (Anadara granosa) and exposure to contaminated water and sediments along the west coast of Peninsular Malaysia.

PubMed

Mirsadeghi, Seiedeh Aghileh; Zakari, Mohamad Pauzi; Yap, Chee Kong; Shahbazi, Azadeh

2011-01-01

The concentration of carcinogenic polycyclic aromatic hydrocarbons (c-PAHs) present in the sediment and water of Peninsular Malaysia as well as in the cockle Anadara granosa was investigated. Samples were extracted and analysed with gas chromatography-mass spectrometry. The concentrations of total carcinogenic polycyclic aromatic hydrocarbons (t-PAHs) were measured between 0.80 +/- 0.04 to 162.96 +/- 14.74 ng/g wet weight (ww) in sediment, between 21.85 +/- 2.18 to 76.2 +/- 10.82 ng/L in water samples and between 3.34 +/- 0.77 to 46.85 +/- 5.50 ng/g ww in the cockle tissue. The risk assessment of probable human carcinogens in the Group B2 PAHs was calculated and assessed in accordance with the standards of the United States Environmental Protection Agency (US EPA). Case I in the toxicity assessment analysed the cancer risk to consumers of Malaysian blood cockle. Case II assessed the risk of cancer from exposure to PAHs from multiple pathways. The average cancer risk of case I and case II were found to be classifiable as unsafe according to the US EPA standard. The cancer risk due to c-PAHs acquired by the ingestion of blood cockle was (8.82 +/- 0.54) x 10-6 to (2.67 +/- 0.06) x 10(-2), higher than the US EPA risk management criterion. The non-cancer risks associated with multiple pathways in Kuala Gula, Kuala Juru and Kuala Perlis were higher than the U.S. EPA safe level, but the non-cancer risk for eating blood cockle was below the level of U.S. EPA concern.

A novel aromatic alcohol dehydrogenase in higher plants: molecular cloning and expression.

PubMed

Goffner, D; Van Doorsselaere, J; Yahiaoui, N; Samaj, J; Grima-Pettenati, J; Boudet, A M

1998-03-01

Cinnamyl alcohol dehydrogenase (CAD; EC 1.1.195) catalyses the conversion of p-hydroxy-cinnamaldehydes to the corresponding alcohols and is considered a key enzyme in lignin biosynthesis. In a previous study, an atypical form of CAD (CAD 1) was identified in Eucalyptus gunnii [12]. We report here the molecular cloning and characterization of the corresponding cDNA, CAD 1-5, which encodes this novel aromatic alcohol dehydrogenase. The identity of CAD 1-5 was unambiguously confirmed by sequence comparison of the cDNA with peptide sequences derived from purified CAD 1 protein and by functional expression of CAD 1 recombinant protein in Escherichia coli. Both native and recombinant CAD 1 exhibit high affinity towards lignin precursors including 4-coumaraldehyde and coniferaldehyde, but they do not accept sinapaldehyde. Moreover, recombinant CAD 1 can also utilize a wide range of aromatic substrates including unsubstituted and substituted benzaldehydes. The open reading frame of CAD 1-5 encodes a protein with a calculated molecular mass of 35,790 Da and an isoelectric point of 8.1. Although sequence comparisons with proteins in databases revealed significant similarities with dihydroflavonol-4-reductases (DFR; EC 1.1.1.219) from a wide range of plant species, the most striking similarity was found with cinnamoyl-CoA reductase (CCR; EC 1.2.1.44), the enzyme which directly precedes CAD in the lignin biosynthetic pathway. RNA blot analysis and immunolocalization experiments indicated that CAD 1 is expressed in both lignified and unlignified tissues/cells. Based on the catalytic activity of CAD 1 in vitro and its localization in planta, CAD 1 may function as an 'alternative' enzyme in the lignin biosynthetic pathway. However, additional roles in phenolic metabolism are not excluded.

Final Report: Investigation of Catalytic Pathways for Lignin Breakdown into Monomers and Fuels

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

Gluckstein, Jeffrey A; Hu, Michael Z.; Kidder, Michelle

2010-12-01

Lignin is a biopolymer that comprises up to 35% of woody biomass by dry weight. It is currently underutilized compared to cellulose and hemicellulose, the other two primary components of woody biomass. Lignin has an irregular structure of methoxylated aromatic groups linked by a suite of ether and alkyl bonds which makes it difficult to degrade selectively. However, the aromatic components of lignin also make it promising as a base material for the production of aromatic fuel additives and cyclic chemical feed stocks such as styrene, benzene, and cyclohexanol. Our laboratory research focused on three methods to selectively cleave andmore » deoxygenate purified lignin under mild conditions: acidolysis, hydrogenation and electrocatalysis. (1) Acidolysis was undertaken in CH2Cl2 at room temperature. (2) Hydrogenation was carried out by dissolving lignin and a rhodium catalyst in 1:1 water:methoxyethanol under a 1 atm H2 environment. (3) Electrocatalysis of lignin involved reacting electrically generated hydrogen atoms at a catalytic palladium cathode with lignin dissolved in a solution of aqueous methanol. In all of the experiments, the lignin degradation products were identified and quantified by gas chromatography mass spectroscopy and flame ionization detection. Yields were low, but this may have reflected the difficulty in recovering the various fractions after conversion. The homogeneous hydrogenation of lignin showed fragmentation into monomers, while the electrocatalytic hydrogenation showed production of polyaromatic hydrocarbons and substituted benzenes. In addition to the experiments, promising pathways for the conversion of lignin were assessed. Three conversion methods were compared based on their material and energy inputs and proposed improvements using better catalyst and process technology. A variety of areas were noted as needing further experimental and theoretical effort to increase the feasibility of lignin conversion to fuels.« less

Petroleum and individual polycyclic aromatic hydrocarbons

USGS Publications Warehouse

Albers, Peter H.; Hoffman, David J.; Rattner, Barnett A.; Burton, G. Allen; Cairns, John

1995-01-01

Crude petroleum, refined-petroleum products, and individual polycyclic aromatic hydrocarbons (PAHs) contained within petroleum are found throughout the world. their presence has been detected in living and nonliving components of ecosystems. Petroleum can be an environmental hazard for wild animals and plants. Individual PAHs are also hazardous to wildlife, but they are most commonly associated with human illnesses. Because petroleum is a major environmental source of these PAHs, petroleum and PAHs are jointly presented in this chapter. Composition, sources, environmental fate, and toxic effects on all living components of aquatic and terrestrial environments are addessed.

Dissociation reactions of protonated anthracycline antibiotics following electrospray ionization-tandem mass spectrometry

NASA Astrophysics Data System (ADS)

Sleno, Lekha; Campagna-Slater, Valerie; Volmer, Dietrich A.

2006-09-01

Fragmentation pathways of doxorubicin, a common cancer therapy agent, and three closely related analogs (epirubicin, daunorubicin, idarubicin) were compared using electrospray ionization with tandem mass spectrometry. This class of antibiotics with anti-tumour activity has important structural features, with a tetracyclic aromatic, polyketide portion, which is glycosylated with an amino sugar in order to exhibit its biological activity. Collision-induced dissociation spectra revealed very similar product ions for each analog, however, important differences were seen in the relative abundances and the ease at which certain fragments were formed. Fragment ions observed included those from cleavage of the glycosidic bond, loss of the side chain from the aglycone moiety, water losses and loss of a methyl radical. Following cleavage of the glycosidic bond, the charge can either reside on the aglycone portion or the sugar moiety, and each of these primary fragments undergoes several secondary dissociation pathways, depending on the collision energy. By ramping the collision voltage, we were able to correlate the changes in fragmentation behavior with small alterations in the structure of the precursor ion. The detailed study of the fragmentation behavior of doxorubicin was supported by accurate mass measurements, using an electrospray-time of flight instrument, as well as MS3 data from a quadrupole-linear ion trap mass spectrometer. Computational studies were also performed to help explain the role of certain functional groups in the fragmentation reactions.

2-Aminoadipic acid is a biomarker for diabetes risk

PubMed Central

Wang, Thomas J.; Ngo, Debby; Psychogios, Nikolaos; Dejam, Andre; Larson, Martin G.; Vasan, Ramachandran S.; Ghorbani, Anahita; O’Sullivan, John; Cheng, Susan; Rhee, Eugene P.; Sinha, Sumita; McCabe, Elizabeth; Fox, Caroline S.; O’Donnell, Christopher J.; Ho, Jennifer E.; Florez, Jose C.; Magnusson, Martin; Pierce, Kerry A.; Souza, Amanda L.; Yu, Yi; Carter, Christian; Light, Peter E.; Melander, Olle; Clish, Clary B.; Gerszten, Robert E.

2013-01-01

Improvements in metabolite-profiling techniques are providing increased breadth of coverage of the human metabolome and may highlight biomarkers and pathways in common diseases such as diabetes. Using a metabolomics platform that analyzes intermediary organic acids, purines, pyrimidines, and other compounds, we performed a nested case-control study of 188 individuals who developed diabetes and 188 propensity-matched controls from 2,422 normoglycemic participants followed for 12 years in the Framingham Heart Study. The metabolite 2-aminoadipic acid (2-AAA) was most strongly associated with the risk of developing diabetes. Individuals with 2-AAA concentrations in the top quartile had greater than a 4-fold risk of developing diabetes. Levels of 2-AAA were not well correlated with other metabolite biomarkers of diabetes, such as branched chain amino acids and aromatic amino acids, suggesting they report on a distinct pathophysiological pathway. In experimental studies, administration of 2-AAA lowered fasting plasma glucose levels in mice fed both standard chow and high-fat diets. Further, 2-AAA treatment enhanced insulin secretion from a pancreatic β cell line as well as murine and human islets. These data highlight a metabolite not previously associated with diabetes risk that is increased up to 12 years before the onset of overt disease. Our findings suggest that 2-AAA is a marker of diabetes risk and a potential modulator of glucose homeostasis in humans. PMID:24091325

2-Aminoadipic acid is a biomarker for diabetes risk.

PubMed

Wang, Thomas J; Ngo, Debby; Psychogios, Nikolaos; Dejam, Andre; Larson, Martin G; Vasan, Ramachandran S; Ghorbani, Anahita; O'Sullivan, John; Cheng, Susan; Rhee, Eugene P; Sinha, Sumita; McCabe, Elizabeth; Fox, Caroline S; O'Donnell, Christopher J; Ho, Jennifer E; Florez, Jose C; Magnusson, Martin; Pierce, Kerry A; Souza, Amanda L; Yu, Yi; Carter, Christian; Light, Peter E; Melander, Olle; Clish, Clary B; Gerszten, Robert E

2013-10-01

Improvements in metabolite-profiling techniques are providing increased breadth of coverage of the human metabolome and may highlight biomarkers and pathways in common diseases such as diabetes. Using a metabolomics platform that analyzes intermediary organic acids, purines, pyrimidines, and other compounds, we performed a nested case-control study of 188 individuals who developed diabetes and 188 propensity-matched controls from 2,422 normoglycemic participants followed for 12 years in the Framingham Heart Study. The metabolite 2-aminoadipic acid (2-AAA) was most strongly associated with the risk of developing diabetes. Individuals with 2-AAA concentrations in the top quartile had greater than a 4-fold risk of developing diabetes. Levels of 2-AAA were not well correlated with other metabolite biomarkers of diabetes, such as branched chain amino acids and aromatic amino acids, suggesting they report on a distinct pathophysiological pathway. In experimental studies, administration of 2-AAA lowered fasting plasma glucose levels in mice fed both standard chow and high-fat diets. Further, 2-AAA treatment enhanced insulin secretion from a pancreatic β cell line as well as murine and human islets. These data highlight a metabolite not previously associated with diabetes risk that is increased up to 12 years before the onset of overt disease. Our findings suggest that 2-AAA is a marker of diabetes risk and a potential modulator of glucose homeostasis in humans.

Metabolism of tetralin (1,2,3,4-tetrahydronaphthalene) in Corynebacterium sp. strain C125

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

Sikkema, J.; Bont, J.A.M. de

1993-02-01

Tetralin, widely used as a solvent in the petrochemical industry and in paints and waxes, degrades slowly in mixed cultures of microorganisms or in the presence of cosubstrates. This study reports on the metabolism of tetralin in the o-xylene-isolated Corynebacterium sp. strain C125. The researchers found that this organism attacks tetralin by an initial oxidation of the aromatic nucleus at positions C-5 and C-6 and they propose a four step inducible degradation pathway for tetralin starting at that point. The presence of the pathway makes this bacteria an excellent catalyst for the specific production of special cis-dihydro diols.

Carbon Source-Dependent Inducible Metabolism of Veratryl Alcohol and Ferulic Acid in Pseudomonas putida CSV86

PubMed Central

Mohan, Karishma

2017-01-01

ABSTRACT Pseudomonas putida CSV86 degrades lignin-derived metabolic intermediates, viz., veratryl alcohol, ferulic acid, vanillin, and vanillic acid, as the sole sources of carbon and energy. Strain CSV86 also degraded lignin sulfonate. Cell respiration, enzyme activity, biotransformation, and high-pressure liquid chromatography (HPLC) analyses suggest that veratryl alcohol and ferulic acid are metabolized to vanillic acid by two distinct carbon source-dependent inducible pathways. Vanillic acid was further metabolized to protocatechuic acid and entered the central carbon pathway via the β-ketoadipate route after ortho ring cleavage. Genes encoding putative enzymes involved in the degradation were found to be present at fer, ver, and van loci. The transcriptional analysis suggests a carbon source-dependent cotranscription of these loci, substantiating the metabolic studies. Biochemical and quantitative real-time (qRT)-PCR studies revealed the presence of two distinct O-demethylases, viz., VerAB and VanAB, involved in the oxidative demethylation of veratric acid and vanillic acid, respectively. This report describes the various steps involved in metabolizing lignin-derived aromatic compounds at the biochemical level and identifies the genes involved in degrading veratric acid and the arrangement of phenylpropanoid metabolic genes as three distinct inducible transcription units/operons. This study provides insight into the bacterial degradation of lignin-derived aromatics and the potential of P. putida CSV86 as a suitable candidate for producing valuable products. IMPORTANCE Pseudomonas putida CSV86 metabolizes lignin and its metabolic intermediates as a carbon source. Strain CSV86 displays a unique property of preferential utilization of aromatics, including for phenylpropanoids over glucose. This report unravels veratryl alcohol metabolism and genes encoding veratric acid O-demethylase, hitherto unknown in pseudomonads, thereby providing new insight into the metabolic pathway and gene pool for lignin degradation in bacteria. The biochemical and genetic characterization of phenylpropanoid metabolism makes it a prospective system for its application in producing valuable products, such as vanillin and vanillic acid, from lignocellulose. This study supports the immense potential of P. putida CSV86 as a suitable candidate for bioremediation and biorefinery. PMID:28188206

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

Single gene insertion drives bioalcohol production by a thermophilic archaeon

PubMed Central

Basen, Mirko; Schut, Gerrit J.; Nguyen, Diep M.; Lipscomb, Gina L.; Benn, Robert A.; Prybol, Cameron J.; Vaccaro, Brian J.; Poole, Farris L.; Kelly, Robert M.; Adams, Michael W. W.

2014-01-01

Bioethanol production is achieved by only two metabolic pathways and only at moderate temperatures. Herein a fundamentally different synthetic pathway for bioalcohol production at 70 °C was constructed by insertion of the gene for bacterial alcohol dehydrogenase (AdhA) into the archaeon Pyrococcus furiosus. The engineered strain converted glucose to ethanol via acetate and acetaldehyde, catalyzed by the host-encoded aldehyde ferredoxin oxidoreductase (AOR) and heterologously expressed AdhA, in an energy-conserving, redox-balanced pathway. Furthermore, the AOR/AdhA pathway also converted exogenously added aliphatic and aromatic carboxylic acids to the corresponding alcohol using glucose, pyruvate, and/or hydrogen as the source of reductant. By heterologous coexpression of a membrane-bound carbon monoxide dehydrogenase, CO was used as a reductant for converting carboxylic acids to alcohols. Redirecting the fermentative metabolism of P. furiosus through strategic insertion of foreign genes creates unprecedented opportunities for thermophilic bioalcohol production. Moreover, the AOR/AdhA pathway is a potentially game-changing strategy for syngas fermentation, especially in combination with carbon chain elongation pathways. PMID:25368184

Single gene insertion drives bioalcohol production by a thermophilic archaeon

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

Basen, M; Schut, GJ; Nguyen, DM

2014-12-09

Bioethanol production is achieved by only two metabolic pathways and only at moderate temperatures. Herein a fundamentally different synthetic pathway for bioalcohol production at 70 degrees C was constructed by insertion of the gene for bacterial alcohol dehydrogenase (AdhA) into the archaeon Pyrococcus furiosus. The engineered strain converted glucose to ethanol via acetate and acetaldehyde, catalyzed by the host-encoded aldehyde ferredoxin oxidoreductase (AOR) and heterologously expressed AdhA, in an energy-conserving, redox-balanced pathway. Furthermore, the AOR/AdhA pathway also converted exogenously added aliphatic and aromatic carboxylic acids to the corresponding alcohol using glucose, pyruvate, and/or hydrogen as the source of reductant. Bymore » heterologous coexpression of a membrane-bound carbon monoxide dehydrogenase, CO was used as a reductant for converting carboxylic acids to alcohols. Redirecting the fermentative metabolism of P. furiosus through strategic insertion of foreign genes creates unprecedented opportunities for thermophilic bioalcohol production. Moreover, the AOR/AdhA pathway is a potentially game-changing strategy for syngas fermentation, especially in combination with carbon chain elongation pathways.« less

Mycotoxicogenic fungal inhibition by innovative cheese cover with aromatic plants.

PubMed

Moro, Armando; Librán, Celia M; Berruga, M Isabel; Zalacain, Amaya; Carmona, Manuel

2013-03-30

The use of aromatic plants and their extracts with antimicrobial properties may be compromised in the case of cheese, as some type of fungal starter is needed during its production. Penicillium verrucosum is considered a common cheese spoiler. The aim of this study was to evaluate the innovative use of certain aromatic plants as natural cheese covers in order to prevent mycotoxicogenic fungal growth (P. verrucosum). A collection of 12 essential oils (EOs) was obtained from various aromatic plants by solvent-free microwave extraction technology, and volatile characterisation of the EOs was carried out by gas chromatography/mass spectrometry. The most effective EOs against P. verrucosum were obtained from Anethum graveolens, Hyssopus officinalis and Chamaemelum nobile, yielding 50% inhibition of fungal growth at concentration values lower than 0.02 µL mL⁻¹. All EOs showed high volatile heterogeneity, with α-phellandrene, pinocamphone, isopinocamphone, α-pinene, camphene, 1,8-cineole, carvacrol and trans-anethole being found to be statistically significant in the antifungal model. The use of these aromatic plants as natural covers on cheese can satisfactorily inhibit the growth of some mycotoxicogenic fungal spoilers. Among the volatile compounds present, α- and β-phellandrene were confirmed as the most relevant in the inhibition. © 2012 Society of Chemical Industry.

Effects of Fuel Composition on Combustion Stability and NO X Emissions for Traditional and Alternative Jet Fuels

NASA Astrophysics Data System (ADS)

Vijlee, Shazib Z.

Synthetic jet fuels are studied to help understand their viability as alternatives to traditionally derived jet fuel. Two combustion parameters -- flame stability and NOX emissions -- are used to compare these fuels through experiments and models. At its core, this is a fuels study comparing how chemical makeup and behavior relate. Six 'real', complex fuels are studied in this work -- four are synthetic from alternative sources and two are traditional from petroleum sources. Two of the synthetic fuels are derived from natural gas and coal via the Fischer Tropsch catalytic process. The other two are derived from Camelina oil and tallow via hydroprocessing. The traditional military jet fuel, JP8, is used as a baseline as it is derived from petroleum. The sixth fuel is derived from petroleum and is used to study the effects of aromatic content on the synthetic fuels. The synthetic fuels lack aromatic compounds, which are an important class of hydrocarbons necessary for fuel handling systems to function properly. Several single-component fuels are studied (through models and/or experiments) to facilitate interpretation and understanding. The flame stability study first compares all the 'real', complex fuels for blowout. A toroidal stirred reactor is used to try and isolate temperature and chemical effects. The modeling study of blowout in the toroidal reactor is the key to understanding any fuel-based differences in blowout behavior. A detailed, reacting CFD model of methane is used to understand how the reactor stabilizes the flame and how that changes as the reactor approaches blowout. A 22 species reduced form of GRI 3.0 is used to model methane chemistry. The knowledge of the radical species role is utilized to investigate the differences between a highly aliphatic fuel (surrogated by iso-octane) and a highly aromatic fuel (surrogated by toluene). A perfectly stirred reactor model is used to study the chemical kinetic pathways for these fuels near blowout. The differences in flame stabilization can be attributed to the rate at which these fuels are attacked and destroyed by radical species. The slow disintegration of the aromatic rings reduces the radical pool available for chain-initiating and chain-branching, which ultimately leads to an earlier blowout. The NOX study compares JP8, the aromatic additive, the synthetic fuels with and without an aromatic additive, and an aromatic surrogate (1,3,5-trimethylbenzene). A jet stirred reactor is used to try and isolate temperature and chemical effects. The reactor has a volume of 15.8 mL and a residence time of approximately 2.5 ms. The fuel flow rate (hence equivalence ratio) is adjusted to achieve nominally consistent temperatures of 1800, 1850, and 1900K. Small oscillations in fuel flow rate cause the data to appear in bands, which facilitated Arrhenius-type NOX-temperature correlations for direct comparison between fuels. The fuel comparisons are somewhat inconsistent, especially when the aromatic fuel is blended into the synthetic fuels. In general, the aromatic surrogate (1,3,5-trimethylbenzene) produces the most NOX, followed by JP8. The synthetic fuels (without aromatic additive) are always in the same ranking order for NOX production (HP Camelina > FT Coal > FT Natural Gas > HP Tallow). The aromatic additive ranks differently based on the temperature, which appears to indicate that some of the differences in NOX formation are due to the Zeldovich NOX formation pathway. The aromatic additive increases NOX for the HP Tallow and decreases NOX for the FT Coal. The aromatic additive causes increased NOX at low temperatures but decreases NOX at high temperatures for the HP Camelina and FT Natural Gas. A single perfectly stirred reactor model is used with several chemical kinetic mechanisms to study the effects of fuel (and fuel class) on NO X formation. The 27 unique NOX formation reactions from GRI 3.0 are added to published mechanisms for jet fuel surrogates. The investigation first looked at iso-octane and toluene and found that toluene produces more NOX because of a larger pool of O radical. The O radical concentration was lower for iso-octane because of an increased concentration of methyl (CH 3) radical that consumes O radical readily. Several surrogate fuels (iso-octane, toluene, propylcyclohexane, n-octane, and 1,3,5-trimethylbenzene) are modeled to look for differences in NOX production. The trend (increased CH3 → decreased O → decreased NOX) is consistently true for all surrogate fuels with multiple kinetic mechanisms. It appears that the manner in which the fuel disintegrates and creates methyl radical is an extremely important aspect of how much NOX a fuel will produce. (Abstract shortened by UMI.).

Synthesis and accumulation of aromatic aldehydes in an engineered strain of Escherichia coli.

PubMed

Kunjapur, Aditya M; Tarasova, Yekaterina; Prather, Kristala L J

2014-08-20

Aromatic aldehydes are useful in numerous applications, especially as flavors, fragrances, and pharmaceutical precursors. However, microbial synthesis of aldehydes is hindered by rapid, endogenous, and redundant conversion of aldehydes to their corresponding alcohols. We report the construction of an Escherichia coli K-12 MG1655 strain with reduced aromatic aldehyde reduction (RARE) that serves as a platform for aromatic aldehyde biosynthesis. Six genes with reported activity on the model substrate benzaldehyde were rationally targeted for deletion: three genes that encode aldo-keto reductases and three genes that encode alcohol dehydrogenases. Upon expression of a recombinant carboxylic acid reductase in the RARE strain and addition of benzoate during growth, benzaldehyde remained in the culture after 24 h, with less than 12% conversion of benzaldehyde to benzyl alcohol. Although individual overexpression results demonstrated that all six genes could contribute to benzaldehyde reduction in vivo, additional experiments featuring subset deletion strains revealed that two of the gene deletions were dispensable under the conditions tested. The engineered strain was next investigated for the production of vanillin from vanillate and succeeded in preventing formation of the byproduct vanillyl alcohol. A pathway for the biosynthesis of vanillin directly from glucose was introduced and resulted in a 55-fold improvement in vanillin titer when using the RARE strain versus the wild-type strain. Finally, synthesis of the chiral pharmaceutical intermediate L-phenylacetylcarbinol (L-PAC) was demonstrated from benzaldehyde and glucose upon expression of a recombinant mutant pyruvate decarboxylase in the RARE strain. Beyond allowing accumulation of aromatic aldehydes as end products in E. coli, the RARE strain expands the classes of chemicals that can be produced microbially via aldehyde intermediates.

Aromatic Rings Commonly Used in Medicinal Chemistry: Force Fields Comparison and Interactions With Water Toward the Design of New Chemical Entities.

PubMed

Polêto, Marcelo D; Rusu, Victor H; Grisci, Bruno I; Dorn, Marcio; Lins, Roberto D; Verli, Hugo

2018-01-01

The identification of lead compounds usually includes a step of chemical diversity generation. Its rationale may be supported by both qualitative (SAR) and quantitative (QSAR) approaches, offering models of the putative ligand-receptor interactions. In both scenarios, our understanding of which interactions functional groups can perform is mostly based on their chemical nature (such as electronegativity, volume, melting point, lipophilicity etc.) instead of their dynamics in aqueous, biological solutions (solvent accessibility, lifetime of hydrogen bonds, solvent structure etc.). As a consequence, it is challenging to predict from 2D structures which functional groups will be able to perform interactions with the target receptor, at which intensity and relative abundance in the biological environment, all of which will contribute to ligand potency and intrinsic activity. With this in mind, the aim of this work is to assess properties of aromatic rings, commonly used for drug design, in aqueous solution through molecular dynamics simulations in order to characterize their chemical features and infer their impact in complexation dynamics. For this, common aromatic and heteroaromatic rings were selected and received new atomic charge set based on the direction and module of the dipole moment from MP2/6-31G * calculations, while other topological terms were taken from GROMOS53A6 force field. Afterwards, liquid physicochemical properties were simulated for a calibration set composed by nearly 40 molecules and compared to their respective experimental data, in order to validate each topology. Based on the reliance of the employed strategy, we expanded the dataset to more than 100 aromatic rings. Properties in aqueous solution such as solvent accessible surface area, H-bonds availability, H-bonds residence time, and water structure around heteroatoms were calculated for each ring, creating a database of potential interactions, shedding light on features of drugs in biological solutions, on the structural basis for bioisosterism and on the enthalpic/entropic costs for ligand-receptor complexation dynamics.

Polycyclic aromatic hydrocarbon metabolic network in Mycobacterium vanbaalenii PYR-1.

PubMed

Kweon, Ohgew; Kim, Seong-Jae; Holland, Ricky D; Chen, Hongyan; Kim, Dae-Wi; Gao, Yuan; Yu, Li-Rong; Baek, Songjoon; Baek, Dong-Heon; Ahn, Hongsik; Cerniglia, Carl E

2011-09-01

This study investigated a metabolic network (MN) from Mycobacterium vanbaalenii PYR-1 for polycyclic aromatic hydrocarbons (PAHs) from the perspective of structure, behavior, and evolution, in which multilayer omics data are integrated. Initially, we utilized a high-throughput proteomic analysis to assess the protein expression response of M. vanbaalenii PYR-1 to seven different aromatic compounds. A total of 3,431 proteins (57.38% of the genome-predicted proteins) were identified, which included 160 proteins that seemed to be involved in the degradation of aromatic hydrocarbons. Based on the proteomic data and the previous metabolic, biochemical, physiological, and genomic information, we reconstructed an experiment-based system-level PAH-MN. The structure of PAH-MN, with 183 metabolic compounds and 224 chemical reactions, has a typical scale-free nature. The behavior and evolution of the PAH-MN reveals a hierarchical modularity with funnel effects in structure/function and intimate association with evolutionary modules of the functional modules, which are the ring cleavage process (RCP), side chain process (SCP), and central aromatic process (CAP). The 189 commonly upregulated proteins in all aromatic hydrocarbon treatments provide insights into the global adaptation to facilitate the PAH metabolism. Taken together, the findings of our study provide the hierarchical viewpoint from genes/proteins/metabolites to the network via functional modules of the PAH-MN equipped with the engineering-driven approaches of modularization and rationalization, which may expand our understanding of the metabolic potential of M. vanbaalenii PYR-1 for bioremediation applications.

The effects of ionizing radiations on L-, DL-phenylalanine and L-, DL- tryptophase studied by ultra-violet and infra-red spectrophotometry

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

Korgaonkar, K S; Donde, R B

Aqueous solutions of L-, DL-phenylalanlne and L-, DLtryptophane were irradiated with Co 60 gamma rays. Marked changes in the ultraviolet spectra of the samples and in the infra-red spectra of their solid residues were noted. The radiosensitivities of these irradiated molecules in terms of G-values were determined, and the modes of action and the nature of irradiation products are discussed. A common order of radiosensitivities among the three aromatic amino acids both L-, and DL-forms is observed. Apparent differences In the ultraviolet spectral responses of tryptophane on the one hand and phenylalanine and tyrosine on the other are explained. Evidencemore » is presented suggesting some common radiation end-product of a cellulose or sugar type from these aromatic amino acids.« less

[Analysis of phthalates in aromatic and deodorant aerosol products and evaluation of exposure risk].

PubMed

Sato, Yoshiki; Sugaya, Naeko; Nakagawa, Tomoo; Morita, Masatoshi

2015-01-01

We established an analytical method for the detection of seven phthalates, dimethyl phthalate, diethyl phthalate (DEP), benzyl butyl phthalate, di-i-butyl phthalate, dibutyl phthalate (DBP), diethylhexyl phthalate (DEHP), and di-n-octhyl phthalate, using an ultra high performance liquid chromatograph equipped with a photodiode array detector. This method is quick, with minimal contamination, and was applied to the analysis of aromatic and deodorant aerosol products. Phthalates were detected in 15 of 52 samples purchased from 1999 to 2012 in Yokohama. Three types of phthalate (DEP, DBP, DEHP) were detected, and their concentrations ranged from 0.0085-0.23% DEP in nine samples, 0.012-0.045% DBP in four samples, and 0.012-0.033% DEHP in four samples. No other phthalate esters were detected. Furthermore, we estimated phthalate exposure via breathing in commonly used aromatic and deodorant aerosol products, then evaluated the associated risk. The estimated levels of phthalate exposure were lower than the tolerated daily limit, but the results indicated that aromatic and deodorant aerosol products could be a significant source of phthalate exposure.

Light-induced radical formation and isomerization of an aromatic thiol in solution followed by time-resolved x-ray absorption spectroscopy at the sulfur K-edge

DOE PAGES

Ochmann, Miguel; von Ahnen, Inga; Cordones, Amy A.; ...

2017-02-20

Here, we applied time-resolved sulfur-1s absorption spectroscopy to a model aromatic thiol system as a promising method for tracking chemical reactions in solution. Sulfur-1s absorption spectroscopy allows tracking multiple sulfur species with a time resolution of ~70 ps at synchrotron radiation facilities. Experimental transient spectra combined with high-level electronic structure theory allow identification of a radical and two thione isomers, which are generated upon illumination with 267 nm radiation. Moreover, the regioselectivity of the thione isomerization is explained by the resulting radical frontier orbitals. This work demonstrates the usefulness and potential of time-resolved sulfur-1s absorption spectroscopy for tracking multiple chemicalmore » reaction pathways and transient products of sulfur-containing molecules in solution.« less

Airborne polycyclic aromatic hydrocarbons trigger human skin cells aging through aryl hydrocarbon receptor.

PubMed

Qiao, Yuan; Li, Qiang; Du, Hong-Yang; Wang, Qiao-Wei; Huang, Ye; Liu, Wei

2017-07-01

Accumulating evidence suggests that polycyclic aromatic hydrocarbons (PAH) which adsorbed on the surface of ambient air particulate matters (PM), are the major toxic compound to cause cardiovascular and respiratory diseases, even cancer. However, its detrimental effects on human skin cell remain unclear. Here, we demonstrated that SRM1649b, a reference urban dust material of PAH, triggers human skin cells aging through cell cycle arrest, cell growth inhibition and apoptosis. Principally, SRM1649b facilitated Aryl hydrocarbon receptor (AhR) translocated into nucleus, subsequently activated ERK/MAPK signaling pathway, and upregulated aging-related genes expression. Most important, we found that AhR antagonist efficiently revert the aging of skin cells. Thus our novel findings firstly revealed the mechanism of skin aging under PAH contamination and provided potential strategy for clinical application. Copyright © 2017. Published by Elsevier Inc.

Deciphering the Functional Composition of Fusogenic Liposomes

PubMed Central

Kolašinac, Rejhana; Kleusch, Christian; Braun, Tobias; Merkel, Rudolf; Csiszár, Agnes

2018-01-01

Cationic liposomes are frequently used as carrier particles for nucleic acid delivery. The most popular formulation is the equimolar mixture of two components, a cationic lipid and a neutral phosphoethanolamine. Its uptake pathway has been described as endocytosis. The presence of an aromatic molecule as a third component strongly influences the cellular uptake process and results in complete membrane fusion instead of endocytosis. Here, we systematically varied all three components of this lipid mixture and determined how efficiently the resulting particles fused with the plasma membrane of living mammalian cells. Our results show that an aromatic molecule and a cationic lipid component with conical molecular shape are essential for efficient fusion induction. While a neutral lipid is not mandatory, it can be used to control fusion efficiency and, in the most extreme case, to revert the uptake mechanism back to endocytosis. PMID:29364187

Draft genome sequence of Mycobacterium rufum JS14(T), a polycyclic-aromatic-hydrocarbon-degrading bacterium from petroleum-contaminated soil in Hawaii.

PubMed

Kwak, Yunyoung; Li, Qing X; Shin, Jae-Ho

2016-01-01

Mycobacterium rufum JS14(T) (=ATCC BAA-1377(T), CIP 109273(T), JCM 16372(T), DSM 45406(T)), a type strain of the species Mycobacterium rufum sp. . belonging to the family Mycobacteriaceae, was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil in Hilo (HI, USA) because it harbors the capability of degrading PAH. Here, we describe the first genome sequence of strain JS14(T), with brief phenotypic characteristics. The genome is composed of 6,176,413 bp with 69.25 % G + C content and contains 5810 protein-coding genes with 54 RNA genes. The genome information on M. rufum JS14(T) will provide a better understanding of the complexity of bacterial catabolic pathways for degradation of specific chemicals.

Light-induced radical formation and isomerization of an aromatic thiol in solution followed by time-resolved x-ray absorption spectroscopy at the sulfur K-edge

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

Ochmann, Miguel; von Ahnen, Inga; Cordones, Amy A.

Here, we applied time-resolved sulfur-1s absorption spectroscopy to a model aromatic thiol system as a promising method for tracking chemical reactions in solution. Sulfur-1s absorption spectroscopy allows tracking multiple sulfur species with a time resolution of ~70 ps at synchrotron radiation facilities. Experimental transient spectra combined with high-level electronic structure theory allow identification of a radical and two thione isomers, which are generated upon illumination with 267 nm radiation. Moreover, the regioselectivity of the thione isomerization is explained by the resulting radical frontier orbitals. This work demonstrates the usefulness and potential of time-resolved sulfur-1s absorption spectroscopy for tracking multiple chemicalmore » reaction pathways and transient products of sulfur-containing molecules in solution.« less

Which kind of aromatic structures are produced during biomass charring? New insights provided by modern solid-state NMR spectroscopy

NASA Astrophysics Data System (ADS)

Knicker, Heike; Paneque-Carmona, Marina; Velasco-Molina, Marta; de la Rosa, José Maria; León-Ovelar, Laura Regina; Fernandez-Boy, Elena

2017-04-01

Intense research on biochar and charcoal of the last years has revealed that depending on the production conditions, the chemical and physical characteristics of their aromatic network can greatly vary. Since such variations are determining the behavior and stability of charred material in soils, a better understanding of the structural changes occurring during their heating and the impact of those changes on their function is needed. One method to characterize pyrogenic organic matter (PyOM) represents solid-state 13C NMR spectroscopy applying the cross polarization (CP) magic angle spinning technique (MAS). A drawback of this technique is that the quantification of NMR spectra of samples with highly condensed and proton-depleted structures is assumed to be bias. Typical samples with such attributes are charcoals produced at temperatures above 700°C under pyrolytic conditions. Commonly their high condensation degree leads to graphenic structures that are not only reducing the CP efficiency but create also a conductive lattice which acts as a shield and prevents the entering of the excitation pulse into the sample during the NMR experiments. Since the latter can damage the NMR probe and in the most cases the obtained NMR spectra show only one broad signal assignable to aromatic C, this technique is rarely applied for characterizing high temperature chars or soot. As a consequence, a more detailed knowledge of the nature of the aromatic ring systems is still missing. The latter is also true for the aromatic domains of PyOM produced at lower temperatures, since older NMR instruments operating at low magnetic fields deliver solid-state 13C NMR spectra with low resolution which turns a more detailed analysis of the aromatic chemical shift region into a challenging task. In order to overcome this disadvantages, modern NMR spectroscopy offers not only instruments with greatly improved resolution but also special pulse sequences for NMR experiments which allow a more detailed chemical shift assignment. Applying the latter to various charcoals and biochars, we intended to test their usefulness for a better characterization of PyOM and elucidation how specific aromatic features can affect their behavior in soils. We could demonstrate that furans represent the major compound class of low temperature chars produced from woody material. As indicated by 2D techniques, residual alkyl C in such chars has minor covalent binding to the aromatic network. Reducing the electrical conductivity of high-temperature chars by addition of aluminum oxide permitted the application of the cross CP technique. Determination of the relaxation and CP dynamics confirmed high rigidity of their aromatic domains which were dominated by coronene-type moieties. In contrast to common view, we could demonstrate that quantifiable CP NMR spectra can be obtained from high temperature chars with contact times of 3 to 5 ms and pulse delays > 3 s.

Enhanced adsorbability and photocatalytic activity of TiO2-graphene composite for polycyclic aromatic hydrocarbons removal in aqueous phase.

PubMed

Bai, Hongzhen; Zhou, Jun; Zhang, Hongjian; Tang, Guping

2017-02-01

Photodegradation via titanium dioxide (TiO 2 ) has been used to remove polycyclic aromatic hydrocarbons (PAHs) from environmental media broadly. In this study, a series of TiO 2 -graphene composites (P25-GR) with different GR weight ratios were synthesized via hydrothermal reaction of graphene oxide (GO) and P25. Their structures were characterized and the proprieties were tested in aqueous phase. Phenanthrene (PHE), fluoranthene (FLAN), and benzo[a]pyrene (BaP) were selected as models of PAHs. The experiment indicated that P25-2.5%GR exhibited enhancement in both adsorption and photodegradation, ∼80% of PAHs were removed after 2h photocatalysis. The influence of photodegradation rate was studied, including PAHs initial concentration and pH. Aromatic intermediates were identified during the reaction process and the degradation pathways were portrayed. This work explored the enhanced photocatalysis performance was attributed to the PAH-selective adsorbability and the strong electron transfer ability of the composite. The analysis of the degradation intermediates confirmed that the reaction proceeded with the formation of free radicals, leading to the gradual PAH mineralization. Copyright © 2016 Elsevier B.V. All rights reserved.

Metabolism and Biomarkers of Heterocyclic Aromatic Amines in Molecular Epidemiology Studies: Lessons Learned from Aromatic Amines

PubMed Central

2011-01-01

Aromatic amines and heterocyclic aromatic amines (HAAs) are structurally related classes of carcinogens that are formed during the combustion of tobacco or during the high-temperature cooking of meats. Both classes of procarcinogens undergo metabolic activation by N-hydroxylation of the exocyclic amine group, to produce a common proposed intermediate, the arylnitrenium ion, which is the critical metabolite implicated in toxicity and DNA damage. However, the biochemistry and chemical properties of these compounds are distinct and different biomarkers of aromatic amines and HAAs have been developed for human biomonitoring studies. Hemoglobin adducts have been extensively used as biomarkers to monitor occupational and environmental exposures to a number of aromatic amines; however, HAAs do not form hemoglobin adducts at appreciable levels and other biomarkers have been sought. A number of epidemiologic studies that have investigated dietary consumption of well-done meat in relation to various tumor sites reported a positive association between cancer risk and well-done meat consumption, although some studies have shown no associations between well-done meat and cancer risk. A major limiting factor in most epidemiological studies is the uncertainty in quantitative estimates of chronic exposure to HAAs and, thus, the association of HAAs formed in cooked meat and cancer risk has been difficult to establish. There is a critical need to establish long-term biomarkers of HAAs that can be implemented in molecular epidemioIogy studies. In this review article, we highlight and contrast the biochemistry of several prototypical carcinogenic aromatic amines and HAAs to which humans are chronically exposed. The biochemical properties and the impact of polymorphisms of the major xenobiotic-metabolizing enzymes on the biological effects of these chemicals are examined. Lastly, the analytical approaches that have been successfully employed to biomonitor aromatic amines and HAAs, and emerging biomarkers of HAAs that may be implemented in molecular epidemiology studies are discussed. PMID:21688801

Genetic susceptibility to the cross-reactivity of aromatic antiepileptic drugs-induced cutaneous adverse reactions.

PubMed

Wang, Wei; Hu, Fa-Yun; Wu, Xin-Tong; An, Dong-Mei; Yan, Bo; Zhou, Dong

2014-08-01

The cross-allergic reactions among aromatic antiepileptic drugs (AEDs) are common, but little is known about the genetic mechanisms. The aim of this study was to investigate the genetic associations of the human leukocyte antigen (HLA) genes with the cross-reactivity of cutaneous adverse drug reactions (cADRs) induced by different aromatic AEDs. We reviewed 60 Chinese patients with a history of cADRs induced by an aromatic AED, and which re-challenged other aromatic AEDs as an alternative to the causative AED owing to some particular reasons. According to whether developing another episode of cADRs, these patients were automatically divided into the cross-reactivity group and tolerant control group. High-resolution HLA-A, -B, -DRB1 genotyping were performed for each patient. One out of 10 patients (10%, 1/10) carried the HLA-A*2402 allele in the cross-reactivity group. However, 23 patients (46%, 23/50) carried this allele in the tolerant control group. The difference of the HLA-A*2402 allele between the two groups is statistically significant (P=0.040, OR=0.130, 95% CI: 0.015-1.108). In addition, the frequency differences of other HLA alleles between the two groups, including the HLA-B*1502 allele, did not reach statistical significance (P>0.05). The HLA genes contribute to the genetic susceptibility of the cross-reactivity of cADRs among aromatic AEDs. Our results suggest that HLA-B*1502 is not a major responsible allele for the cross-reactivity of cADRs to aromatic AEDs, but the HLA-A*2402 allele may be a protective marker for the cross-allergic reactions among aromatic AEDs in Han Chinese. Further studies are warranted to test the potential predictive value of the HLA-A*2402 allele in future. Copyright © 2014. Published by Elsevier B.V.

Radical Rearrangement Chemistry in Ultraviolet Photodissociation of Iodotyrosine Systems: Insights from Metastable Dissociation, Infrared Ion Spectroscopy, and Reaction Pathway Calculations.

PubMed

Ranka, Karnamohit; Zhao, Ning; Yu, Long; Stanton, John F; Polfer, Nicolas C

2018-05-29

We report on the ultraviolet photodissociation (UVPD) chemistry of protonated tyrosine, iodotyrosine, and diiodotyrosine. Distonic loss of the iodine creates a high-energy radical at the aromatic ring that engages in hydrogen/proton rearrangement chemistry. Based on UVPD kinetics measurements, the appearance of this radical is coincident with the UV irradiation pulse (8 ns). Conversely, sequential UVPD product ions exhibit metastable decay on ca. 100 ns timescales. Infrared ion spectroscopy is capable of confirming putative structures of the rearrangement products as proton transfers from the imine and β-carbon hydrogens. Potential energy surfaces for the various reaction pathways indicate that the rearrangement chemistry is highly complex, compatible with a cascade of rearrangements, and that there is no preferred rearrangement pathway even in small molecular systems like these. Graphical Abstract.

Kinetic Behavior of Leucine and Other Amino Acids Modulating Cognitive Performance via mTOR Pathway

DTIC Science & Technology

2011-12-02

is a potential target for modulation with leucine (or other therapeutic agents), to maintain/enhance normal functioning under stress conditions. Such... functioning under stress conditions. Such an effect has potential for optimizing warfighter cognitive performance under high demand conditions. The... Isoleucine L1 Essential Neutral Non-polar Branched chain Lysine Basic Y+ Essential Basic Polar Proline L1? Neutral Non-polar Aromatic Asparagine Neutral

Leucine Modulation of the mTOR Pathway for Cognition Modulation: Kinetic and In Vitro Studies and Model Development

DTIC Science & Technology

2015-09-30

isoleucine non-polar L1 131 Aromatic side chain phenylalanine non-polar L1 165 tyrosine polar L1 181 tryptophan slightly...Human Performance Wing Human Effectiveness Directorate Bioeffects Division Molecular Bioeffects Branch Wright-Patterson AFB OH 45433-5707 NOTICE...IV, DAF Chief, Bioeffects Division Human Effectiveness Directorate 711th Human Performance Wing Air Force Research Laboratory This report is

Photoredox-catalyzed Direct Reductive Amination of Aldehydes without an External Hydrogen/Hydride Source.

PubMed

Alam, Rauful; Molander, Gary A

2018-05-04

The direct reductive amination of aromatic aldehydes has been realized using a photocatalyst under visible light irradiation. The single electron oxidation of an in situ formed aminal species generates the putative α-amino radical that eventually delivers the reductive amination product. This method is operationally simple, highly selective, and functional group tolerant, which allows the direct synthesis of benzylic amines by a unique mechanistic pathway.

Arylamine N-acetyltransferase activity in bronchial epithelial cells and its inhibition by cellular oxidants

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

Dairou, Julien; Petit, Emile; Ragunathan, Nilusha

2009-05-01

Bronchial epithelial cells express xenobiotic-metabolizing enzymes (XMEs) that are involved in the biotransformation of inhaled toxic compounds. The activities of these XMEs in the lung may modulate respiratory toxicity and have been linked to several diseases of the airways. Arylamine N-acetyltransferases (NAT) are conjugating XMEs that play a key role in the biotransformation of aromatic amine pollutants such as the tobacco-smoke carcinogens 4-aminobiphenyl (4-ABP) and {beta}-naphthylamine ({beta}-NA). We show here that functional human NAT1 or its murine counterpart Nat2 are present in different lung epithelial cells i.e. Clara cells, type II alveolar cells and bronchial epithelial cells, thus indicating thatmore » inhaled aromatic amines may undergo NAT-dependent biotransformation in lung epithelium. Exposure of these cells to pathophysiologically relevant amounts of oxidants known to contribute to lung dysfunction, such as H{sub 2}O{sub 2} or peroxynitrite, was found to impair the NAT1/Nat2-dependent cellular biotransformation of aromatic amines. Genetic and non genetic impairment of intracellular NAT enzyme activities has been suggested to compromise the important detoxification pathway of aromatic amine N-acetylation and subsequently to contribute to an exacerbation of untoward effects of these pollutants on health. Our study suggests that oxidative/nitroxidative stress in lung epithelial cells, due to air pollution and/or inflammation, could contribute to local and/or systemic dysfunctions through the alteration of the functions of pulmonary NAT enzymes.« less

De Novo Sequencing and Analysis of Lemongrass Transcriptome Provide First Insights into the Essential Oil Biosynthesis of Aromatic Grasses.

PubMed

Meena, Seema; Kumar, Sarma R; Venkata Rao, D K; Dwivedi, Varun; Shilpashree, H B; Rastogi, Shubhra; Shasany, Ajit K; Nagegowda, Dinesh A

2016-01-01

Aromatic grasses of the genus Cymbopogon (Poaceae family) represent unique group of plants that produce diverse composition of monoterpene rich essential oils, which have great value in flavor, fragrance, cosmetic, and aromatherapy industries. Despite the commercial importance of these natural aromatic oils, their biosynthesis at the molecular level remains unexplored. As the first step toward understanding the essential oil biosynthesis, we performed de novo transcriptome assembly and analysis of C. flexuosus (lemongrass) by employing Illumina sequencing. Mining of transcriptome data and subsequent phylogenetic analysis led to identification of terpene synthases, pyrophosphatases, alcohol dehydrogenases, aldo-keto reductases, carotenoid cleavage dioxygenases, alcohol acetyltransferases, and aldehyde dehydrogenases, which are potentially involved in essential oil biosynthesis. Comparative essential oil profiling and mRNA expression analysis in three Cymbopogon species (C. flexuosus, aldehyde type; C. martinii, alcohol type; and C. winterianus, intermediate type) with varying essential oil composition indicated the involvement of identified candidate genes in the formation of alcohols, aldehydes, and acetates. Molecular modeling and docking further supported the role of identified protein sequences in aroma formation in Cymbopogon. Also, simple sequence repeats were found in the transcriptome with many linked to terpene pathway genes including the genes potentially involved in aroma biosynthesis. This work provides the first insights into the essential oil biosynthesis of aromatic grasses, and the identified candidate genes and markers can be a great resource for biotechnological and molecular breeding approaches to modulate the essential oil composition.

Sulfur Transformation during Microwave and Conventional Pyrolysis of Sewage Sludge.

PubMed

Zhang, Jun; Zuo, Wei; Tian, Yu; Chen, Lin; Yin, Linlin; Zhang, Jie

2017-01-03

The sulfur distributions and evolution of sulfur-containing compounds in the char, tar and gas fractions were investigated during the microwave and conventional pyrolysis of sewage sludge. Increased accumulation of sulfur in the char and less production of H 2 S were obtained from microwave pyrolysis at higher temperatures (500-800 °C). Three similar conversion pathways were identified for the formation of H 2 S during microwave and conventional pyrolysis. The cracking of unstable mercaptan structure in the sludge contributed to the release of H 2 S below 300 °C. The decomposition of aliphatic-S compounds in the tars led to the formation of H 2 S (300-500 °C). The thermal decomposition of aromatic-S compounds in the tars generated H 2 S from 500 to 800 °C. However, the secondary decomposition of thiophene-S compounds took place only in conventional pyrolysis above 700 °C. Comparing the H 2 S contributions from microwave and conventional pyrolysis, the significant increase of H 2 S yields in conventional pyrolysis was mainly attributed to the decomposition of aromatic-S (increasing by 10.4%) and thiophene-S compounds (11.3%). Further investigation on the inhibition mechanism of H 2 S formation during microwave pyrolysis confirmed that, with the special heating characteristics and relative shorter residence time, microwave pyrolysis promoted the retention of H 2 S on CaO and inhibited the secondary cracking of thiophene-S compounds at higher temperatures.

De Novo Sequencing and Analysis of Lemongrass Transcriptome Provide First Insights into the Essential Oil Biosynthesis of Aromatic Grasses

PubMed Central

Meena, Seema; Kumar, Sarma R.; Venkata Rao, D. K.; Dwivedi, Varun; Shilpashree, H. B.; Rastogi, Shubhra; Shasany, Ajit K.; Nagegowda, Dinesh A.

2016-01-01

Aromatic grasses of the genus Cymbopogon (Poaceae family) represent unique group of plants that produce diverse composition of monoterpene rich essential oils, which have great value in flavor, fragrance, cosmetic, and aromatherapy industries. Despite the commercial importance of these natural aromatic oils, their biosynthesis at the molecular level remains unexplored. As the first step toward understanding the essential oil biosynthesis, we performed de novo transcriptome assembly and analysis of C. flexuosus (lemongrass) by employing Illumina sequencing. Mining of transcriptome data and subsequent phylogenetic analysis led to identification of terpene synthases, pyrophosphatases, alcohol dehydrogenases, aldo-keto reductases, carotenoid cleavage dioxygenases, alcohol acetyltransferases, and aldehyde dehydrogenases, which are potentially involved in essential oil biosynthesis. Comparative essential oil profiling and mRNA expression analysis in three Cymbopogon species (C. flexuosus, aldehyde type; C. martinii, alcohol type; and C. winterianus, intermediate type) with varying essential oil composition indicated the involvement of identified candidate genes in the formation of alcohols, aldehydes, and acetates. Molecular modeling and docking further supported the role of identified protein sequences in aroma formation in Cymbopogon. Also, simple sequence repeats were found in the transcriptome with many linked to terpene pathway genes including the genes potentially involved in aroma biosynthesis. This work provides the first insights into the essential oil biosynthesis of aromatic grasses, and the identified candidate genes and markers can be a great resource for biotechnological and molecular breeding approaches to modulate the essential oil composition. PMID:27516768

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota.

PubMed

Defois, Clémence; Ratel, Jérémy; Denis, Sylvain; Batut, Bérénice; Beugnot, Réjane; Peyretaillade, Eric; Engel, Erwan; Peyret, Pierre

2017-01-01

Benzo[ a ]pyrene (B[ a ]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces the pollutant to the digestive tract. Although the metabolism of B[ a ]P by host cells is well known, its impacts on the human gut microbiota, which plays a key role in health and disease, remain unexplored. We performed an in vitro assay using 16S barcoding, metatranscriptomics and volatile metabolomics to study the impact of B[ a ]P on two distinct human fecal microbiota. B[ a ]P exposure did not induce a significant change in the microbial structure; however, it altered the microbial volatolome in a dose-dependent manner. The transcript levels related to several metabolic pathways, such as vitamin and cofactor metabolism, cell wall compound metabolism, DNA repair and replication systems, and aromatic compound metabolism, were upregulated, whereas the transcript levels related to the glycolysis-gluconeogenesis pathway and bacterial chemotaxis toward simple carbohydrates were downregulated. These primary findings show that food pollutants, such as B[ a ]P, alter human gut microbiota activity. The observed shift in the volatolome demonstrates that B[ a ]P induces a specific deviation in the microbial metabolism.

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota

PubMed Central

Defois, Clémence; Ratel, Jérémy; Denis, Sylvain; Batut, Bérénice; Beugnot, Réjane; Peyretaillade, Eric; Engel, Erwan; Peyret, Pierre

2017-01-01

Benzo[a]pyrene (B[a]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces the pollutant to the digestive tract. Although the metabolism of B[a]P by host cells is well known, its impacts on the human gut microbiota, which plays a key role in health and disease, remain unexplored. We performed an in vitro assay using 16S barcoding, metatranscriptomics and volatile metabolomics to study the impact of B[a]P on two distinct human fecal microbiota. B[a]P exposure did not induce a significant change in the microbial structure; however, it altered the microbial volatolome in a dose-dependent manner. The transcript levels related to several metabolic pathways, such as vitamin and cofactor metabolism, cell wall compound metabolism, DNA repair and replication systems, and aromatic compound metabolism, were upregulated, whereas the transcript levels related to the glycolysis-gluconeogenesis pathway and bacterial chemotaxis toward simple carbohydrates were downregulated. These primary findings show that food pollutants, such as B[a]P, alter human gut microbiota activity. The observed shift in the volatolome demonstrates that B[a]P induces a specific deviation in the microbial metabolism. PMID:28861070

Bioanalytical evidence that chemicals in tattoo ink can induce adaptive stress responses.

PubMed

Neale, Peta A; Stalter, Daniel; Tang, Janet Y M; Escher, Beate I

2015-10-15

Tattooing is becoming increasingly popular, particularly amongst young people. However, tattoo inks contain a complex mixture of chemical impurities that may pose a long-term risk for human health. As a first step towards the risk assessment of these complex mixtures we propose to assess the toxicological hazard potential of tattoo ink chemicals with cell-based bioassays. Targeted modes of toxic action and cellular endpoints included cytotoxicity, genotoxicity and adaptive stress response pathways. The studied tattoo inks, which were extracted with hexane as a proxy for the bioavailable fraction, caused effects in all bioassays, with the red and yellow tattoo inks having the greatest response, particularly inducing genotoxicity and oxidative stress response endpoints. Chemical analysis revealed the presence of polycyclic aromatic hydrocarbons in the tested black tattoo ink at concentrations twice the recommended level. The detected polycyclic aromatic hydrocarbons only explained 0.06% of the oxidative stress response of the black tattoo ink, thus the majority of the effect was caused by unidentified components. The study indicates that currently available tattoo inks contain components that induce adaptive stress response pathways, but to evaluate the risk to human health further work is required to understand the toxicokinetics of tattoo ink chemicals in the body. Copyright © 2015 Elsevier B.V. All rights reserved.

Distribution, partition and removal of polycyclic aromatic hydrocarbons (PAHs) during coking wastewater treatment processes.

PubMed

Zhang, Wanhui; Wei, Chaohai; An, Guanfeng

2015-05-01

In this study, we report the performance of a full-scale conventional activated sludge (A-O1-O2) treatment in eliminating polycyclic aromatic hydrocarbons (PAHs). Both aqueous and solid phases along with the coking wastewater treatment processes were analyzed for the presence of 18 PAHs. It was found that the target compounds occurred widely in raw coking wastewater, treated effluent and sludge samples. In the coking wastewater treatment system, 4-5 ring PAHs were the dominant compounds, while 4 rings PAHs predominated in the sludge samples. Over 98% of the PAH removal was achieved in the coking wastewater treatment plant (WWTP), with the total concentration of PAHs being 21.3 ± 1.9 μg L(-1) in the final effluent. During the coking wastewater treatment processes, the association of the lower molecular weight PAH with suspended solids was generally less than 60%, while the association of higher molecular weight PAHs was greater than 90%. High distribution efficiencies (Kdp and Kds) were found, suggesting that adsorption was the potential removal pathway of PAHs. Finally, the mass balances of PAHs in various stages of the coking WWTP were obtained, and the results indicated that adsorption to sludge was the main removal pathway for PAHs in the coking wastewater treatment processes.

A cluster of bacterial genes for anaerobic benzene ring biodegradation

PubMed Central

Egland, Paul G.; Pelletier, Dale A.; Dispensa, Marilyn; Gibson, Jane; Harwood, Caroline S.

1997-01-01

A reductive benzoate pathway is the central conduit for the anaerobic biodegradation of aromatic pollutants and lignin monomers. Benzene ring reduction requires a large input of energy and this metabolic capability has, so far, been reported only in bacteria. To determine the molecular basis for this environmentally important process, we cloned and analyzed genes required for the anaerobic degradation of benzoate and related compounds from the phototrophic bacterium, Rhodopseudomonas palustris. A cluster of 24 genes was identified that includes twelve genes likely to be involved in anaerobic benzoate degradation and additional genes that convert the related compounds 4-hydroxybenzoate and cyclohexanecarboxylate to benzoyl-CoA. Genes encoding benzoyl-CoA reductase, a novel enzyme able to overcome the resonance stability of the aromatic ring, were identified by directed mutagenesis. The gene encoding the ring-cleavage enzyme, 2-ketocyclohexanecarboxyl-CoA hydrolase, was identified by assaying the enzymatic activity of the protein expressed in Escherichia coli. Physiological data and DNA sequence analyses indicate that the benzoate pathway consists of unusual enzymes for ring reduction and cleavage interposed among enzymes homologous to those catalyzing fatty acid degradation. The cloned genes should be useful as probes to identify benzoate degradation genes from other metabolically distinct groups of anaerobic bacteria, such as denitrifying bacteria and sulfate-reducing bacteria. PMID:9177244

Differential metabolism of L-phenylalanine in the formation of aromatic volatiles in melon (Cucumis melo L.) fruit.

PubMed

Gonda, Itay; Davidovich-Rikanati, Rachel; Bar, Einat; Lev, Shery; Jhirad, Pliaa; Meshulam, Yuval; Wissotsky, Guy; Portnoy, Vitaly; Burger, Joseph; Schaffer, Arthur A; Tadmor, Yaakov; Giovannoni, James J; Fei, Zhangjun; Fait, Aaron; Katzir, Nurit; Lewinsohn, Efraim

2018-04-01

Studies on the active pathways and the genes involved in the biosynthesis of L-phenylalanine-derived volatiles in fleshy fruits are sparse. Melon fruit rinds converted stable-isotope labeled L-phe into more than 20 volatiles. Phenylpropanes, phenylpropenes and benzenoids are apparently produced via the well-known phenylpropanoid pathway involving phenylalanine ammonia lyase (PAL) and being (E)-cinnamic acid a key intermediate. Phenethyl derivatives seemed to be derived from L-phe via a separate biosynthetic route not involving (E)-cinnamic acid and PAL. To explore for a biosynthetic route to (E)-cinnamaldehyde in melon rinds, soluble protein cell-free extracts were assayed with (E)-cinnamic acid, CoA, ATP, NADPH and MgSO 4 , producing (E)-cinnamaldehyde in vitro. In this context, we characterized CmCNL, a gene encoding for (E)-cinnamic acid:coenzyme A ligase, inferred to be involved in the biosynthesis of (E)-cinnamaldehyde. Additionally we describe CmBAMT, a SABATH gene family member encoding a benzoic acid:S-adenosyl-L-methionine carboxyl methyltransferase having a role in the accumulation of methyl benzoate. Our approach leads to a more comprehensive understanding of L-phe metabolism into aromatic volatiles in melon fruit. Copyright © 2018 Elsevier Ltd. All rights reserved.

Organization and control of genes encoding catabolic enzymes in Rhizobiaceae. Progress report, March 1993

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

Parke, D.; Ornston, L.N.

1993-03-01

Rhizobiaceae, a diverse bacterial group comprising rhizobia and agrobacteria, symbiotic partnership with plants form nitrogen-fixing nodules on plant roots or are plant pathogens. Phenolic compounds produced by plants serve as inducers of rhizobial nodulation genes and agrobacterial virulence genes reflect their capacity to utilize numerous aromatics, including phenolics, as a source of carbon and energy. In many microbes the aerobic degradation of numerous aromatic compounds to tricarboxylic acid cycle intermediates is achieved by the {beta}-ketoadipate pathway. Our initial studies focused on the organization and regulation of the ketoadipate pathway in Agrobacterium tumefaciens. We have cloned, identified and characterized a novelmore » regulatory gene that modulates expression of an adjacent pca (protocatechuate) structural gene, pcaD. Regulation of pcaD is mediated by the regulatory gene, termed pcaQ, in concert with the intermediate {beta}-carboxy-cis,cis-muconate. {beta}-carboxy-cis,cismuconate is an unstable chemical, not marketed commercially, and it is unlikely to permeate Escherichia coli cells if supplied in media. Because of these factors, characterization of pcaQ in E. coli required an in vivo delivery system for {beta}-carboxycis,cis-muconate. This was accomplished by designing an E. coli strain that expressed an Acinetobacter calcoaceticus pcaA gene for conversion of protocatechuate to {beta}-carboxy-cis,cis-muconate.« less

Organization and control of genes encoding catabolic enzymes in Rhizobiaceae

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

Parke, D.; Ornston, L.N.

1993-03-01

Rhizobiaceae, a diverse bacterial group comprising rhizobia and agrobacteria, symbiotic partnership with plants form nitrogen-fixing nodules on plant roots or are plant pathogens. Phenolic compounds produced by plants serve as inducers of rhizobial nodulation genes and agrobacterial virulence genes reflect their capacity to utilize numerous aromatics, including phenolics, as a source of carbon and energy. In many microbes the aerobic degradation of numerous aromatic compounds to tricarboxylic acid cycle intermediates is achieved by the [beta]-ketoadipate pathway. Our initial studies focused on the organization and regulation of the ketoadipate pathway in Agrobacterium tumefaciens. We have cloned, identified and characterized a novelmore » regulatory gene that modulates expression of an adjacent pca (protocatechuate) structural gene, pcaD. Regulation of pcaD is mediated by the regulatory gene, termed pcaQ, in concert with the intermediate [beta]-carboxy-cis,cis-muconate. [beta]-carboxy-cis,cismuconate is an unstable chemical, not marketed commercially, and it is unlikely to permeate Escherichia coli cells if supplied in media. Because of these factors, characterization of pcaQ in E. coli required an in vivo delivery system for [beta]-carboxycis,cis-muconate. This was accomplished by designing an E. coli strain that expressed an Acinetobacter calcoaceticus pcaA gene for conversion of protocatechuate to [beta]-carboxy-cis,cis-muconate.« less

Structural and Biochemical Characterization of Gentisate 1,2-Dioxygenase from Escherichia coli O157:H7.

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

Adams,M.; Singh, V.; Keller, B.

2006-01-01

Gentisic acid (2,5-dihydroxybenzoic acid) is a key intermediate in aerobic bacterial pathways that are responsible for the metabolism of a large number of aromatic compounds. The critical step of these pathways is the oxygen-dependent reaction catalysed by gentisate 1,2-dioxygenase which opens the aromatic ring of gentisate to form maleylpyruvate. From gentisic acid, the cell derives carbon and energy through the conversion of maleylpyruvate to central metabolites. We have confirmed the annotation of a gentisate 1,2-dioygenase from the pathogenic O157:H7 Escherichia coli strain and present the first structural characterization of this family of enzymes. The identity of the reaction product wasmore » revealed using tandem mass spectroscopy. The operon responsible for the degradation of gentisate in this organism exhibits a high degree of conservation with the gentisate-degrading operons of other pathogenic bacteria, including the Shiga toxin-producing E. coli O103:H2, but does not appear to be present in non-pathogenic strains. The acquisition of the gentisate operon may represent a special adaptation to meet carbon source requirements under conditions of environmental stress and may provide a selective advantage for enterohaemorrhagic E. coli relative to their non-pathogenic counterparts.« less

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.

PubMed

Pereira, Jose Henrique; Heins, Richard A; Gall, Daniel L; McAndrew, Ryan P; Deng, Kai; Holland, Keefe C; Donohue, Timothy J; Noguera, Daniel R; Simmons, Blake A; Sale, Kenneth L; Ralph, John; Adams, Paul D

2016-05-06

There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of β-aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. β-Aryl ether units are typically abundant in lignin, corresponding to 50-70% of all of the intermonomer linkages. Consequently, a comprehensive understanding of enzymatic β-aryl ether (β-ether) cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, and LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the β-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites and on the catalytic mechanisms of these enzymes, comparing them with other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Transport of terrigenous polycyclic aromatic hydrocarbons affected by the coastal upwelling in the northwestern coast of South China Sea.

PubMed

Ya, Miaolei; Wu, Yuling; Li, Yongyu; Wang, Xinhong

2017-10-01

Coastal upwelling prevails in the coast of Hainan Island, the northern South China Sea (SCS) during summer. We studied the influences of the upwelling on the horizontal and vertical transport of terrigenous polycyclic aromatic hydrocarbons (PAHs). PAHs in dissolved and suspended particulate phase of water samples were determined in the upper (depth < 1 m) and water column (depth > 10 m). PAH levels decreased sharply from inshore to offshore to open sea. The results showed that terrestrial input was the main source of coastal PAHs. Perylene, an important indicator of land plant-derived PAH, showed the significant correlation with PAHs (p < 0.005). This implied that fluvial transport was the primary pathway of terrigenous PAHs into the coast of northern SCS. Variations of the concentrations, compositions and diagnostic ratios of PAHs, accompanied the partition equilibrium in the water column, could indicate the selective degradation of PAHs by the plankton affected by upwelling. Different from the "traditional" transport pathway of PAHs in the water column (surface enrichment-depth depletion distribution), the upwelling could provide the original driver to elevate the upward diffusion of sediment entrained contaminants towards the intermediate even the upper waters. It could also enhance the outward diffusion of terrigenous PAHs accompanied by the offshore transport of the upper waters. Therefore, the transport pathway of PAHs can be summarized by the coastal upwelling rising PAHs with their subsequent transport offshore and settling in the adjacent open sea. Copyright © 2017 Elsevier Ltd. All rights reserved.

Discovery of biaryl-4-carbonitriles as antihyperglycemic agents that may act through AMPK-p38 MAPK pathway.

PubMed

Goel, Atul; Nag, Pankaj; Rahuja, Neha; Srivastava, Rohit; Chaurasia, Sumit; Gautam, Sudeep; Chandra, Sharat; Siddiqi, Mohammad Imran; Srivastava, Arvind K

2014-08-25

A series of functionalized biaryl-4-carbonitriles was synthesized in three steps and evaluated for PTP-1B inhibitory activity. Among the synthesized compounds, four biaryls 6a-d showed inhibition (IC50 58-75 μM) against in vitro PTP-1B assay possibly due to interaction with amino acid residues Lys120, Tyr46 through hydrogen bonding and aromatic-aromatic interactions, respectively. Two biaryl-4-carbonitriles 6b and 6c showed improved glucose tolerance, fasting as well as postprandial blood glucose, serum total triglycerides, and increased high-density lipoprotein-cholesterol in SLM, STZ, STZ-S and C57BL/KsJ-db/db animal models. The bioanalysis of 4'-bromo-2,3-dimethyl-5-(piperidin-1-yl)biphenyl-4-carbonitrile (6b) revealed that like insulin, it increased 2-deoxyglucose uptake in skeletal muscle cells (L6 and C2C12 myotubes). The compound 6b significantly up-regulated the genes related to the insulin signaling pathways like AMPK, MAPK including glucose transporter-4 (GLUT-4) gene in muscle tissue of C57BL/KsJ-db/db mice. Furthermore, it was observed that the compound 6b up-regulated PPARα, UCP2 and HNF4α, which are key regulator of glucose, lipid, and fatty acid metabolism. Western blot analysis of the compound 6b showed that it significantly increased the phosphorylation of AMPK and p38 MAPK and ameliorated glucose uptake in C57BL/KsJ-db/db mice through the AMPK-p38 MAPK pathway. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6

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

Pereira, Jose Henrique; Heins, Richard A.; Gall, Daniel L.

There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of β-aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. β-Aryl ether units are typically abundant in lignin, corresponding tomore » 50–70% of all of the intermonomer linkages. Consequently, a comprehensive understanding of enzymatic β-aryl ether (β-ether) cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, and LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the β-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites and on the catalytic mechanisms of these enzymes, comparing them with other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts.« less

Evaluating officially reported polycyclic aromatic hydrocarbon emissions in the Athabasca oil sands region with a multimedia fate model.

PubMed

Parajulee, Abha; Wania, Frank

2014-03-04

Emissions of organic substances with potential toxicity to humans and the environment are a major concern surrounding the rapid industrial development in the Athabasca oil sands region (AOSR). Although concentrations of polycyclic aromatic hydrocarbons (PAHs) in some environmental samples have been reported, a comprehensive picture of organic contaminant sources, pathways, and sinks within the AOSR has yet to be elucidated. We sought to use a dynamic multimedia environmental fate model to reconcile the emissions and residue levels reported for three representative PAHs in the AOSR. Data describing emissions to air compiled from two official sources result in simulated concentrations in air, soil, water, and foliage that tend to fall close to or below the minimum measured concentrations of phenanthrene, pyrene, and benzo(a)pyrene in the environment. Accounting for evaporative emissions (e.g., from tailings pond disposal) provides a more realistic representation of PAH distribution in the AOSR. Such indirect emissions to air were found to be a greater contributor of PAHs to the AOSR atmosphere relative to reported direct emissions to air. The indirect pathway transporting uncontrolled releases of PAHs to aquatic systems via the atmosphere may be as significant a contributor of PAHs to aquatic systems as other supply pathways. Emission density estimates for the three PAHs that account for tailings pond disposal are much closer to estimated global averages than estimates based on the available emissions datasets, which fall close to the global minima. Our results highlight the need for improved accounting of PAH emissions from oil sands operations, especially in light of continued expansion of these operations.

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6

DOE PAGES

Pereira, Jose Henrique; Heins, Richard A.; Gall, Daniel L.; ...

2016-03-03

There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of β-aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. β-Aryl ether units are typically abundant in lignin, corresponding tomore » 50–70% of all of the intermonomer linkages. Consequently, a comprehensive understanding of enzymatic β-aryl ether (β-ether) cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, and LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the β-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites and on the catalytic mechanisms of these enzymes, comparing them with other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts.« less

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6*

PubMed Central

Pereira, Jose Henrique; Heins, Richard A.; Gall, Daniel L.; McAndrew, Ryan P.; Deng, Kai; Holland, Keefe C.; Donohue, Timothy J.; Noguera, Daniel R.; Simmons, Blake A.; Sale, Kenneth L.; Ralph, John; Adams, Paul D.

2016-01-01

There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of β-aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. β-Aryl ether units are typically abundant in lignin, corresponding to 50–70% of all of the intermonomer linkages. Consequently, a comprehensive understanding of enzymatic β-aryl ether (β-ether) cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, and LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the β-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites and on the catalytic mechanisms of these enzymes, comparing them with other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts. PMID:26940872

Stereochemical Consequences of Vinylpyruvate Hydratase-Catalyzed Reactions.

PubMed

Johnson, William H; Stack, Tyler M M; Taylor, Stephanie M; Burks, Elizabeth A; Whitman, Christian P

2016-07-26

A stereochemical analysis has been carried out on two vinylpyruvate hydratases (VPH), which convert 2-hydroxy-2,4-pentadienoate to 2-keto-4S-hydroxypentanoate in meta-fission pathways. Bacterial strains with this pathway can use aromatic compounds as sole sources of energy and carbon. The analysis was carried out using the 5-methyl and 5-chloro derivatives of 2-hydroxy-2,4-pentadienoate with the enzymes from Pseudomonas putida mt-2 (Pp) and Leptothrix cholodnii SP-6 (Lc). In both organisms, VPH is in a complex with the preceding enzyme in the pathway, 4-oxalocrotonate decarboxylase (4-OD). In D2O, a deuteron is incorporated stereospecifically at the C-3 and C-5 positions of product by both Pp and Lc enzymes. Accordingly, the complexes generate (3S,5S)-3,5-[di-D]-2-keto-4S-hydroxyhexanoate and (3S,5R)-3,5-[di-D]-2-keto-4R-hydroxy-5-chloropentanoate (4R and 5R due to a priority numbering change). The substitution at C-5 (CH3 or Cl) or the source of the enzyme (Pp or Lc) does not change the stereochemical outcome. One mechanism that can account for the results is the ketonization of the 5-substituted dienol to the α,β-unsaturated ketone (placing a deuteron at C-5 in D2O), followed by the conjugate addition of water (placing a deuteron at C-3). The stereochemical outcome for VPH (from Pp and Lc) is the same as that reported for a related enzyme, 2-oxo-hept-4-ene-1,7-dioate hydratase, from Escherichia coli C. The combined observations suggest similar mechanisms for these three enzymes that could possibly be common to this group of enzymes.

Genomic and physiological characterization of a laboratory-isolated Acinetobacter schindleri ACE strain that quickly and efficiently catabolizes acetate.

PubMed

Sigala, Juan-Carlos; Suárez, Brisa Paola; Lara, Alvaro R; Borgne, Sylvie Le; Bustos, Patricia; Santamaría, Rosa Isela; González, Víctor; Martinez, Alfredo

2017-07-01

An Acinetobacter strain, designated ACE, was isolated in the laboratory. Phylogenetic tests and average nucleotide identity value comparisons suggested that ACE belongs to the species Acinetobacterschindleri. We report for the first time the complete genome sequence of an A. schindleri strain, which consists of a single circular chromosome of 3 001 209 bp with an overall DNA G+C content of 42.9 mol% and six plasmids that account for 266 844 bp of extrachromosomal material. The presence or absence of genes related to carbon catabolism and antibiotic resistance were in agreement with the phenotypic characterization of ACE. This strain grew faster and with a higher biomass yield on acetate than the reference strain Acinetobacter baylyi ADP1. However, ACE did not use aromatic compounds and was unable to grow on common carbon sources, such as glucose, xylose, glycerol or citrate. The gluconeogenic and the catechol pathways are complete in ACE, but compounds that are converted to protocatechuate did not sustain growth since some genes of this pathway are missing. Likewise, this strain could not grow on glucose because it lacks the genes of the Entner-Doudoroff pathway. Minimal inhibitory concentration data showed that ACE was susceptible to most of the antimicrobial agents recommended for the clinical treatment of Acinetobacter spp. Some genes related to a possible human-microbe interaction were found in the ACE genome. ACE is likely to have a low pathogenic risk, as is the case with other A. schindleri strains. These results provide a valuable reference for broadening the knowledge of the biology of Acinetobacter.

Metabolic transcription analysis of engineered Escherichia coli strains that overproduce L-phenylalanine

PubMed Central

Báez-Viveros, José Luis; Flores, Noemí; Juárez, Katy; Castillo-España, Patricia; Bolivar, Francisco; Gosset, Guillermo

2007-01-01

Background The rational design of L-phenylalanine (L-Phe) overproducing microorganisms has been successfully achieved by combining different genetic strategies such as inactivation of the phosphoenolpyruvate: phosphotransferase transport system (PTS) and overexpression of key genes (DAHP synthase, transketolase and chorismate mutase-prephenate dehydratase), reaching yields of 0.33 (g-Phe/g-Glc), which correspond to 60% of theoretical maximum. Although genetic modifications introduced into the cell for the generation of overproducing organisms are specifically targeted to a particular pathway, these can trigger unexpected transcriptional responses of several genes. In the current work, metabolic transcription analysis (MTA) of both L-Phe overproducing and non-engineered strains using Real-Time PCR was performed, allowing the detection of transcriptional responses to PTS deletion and plasmid presence of genes related to central carbon metabolism. This MTA included 86 genes encoding enzymes of glycolysis, gluconeogenesis, pentoses phosphate, tricarboxylic acid cycle, fermentative and aromatic amino acid pathways. In addition, 30 genes encoding regulatory proteins and transporters for aromatic compounds and carbohydrates were also analyzed. Results MTA revealed that a set of genes encoding carbohydrate transporters (galP, mglB), gluconeogenic (ppsA, pckA) and fermentative enzymes (ldhA) were significantly induced, while some others were down-regulated such as ppc, pflB, pta and ackA, as a consequence of PTS inactivation. One of the most relevant findings was the coordinated up-regulation of several genes that are exclusively gluconeogenic (fbp, ppsA, pckA, maeB, sfcA, and glyoxylate shunt) in the best PTS- L-Phe overproducing strain (PB12-ev2). Furthermore, it was noticeable that most of the TCA genes showed a strong up-regulation in the presence of multicopy plasmids by an unknown mechanism. A group of genes exhibited transcriptional responses to both PTS inactivation and the presence of plasmids. For instance, acs-ackA, sucABCD, and sdhABCD operons were up-regulated in PB12 (PTS mutant that carries an arcB- mutation). The induction of these operons was further increased by the presence of plasmids in PB12-ev2. Some genes involved in the shikimate and specific aromatic amino acid pathways showed down-regulation in the L-Phe overproducing strains, might cause possible metabolic limitations in the shikimate pathway. Conclusion The identification of potential rate-limiting steps and the detection of transcriptional responses in overproducing microorganisms may suggest "reverse engineering" strategies for the further improvement of L-Phe production strains. PMID:17880710

Evidence that Polycyclic Aromatic Hydrocarbons in Two Carbonaceous Chondrites Predate Parent-Body Formation

NASA Technical Reports Server (NTRS)

Plows, F. L.; Elsila, J. E.; Zare, R. N.; Buseck, P. R.

2003-01-01

Organic material in meteorites provides insight into the cosmochemistry of the early solar system. The distribution of polycyclic aromatic hydrocarbons (PAHs) in the Allende and Murchison carbonaceous chondrites was investigated using spatially resolved microprobe laser-desorption laser-ionization mass spectrometry. Sharp chemical gradients of PAHs are associated with specific meteorite features. The ratios of various PAH intensities relative to the smallest PAH, naphthalene, are nearly constant across the sample. These findings suggest a common origin for PAHs dating prior to or contemporary with the formation of the parent body, consistent with proposed interstellar formation mechanisms.

Ingredients for Life (Artist's Concept)

NASA Technical Reports Server (NTRS)

2005-01-01

[figure removed for brevity, see original site] Figure 1: Artist's Conception Symbolically Represents Complex Organic Molecules

This artist's conception symbolically represents complex organic molecules, known as polycyclic aromatic hydrocarbons, seen in the early universe. These large molecules, comprised of carbon and hydrogen, are considered among the building blocks of life.

NASA's Spitzer Space Telescope is the first telescope to see polycyclic aromatic hydrocarbons so early -- 10 billion years further back in time than seen previously. Spitzer detected these molecules in galaxies when our universe was one-fourth of its current age of about 14 billion years.

These complex molecules are very common on Earth. They form any time carbon-based materials are not burned completely. They can be found in sooty exhaust from cars and airplanes, and in charcoal broiled hamburgers and burnt toast.

Polycyclic aromatic hydrocarbons are pervasive in galaxies like our own Milky Way, and play a significant role in star and planet formation.

Essential Oils’ Chemical Characterization and Investigation of Some Biological Activities: A Critical Review

PubMed Central

Dhifi, Wissal; Bellili, Sana; Jazi, Sabrine; Bahloul, Nada; Mnif, Wissem

2016-01-01

This review covers literature data summarizing, on one hand, the chemistry of essential oils and, on the other hand, their most important activities. Essential oils, which are complex mixtures of volatile compounds particularly abundant in aromatic plants, are mainly composed of terpenes biogenerated by the mevalonate pathway. These volatile molecules include monoterpenes (hydrocarbon and oxygenated monoterpens), and also sesquiterpenes (hydrocarbon and oxygenated sesquiterpens). Furthermore, they contain phenolic compounds, which are derived via the shikimate pathway. Thanks to their chemical composition, essential oils possess numerous biological activities (antioxidant, anti-inflammatory, antimicrobial, etc…) of great interest in food and cosmetic industries, as well as in the human health field. PMID:28930135

Gone or just out of sight? The apparent disappearance of aromatic litter components in soils

NASA Astrophysics Data System (ADS)

Klotzbücher, Thimo; Kalbitz, Karsten; Cerli, Chiara; Hernes, Peter J.; Kaiser, Klaus

2016-07-01

Uncertainties concerning stabilization of organic compounds in soil limit our basic understanding on soil organic matter (SOM) formation and our ability to model and manage effects of global change on SOM stocks. One controversially debated aspect is the contribution of aromatic litter components, such as lignin and tannins, to stable SOM forms. In the present opinion paper, we summarize and discuss the inconsistencies and propose research options to clear them. Lignin degradation takes place stepwise, starting with (i) depolymerization and followed by (ii) transformation of the water-soluble depolymerization products. The long-term fate of the depolymerization products and other soluble aromatics, e.g., tannins, in the mineral soils is still a mystery. Research on dissolved organic matter (DOM) composition and fluxes indicates dissolved aromatics are important precursors of stable SOM attached to mineral surfaces and persist in soils for centuries to millennia. Evidence comes from flux analyses in soil profiles, biodegradation assays, and sorption experiments. In contrast, studies on composition of mineral-associated SOM indicate the prevalence of non-aromatic microbial-derived compounds. Other studies suggest the turnover of lignin in soil can be faster than the turnover of bulk SOM. Mechanisms that can explain the apparent fast disappearance of lignin in mineral soils are, however, not yet identified. The contradictions might be explained by analytical problems. Commonly used methods probably detect only a fraction of the aromatics stored in the mineral soil. Careful data interpretation, critical assessment of analytical limitations, and combined studies on DOM and solid-phase SOM could thus be ways to unveil the issues.

Gone or just out of sight? The apparent disappearance of aromatic litter components in soils

NASA Astrophysics Data System (ADS)

Klotzbücher, Thimo; Kalbitz, Karsten; Cerli, Chiara; Hernes, Peter; Kaiser, Klaus

2016-04-01

Uncertainties concerning stabilization of organic compounds in soil limit our basic understanding on soil organic matter (SOM) formation and our ability to model and manage effects of global change on SOM stocks. One controversially debated aspect is the contribution of aromatic litter components, such as lignin and tannins, to stable SOM forms. Here we summarize and discuss the inconsistencies and propose research options to clear them. Lignin degradation takes place step-wise, starting with (i) depolymerisation, followed by (ii) transformation of the water-soluble depolymerization products. The long-term fate of the depolymerization products and other soluble aromatics, e.g., tannins, in the mineral soils is still a mystery. Research on dissolved organic matter (DOM) composition and fluxes indicates dissolved aromatics are important precursors of stable SOM attached to mineral surfaces and persist in soils for centuries to millennia. Evidence comes from flux analyses in soil profiles, biodegradation assays, and sorption experiments. In contrast, studies on composition of mineral-associated SOM indicate the prevalence of non-aromatic microbial-derived compounds. Other studies suggest the turnover of lignin in soil can be faster than the turnover of bulk SOM. Mechanisms that can explain the apparent fast disappearance of lignin in mineral soils are, however, not yet identified. The contradictions might be explained by analytical problems. Commonly used methods probably detect only a fraction of the aromatics stored in the mineral soil. Careful data interpretation, critical assessment of analytical limitations, and combined studies on DOM and solid-phase SOM could thus be ways to unveil the issues.

Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit

PubMed Central

Gupta, Apoorv; Brockman Reizman, Irene M.; Reisch, Christopher R.; Prather, Kristala L. J.

2017-01-01

Metabolic engineering of microorganisms to produce desirable products on an industrial scale can result in unbalanced cellular metabolic networks that reduce productivity and yield. Metabolic fluxes can be rebalanced using dynamic pathway regulation, but few broadly applicable tools are available to achieve this. We present a pathway-independent genetic control module that can be used to dynamically regulate the expression of target genes. We applied our module to identify the optimal point to redirect glycolytic flux into heterologous engineered pathways in Escherichia coli, resulting in 5.5-fold increased titres of myo-inositol and titers of glucaric acid that improved from unmeasurable quantities to >0.8 g/L. Scaled-up production in benchtop bioreactors resulted in almost 10-fold and 5-fold increases in titers of myo-inositol and glucaric acid. We also used our module to control flux into aromatic amino acid biosynthesis to increase titers of shikimate in E. coli from unmeasurable quantities to >100 mg/L. PMID:28191902

Indole-3-acetic acid biosynthesis in Fusarium delphinoides strain GPK, a causal agent of Wilt in Chickpea.

PubMed

Kulkarni, Guruprasad B; Sanjeevkumar, S; Kirankumar, B; Santoshkumar, M; Karegoudar, T B

2013-02-01

Fusarium delphinoides (Ascomycota; Nectriaceae) is an indole-3-acetic acid (IAA) producing plant pathogen and a causal agent of wilt in chickpea. The IAA biosynthetic pathway in F. delphinoides strain GPK (FDG) was examined by analyzing metabolic intermediates and by feeding experiments. Gas chromatograph (GC) analysis of FDG culture filtrates showed the presence of metabolic intermediates of indole-3-pyruvic acid (IPyA), indole-3-acetamide (IAM), and tryptamine (TRA) pathways. The different IAA biosynthetic pathways were further confirmed by identifying the presence of different enzymes of these pathways. Substrate specificity study of aromatic amino acid aminotransferase revealed that the enzyme is highly specific for tryptophan (Trp) and α-ketoglutarate (α-kg) as amino group donor and acceptor, respectively. Furthermore, the concentration-dependent effect of exogenous IAA on fungal growth was established. Low concentration of exogenous IAA increases the fungal growth and at high concentration it decreases the growth of FDG.

Yeast: the soul of beer's aroma--a review of flavour-active esters and higher alcohols produced by the brewing yeast.

PubMed

Pires, Eduardo J; Teixeira, José A; Brányik, Tomás; Vicente, António A

2014-03-01

Among the most important factors influencing beer quality is the presence of well-adjusted amounts of higher alcohols and esters. Thus, a heavy body of literature focuses on these substances and on the parameters influencing their production by the brewing yeast. Additionally, the complex metabolic pathways involved in their synthesis require special attention. More than a century of data, mainly in genetic and proteomic fields, has built up enough information to describe in detail each step in the pathway for the synthesis of higher alcohols and their esters, but there is still place for more. Higher alcohols are formed either by anabolism or catabolism (Ehrlich pathway) of amino acids. Esters are formed by enzymatic condensation of organic acids and alcohols. The current paper reviews the up-to-date knowledge in the pathways involving the synthesis of higher alcohols and esters by brewing yeasts. Fermentation parameters affecting yeast response during biosynthesis of these aromatic substances are also fully reviewed.

Aromatic-degrading Sphingomonas isolates from the deep subsurface

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

Fredrickson, J.K.; Romine, M.F.; Balkwill, D.L.

An obligately aerobic chemoheterotrophic bacterium (strain F199) previously isolated from Southeast Coastal Plain subsurface sediments and shown to degrade toluene, naphthalene, and other aromatic compounds was characterized by analysis of its 16S rRNA nucleotide base sequence and cellular lipid composition. Strain F199 contained 2-OH14:0 and 18:1{omega}7c as the predominant cellular fatty acids and sphingolipids that are characteristic of the genus Sphingomonas. Phylogenetic analysis of its 16SrRNA sequence indicated that F199 was most closely related to Sphingomonas capsulata among the bacteria currently in the Ribosomal Database. Five additional isolates from deep Southeast Coastal Plain sediments were determined by 16S rRNA sequencemore » analysis to be closely related to F199. These strains also contained characteristic sphingolipids. Four of these five strains could also grow on a broad range of aromatic compounds and could mineralize [{sup 14C}]toluene and [{sup 14C}]naphthalene. S. capsulata (ATCC 14666), Sphingomonas paucimobiolis (ATCC 29837), and one of the subsurface isolates were unable to grow on any of the aromatic compounds or mineralize toluene or naphthalene. These results indicate that bacteria within the genus Sphingomonas are present in Southeast Coastal Plain subsurface sediments and that the capacity for degrading a broad range of substituted aromatic compounds appears to be common among Sphingomonas species from this environment. 41 refs., 2 figs., 5 tabs.« less

Structure-Activity Relationships for Rates of Aromatic Amine Oxidation by Manganese Dioxide.

PubMed

Salter-Blanc, Alexandra J; Bylaska, Eric J; Lyon, Molly A; Ness, Stuart C; Tratnyek, Paul G

2016-05-17

New energetic compounds are designed to minimize their potential environmental impacts, which includes their transformation and the fate and effects of their transformation products. The nitro groups of energetic compounds are readily reduced to amines, and the resulting aromatic amines are subject to oxidation and coupling reactions. Manganese dioxide (MnO2) is a common environmental oxidant and model system for kinetic studies of aromatic amine oxidation. In this study, a training set of new and previously reported kinetic data for the oxidation of model and energetic-derived aromatic amines was assembled and subjected to correlation analysis against descriptor variables that ranged from general purpose [Hammett σ constants (σ(-)), pKas of the amines, and energies of the highest occupied molecular orbital (EHOMO)] to specific for the likely rate-limiting step [one-electron oxidation potentials (Eox)]. The selection of calculated descriptors (pKa, EHOMO, and Eox) was based on validation with experimental data. All of the correlations gave satisfactory quantitative structure-activity relationships (QSARs), but they improved with the specificity of the descriptor. The scope of correlation analysis was extended beyond MnO2 to include literature data on aromatic amine oxidation by other environmentally relevant oxidants (ozone, chlorine dioxide, and phosphate and carbonate radicals) by correlating relative rate constants (normalized to 4-chloroaniline) to EHOMO (calculated with a modest level of theory).

Biodegradation of polycyclic aromatic hydrocarbons by Trichoderma species: a mini review.

PubMed

Zafra, German; Cortés-Espinosa, Diana V

2015-12-01

Fungi belonging to Trichoderma genus are ascomycetes found in soils worldwide. Trichoderma has been studied in relation to diverse biotechnological applications and are known as successful colonizers of their common habitats. Members of this genus have been well described as effective biocontrol organisms through the production of secondary metabolites with potential applications as new antibiotics. Even though members of Trichoderma are commonly used for the commercial production of lytic enzymes, as a biological control agent, and also in the food industry, their use in xenobiotic biodegradation is limited. Trichoderma stands out as a genus with a great range of substrate utilization, a high production of antimicrobial compounds, and its ability for environmental opportunism. In this review, we focused on the recent advances in the research of Trichoderma species as potent and efficient aromatic hydrocarbon-degrading organisms, as well as aimed to provide insight into its potential role in the bioremediation of soils contaminated with heavy hydrocarbons. Several Trichoderma species are associated with the ability to metabolize a variety of both high and low molecular weight polycyclic aromatic hydrocarbons (PAHs) such as naphthalene, phenanthrene, chrysene, pyrene, and benzo[a]pyrene. PAH-degrading species include Trichoderma hamatum, Trichoderma harzianum, Trichoderma reesei, Trichoderma koningii, Trichoderma viride, Trichoderma virens, and Trichoderma asperellum using alternate enzyme systems commonly seen in other organisms, such as multicooper laccases, peroxidases, and ring-cleavage dioxygenases. Within these species, T. asperellum stands out as a versatile organism with remarkable degrading abilities, high tolerance, and a remarkable potential to be used as a remediation agent in polluted soils.

Sources and pathways of polycyclic aromatic and saturated hydrocarbons in the Arkona Basin (Southern Baltic Sea, Central Europe)

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

Schulz, H.M.

The Baltic Sea (Central Europe) is surrounded by coastal regions with long histories of industrialization. The heavy metal profiles in the sediments in the center of the Arkona Basin, one of the depressions of the southern Baltic Sea area, clearly reflect the historical anthropogenic influence. The Arkona Basin-is the final sink for materials derived from the Oder river which drains a highly polluted industrial area of Eastern Europe. Surficial muddy sediments from a close-meshed field of sampling-points were analyzed for distribution patterns of aliphatics and quantities and ratios of selected polycyclic aromatic hydrocarbons (PAH). These compounds are thought to reflectmore » anthropogenic pollution related to emissions from traffic, heating, etc. We use these marker substances to test if the basin sediments reflect riverine input, and if additional sources can be identified.« less

Expression of gentisate 1,2-dioxygenase (gdoA) genes involved in aromatic degradation in two haloarchaeal genera.

PubMed

Fairley, D J; Wang, G; Rensing, C; Pepper, I L; Larkin, M J

2006-12-01

Gentisate-1,2-dioxygenase genes (gdoA), with homology to a number of bacterial dioxygenases, and genes encoding a putative coenzyme A (CoA)-synthetase subunit (acdB) and a CoA-thioesterase (tieA) were identified in two haloarchaeal isolates. In Haloarcula sp. D1, gdoA was expressed during growth on 4-hydroxybenzoate but not benzoate, and acdB and tieA were not expressed during growth on any of the aromatic substrates tested. In contrast, gdoA was expressed in Haloferax sp. D1227 during growth on benzoate, 3-hydroxybenzoate, cinnamate and phenylpropionate, and both acdB and tieA were expressed during growth on benzoate, cinnamate and phenylpropionate, but not on 3-hydroxybenzoate. This pattern of induction is consistent with these genes encoding steps in a CoA-mediated benzoate pathway in this strain.

Molecular-Barrier-Enhanced Aromatic Fluorophores in Cocrystals with Unity Quantum Efficiency.

PubMed

Ye, Huanqing; Liu, Guangfeng; Liu, Sheng; Casanova, David; Ye, Xin; Tao, Xutang; Zhang, Qichun; Xiong, Qihua

2018-02-12

Singlet-triplet conversion in organic light-emitting materials introduces non-emissive (dark) and long-lived triplet states, which represents a significant challenge in constraining the optical properties. There have been considerable attempts at separating singlets and triplets in long-chain polymers, scavenging triplets, and quenching triplets with heavy metals; nonetheless, such triplet-induced loss cannot be fully eliminated. Herein, a new strategy of crafting a periodic molecular barrier into the π-conjugated matrices of organic aromatic fluorophores is reported. The molecular barriers effectively block the singlet-to-triplet pathway, resulting in near-unity photoluminescence quantum efficiency (PLQE) of the organic fluorophores. The transient optical spectroscopy measurements confirm the absence of the triplet absorption. These studies provide a general approach to preventing the formation of dark triplet states in organic semiconductors and bring new opportunities for the development of advanced organic optics and photonics. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atmospheric reactions of ortho cresol: Gas phase and aerosol products

NASA Astrophysics Data System (ADS)

Grosjean, Daniel

Photo-oxidation of ortho-cresol (0.5-1.1 ppm) and oxides of nitrogen (0.12-0.66 ppm) in air yielded the following gas-phase products: pyruvic acid, acetaldehyde, formaldehyde, peroxyacetylnitrate, nitrocresol and trace levels of nitric acid and methyl nitrate. particulate phase products included 2-hydroxy3-nitro toluene, 2-hydroxy-5-nitro toluene, 2-hydroxy-3,5-dinitrotoluene and, tentatively, several hydroxynitrocresol isomers. Yields of gas-phase products (0.8 % for pyruvic acid, 5-11 % for the sum of the aromatic ring fragmentation products) and of aerosol products (5-19% on a carbon basis, with particulate carbon formation rates of 30-80 μ g m -3 h -1) are discussed in terms of photochemical reaction pathways. From 60 to 89 % of the initial NO x was consumed in these reactions and a significant fraction of the reacted NO x could be accounted for as particulate nitro-aromatic products.

Evaluating the Substrate Selectivity of Alkyladenine DNA Glycosylase: The Synergistic Interplay of Active Site Flexibility and Water Reorganization.

PubMed

Lenz, Stefan A P; Wetmore, Stacey D

2016-02-09

Human alkyladenine DNA glycosylase (AAG) functions as part of the base excision repair (BER) pathway by cleaving the N-glycosidic bond that connects nucleobases to the sugar-phosphate backbone in DNA. AAG targets a range of structurally diverse purine lesions using nonspecific DNA-protein π-π interactions. Nevertheless, the enzyme discriminates against the natural purines and is inhibited by pyrimidine lesions. This study uses molecular dynamics simulations and seven different neutral or charged substrates, inhibitors, or canonical purines to probe how the bound nucleotide affects the conformation of the AAG active site, and the role of active site residues in dictating substrate selectivity. The neutral substrates form a common DNA-protein hydrogen bond, which results in a consistent active site conformation that maximizes π-π interactions between the aromatic residues and the nucleobase required for catalysis. Nevertheless, subtle differences in DNA-enzyme contacts for different neutral substrates explain observed differential catalytic efficiencies. In contrast, the exocyclic amino groups of the natural purines clash with active site residues, which leads to catalytically incompetent DNA-enzyme complexes due to significant reorganization of active site water. Specifically, water resides between the A nucleobase and the active site aromatic amino acids required for catalysis, while a shift in the position of the general base (E125) repositions (potentially nucleophilic) water away from G. Despite sharing common amino groups, the methyl substituents in cationic purine lesions (3MeA and 7MeG) exhibit repulsion with active site residues, which repositions the damaged bases in the active site in a manner that promotes their excision. Overall, we provide a structural explanation for the diverse yet discriminatory substrate selectivity of AAG and rationalize key kinetic data available for the enzyme. Specifically, our results highlight the complex interplay of many different DNA-protein interactions used by AAG to facilitate BER, as well as the crucial role of the general base and water (nucleophile) positioning. The insights gained from our work will aid the understanding of the function of other enzymes that use flexible active sites to exhibit diverse substrate specificity.

Determining aromatic and aliphatic carboxylic acids in biomass-derived oil samples using 2,4-dinitrophenylhydrazine and liquid chromatography-electrospray injection-mass spectrometry/mass spectrometry

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

Lewis, Sr., Samuel A.; Connatser, Raynella M.; Olarte, Mariefel V.

Here, converting biomass to a useful fuel commonly incorporates the pyrolysis of the biomass feed stock. The base liquid fraction usually contains high concentrations of ketones, aldehydes and carboxylic acids, of which each can cause detrimental issues related to the storage and upgrading process. Knowing the carbonyl species and the concentration of each will provide value information to the pyrolysis researchers, specifically as that community branches into more targeted end-products such as jet fuel or biogenic-derived oxygenate-containing fuel products. The analysis of aldehydes, ketones and small alkyl carboxylic acids using 2,4-dinitrophenylhydrazine (DNPH) derivation method has been well documented and themore » method is commonly used the analytical community. By using liquid chromatograph coupled to tandem mass spectrometry, biomass sample analysis can be complete with identification of most carbonyl species. The issue of identifying isobaric ketone and aldehyde compounds can be resolved by utilizing differences in retention time or characteristic fragment ions of ketones and aldehydes. One issue which could not resolved using published methods was identifying aromatic or large non-aromatic carboxylic acids from their corresponding hydroxyl aldehyde or ketone analogs. By modifying the current method for determining carbonyls in biomass samples, carboxylic and hydroxyl-carbonyl can be determined. A careful adjustment of the pH during the extraction procedure and extended heating time of the DNPH solution allowed for the successful derivation of aromatic carboxylic acids. Like other dinitrophenylhydrazones, carboxylic acid derivatives also produce a unique secondary ion pattern, which was useful to distinguish these species from the non-acid analogs.« less

Determining aromatic and aliphatic carboxylic acids in biomass-derived oil samples using 2,4-dinitrophenylhydrazine and liquid chromatography-electrospray injection-mass spectrometry/mass spectrometry

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

Lewis, Samuel A.; Connatser, Raynella M.; Olarte, Mariefel V.

Converting biomass to a useful fuel commonly incorporates the pyrolysis of the biomass feed stock. The base liquid fraction usually contains high concentrations of ketones, aldehydes and carboxylic acids, of which each can cause detrimental issues related to the storage and upgrading process. Knowing the carbonyl species and the concentration of each will provide value information to the pyrolysis researchers, specifically as that community branches into more targeted end-products such as jet fuel or biogenic-derived oxygenate-containing fuel products. The analysis of aldehydes, ketones and small alkyl carboxylic acids using 2,4-dinitrophenylhydrazine (DNPH) derivation method has been well documented and the methodmore » is commonly used the analytical community. By using liquid chromatograph coupled to tandem mass spectrometry, biomass sample analysis can be complete with identification of most carbonyl species. The issue of identifying isobaric ketone and aldehyde compounds can be resolved by utilizing differences in retention time or characteristic fragment ions of ketones and aldehydes. One issue which could not resolved using published methods was identifying aromatic or large non-aromatic carboxylic acids from their corresponding hydroxyl aldehyde or ketone analogs. By modifying the current method for determining carbonyls in biomass samples, carboxylic and hydroxyl-carbonyl can be determined. A careful adjustment of the pH during the extraction procedure and extended heating time of the DNPH solution allowed for the successful derivation of aromatic carboxylic acids. Like other dinitrophenylhydrazones, carboxylic acid derivatives also produce a unique secondary ion pattern, which was useful to distinguish these species from the non-acid analogs.« less

Determining aromatic and aliphatic carboxylic acids in biomass-derived oil samples using 2,4-dinitrophenylhydrazine and liquid chromatography-electrospray injection-mass spectrometry/mass spectrometry

DOE PAGES

Lewis, Sr., Samuel A.; Connatser, Raynella M.; Olarte, Mariefel V.; ...

2017-11-22

Here, converting biomass to a useful fuel commonly incorporates the pyrolysis of the biomass feed stock. The base liquid fraction usually contains high concentrations of ketones, aldehydes and carboxylic acids, of which each can cause detrimental issues related to the storage and upgrading process. Knowing the carbonyl species and the concentration of each will provide value information to the pyrolysis researchers, specifically as that community branches into more targeted end-products such as jet fuel or biogenic-derived oxygenate-containing fuel products. The analysis of aldehydes, ketones and small alkyl carboxylic acids using 2,4-dinitrophenylhydrazine (DNPH) derivation method has been well documented and themore » method is commonly used the analytical community. By using liquid chromatograph coupled to tandem mass spectrometry, biomass sample analysis can be complete with identification of most carbonyl species. The issue of identifying isobaric ketone and aldehyde compounds can be resolved by utilizing differences in retention time or characteristic fragment ions of ketones and aldehydes. One issue which could not resolved using published methods was identifying aromatic or large non-aromatic carboxylic acids from their corresponding hydroxyl aldehyde or ketone analogs. By modifying the current method for determining carbonyls in biomass samples, carboxylic and hydroxyl-carbonyl can be determined. A careful adjustment of the pH during the extraction procedure and extended heating time of the DNPH solution allowed for the successful derivation of aromatic carboxylic acids. Like other dinitrophenylhydrazones, carboxylic acid derivatives also produce a unique secondary ion pattern, which was useful to distinguish these species from the non-acid analogs.« less

Experimental and Computational Studies of Oxidizer and Fuel Side Addition of Ethanol to Opposed Flow Air/Ethylene Flames

DTIC Science & Technology

2005-02-01

literature to be used in modeling of the results (10). 2. Background The separation of the regions of highest particulate and aromatic concentrations... modeling calculations incorporating the well-characterized C2 combustion mechanism of Frenklach et al. (10). This mechanism was developed for...experimentally and modeled , and shown to occur via different pathways within the context of a detailed chemical mechanism. In particular, ethanol

Heterolytic Activation of Hydrogen Promoted by Ruthenium Nanoparticles immobilized on Basic Supports and Hydrogenation of Aromatic Compounds

NASA Astrophysics Data System (ADS)

Fang, Minfeng

Despite the aggressive development and deployment of new renewable and nuclear technologies, petroleum-derived transportation fuels---gasoline, diesel and jet fuels---will continue to dominate the markets for decades. Environmental legislation imposes severe limits on the tolerable proportion of aromatics, sulfur and nitrogen contents in transportation fuels, which is difficult to achieve with current refining technologies. Catalytic hydrogenation plays an important role in the production of cleaner fuels, both as a direct means to reduce the aromatics and as a key step in the hydrodenitrogenation (HDN) and hydrodesulfurization (HDS) processes. However, conventional catalysts require drastic conditions and/or are easily poisoned by S or N aromatics. Therefore, there is still a need for new efficient catalysts for hydrogenation reactions relevant to the production of cleaner fossil fuels. Our catalyst design involves metallic nanoparticles intimately associated with a basic support, with the aim of creating a nanostructure capable of promoting the heterolytic activation of hydrogen and ionic hydrogenation mechanisms, as a strategy to avoid catalyst poisoning and enhance catalytic activity. We have designed and prepared a new nanostructured catalytic material composed of RuNPs immobilized on the basic polymer P4VPy. We have demonstrated that the Ru/P4VPy catalyst can promote heterolytic hydrogen activation and a unique surface ionic hydrogenation mechanism for the efficient hydrogenation of N-aromatics. This is the first time these ionic hydrogenation pathways have been demonstrated on solid surfaces. For the RuNPs surfaces without basic sites in close proximity, the conventional homolytic H2 splitting is otherwise involved. Using the mechanistic concepts from Ru/P4VPy, we have designed and prepared the Ru/MgO catalyst, with the aim to improve the catalytic efficiency for the hydrogenation of heteroatom aromatics operating by the ionic hydrogenation mechanism. The Ru/MgO catalyst significantly improves the catalytic efficiency for hydrogenation of a variety of N-/S-heteroaromatics and mono-/polycyclic aromatic hydrocarbons representative of components of petroleum-derived fuels. The catalyst is superior to the few other known supported noble metal catalysts for these reactions. Mechanistic studies also point to the ionic hydrogenation mechanism on the Ru/MgO surfaces. In addition, the Ru/MgO catalyst is highly recyclable and long-lived.

Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp.

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

Fredrickson, Jim K.; Balkwill, David L.; Romine, Margaret F.

Several new species of the genus Sphingomonas including S. aromaticivorans, S. stygia, and S. subterranea that have the capacity for degrading a broad range of aromatic compounds including toluene, naphthalene, xylenes, p-cresol, fluorene, biphenyl, and dibenzothiophene, were isolated from deeply-buried (>200 m) sediments of the US Atlantic coastal plain (ACP). In S. aromaticivorans F199, many of the genes involved in the catabolism of these aromatic compounds are encoded on a 184-kb conjugative plasmid; some of the genes involved in aromatic catabolism are plasmid-encoded in the other strains as well. Members of the genus Sphingomonas were common among aerobic heterotrophic bacteriamore » cultured from ACP sediments and have been detected in deep subsurface environments elsewhere. The major source of organic carbon for heterotrophic metabolism in ACP deep aquifers is lignite that originated from plant material buried with the sediments. We speculate that the ability of the subsurface Sphingomonas strains to degrade a wide array of aromatic compounds represents an adaptation for utilization of sedimentary lignite. These and related subsurface Sphingomonas spp may play an important role in the transformation of sedimentary organic carbon in the aerobic and microaerobic regions of the deep aquifers of the ACP.« less

Anti-aging activities of extracts from Tunisian medicinal halophytes and their aromatic constituents

PubMed Central

Jdey, A.; Falleh, H.; Ben Jannet, S.; Mkadmini Hammi, K.; Dauvergne, X.; Magné, C.; Ksouri, R.

2017-01-01

Six medicinal halophytes widely represented in North Africa and commonly used in traditional medicine were screened for pharmacological properties to set out new promising sources of natural ingredients for cosmetic or nutraceutical applications. Thus, Citrullus colocynthis, Cleome arabica, Daemia cordata, Haloxylon articulatum, Pituranthos scoparius and Scorzonera undulata were examined for their in vitro antioxidant (DPPH scavenging and superoxide anion-scavenging, β-carotene bleaching inhibition and iron-reducing tests), antibacterial (microdilution method, against four human pathogenic bacteria) and anti-tyrosinase activities. Besides, their aromatic composition was determined by RP-HPLC. H. articulatum shoot extracts exhibited the strongest antioxidant activity and inhibited efficiently the growth of Salmonella enterica and Escherichia coli. P. scoparius and C. arabica inhibited slightly monophenolase, whereas H. articulatum was the most efficient inhibitor of diphenolase activity. Furthermore, H. articulatum exhibited the highest aromatic content (3.4 % DW), with dopamine as the major compound. These observations suggest that shoot extract of H. articulatum, and to a lesser extent of C. arabica, could be used as antioxidant, antibiotic as well as new natural skin lightening agents. Also, possible implication of aromatic compounds in anti-tyrosinase activity is discussed. PMID:28827992

Anti-aging activities of extracts from Tunisian medicinal halophytes and their aromatic constituents.

PubMed

Jdey, A; Falleh, H; Ben Jannet, S; Mkadmini Hammi, K; Dauvergne, X; Magné, C; Ksouri, R

2017-01-01

Six medicinal halophytes widely represented in North Africa and commonly used in traditional medicine were screened for pharmacological properties to set out new promising sources of natural ingredients for cosmetic or nutraceutical applications. Thus, Citrullus colocynthis , Cleome arabica , Daemia cordata , Haloxylon articulatum , Pituranthos scoparius and Scorzonera undulata were examined for their in vitro antioxidant (DPPH scavenging and superoxide anion-scavenging, β -carotene bleaching inhibition and iron-reducing tests), antibacterial (microdilution method, against four human pathogenic bacteria) and anti-tyrosinase activities. Besides, their aromatic composition was determined by RP-HPLC. H. articulatum shoot extracts exhibited the strongest antioxidant activity and inhibited efficiently the growth of Salmonella enterica and Escherichia coli . P. scoparius and C. arabica inhibited slightly monophenolase, whereas H. articulatum was the most efficient inhibitor of diphenolase activity. Furthermore, H. articulatum exhibited the highest aromatic content (3.4 % DW), with dopamine as the major compound. These observations suggest that shoot extract of H. articulatum , and to a lesser extent of C. arabica , could be used as antioxidant, antibiotic as well as new natural skin lightening agents. Also, possible implication of aromatic compounds in anti-tyrosinase activity is discussed.

Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp.

PubMed

Fredrickson, J K; Balkwill, D L; Romine, M F; Shi, T

1999-10-01

Several new species of the genus Sphingomonas including S. aromaticivorans, S. stygia, and S. subterranea that have the capacity for degrading a broad range of aromatic compounds including toluene, naphthalene, xylenes, p-cresol, fluorene, biphenyl, and dibenzothiophene, were isolated from deeply-buried (>200 m) sediments of the US Atlantic coastal plain (ACP). In S. aromaticivorans F199, many of the genes involved in the catabolism of these aromatic compounds are encoded on a 184-kb conjugative plasmid; some of the genes involved in aromatic catabolism are plasmid-encoded in the other strains as well. Members of the genus Sphingomonas were common among aerobic heterotrophic bacteria cultured from ACP sediments and have been detected in deep subsurface environments elsewhere. The major source of organic carbon for heterotrophic metabolism in ACP deep aquifers is lignite that originated from plant material buried with the sediments. We speculate that the ability of the subsurface Sphingomonas strains to degrade a wide array of aromatic compounds represents an adaptation for utilization of sedimentary lignite. These and related subsurface Sphingomonas spp may play an important role in the transformation of sedimentary organic carbon in the aerobic and microaerobic regions of the deep aquifers of the ACP.

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.

L-Tryptophan Production in Escherichia coli Improved by Weakening the Pta-AckA Pathway

PubMed Central

Liu, Lina; Duan, Xuguo; Wu, Jing

2016-01-01

Acetate accumulation during the fermentation process of Escherichia coli FB-04, an L-tryptophan production strain, is detrimental to L-tryptophan production. In an initial attempt to reduce acetate formation, the phosphate acetyltransferase gene (pta) from E. coli FB-04 was deleted, forming strain FB-04(Δpta). Unfortunately, FB-04(Δpta) exhibited a growth defect. Therefore, pta was replaced with a pta variant (pta1) from E. coli CCTCC M 2016009, forming strain FB-04(pta1). Pta1 exhibits lower catalytic capacity and substrate affinity than Pta because of a single amino acid substitution (Pro69Leu). FB-04(pta1) lacked the growth defect of FB-04(Δpta) and showed improved fermentation performance. Strain FB-04(pta1) showed a 91% increase in L-tryptophan yield in flask fermentation experiments, while acetate production decreased by 35%, compared with its parent FB-04. Throughout the fed-batch fermentation process, acetate accumulation by FB-04(pta1) was slower than that by FB-04. The final L-tryptophan titer of FB-04(pta1) reached 44.0 g/L, representing a 15% increase over that of FB-04. Metabolomics analysis showed that the pta1 genomic substitution slightly decreased carbon flux through glycolysis and significantly increased carbon fluxes through the pentose phosphate and common aromatic pathways. These results indicate that this strategy enhances L-tryptophan production and decreases acetate accumulation during the L-tryptophan fermentation process. PMID:27348810

The transformation of triclosan by laccase: Effect of humic acid on the reaction kinetics, products and pathway.

PubMed

Dou, Rong-Ni; Wang, Jing-Hao; Chen, Yuan-Cai; Hu, Yong-You

2018-03-01

This study systematically explored the effect of humic acid (HA) (as model of natural organic matter) on the kinetics, products and transformation pathway of triclosan (TCS) by laccase-catalyzed oxidation. It was found that TCS could be effectively transformed by laccase-catalysis, with the apparent second-order rate constant being 0.056 U -1 mL min -1 . HA inhibited the removal rate of TCS. HA-induced inhibition was negatively correlated with HA concentration in the range of 0-10 mg L -1 and pH-dependent from 3.5 to 9.5. FT-IR and 13 C NMR spectra showed a decrease of aromatic hydroxyl (phenolic) groups and an increase of aromatic ether groups, indicating the cross-linking of HA via C-O-C and C-N-C bonds during enzyme-catalyzed oxidation. Ten principle oxidative products, including two quinone-like products (2-chlorohydroquinone, 2-chloro-5-(2,4-dichlodichlorophenoxy)-(1,4)benzoquinone), one chlorinated phenol (2,4-dichlorophenol (2,4-DCP)), three dimers, two trimmers and two tetramers, were detected by gas chromatograghy/mass spectrometry (GC-MS) and high performance liquid chromatography/quadrupole time-of-flight/mass spectrometry (HPLC/Q-TOF/MS). The presence of HA induced significantly lesser generation of self-polymers and enhanced cross-coupling between HA and self-polymers via C-O-C, C-N-C and C-C coupling pathways. A plausible transformation pathway was proposed as follows: TCS was initially oxidized to form reactive phenoxyl radicals, which self-coupled to each other subsequently by C-C and C-O pathway, yielding self-polymers. In addition, the scission of ether bond was also observed. The presence of HA can promote scission of ether bond and further oxidation of phenoxyl radicals, forming hydroxylated or quinone-like TCS. This study shed light on the behavior of TCS in natural environment and engineered processes, as well provided a perspective for the water/wastewater treatment using enzyme-catalyzed oxidation techniques. Copyright © 2017 Elsevier Ltd. All rights reserved.

Phenol and Benzoate Metabolism by Pseudomonas putida: Regulation of Tangential Pathways

PubMed Central

Feist, Carol F.; Hegeman, G. D.

1969-01-01

Catechol occurs as an intermediate in the metabolism of both benzoate and phenol by strains of Pseudomonas putida. During growth at the expense of benzoate, catechol is cleaved ortho (1,2-oxygenase) and metabolized via the β-ketoadipate pathway; during growth at the expense of phenol or cresols, the catechol or substituted catechols formed are metabolized by a separate pathway following meta (2,3-oxygenase) cleavage of the aromatic ring of catechol. It is possible to explain the mutually exclusive occurrence of the meta and ortho pathway enzymes in phenol- and benzoate-grown cells of P. putida on the basis of differences in the mode of regulation of these two pathways. By use of both nonmetabolizable inducers and blocked mutants, gratuitous synthesis of some of the meta pathway enzymes was obtained. All four enzymes of the meta pathway are induced by the primary substrate, cresol or phenol, or its analogue. Three enzymes of the ortho pathway that catalyze the conversion of catechol to β-ketoadipate enol-lactone are induced by cis,cis-muconate, produced from catechol by 1,2-oxygenase-mediated cleavage. Observations on the differences in specificity of induction and function of the two pathways suggest that they are not really either tangential or redundant. The meta pathway serves as a general mechanism for catabolism of various alkyl derivatives of catechol derived from substituted phenolic compounds. The ortho pathway is more specific and serves primarily in the catabolism of precursors of catechol and catechol itself. PMID:5354952

Genome wide transcriptome profiling reveals differential gene expression in secondary metabolite pathway of Cymbopogon winterianus.

PubMed

Devi, Kamalakshi; Mishra, Surajit K; Sahu, Jagajjit; Panda, Debashis; Modi, Mahendra K; Sen, Priyabrata

2016-02-15

Advances in transcriptome sequencing provide fast, cost-effective and reliable approach to generate large expression datasets especially suitable for non-model species to identify putative genes, key pathway and regulatory mechanism. Citronella (Cymbopogon winterianus) is an aromatic medicinal grass used for anti-tumoral, antibacterial, anti-fungal, antiviral, detoxifying and natural insect repellent properties. Despite of having number of utilities, the genes involved in terpenes biosynthetic pathway is not yet clearly elucidated. The present study is a pioneering attempt to generate an exhaustive molecular information of secondary metabolite pathway and to increase genomic resources in Citronella. Using high-throughput RNA-Seq technology, root and leaf transcriptome was analysed at an unprecedented depth (11.7 Gb). Targeted searches identified majority of the genes associated with metabolic pathway and other natural product pathway viz. antibiotics synthesis along with many novel genes. Terpenoid biosynthesis genes comparative expression results were validated for 15 unigenes by RT-PCR and qRT-PCR. Thus the coverage of these transcriptome is comprehensive enough to discover all known genes of major metabolic pathways. This transcriptome dataset can serve as important public information for gene expression, genomics and function genomics studies in Citronella and shall act as a benchmark for future improvement of the crop.

Elemental carbon and polycyclic aromatic compounds in a 150-year sediment core from Lake Qinghai, Tibetan Plateau, China: influence of regional and local sources and transport pathways.

PubMed

Han, Y M; Wei, C; Bandowe, B A M; Wilcke, W; Cao, J J; Xu, B Q; Gao, S P; Tie, X X; Li, G H; Jin, Z D; An, Z S

2015-04-07

Elemental carbon (EC) and polycyclic aromatic compounds (PACs) are potential proxies for the reconstruction of change in human activities and the origin of air masses in historic times. In this study, the historic deposition of char and soot (the two subtypes of EC) and PACs in a 150-year sediment core from different topographic subbasins of Lake Qinghai on the Qinghai Tibetan Plateau (QTP) were reconstructed. The objective was to explore how the variations in the concentrations of EC and PACs, in the ratios of char to soot and of oxygenated polycyclic aromatic hydrocarbons (OPAHs) to parent PAHs, and in the composition of the PAC mixtures reflect historical changes in climate and human activity and the origin of air masses arriving at the QTP. The deposition fluxes of soot in the different subbasins were similar, averaging 0.18 (range of 0.15-0.25) and 0.16 (0.13-0.23) g m(-2) year(-1), respectively, but they varied for char (averaging 0.11 and 0.22 g m(-2) year(-1), respectively), suggesting ubiquitous atmospheric deposition of soot and local river inputs of char. The different vertical distributions of the char/soot ratios in the different subbasins can be interpreted in terms of the different transport mechanisms of char and soot. An abrupt increase in soot concentrations since 1980 coincides with results from the QTP ice cores that were interpreted to be indicative of soot transport from South Asia. Similar concentration patterns of PAHs with soot and 9,10-anthraquinone/anthracene (9,10-AQ/ANT) ratios all >2.0 suggest regional PAC sources. Increasing PAH/soot ratios and decreasing 9,10-AQ/ANT ratios since the beginning of the 1970s indicate increasing local emissions. The historical trends of these diagnostic ratios indicate an increase in the fossil-fuel contribution since the beginning of the 1970s. The increase of perylene concentrations with increasing core depth and the ratio of perylene to its penta-aromatic isomers indicate that perylene originates mainly from in situ biogenic diagenesis. We demonstrate that the concentrations of EC, char, soot, and PACs in sediments can be used to reconstruct local, regional, and remote sources and transport pathways of pollutants to the QTP.

Recent trends in aviation turbine fuel properties

NASA Technical Reports Server (NTRS)

Friedman, R.

1982-01-01

Plots and tables, compiled from Department of Energy (and predecessor agency) inspection reports from 1969 to 1980, present ranges, averages, extremes, and trends for most of the 22 properties of Jet A aviation turbine fuel. In recent years, average values of aromatics content, mercaptan sulfur content, distillation temperature of 10 percent recovered, smoke point, and freezing point show small but recognizable trends toward their specification limits. About 80 percent of the fuel samples had at least one property near specification, defined as within a standard band about the specification limit. By far the most common near-specification properties were aromatics content, smoke point, and freezing point.

Aromatic interactions and rotational strengths within protein environment: An electronic structural study on β-lactamases from class A

NASA Astrophysics Data System (ADS)

Christov, Christo; Karabencheva, Tatyana; Lodola, Alessio

2008-04-01

β-Lactamases are important enzymes, responsible for bacterial resistance against β-lactam antibiotics. The enzymes from class A are the most common and the most intensively studied. Here we present our electronic structural study on the relationships between electrostatic interactions and chiroptical properties of three enzymes from class A in the following directions: (i) an integrated influence of environment and ionization state on the rotational strengths mechanisms of tyrosine chromophore in TEM-1 β-lactamase; (ii) an effect of electrostatic environment on the mechanisms of aromatic rotational strengths in β-lactamases from Streptomyces albus and Staphylococcus aureus.

Reductive Detoxication of Arylhydroxylamine Carcinogens by Human NADH Cytochrome b5 Reductase and Cytochrome b5

PubMed Central

Kurian, Joseph R.; Chin, Nathaniel A.; Longlais, Brett J.; Hayes, Kristie L.; Trepanier, Lauren A.

2008-01-01

Heterocyclic and aromatic amine carcinogens are thought to lead to tumor initiation via the formation of DNA adducts, and bioactivation to arylhydroxylamine metabolites is necessary for reactivity with DNA. Carcinogenic arylhydroxylamine metabolites are cleared by a microsomal, NADH-dependent, oxygen-insensitive reduction pathway in humans, which may be a source of inter-individual variability in response to aromatic amine carcinogens. The purpose of this study was to characterize the identity of this reduction pathway in human liver. Based on our findings with structurally similar arylhydroxylamine metabolites of therapeutic drugs, we hypothesized that the reductive detoxication of arylhydroxylamine carcinogens was catalyzed by NADH cytochrome b5 reductase (b5R) and cytochrome b5 (cyt b5). We found that reduction of the carcinogenic hydroxylamines of the aromatic amine 4-aminobiphenyl (4-ABP; found in cigarette smoke) and the heterocyclic amine 2- amino-1-methyl-6-phenylimidazo [4,5-b] pyridine (PhIP; found in grilled meats) was indeed catalyzed by a purified system containing only human b5R and cyt b5. Specific activities were 56 to 346-fold higher in the purified system compared to human liver microsomes (HLM), with similar Michaelis-Menten constants (Km values) in both systems. The stoichiometry for b5R and cyt b5 that yielded the highest activity in the purified system was also similar to that found in native HLM (∼1:8 to 1:10). Polyclonal antisera to either b5R or cyt b5 significantly inhibited N-hydroxy-4-aminobiphenyl (NHOH-4-ABP) reduction by 95 and 89%, respectively, and immunoreactive cyt b5 protein content in individual HLM was significantly correlated with individual reduction of both NHOH-4-ABP and N-hydroxy-PhIP (NHOH-PhIP). Finally, titration of HLM into the purified b5R/cyt b5 system did not enhance the efficiency of reduction activity. We conclude that b5R and cyt b5 are together solely capable of the reduction of arylhydroxylamine carcinogens, and we further hypothesize that this pathway may be a source of individual variability with respect to cancer susceptibility following 4-ABP or PhIP exposure. PMID:17040106

Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium

PubMed Central

Kuever, Jan; Visser, Michael; Loeffler, Claudia; Boll, Matthias; Worm, Petra; Sousa, Diana Z.; Plugge, Caroline M.; Schaap, Peter J.; Muyzer, Gerard; Pereira, Ines A.C.; Parshina, Sofiya N.; Goodwin, Lynne A.; Kyrpides, Nikos C.; Detter, Janine; Woyke, Tanja; Chain, Patrick; Davenport, Karen W.; Rohde, Manfred; Spring, Stefan; Klenk, Hans-Peter; Stams, Alfons J.M.

2014-01-01

Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It does not require any vitamins for growth. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes. PMID:25197466

Oxidative degradation of pentachlorophenol by permanganate for ISCO application.

PubMed

Matta, Roger; Chiron, Serge

2018-03-01

Potassium permanganate (KMnO 4 ) has been an effective technology for the in situ chemical oxidation (ISCO) of many organic compounds including chlorinated alkanes and alkenes, but it has rarely been applied for oxidizing aromatic organochlorines. This study confirms the ability of permanganate to oxidize an aromatic chlorinated compound, pentachlorophenol (PCP), in an efficient manner at neutral pH. The rate of the reaction between KMnO 4 and PCP was calculated and the results indicated that the reaction between PCP and permanganate is relatively fast with a second-order rate constant k″ ∼ 30 M -1  s -1 . Besides the kinetic aspect, the authors identified the main reaction by-products, and proposed a possible reaction mechanism scheme. The general pathway shows the formation of chlorinated intermediates, and ultimately, the complete mineralization to chloride, water, and CO 2 confirmed by total organic carbon and chloride measurement in solution. Flow-through column experiments, consisting of flushing a PCP-contaminated sandy or natural soil with oxidant, showed the good ability of permanganate to eliminate the pollutant. After 24 h of treatment, 77% and 56% of PCP abatement were obtained for sandy and natural soil, respectively. These findings show the high potential of permanganate for the in situ remediation of aromatic organochlorine contaminated soils.

Enhanced Photoreduction of Nitro-aromatic Compounds by Hydrated Electrons Derived from Indole on Natural Montmorillonite.

PubMed

Tian, Haoting; Guo, Yong; Pan, Bo; Gu, Cheng; Li, Hui; Boyd, Stephen A

2015-07-07

A new photoreduction pathway for nitro-aromatic compounds (NACs) and the underlying degradation mechanism are described. 1,3-Dinitrobenzene was reduced to 3-nitroaniline by the widely distributed aromatic molecule indole; the reaction is facilitated by montmorillonite clay mineral under both simulated and natural sunlight irradiation. The novel chemical reaction is strongly affected by the type of exchangeable cation present on montmorillonite. The photoreduction reaction is initiated by the adsorption of 1,3-dinitrobenzene and indole in clay interlayers. Under light irradiation, the excited indole molecule generates a hydrated electron and the indole radical cation. The structural negative charge of montmorillonite plausibly stabilizes the radical cation hence preventing charge recombination. This promotes the release of reactive hydrated electrons for further reductive reactions. Similar results were observed for the photoreduction of nitrobenzene. In situ irradiation time-resolved electron paramagnetic resonance and Fourier transform infrared spectroscopies provided direct evidence for the generation of hydrated electrons and the indole radical cations, which supported the proposed degradation mechanism. In the photoreduction process, the role of clay mineral is to both enhance the generation of hydrated electrons and to provide a constrained reaction environment in the galley regions, which increases the probability of contact between NACs and hydrated electrons.

Pseudomonas putida as a platform for the synthesis of aromatic compounds.

PubMed

Molina-Santiago, Carlos; Cordero, Baldo F; Daddaoua, Abdelali; Udaondo, Zulema; Manzano, Javier; Valdivia, Miguel; Segura, Ana; Ramos, Juan-Luis; Duque, Estrella

2016-09-01

Aromatic compounds such as l-phenylalanine, 2-phenylethanol and trans-cinnamate are aromatic compounds of industrial interest. Current trends support replacement of chemical synthesis of these compounds by 'green' alternatives produced in microbial cell factories. The solvent-tolerant Pseudomonas putida DOT-T1E strain was genetically modified to produce up to 1 g l-1 of l-phenylalanine. In order to engineer this strain, we carried out the following stepwise process: (1) we selected random mutants that are resistant to toxic phenylalanine analogues; (2) we then deleted up to five genes belonging to phenylalanine metabolism pathways, which greatly diminished the internal metabolism of phenylalanine; and (3) in these mutants, we overexpressed the pheAfbr gene, which encodes a recombinant variant of PheA that is insensitive to feedback inhibition by phenylalanine. Furthermore, by introducing new genes, we were able to further extend the diversity of compounds produced. Introduction of histidinol phosphate transferase (PP_0967), phenylpyruvate decarboxylase (kdc) and an alcohol dehydrogenase (adh) enabled the strain to produce up to 180 mg l-1 2-phenylethanol. When phenylalanine ammonia lyase (pal) was introduced, the resulting strain produced up to 200 mg l-1 of trans-cinnamate. These results demonstrate that P. putida can serve as a promising microbial cell factory for the production of l-phenylalanine and related compounds.

Reflectance spectroscopy (350-2500 nm) of solid-state polycyclic aromatic hydrocarbons (PAHs)

NASA Astrophysics Data System (ADS)

Izawa, M. R. M.; Applin, D. M.; Norman, L.; Cloutis, E. A.

2014-07-01

Polycyclic aromatic hydrocarbons (PAHs) are organic compounds based on fused aromatic rings, and are formed in a variety of astrophysical, solar nebula and planetary processes. Polycyclic aromatic hydrocarbons are known or suspected to occur in a wide variety of planetary settings including icy satellites, Titan’s hazes, carbonaceous meteorites, comet nuclei, ring particles; and terrestrial organic-rich lithologies such as coals, asphaltites, and bituminous sands. Relatively few measurements of the visible and near-infrared spectra of PAHs exist, yet this wavelength region (350-2500 nm) is widely used for remote sensing. This study presents detailed analyses of the 350-2500 nm reflectance spectra of 47 fine-grained powders of different high-purity solid-state PAHs. Spectral properties of PAHs change with variations in the number and connectivity of linked aromatic rings and the presence and type of side-groups and heterocycles. PAH spectra are characterized by three strong features near ∼880 nm, ∼1145 nm, and ∼1687 nm due to overtones of νCH fundamental stretching vibrations. Some PAHs are amenable to remote detection due to the presence of diagnostic spectral features, including: Nsbnd H stretching overtones at 1490-1515 nm in NH- and NH2-bearing PAHs, aliphatic or saturated bond Csbnd H overtone vibrations at ∼1180-1280 nm and ∼1700-1860 nm; a broad asymmetric feature between ∼1450 nm and ∼1900 nm due to Osbnd H stretching overtones in aromatic alcohols, Csbnd H and Cdbnd O combinations near ∼2000-2010 nm and ∼2060-2270 nm in acetyl and carboxyl-bearing PAHs. Other substituents such as sulphonyl, thioether ether and carboxyl heterocycles, or cyano, nitrate, and aromatic side groups, do not produce well-resolved diagnostic spectral features but do cause shifts in the positions of the aromatic Csbnd H vibrational overtone features. Fluorescence is commonly suppressed by the presence of heterocycles, side-groups and in many non-alternant PAHs. The spectral characteristics of PAHs offer the potential, under suitable circumstances, for remote characterization of the classes of PAH present and in some cases, identification of particular heterocyclic or side-group substituents.

Evaluating officially reported polycyclic aromatic hydrocarbon emissions in the Athabasca oil sands region with a multimedia fate model

PubMed Central

Parajulee, Abha; Wania, Frank

2014-01-01

Emissions of organic substances with potential toxicity to humans and the environment are a major concern surrounding the rapid industrial development in the Athabasca oil sands region (AOSR). Although concentrations of polycyclic aromatic hydrocarbons (PAHs) in some environmental samples have been reported, a comprehensive picture of organic contaminant sources, pathways, and sinks within the AOSR has yet to be elucidated. We sought to use a dynamic multimedia environmental fate model to reconcile the emissions and residue levels reported for three representative PAHs in the AOSR. Data describing emissions to air compiled from two official sources result in simulated concentrations in air, soil, water, and foliage that tend to fall close to or below the minimum measured concentrations of phenanthrene, pyrene, and benzo(a)pyrene in the environment. Accounting for evaporative emissions (e.g., from tailings pond disposal) provides a more realistic representation of PAH distribution in the AOSR. Such indirect emissions to air were found to be a greater contributor of PAHs to the AOSR atmosphere relative to reported direct emissions to air. The indirect pathway transporting uncontrolled releases of PAHs to aquatic systems via the atmosphere may be as significant a contributor of PAHs to aquatic systems as other supply pathways. Emission density estimates for the three PAHs that account for tailings pond disposal are much closer to estimated global averages than estimates based on the available emissions datasets, which fall close to the global minima. Our results highlight the need for improved accounting of PAH emissions from oil sands operations, especially in light of continued expansion of these operations. PMID:24596429

Sources and mass inventory of sedimentary polycyclic aromatic hydrocarbons in the Gulf of Thailand: Implications for pathways and energy structure in SE Asia.

PubMed

Hu, Limin; Shi, Xuefa; Qiao, Shuqing; Lin, Tian; Li, Yuanyuan; Bai, Yazhi; Wu, Bin; Liu, Shengfa; Kornkanitnan, Narumol; Khokiattiwong, Somkiat

2017-01-01

Surface sediments obtained from a matrix of 92 sample sites in the Gulf of Thailand (GOT) were analyzed for a comprehensive study of the distribution, sources, and mass inventory of polycyclic aromatic hydrocarbons (PAHs) to assess their input pathways and impacts of the regional land-based energy structure on the deposition of PAHs on the adjacent continental margins. The concentration of 16 PAHs in the GOT ranged from 2.6 to 78.1ng/g (dry weight), and the mean concentration was 19.4±15.1ng/g. The spatial distribution pattern of 16 PAH was generally consistent with that of sediment grain size, suggesting the influence of regional hydrodynamic conditions. Correlation and principal component analysis of the PAHs indicated that direct land-based inputs were dominantly responsible for the occurrence of PAHs in the upper GOT and the low molecular weight (LMW) PAHs in the coastal region could be from petrogenic sources. A positive matrix factorization (PMF) model apportioned five contributors: petroleum residues (~44%), biomass burning (~13%), vehicular emissions (~11%), coal combustion (~6%), and air-water exchange (~25%). Gas absorption may be a significant external input pathway for the volatile PAHs in the open GOT, which further implies that atmospheric loading could be important for the sink of PAHs in the open sea of the Southeast Asia (SE Asia). The different PAH source patterns obtained and a significant disparity of PAH mass inventory in the sediments along the East and Southeast Asia continental margins can be ascribed mainly to different land-based PAH emission features under the varied regional energy structure in addition to the depositional environment and climatic conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous β-Keto Acid.

PubMed

Guimarães, Samuel L; Coitinho, Juliana B; Costa, Débora M A; Araújo, Simara S; Whitman, Christian P; Nagem, Ronaldo A P

2016-05-10

The enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. In a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria Pseudomonas putida G7. In this organism, the 83 kb NAH7 plasmid carries several genes involved in this biotransformation process. One enzyme in this route, NahK, a 4-oxalocrotonate decarboxylase (4-OD), converts 2-oxo-3-hexenedioate to 2-hydroxy-2,4-pentadienoate using Mg(2+) as a cofactor. Efforts to study how 4-OD catalyzes this decarboxylation have been hampered because 4-OD is present in a complex with vinylpyruvate hydratase (VPH), which is the next enzyme in the same pathway. For the first time, a monomeric, stable, and active 4-OD has been expressed and purified in the absence of VPH. Crystal structures for NahK in the apo form and bonded with five substrate analogues were obtained using two distinct crystallization conditions. Analysis of the crystal structures implicates a lid domain in substrate binding and suggests roles for specific residues in a proposed reaction mechanism. In addition, we assign a possible function for the NahK N-terminal domain, which differs from most of the other members of the fumarylacetoacetate hydrolase superfamily. Although the structural basis for metal-dependent β-keto acid decarboxylases has been reported, this is the first structural report for that of a vinylogous β-keto acid decarboxylase and the first crystal structure of a 4-OD.

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

PubMed Central

Mason, Olivia U; Scott, Nicole M; Gonzalez, Antonio; Robbins-Pianka, Adam; Bælum, Jacob; Kimbrel, Jeffrey; Bouskill, Nicholas J; Prestat, Emmanuel; Borglin, Sharon; Joyner, Dominique C; Fortney, Julian L; Jurelevicius, Diogo; Stringfellow, William T; Alvarez-Cohen, Lisa; Hazen, Terry C; Knight, Rob; Gilbert, Jack A; Jansson, Janet K

2014-01-01

The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ∼4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using 14C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of 14C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)'s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem. PMID:24451203

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

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

Mason, Olivia U.; Scott, Nicole M.; Gonzalez, Antonio

The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ~4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using 14C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, bothmore » of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of 14C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)’s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem.« less

Analysis of the magnetically induced current density of molecules consisting of annelated aromatic and antiaromatic hydrocarbon rings.

PubMed

Sundholm, Dage; Berger, Raphael J F; Fliegl, Heike

2016-06-21

Magnetically induced current susceptibilities and current pathways have been calculated for molecules consisting of two pentalene groups annelated with a benzene (1) or naphthalene (2) moiety. Current strength susceptibilities have been obtained by numerically integrating separately the diatropic and paratropic contributions to the current flow passing planes through chosen bonds of the molecules. The current density calculations provide novel and unambiguous current pathways for the unusual molecules with annelated aromatic and antiaromatic hydrocarbon moieties. The calculations show that the benzene and naphthalene moieties annelated with two pentalene units as in molecules 1 and 2, respectively, are unexpectedly antiaromatic sustaining only a local paratropic ring current around the ring, whereas a weak diatropic current flows around the C-H moiety of the benzene ring. For 1 and 2, the individual five-membered rings of the pentalenes are antiaromatic and a slightly weaker semilocal paratropic current flows around the two pentalene rings. Molecules 1 and 2 do not sustain any net global ring current. The naphthalene moiety of the molecule consisting of a naphthalene annelated with two pentalene units (3) does not sustain any strong ring current that is typical for naphthalene. Instead, half of the diatropic current passing the naphthalene moiety forms a zig-zag pattern along the C-C bonds of the naphthalene moiety that are not shared with the pentalene moieties and one third of the current continues around the whole molecule partially cancelling the very strong paratropic semilocal ring current of the pentalenes. For molecule 3, the pentalene moieties and the individual five-membered rings of the pentalenes are more antiaromatic than for 1 and 2. The calculated current patterns elucidate why the compounds with formally [4n + 2] π-electrons have unusual aromatic properties violating the Hückel π-electron count rule. The current density calculations also provide valuable information for interpreting the measured (1)H NMR spectra.

Comparison of UV/hydrogen peroxide, potassium ferrate(VI), and ozone in oxidizing the organic fraction of oil sands process-affected water (OSPW).

PubMed

Wang, Chengjin; Klamerth, Nikolaus; Messele, Selamawit Ashagre; Singh, Arvinder; Belosevic, Miodrag; Gamal El-Din, Mohamed

2016-09-01

The efficiency of three different oxidation processes, UV/H2O2 oxidation, ferrate(VI) oxidation, and ozonation with and without hydroxyl radical (OH) scavenger tert-butyl alcohol (TBA) on the removal of organic compounds from oil sands process-affected water (OSPW) was investigated and compared. The removal of aromatics and naphthenic acids (NAs) was explored by synchronous fluorescence spectra (SFS), ion mobility spectra (IMS), proton and carbon nuclear magnetic resonance ((1)H and (13)C NMR), and ultra-performance liquid chromatography coupled with time-of-flight mass spectrometry (UPLC TOF-MS). UV/H2O2 oxidation occurred through radical reaction and photolysis, transforming one-ring, two-ring, and three-ring fluorescing aromatics simultaneously and achieving 42.4% of classical NAs removal at 2.0 mM H2O2 and 950 mJ/cm(2) UV dose provided with medium pressure mercury lamp. Ferrate(VI) oxidation exhibited high selectivity, preferentially removing two-ring and three-ring fluorescing aromatics, sulfur-containing NAs (NAs + S), and NAs with high carbon and high hydrogen deficiency. At 2.0 mM Fe(VI), 46.7% of classical NAs was removed. Ozonation achieved almost complete removal of fluorescing aromatics, NAs + S, and classical NAs (NAs with two oxygen atoms) at the dose of 2.0 mM O3. Both molecular ozone reaction and OH reaction were important pathways in transforming the organics in OSPW as supported by ozonation performance with and without TBA. (1)H NMR analyses further confirmed the removal of aromatics and NAs both qualitatively and quantitatively. All the three oxidation processes reduced the acute toxicity towards Vibrio fischeri and on goldfish primary kidney macrophages (PKMs), with ozonation being the most efficient. Copyright © 2016 Elsevier Ltd. All rights reserved.

Intra- versus intermolecular electron transfer in radical nucleophilic aromatic substitution of dihalo(hetero)arenes – a tool for estimating π-conjugation in aromatic systems† †Electronic supplementary information (ESI) available: Experimental details and procedures, 1H and 13C NMR data, GC traces and mass spectra. CCDC 1526301 and 1526302. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc00100b Click here for additional data file. Click here for additional data file.

PubMed Central

Janhsen, B.; Daniliuc, C. G.

2017-01-01

In this paper, the application of the double radical nucleophilic aromatic substitution (SRN1) in various dihalogenated, mostly diiodinated, π-conjugated systems as a tool for qualitatively estimating their π-conjugation is described. This approach uses electron delocalisation as a measure of π-conjugation. Electron injection into the π-system is achieved via reaction of an intermediate aryl radical, itself generated from a dihalogenated π-system via SET-reduction of the C–I bond and subsequent reaction with a thiolate anion. The generated arene radical anion can then further react with the second aryl-halogen moiety within the π-system via an intramolecular electron transfer process. The efficiency of this intramolecular electron transfer is related to the π-conjugation of the radical anion. If the π-conjugation within the aromatic unit is weak, the arene radical anion reacts via an intermolecular ET with the starting dihalide. The intramolecular ET process delivers a product of a double SRN1 substitution whereas the intermolecular ET pathway provides a product of a mono- SRN1 substitution. By simple product analysis of mono- versus double substitution, π-conjugation can be qualitatively evaluated. This mechanistic tool is applied to various dihalogenated π-conjugated systems and the results are discussed within the context of π-conjugation. The conjugation mode within the π-system and the length of the aromatic system are varied, and the effect of relative positioning of the two halides within small π-systems is also addressed. PMID:28580099

Fragmentation pathways of O-alkyl methylphosphonothionocyanidates in the gas phase: toward unambiguous structural characterization of chemicals in the Chemical Weapons Convention framework.

PubMed

Saeidian, Hamid; Babri, Mehran; Ashrafi, Davood; Sarabadani, Mansour; Naseri, Mohammad Taghi

2013-08-01

The electron-impact (EI) mass spectra of a series of O-alkyl methylphosphonothionocyanidates were studied for Chemical Weapons Convention (CWC) purposes. General EI fragmentation pathways were constructed and discussed, and collision-induced dissociation studies of the major EI ions were performed to confirm proposed fragment structures by analyzing fragment ions of deuterated analogs and by use of density functional theory (DFT) calculations. Thiono-thiolo rearrangement, McLafferty-type rearrangement, and a previously unknown intramolecular electrophilic aromatic substitution reaction were observed and confirmed. The study also focused on differentiation of isomeric compounds. Retention indices for all compounds, and an electrophilicity index for several compounds, are reported and interpreted.

Biodegradation of 3-Nitrotyrosine by Burkholderia sp. Strain JS165 and Variovorax paradoxus JS171

DTIC Science & Technology

2006-02-01

Bukhalid, D. M. Gibson, B. R. Crane, and R. Loria. 2004. Nitration of a peptide phytotoxin by bacterial nitric oxide synthase. Nature 429:79–82. 15...The facile isolation and the specific, regulated pathway for 3-nitrotyrosine degradation in natural ecosystems suggest that there is a significant...mechanisms have been established (19). No information is available on the biodegradation of natural nitro- aromatic compounds, such as 3NTyr. We

Draft Genome Sequence of Pseudomonas pachastrellae Strain CCUG 46540T, a Deep-Sea Bacterium.

PubMed

Gomila, Margarita; Mulet, Magdalena; Lalucat, Jorge; García-Valdés, Elena

2017-04-06

Pseudomonas pachastrellae strain CCUG 46540 T (KMM 330 T ) was isolated from a deep-sea sponge specimen collected in the Philippine Sea at a depth of 750 m. The draft genome has an estimated size of 4.0 Mb, exhibits a G+C content of 61.2 mol%, and is predicted to encode 3,592 proteins, including pathways for the degradation of aromatic compounds. Copyright © 2017 Gomila et al.

Draft Genome Sequence of Pseudomonas pachastrellae Strain CCUG 46540T, a Deep-Sea Bacterium

PubMed Central

2017-01-01

ABSTRACT Pseudomonas pachastrellae strain CCUG 46540T (KMM 330T) was isolated from a deep-sea sponge specimen collected in the Philippine Sea at a depth of 750 m. The draft genome has an estimated size of 4.0 Mb, exhibits a G+C content of 61.2 mol%, and is predicted to encode 3,592 proteins, including pathways for the degradation of aromatic compounds. PMID:28385850

Structure-Activity Relationships for Rates of Aromatic Amine Oxidation by Manganese Dioxide

DOE PAGES

Salter-Blanc, Alexandra J.; Bylaska, Eric J.; Lyon, Molly A.; ...

2016-04-13

New energetic compounds are designed to minimize their potential environmental impacts, which includes their transformation and the fate and effects of their transformation products. The nitro groups of energetic compounds are readily reduced to amines, and the resulting aromatic amines are subject to oxidation and coupling reactions. Manganese dioxide (MnO 2) is a common environmental oxidant and model system for kinetic studies of aromatic amine oxidation. Here in this study, a training set of new and previously reported kinetic data for the oxidation of model and energetic-derived aromatic amines was assembled and subjected to correlation analysis against descriptor variables that ranged from general purpose [Hammettmore » $$\\sigma$$ constants ($$\\sigma^-$$), pK as of the amines, and energies of the highest occupied molecular orbital (E HOMO)] to specific for the likely rate-limiting step [one-electron oxidation potentials (E ox)]. The selection of calculated descriptors (pK a), E HOMO, and E ox) was based on validation with experimental data. All of the correlations gave satisfactory quantitative structure-activity relationships (QSARs), but they improved with the specificity of the descriptor. The scope of correlation analysis was extended beyond MnO 2 to include literature data on aromatic amine oxidation by other environmentally relevant oxidants (ozone, chlorine dioxide, and phosphate and carbonate radicals) by correlating relative rate constants (normalized to 4-chloroaniline) to E HOMO (calculated with a modest level of theory).« less

Structure-Activity Relationships for Rates of Aromatic Amine Oxidation by Manganese Dioxide

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

Salter-Blanc, Alexandra J.; Bylaska, Eric J.; Lyon, Molly A.

New energetic compounds are designed to minimize their potential environmental impacts, which includes their transformation and the fate and effects of their transformation products. The nitro groups of energetic compounds are readily reduced to amines, and the resulting aromatic amines are subject to oxidation and coupling reactions. Manganese dioxide (MnO 2) is a common environmental oxidant and model system for kinetic studies of aromatic amine oxidation. Here in this study, a training set of new and previously reported kinetic data for the oxidation of model and energetic-derived aromatic amines was assembled and subjected to correlation analysis against descriptor variables that ranged from general purpose [Hammettmore » $$\\sigma$$ constants ($$\\sigma^-$$), pK as of the amines, and energies of the highest occupied molecular orbital (E HOMO)] to specific for the likely rate-limiting step [one-electron oxidation potentials (E ox)]. The selection of calculated descriptors (pK a), E HOMO, and E ox) was based on validation with experimental data. All of the correlations gave satisfactory quantitative structure-activity relationships (QSARs), but they improved with the specificity of the descriptor. The scope of correlation analysis was extended beyond MnO 2 to include literature data on aromatic amine oxidation by other environmentally relevant oxidants (ozone, chlorine dioxide, and phosphate and carbonate radicals) by correlating relative rate constants (normalized to 4-chloroaniline) to E HOMO (calculated with a modest level of theory).« less

Biotransformation of Trichoderma spp. and their tolerance to aromatic amines, a major class of pollutants.

PubMed

Cocaign, Angélique; Bui, Linh-Chi; Silar, Philippe; Chan Ho Tong, Laetitia; Busi, Florent; Lamouri, Aazdine; Mougin, Christian; Rodrigues-Lima, Fernando; Dupret, Jean-Marie; Dairou, Julien

2013-08-01

Trichoderma spp. are cosmopolitan soil fungi that are highly resistant to many toxic compounds. Here, we show that Trichoderma virens and T. reesei are tolerant to aromatic amines (AA), a major class of pollutants including the highly toxic pesticide residue 3,4-dichloroaniline (3,4-DCA). In a previous study, we provided proof-of-concept remediation experiments in which another soil fungus, Podospora anserina, detoxifies 3,4-DCA through its arylamine N-acetyltransferase (NAT), a xenobiotic-metabolizing enzyme that enables acetyl coenzyme A-dependent detoxification of AA. To assess whether the N-acetylation pathway enables AA tolerance in Trichoderma spp., we cloned and characterized NATs from T. virens and T. reesei. We characterized recombinant enzymes by determining their catalytic efficiencies toward several toxic AA. Through a complementary approach, we also demonstrate that both Trichoderma species efficiently metabolize 3,4-DCA. Finally, we provide evidence that NAT-independent transformation is solely (in T. virens) or mainly (in T. reesei) responsible for the observed removal of 3,4-DCA. We conclude that T. virens and, to a lesser extent, T. reesei likely utilize another, unidentified, metabolic pathway for the detoxification of AA aside from acetylation. This is the first molecular and functional characterization of AA biotransformation in Trichoderma spp. Given the potential of Trichoderma for cleanup of contaminated soils, these results reveal new possibilities in the fungal remediation of AA-contaminated soil.

Photochemical processes on Titan: Irradiation of mixtures of gases that simulate Titan's atmosphere

NASA Astrophysics Data System (ADS)

Tran, Buu N.; Joseph, Jeffrey C.; Force, Michael; Briggs, Robert G.; Vuitton, Veronique; Ferris, James P.

2005-09-01

Photochemical reaction pathways in Titan's atmosphere were investigated by irradiation of the individual components and the mixture containing nitrogen, methane, hydrogen, acetylene, ethylene, and cyanoacetylene. The quantum yields for the loss of the reactants and the formation of products were determined. Photolysis of ethylene yields mainly saturated compounds (ethane, propane, and butane) while photolysis of acetylene yields the same saturated compounds as well as ethylene and diacetylene. Irradiation of cyanoacetylene yields mainly hydrogen cyanide and small amounts of acetonitrile. When an amount of methane corresponding to its mixing ratio on Titan was added to these mixtures the quantum yields for the loss of reactants decreased and the quantum yields for hydrocarbon formation increased indicative of a hydrogen atom abstraction from methane by the photochemically generated radicals. GC/MS analysis of the products formed by irradiation of mixtures of all these gases generated over 120 compounds which were mainly aliphatic hydrocarbons containing double and triple bonds along with much smaller amounts of aromatic compounds like benzene, toluene and phenylacetylene. The reaction pathways were investigated by the use of 13C acetylene in these gas mixtures. No polycyclic aromatic compounds were detected. Vapor pressures of these compounds under conditions present in Titan's atmosphere were calculated. The low molecular weight compounds likely to be present in the atmosphere and aerosols of Titan as a result of photochemical processes are proposed.

Correlation between degradation pathway and toxicity of acetaminophen and its by-products by using the electro-Fenton process in aqueous media.

PubMed

Le, Thi Xuan Huong; Nguyen, Thi Van; Amadou Yacouba, Zoulkifli; Zoungrana, Laetitia; Avril, Florent; Nguyen, Duy Linh; Petit, Eddy; Mendret, Julie; Bonniol, Valerie; Bechelany, Mikhael; Lacour, Stella; Lesage, Geoffroy; Cretin, Marc

2017-04-01

The evolution of the degradation by-products of an acetaminophen (ACE) solution was monitored by HPLC-UV/MS and IC in parallel with its ecotoxicity (Vibrio fischeri 81.9%, Microtox ® screening tests) during electro-Fenton (EF) oxidation performed on carbon felt. The aromatic compounds 2-hydroxy-4-(N-acetyl) aminophenol, 1,4-benzoquinone, benzaldehyde and benzoic acid were identified as toxic sub-products during the first stage of the electrochemical treatment, whereas aliphatic short-chain carboxylic acids (oxalic, maleic, oxamic, formic, acetic and fumaric acids) and inorganic ions (ammonium and nitrate) were well identified as non-toxic terminal sub-products. Electrogenerated hydroxyl radicals then converted the eco-toxic and bio-refractory property of initial ACE molecule (500 mL, 1 mM) and subsequent aromatic sub-products into non-toxic compounds after 2 h of EF treatment. The toxicity of every intermediate produced during the mineralization of ACE was quantified, and a relationship was established between the degradation pathway of ACE and the global toxicity evolution of the solution. After 8 h of treatment, a total organic carbon removal of 86.9% could be reached for 0.1 mM ACE at applied current of 500 mA with 0.2 mM of Fe 2+ used as catalyst. Copyright © 2016 Elsevier Ltd. All rights reserved.

Isolation and Characterization of Thermophilic Bacilli Degrading Cinnamic, 4-Coumaric, and Ferulic Acids

PubMed Central

Peng, Xue; Misawa, Norihiko; Harayama, Shigeaki

2003-01-01

Thirty-four thermophilic Bacillus sp. strains were isolated from decayed wood bark and a hot spring water sample based on their ability to degrade vanillic acid under thermophilic conditions. It was found that these bacteria were able to degrade a wide range of aromatic acids such as cinnamic, 4-coumaric, 3-phenylpropionic, 3-(p-hydroxyphenyl)propionic, ferulic, benzoic, and 4-hydroxybenzoic acids. The metabolic pathways for the degradation of these aromatic acids at 60°C were examined by using one of the isolates, strain B1. Benzoic and 4-hydroxybenzoic acids were detected as breakdown products from cinnamic and 4-coumaric acids, respectively. The β-oxidative mechanism was proposed to be responsible for these conversions. The degradation of benzoic and 4-hydroxybenzoic acids was determined to proceed through catechol and gentisic acid, respectively, for their ring fission. It is likely that a non-β-oxidative mechanism is the case in the ferulic acid catabolism, which involved 4-hydroxy-3-methoxyphenyl-β-hydroxypropionic acid, vanillin, and vanillic acid as the intermediates. Other strains examined, which are V0, D1, E1, G2, ZI3, and H4, were found to have the same pathways as those of strain B1, except that strains V0, D1, and H4 had the ability to transform 3-hydroxybenzoic acid to gentisic acid, which strain B1 could not do. PMID:12620824

Direct Photolysis Rates and Transformation Pathways of the Lampricides TFM and Niclosamide in Simulated Sunlight.

PubMed

McConville, Megan B; Hubert, Terrance D; Remucal, Christina K

2016-09-20

The lampricides 3-trifluoromethyl-4-nitrophenol (TFM) and 2',5-dichloro-4'-nitrosalicylanilide (niclosamide) are directly added to many tributaries of the Great Lakes that harbor the invasive parasitic sea lamprey. Despite their long history of use, the fate of lampricides is not well understood. This study evaluates the rate and pathway of direct photodegradation of both lampricides under simulated sunlight. The estimated half-lives of TFM range from 16.6 ± 0.2 h (pH 9) to 32.9 ± 1.0 h (pH 6), while the half-lives of niclosamide range from 8.88 ± 0.52 days (pH 6) to 382 ± 83 days (pH 9) assuming continuous irradiation over a water depth of 55 cm. Both compounds degrade to form a series of aromatic intermediates, simple organic acids, ring cleavage products, and inorganic ions. Experimental data were used to construct a kinetic model which demonstrates that the aromatic products of TFM undergo rapid photolysis and emphasizes that niclosamide degradation is the rate-limiting step to dehalogenation and mineralization of the lampricide. This study demonstrates that TFM photodegradation is likely to occur on the time scale of lampricide applications (2-5 days), while niclosamide, the less selective lampricide, will undergo minimal direct photodegradation during its passage to the Great Lakes.

Biotransformation of Trichoderma spp. and Their Tolerance to Aromatic Amines, a Major Class of Pollutants

PubMed Central

Cocaign, Angélique; Bui, Linh-Chi; Silar, Philippe; Chan Ho Tong, Laetitia; Busi, Florent; Lamouri, Aazdine; Mougin, Christian; Rodrigues-Lima, Fernando

2013-01-01

Trichoderma spp. are cosmopolitan soil fungi that are highly resistant to many toxic compounds. Here, we show that Trichoderma virens and T. reesei are tolerant to aromatic amines (AA), a major class of pollutants including the highly toxic pesticide residue 3,4-dichloroaniline (3,4-DCA). In a previous study, we provided proof-of-concept remediation experiments in which another soil fungus, Podospora anserina, detoxifies 3,4-DCA through its arylamine N-acetyltransferase (NAT), a xenobiotic-metabolizing enzyme that enables acetyl coenzyme A-dependent detoxification of AA. To assess whether the N-acetylation pathway enables AA tolerance in Trichoderma spp., we cloned and characterized NATs from T. virens and T. reesei. We characterized recombinant enzymes by determining their catalytic efficiencies toward several toxic AA. Through a complementary approach, we also demonstrate that both Trichoderma species efficiently metabolize 3,4-DCA. Finally, we provide evidence that NAT-independent transformation is solely (in T. virens) or mainly (in T. reesei) responsible for the observed removal of 3,4-DCA. We conclude that T. virens and, to a lesser extent, T. reesei likely utilize another, unidentified, metabolic pathway for the detoxification of AA aside from acetylation. This is the first molecular and functional characterization of AA biotransformation in Trichoderma spp. Given the potential of Trichoderma for cleanup of contaminated soils, these results reveal new possibilities in the fungal remediation of AA-contaminated soil. PMID:23728813

Direct photolysis rates and transformation pathways of the lampricides TFM and niclosamide in simulated sunlight

USGS Publications Warehouse

McConville, Megan B.; Hubert, Terrance D.; Remucal, Christina K.

2016-01-01

The lampricides 3-trifluoromethyl-4-nitrophenol (TFM) and 2′,5-dichloro-4′-nitrosalicylanilide (niclosamide) are directly added to many tributaries of the Great Lakes that harbor the invasive parasitic sea lamprey. Despite their long history of use, the fate of lampricides is not well understood. This study evaluates the rate and pathway of direct photodegradation of both lampricides under simulated sunlight. The estimated half-lives of TFM range from 16.6 ± 0.2 h (pH 9) to 32.9 ± 1.0 h (pH 6), while the half-lives of niclosamide range from 8.88 ± 0.52 days (pH 6) to 382 ± 83 days (pH 9) assuming continuous irradiation over a water depth of 55 cm. Both compounds degrade to form a series of aromatic intermediates, simple organic acids, ring cleavage products, and inorganic ions. Experimental data were used to construct a kinetic model which demonstrates that the aromatic products of TFM undergo rapid photolysis and emphasizes that niclosamide degradation is the rate-limiting step to dehalogenation and mineralization of the lampricide. This study demonstrates that TFM photodegradation is likely to occur on the time scale of lampricide applications (2–5 days), while niclosamide, the less selective lampricide, will undergo minimal direct photodegradation during its passage to the Great Lakes.

Characterization and Transcriptome Analysis of Acinetobacter baumannii Persister Cells.

PubMed

Alkasir, Rashad; Ma, Yanan; Liu, Fei; Li, Jing; Lv, Na; Xue, Yong; Hu, Yongfei; Zhu, Baoli

2018-06-14

Acinetobacter baumannii is a nonfermenting Gram-negative bacillus. A. baumannii resistance is a significant obstacle to clinical infection treatment. The existence of persister cells (persisters) might represent the reason for therapy failure and relapse, and such cells may be the driving force behind rising resistance rates. In this study, A. baumannii ATCC 19606 was used as a target to explore the essential features of A. baumannii persisters. Antibiotic treatment of A. baumannii cultures at 50-fold the minimum inhibitory concentration resulted in a distinct plateau of surviving drug-tolerant persisters. The sensitive bacteria were lysed with ceftazidime, and the nonreplicating bacteria were isolated for transcriptome analysis using RNA sequencing. We analyzed the transcriptome of A. baumannii persisters and identified significantly differentially expressed genes, as well as their enriched pathways. The results showed that both the GP49 (HigB)/Cro (HigA) and DUF1044/RelB toxin/antitoxin systems were significantly increased during the persister incubation period. In addition, the activities of certain metabolic pathways (such as electron transport, adenosine triphosphate [ATP], and the citrate cycle) decreased sharply after antibiotic treatment and remained low during the persister period, while aromatic compound degradation genes were only upregulated in persisters. These results suggest the involvement of aromatic compound degradation genes in persister formation and maintenance. They further provide the first insight into the mechanism of persister formation in A. baumannii.

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

Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.

Here, lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, wemore » present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.« less

The Mechanism of Covalent Bonding: Analysis within the Huckel Model of Electronic Structure

ERIC Educational Resources Information Center

Nordholm, Sture; Back, Andreas; Backsay, George B.

2007-01-01

The commonly used Huckel model of electronic structure is employed to study the mechanisms of covalent bonding, a quantum effect related to electron dynamics. The model also explains the conjugation and aromaticity of planar hydrocarbon molecules completely.

RELATIONSHIP BETWEEN METABOLISM AND BIOACCUMULATION OF BENZO[A]PYRENE IN BENTHIC INVERTEBRATES

EPA Science Inventory

The potential influence of polycyclic aromatic hydrocarbon (PAH) metabolism on bioaccumulation is well accepted, but rarely has been examined in many species of benthic invertebrates that commonly are found in contaminated sediments, or used in bioaccumulation or toxicity tests. ...

TOXICITY OF AROMATIC AEROBIC BIOTRANSFORMATION PRODUCTS OF TOLUENE TO HELA CELLS

EPA Science Inventory

Petroleum contamination of groundwater is widely recognized as a serious environmental problem. Toluene (methylbenzene) occurs naturally in crude oil and is commonly found as a contaminant in the subsurface as a result of waste disposal and storage activities. Biological transf...

In silico comparison of genomic regions containing genes coding for enzymes and transcription factors for the phenylpropanoid pathway in Phaseolus vulgaris L. and Glycine max L. Merr

PubMed Central

Reinprecht, Yarmilla; Yadegari, Zeinab; Perry, Gregory E.; Siddiqua, Mahbuba; Wright, Lori C.; McClean, Phillip E.; Pauls, K. Peter

2013-01-01

Legumes contain a variety of phytochemicals derived from the phenylpropanoid pathway that have important effects on human health as well as seed coat color, plant disease resistance and nodulation. However, the information about the genes involved in this important pathway is fragmentary in common bean (Phaseolus vulgaris L.). The objectives of this research were to isolate genes that function in and control the phenylpropanoid pathway in common bean, determine their genomic locations in silico in common bean and soybean, and analyze sequences of the 4CL gene family in two common bean genotypes. Sequences of phenylpropanoid pathway genes available for common bean or other plant species were aligned, and the conserved regions were used to design sequence-specific primers. The PCR products were cloned and sequenced and the gene sequences along with common bean gene-based (g) markers were BLASTed against the Glycine max v.1.0 genome and the P. vulgaris v.1.0 (Andean) early release genome. In addition, gene sequences were BLASTed against the OAC Rex (Mesoamerican) genome sequence assembly. In total, fragments of 46 structural and regulatory phenylpropanoid pathway genes were characterized in this way and placed in silico on common bean and soybean sequence maps. The maps contain over 250 common bean g and SSR (simple sequence repeat) markers and identify the positions of more than 60 additional phenylpropanoid pathway gene sequences, plus the putative locations of seed coat color genes. The majority of cloned phenylpropanoid pathway gene sequences were mapped to one location in the common bean genome but had two positions in soybean. The comparison of the genomic maps confirmed previous studies, which show that common bean and soybean share genomic regions, including those containing phenylpropanoid pathway gene sequences, with conserved synteny. Indels identified in the comparison of Andean and Mesoamerican common bean 4CL gene sequences might be used to develop inter-pool phenylpropanoid pathway gene-based markers. We anticipate that the information obtained by this study will simplify and accelerate selections of common bean with specific phenylpropanoid pathway alleles to increase the contents of beneficial phenylpropanoids in common bean and other legumes. PMID:24046770

Cardiac toxicity of 5-ring polycyclic aromatic hydrocarbons is differentially dependent on the aryl hydrocarbon receptor 2 isoform during zebrafish development

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

Incardona, John P., E-mail: john.incardona@noaa.gov; Linbo, Tiffany L.; Scholz, Nathaniel L.

Petroleum-derived compounds, including polycyclic aromatic hydrocarbons (PAHs), commonly occur as complex mixtures in the environment. Recent studies using the zebrafish experimental model have shown that PAHs are toxic to the embryonic cardiovascular system, and that the severity and nature of this developmental cardiotoxicity varies by individual PAH. In the present study we characterize the toxicity of the relatively higher molecular weight 5-ring PAHs benzo[a]pyrene (BaP), benzo[e]pyrene (BeP), and benzo[k]fluoranthene (BkF). While all three compounds target the cardiovascular system, the underlying role of the ligand-activated aryl hydrocarbon receptor (AHR2) and the tissue-specific induction of the cytochrome p450 metabolic pathway (CYP1A) weremore » distinct for each. BaP exposure (40 {mu}M) produced AHR2-dependent bradycardia, pericardial edema, and myocardial CYP1A immunofluorescence. By contrast, BkF exposure (4-40 {mu}M) caused more severe pericardial edema, looping defects, and erythrocyte regurgitation through the atrioventricular valve that were AHR2-independent (i.e., absent myocardial or endocardial CYP1A induction). Lastly, exposure to BeP (40 {mu}M) yielded a low level of CYP1A+ signal in the vascular endothelium of the head and trunk, without evident toxic effects on cardiac function or morphogenesis. Combined with earlier work on 3- and 4-ring PAHs, our findings provide a more complete picture of how individual PAHs may drive the cardiotoxicity of mixtures in which they predominate. This will improve toxic injury assessments and risk assessments for wild fish populations that spawn in habitats altered by overlapping petroleum-related human impacts such as oil spills, urban stormwater runoff, or sediments contaminated by legacy industrial activities. -- Highlights: Black-Right-Pointing-Pointer PAH compounds with 5 rings in different arrangements caused differential tissue-specific patterns of CYP1A induction in zebrafish embryos. Black-Right-Pointing-Pointer These compounds produced differential cardiac developmental toxicity that did not strictly correlate with associated CYP1A induction. Black-Right-Pointing-Pointer Cardiotoxicity of benzo(a)pyrene was partially dependent on the AHR2 isoform, while benzo(k)fluoranthene cardiotoxicity was not. Black-Right-Pointing-Pointer Individual PAH compounds have distinct toxicokinetic pathways in fish embryos, and act through different toxic mechanisms.« less

Enzymological Basis for Growth Inhibition by l-Phenylalanine in the Cyanobacterium Synechocystis sp. 29108

PubMed Central

Hall, Geraldine C.; Jensen, Roy A.

1980-01-01

The pattern of allosteric control in the biosynthetic pathway for aromatic amino acids provides a basis to explain vulnerability to growth inhibition by l-phenylalanine (0.2 mM or greater) in the unicellular cyanobacterium Synechocystis sp. 29108. We attribute growth inhibition to the hypersensitivity of 3-deoxy-d-arabinoheptulosonate 7-phosphate synthase to feedback inhibition by l-phenylalanine. Hyperregulation of this initial enzyme of aromatic biosynthesis depletes the supply of precursors needed for biosynthesis of l-tyrosine and l-tryptophan. Consistent with this mechanism is the total reversal of phenylalanine inhibition by a combination of tyrosine and tryptophan. Inhibited cultures also contained decreased levels of phycocyanin pigments, a characteristic previously correlated with amino acid starvation in cyanobacteria. l-Phenylalanine is a potent noncompetitive inhibitor (with both substrates) of 3-deoxy-d-arabinoheptulosonate 7-phosphate synthase, whereas l-tyrosine is a very weak inhibitor. Prephenate dehydratase also displays allosteric sensitivity to phenylalanine (inhibition) and to tyrosine (activation). Both 2-fluoro and 4-fluoro derivatives of phenylalanine were potent analog antimetabolites, and these were used in addition to l-phenylalanine as selective agents for resistant mutants. Mutants were isolated which excreted both phenylalanine and tyrosine, the consequence of an altered 3-deoxy-d-arabinoheptulosonate 7-phosphate synthase no longer sensitive to feedback inhibition. Simultaneous insensitivity to l-tyrosine suggests that l-tyrosine acts as a weak analog mimic of l-phenylalanine at a common binding site. Prephenate dehydratase in the regulatory mutants was unaltered. Surprisingly, in view of the lack of regulation in the tyrosine branchlet of the pathway, such mutants excrete more phenylalanine than tyrosine, indicating that l-tyrosine activation dominates l-phenylalanine inhibition of prephenate dehydratase in vivo. In mutant Phe r19 the loss in allosteric sensitivity of 3-deoxy-d-arabinoheptulosonate 7-phosphate synthase was accompanied by a threefold increase in specific activity. This could suggest that existence of a modest degree of repression control (autogenous) over 3-deoxy-d-arabinoheptulosonate synthase, although other explanations are possible. Specific activities of chorismate mutase, prephenate dehydratase, shikimate/nicotinamide adenine dinucleotide phosphate dehydrogenase, and arogenate/nicotinamide adenine dinucleotide phosphate dehydrogenase in mutant Phe r19 were identical with those of the wild type. PMID:6108316

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.

[Polycyclic aromatic hydrocarbons (PAHs) in herbs and fruit teas].

PubMed

Ciemniak, Artur

2005-01-01

Polycyclic aromatic hydrocarbons (PAHs) of which benzo[a]pyrene is the most commonly studied and measured, are fused - ring aromatic compounds formed in both natural and man made processes and are found widely distributed throughout the human environment. PAHs occur as contaminants in different food categories and beverages including water, vegetables, fruit, cereals, oils and fats, barbecued and smoked meat. The sources of PAHs in food are predominantly from environmental pollution and food processing. PAHs emissions from automobile traffic and industry activities were show to influence the PAHs levels in vegetables and fruits. The present study was carried out to determine levels of 16 basic PAHs in herbs and fruit teas. The method was based on the hexane extraction and cleaned up by florisil cartridge. The extracts were analysed by GC-MS. The levels of total PAHs varied from 48,27 microg/kg (hibiscus tea) to 1703 microg/kg (green tea). The highest level of BaP was found in lime tea (74,2 microg/kg).

Polyether-polyester graft copolymer

NASA Technical Reports Server (NTRS)

Bell, Vernon L. (Inventor)

1987-01-01

Described is a polyether graft polymer having improved solvent resistance and crystalline thermally reversible crosslinks. The copolymer is prepared by a novel process of anionic copolymerization. These polymers exhibit good solvent resistance and are well suited for aircraft parts. Previous aromatic polyethers, also known as polyphenylene oxides, have certain deficiencies which detract from their usefulness. These commercial polymers are often soluble in common solvents including the halocarbon and aromatic hydrocarbon types of paint thinners and removers. This limitation prevents the use of these polyethers in structural articles requiring frequent painting. In addition, the most popular commercially available polyether is a very high melting plastic. This makes it considerably more difficult to fabricate finished parts from this material. These problems are solved by providing an aromatic polyether graft copolymer with improved solvent resistance and crystalline thermally reversible crosslinks. The graft copolymer is formed by converting the carboxyl groups of a carboxylated polyphenylene oxide polymer to ionic carbonyl groups in a suitable solvent, reacting pivalolactone with the dissolved polymer, and adding acid to the solution to produce the graft copolymer.

In Vitro Antifungal Activity of New and Known Geranylated Phenols against Phytophthora cinnamomi Rands.

PubMed

Chavez, María I; Soto, Mauricio; Cimino, Franco A; Olea, Andrés F; Espinoza, Luis; Díaz, Katy; Taborga, Lautaro

2018-05-29

A series of new and known geranylated phenol/methoxyphenol derivatives has been tested in vitro as inhibitor agents of mycelial growth of Phytophthora cinnamomi . The activity of tested compounds is correlated with the nature, number, and position of the substituent group on the aromatic ring. Results indicate that the most active geranylated derivatives are those having two hydroxyl groups (or one ⁻OH and one ⁻OCH₃) attached to the aromatic ring. Interestingly, these derivatives are as active as Metalaxil ® , a commonly used commercial fungicide. Thus, our results suggest that some of these compounds might be of agricultural interest due to their potential use as fungicides against P. cinnamomi . The effect of structure on fungicide activity is discussed in terms of electronic distribution on both the aromatic ring and side geranyl chain. All tested compounds have been synthesized by direct coupling of geraniol and the respective phenol. Interestingly, new digeranylated derivatives were obtained by increasing the reaction time.

Particulate matter from both heavy fuel oil and diesel fuel shipping emissions show strong biological effects on human lung cells at realistic and comparable in vitro exposure conditions.

PubMed

Oeder, Sebastian; Kanashova, Tamara; Sippula, Olli; Sapcariu, Sean C; Streibel, Thorsten; Arteaga-Salas, Jose Manuel; Passig, Johannes; Dilger, Marco; Paur, Hanns-Rudolf; Schlager, Christoph; Mülhopt, Sonja; Diabaté, Silvia; Weiss, Carsten; Stengel, Benjamin; Rabe, Rom; Harndorf, Horst; Torvela, Tiina; Jokiniemi, Jorma K; Hirvonen, Maija-Riitta; Schmidt-Weber, Carsten; Traidl-Hoffmann, Claudia; BéruBé, Kelly A; Wlodarczyk, Anna J; Prytherch, Zoë; Michalke, Bernhard; Krebs, Tobias; Prévôt, André S H; Kelbg, Michael; Tiggesbäumker, Josef; Karg, Erwin; Jakobi, Gert; Scholtes, Sorana; Schnelle-Kreis, Jürgen; Lintelmann, Jutta; Matuschek, Georg; Sklorz, Martin; Klingbeil, Sophie; Orasche, Jürgen; Richthammer, Patrick; Müller, Laarnie; Elsasser, Michael; Reda, Ahmed; Gröger, Thomas; Weggler, Benedikt; Schwemer, Theo; Czech, Hendryk; Rüger, Christopher P; Abbaszade, Gülcin; Radischat, Christian; Hiller, Karsten; Buters, Jeroen T M; Dittmar, Gunnar; Zimmermann, Ralf

2015-01-01

Ship engine emissions are important with regard to lung and cardiovascular diseases especially in coastal regions worldwide. Known cellular responses to combustion particles include oxidative stress and inflammatory signalling. To provide a molecular link between the chemical and physical characteristics of ship emission particles and the cellular responses they elicit and to identify potentially harmful fractions in shipping emission aerosols. Through an air-liquid interface exposure system, we exposed human lung cells under realistic in vitro conditions to exhaust fumes from a ship engine running on either common heavy fuel oil (HFO) or cleaner-burning diesel fuel (DF). Advanced chemical analyses of the exhaust aerosols were combined with transcriptional, proteomic and metabolomic profiling including isotope labelling methods to characterise the lung cell responses. The HFO emissions contained high concentrations of toxic compounds such as metals and polycyclic aromatic hydrocarbon, and were higher in particle mass. These compounds were lower in DF emissions, which in turn had higher concentrations of elemental carbon ("soot"). Common cellular reactions included cellular stress responses and endocytosis. Reactions to HFO emissions were dominated by oxidative stress and inflammatory responses, whereas DF emissions induced generally a broader biological response than HFO emissions and affected essential cellular pathways such as energy metabolism, protein synthesis, and chromatin modification. Despite a lower content of known toxic compounds, combustion particles from the clean shipping fuel DF influenced several essential pathways of lung cell metabolism more strongly than particles from the unrefined fuel HFO. This might be attributable to a higher soot content in DF. Thus the role of diesel soot, which is a known carcinogen in acute air pollution-induced health effects should be further investigated. For the use of HFO and DF we recommend a reduction of carbonaceous soot in the ship emissions by implementation of filtration devices.

Particulate Matter from Both Heavy Fuel Oil and Diesel Fuel Shipping Emissions Show Strong Biological Effects on Human Lung Cells at Realistic and Comparable In Vitro Exposure Conditions

PubMed Central

Dilger, Marco; Paur, Hanns-Rudolf; Schlager, Christoph; Mülhopt, Sonja; Diabaté, Silvia; Weiss, Carsten; Stengel, Benjamin; Rabe, Rom; Harndorf, Horst; Torvela, Tiina; Jokiniemi, Jorma K.; Hirvonen, Maija-Riitta; Schmidt-Weber, Carsten; Traidl-Hoffmann, Claudia; BéruBé, Kelly A.; Wlodarczyk, Anna J.; Prytherch, Zoë; Michalke, Bernhard; Krebs, Tobias; Prévôt, André S. H.; Kelbg, Michael; Tiggesbäumker, Josef; Karg, Erwin; Jakobi, Gert; Scholtes, Sorana; Schnelle-Kreis, Jürgen; Lintelmann, Jutta; Matuschek, Georg; Sklorz, Martin; Klingbeil, Sophie; Orasche, Jürgen; Richthammer, Patrick; Müller, Laarnie; Elsasser, Michael; Reda, Ahmed; Gröger, Thomas; Weggler, Benedikt; Schwemer, Theo; Czech, Hendryk; Rüger, Christopher P.; Abbaszade, Gülcin; Radischat, Christian; Hiller, Karsten; Buters, Jeroen T. M.; Dittmar, Gunnar; Zimmermann, Ralf

2015-01-01

Background Ship engine emissions are important with regard to lung and cardiovascular diseases especially in coastal regions worldwide. Known cellular responses to combustion particles include oxidative stress and inflammatory signalling. Objectives To provide a molecular link between the chemical and physical characteristics of ship emission particles and the cellular responses they elicit and to identify potentially harmful fractions in shipping emission aerosols. Methods Through an air-liquid interface exposure system, we exposed human lung cells under realistic in vitro conditions to exhaust fumes from a ship engine running on either common heavy fuel oil (HFO) or cleaner-burning diesel fuel (DF). Advanced chemical analyses of the exhaust aerosols were combined with transcriptional, proteomic and metabolomic profiling including isotope labelling methods to characterise the lung cell responses. Results The HFO emissions contained high concentrations of toxic compounds such as metals and polycyclic aromatic hydrocarbon, and were higher in particle mass. These compounds were lower in DF emissions, which in turn had higher concentrations of elemental carbon (“soot”). Common cellular reactions included cellular stress responses and endocytosis. Reactions to HFO emissions were dominated by oxidative stress and inflammatory responses, whereas DF emissions induced generally a broader biological response than HFO emissions and affected essential cellular pathways such as energy metabolism, protein synthesis, and chromatin modification. Conclusions Despite a lower content of known toxic compounds, combustion particles from the clean shipping fuel DF influenced several essential pathways of lung cell metabolism more strongly than particles from the unrefined fuel HFO. This might be attributable to a higher soot content in DF. Thus the role of diesel soot, which is a known carcinogen in acute air pollution-induced health effects should be further investigated. For the use of HFO and DF we recommend a reduction of carbonaceous soot in the ship emissions by implementation of filtration devices. PMID:26039251

Common Pharmacophore of Structurally Distinct Small-Molecule Inhibitors of Intracellular Retrograde Trafficking of Ribosome Inactivating Proteins

NASA Astrophysics Data System (ADS)

Yu, Shichao; Park, Jewn Giew; Kahn, Jennifer Nielsen; Tumer, Nilgun E.; Pang, Yuan-Ping

2013-12-01

We reported previously (+/-)-2-(5-methylthiophen-2-yl)-3-phenyl-2,3-dihydroquinazolin-4(1H)-one [(+/-)-Retro-2cycl] as the chemical structure of Retro-2 that showed mouse protection against ricin, a notorious ribosome inactivating protein (RIP). Herein we report our chemical resolution of (+/-)-Retro-2cycl, analog synthesis, and cell-based evaluation showing that the two optically pure enantiomers and their achiral analog have nearly the same degree of cell protection against ricin as (+/-)-Retro-2cycl. We also report our computational studies explaining the lack of stereo preference and revealing a common pharmacophore of structurally distinct inhibitors of intracellular retrograde trafficking of RIPs. This pharmacophore comprises a central aromatic ring o-substituted by an aromatic ring and a moiety bearing an O or S atom attached to sp2 C atom(s). These results offer new insights into lead identification and optimization for RIP antidote development to minimize the global health threat caused by ribosome-inactivating proteins.

Photochemical reactions of aromatic compounds and the concept of the photon as a traceless reagent.

PubMed

Hoffmann, Norbert

2012-11-01

Electronic excitation significantly changes the reactivity of chemical compounds. Compared to ground state reactions, photochemical reactions considerably enlarge the application spectrum of a particular functional group in organic synthesis. Multistep syntheses may be simplified and perspectives for target oriented synthesis (TOS) and diversity oriented synthesis (DOS) are developed. New compound families become available or may be obtained more easily. In contrast to common chemical reagents, photons don't generate side products resulting from the transformation of a chemical reagent. Therefore, they are considered as a traceless reagent. Consequently, photochemical reactions play a central role in the methodology of sustainable chemistry. This aspect has been recognized since the beginning of the 20th century. As with many other photochemical transformations, photochemical reactions of aromatic, benzene-like compounds illustrate well the advantages in this context. Photochemical cycloadditions of aromatic compounds have been investigated for a long time. Currently, they are applied in various fields of organic synthesis. They are also studied in supramolecular structures. The phenomena of reactivity and stereoselectivity are investigated. During recent years, photochemical electron transfer mediated reactions are particularly focused. Such transformations have likewise been performed with aromatic compounds. Reactivity and selectivity as well as application to organic synthesis are studied.

Transformations of Aromatic Compounds by Nitrosomonas europaea

PubMed Central

Keener, William K.; Arp, Daniel J.

1994-01-01

Benzene and a variety of substituted benzenes inhibited ammonia oxidation by intact cells of Nitrosomonas europaea. In most cases, the inhibition was accompanied by transformation of the aromatic compound to a more oxidized product or products. All products detected were aromatic, and substituents were often oxidized but were not separated from the benzene ring. Most transformations were enhanced by (NH4)2SO4 (12.5 mM) and were prevented by C2H2, a mechanism-based inactivator of ammonia monooxygenase (AMO). AMO catalyzed alkyl substituent hydroxylations, styrene epoxidation, ethylbenzene desaturation to styrene, and aniline oxidation to nitrobenzene (and unidentified products). Alkyl substituents were preferred oxidation sites, but the ring was also oxidized to produce phenolic compounds from benzene, ethylbenzene, halobenzenes, phenol, and nitrobenzene. No carboxylic acids were identified. Ethylbenzene was oxidized via styrene to two products common also to oxidation of styrene; production of styrene is suggestive of an electron transfer mechanism for AMO. Iodobenzene and 1,2-dichlorobenzene were oxidized slowly to halophenols; 1,4-dichlorobenzene was not transformed. No 2-halophenols were detected as products. Several hydroxymethyl (-CH2OH)-substituted aromatics and p-cresol were oxidized by C2H2-treated cells to the corresponding aldehydes, benzaldehyde was reduced to benzyl alcohol, and o-cresol and 2,5-dimethylphenol were not depleted. PMID:16349282

Substrate and Enzyme Specificity of the Kinetic Isotope Effects Associated with the Dioxygenation of Nitroaromatic Contaminants.

PubMed

Pati, Sarah G; Kohler, Hans-Peter E; Pabis, Anna; Paneth, Piotr; Parales, Rebecca E; Hofstetter, Thomas B

2016-07-05

Compound-specific isotope analysis (CSIA) is a promising approach for tracking biotransformation of organic pollutants, but isotope fractionation associated with aromatic oxygenations is only poorly understood. We investigated the dioxygenation of a series of nitroaromatic compounds to the corresponding catechols by two enzymes, namely, nitrobenzene and 2-nitrotoluene dioxygenase (NBDO and 2NTDO) to elucidate the enzyme- and substrate-specificity of C and H isotope fractionation. While the apparent (13)C- and (2)H-kinetic isotope effects of nitrobenzene, nitrotoluene isomers, 2,6-dinitrotoluene, and naphthalene dioxygenation by NBDO varied considerably, the correlation of C and H isotope fractionation revealed a common mechanism for nitrobenzene and nitrotoluenes. Similar observations were made for the dioxygenation of these substrates by 2NTDO. Evaluation of reaction kinetics, isotope effects, and commitment-to-catalysis based on experiment and theory showed that rates of dioxygenation are determined by the enzymatic O2 activation and aromatic C oxygenation. The contribution of enzymatic O2 activation to the reaction rate varies for different nitroaromatic substrates of NBDO and 2NTDO. Because aromatic dioxygenation by nonheme iron dioxygenases is frequently the initial step of biodegradation, O2 activation kinetics may also have been responsible for the minor isotope fractionation reported for the oxygenation of other aromatic contaminants.

Lewis Acid Induced Toggle from Ir(II) to Ir(IV) Pathways in Photocatalytic Reactions: Synthesis of Thiomorpholines and Thiazepanes from Aldehydes and SLAP Reagents

PubMed Central

2016-01-01

Redox neutral photocatalytic transformations often require careful pairing of the substrates and photoredox catalysts in order to achieve a catalytic cycle. This can limit the range of viable transformations, as we recently observed in attempting to extend the scope of the photocatalytic synthesis of N-heterocycles using silicon amine protocol (SLAP) reagents to include starting materials that require higher oxidation potentials. We now report that the inclusion of Lewis acids in photocatalytic reactions of organosilanes allows access to a distinct reaction pathway featuring an Ir(III)*/Ir(IV) couple instead of the previously employed Ir(III)*/Ir(II) pathway, enabling the transformation of aromatic and aliphatic aldehydes to thiomorpholines and thiazepanes. The role of the Lewis acid in accepting an electron—either directly or via coordination to an imine—can be extended to other classes of photocatalysts and transformations, including oxidative cyclizations. The combination of light induced reactions and Lewis acids therefore promises access to new pathways and transformations that are not viable using the photocatalysts alone. PMID:28149955

Developmental roles of tyrosine metabolism enzymes in the blood-sucking insect Rhodnius prolixus

PubMed Central

Oliveira, Pedro L.

2017-01-01

The phenylalanine/tyrosine degradation pathway is frequently described as a catabolic pathway that funnels aromatic amino acids into citric acid cycle intermediates. Previously, we demonstrated that the accumulation of tyrosine generated during the hydrolysis of blood meal proteins in Rhodnius prolixus is potentially toxic, a harmful outcome that is prevented by the action of the first two enzymes in the tyrosine degradation pathway. In this work, we further evaluated the relevance of all other enzymes involved in phenylalanine/tyrosine metabolism in the physiology of this insect. The knockdown of most of these enzymes produced a wide spectrum of distinct phenotypes associated with reproduction, development and nymph survival, demonstrating a highly pleiotropic role of tyrosine metabolism. The phenotypes obtained for two of these enzymes, homogentisate dioxygenase and fumarylacetoacetase, have never before been described in any arthropod. To our knowledge, this report is the first comprehensive gene-silencing analysis of an amino acid metabolism pathway in insects. Amino acid metabolism is exceptionally important in haematophagous arthropods due to their particular feeding behaviour. PMID:28469016

Developmental roles of tyrosine metabolism enzymes in the blood-sucking insect Rhodnius prolixus.

PubMed

Sterkel, Marcos; Oliveira, Pedro L

2017-05-17

The phenylalanine/tyrosine degradation pathway is frequently described as a catabolic pathway that funnels aromatic amino acids into citric acid cycle intermediates. Previously, we demonstrated that the accumulation of tyrosine generated during the hydrolysis of blood meal proteins in Rhodnius prolixus is potentially toxic, a harmful outcome that is prevented by the action of the first two enzymes in the tyrosine degradation pathway. In this work, we further evaluated the relevance of all other enzymes involved in phenylalanine/tyrosine metabolism in the physiology of this insect. The knockdown of most of these enzymes produced a wide spectrum of distinct phenotypes associated with reproduction, development and nymph survival, demonstrating a highly pleiotropic role of tyrosine metabolism. The phenotypes obtained for two of these enzymes, homogentisate dioxygenase and fumarylacetoacetase, have never before been described in any arthropod. To our knowledge, this report is the first comprehensive gene-silencing analysis of an amino acid metabolism pathway in insects. Amino acid metabolism is exceptionally important in haematophagous arthropods due to their particular feeding behaviour. © 2017 The Author(s).

Evolution of the biosynthesis of the branched-chain amino acids

NASA Technical Reports Server (NTRS)

Keefe, Anthony D.; Lazcano, Antonio; Miller, Stanley L.

1995-01-01

The origins of the biosynthetic pathways for the branched-chain amino acids cannot be understood in terms of the backwards development of the present acetolactate pathway because it contains unstable intermediates. We propose that the first biosynthesis of the branched-chain amino acids was by the reductive carboxylation of short branched chain fatty acids giving keto acids which were then transaminated. Similar reaction sequences mediated by nonspecific enzymes would produce serine and threomine from the abundant prebiotic compounds glycolic and lactic acids. The aromatic amino acids may also have first been synthesized in this way, e.g. tryptophan from indole acetic acid. The next step would have been the biosynthesis of leucine from alpha-ketoisovalerc acid. The acetolactate pathway developed subsequently. The first version of the Krebs cycle, which was used for amino acid biosynthesis, would have been assembled by making use fo the reductive carboxylation and leucine biosynthesis enzymes, and completed with the development of a single new enzyme, succinate dehydrogenase. This evolutionary scheme suggests that there may be limitations to inferring the origins of metabolism by a simple back extrapolation of current pathways.

[Biosynthesis of indigo and indirubin by whole-cell catalyst designed by combination of protein engineering and metabolic engineering].

PubMed

Li, Yang; Zhu, Junge; Wang, Jianjun; Xia, Huanzhang; Wu, Sheng

2016-01-01

The phenylacetone monooxygenase, isolated from Thermobifida fusca, mainly catalyzes Baeyer-Villiger oxidation reaction towards aromatic compounds. Met446 plays a vital role in catalytic promiscuity, based on the structure and function of phenylacetone monooxygenase. Mutation in Met446 locus can offer enzyme new catalytic feature to activate C-H bond, oxidizing indole to finally generate indigo and indirubin, but the yield was only 1.89 mg/L. In order to further improve the biosynthesis efficiency of the whole-cell catalyst, metabolic engineering was applied to change glucose metabolism pathway of Escherichia coli. Blocking glucose isomerase gene pgi led to pentose phosphate pathway instead of the glycolytic pathway to become the major metabolic pathways of glucose, which provided more cofactor NADPH needed in enzymatic oxidation of indole. Engineering the host E. coli led to synthesis of indigo and indirubin efficiency further increased to 25 mg/L. Combination of protein and metabolic engineering to design efficient whole-cell catalysts not only improves the synthesis of indigo and indirubin, but also provides a novel strategy for whole-cell catalyst development.

Tough soluble aromatic thermoplastic copolyimides

NASA Technical Reports Server (NTRS)

Bryant, Robert G. (Inventor)

2000-01-01

Tough, soluble, aromatic, thermoplastic copolyimides were prepared by reacting 4,4'-oxydiphthalic anhydride, 3,4,3',4'-biphenyltetracarboxylic dianhydride and 3,4'-oxydianiline. Alternatively, these copolyimides may be prepared by reacting 4,4'-oxydiphthalic anhydride with 3,4,3',4'-biphenyltetracarboxylic dianhydride and 3,4'-oxydiisocyanate. Also, the copolyimide may be prepared by reacting the corresponding tetra acid and ester precursors of 4,4'-oxydiphthalic anhydride and 3,4,3',4'-biphenyltetracarboxylic dianhydride with 3,4'-oxydianiline. These copolyimides were found to be soluble in common amide solvents such as N,N'-dimethyl acetamide, N-methylpyrrolidinone, and dimethylformamide allowing them to be applied as the fully imidized copolymer and to be used to prepare a wide range of articles.

A novel withanolide with an unprecedented carbon skeleton from Physalis angulata.

PubMed

Sun, Cheng-Peng; Kutateladze, Andrei G; Zhao, Feng; Chen, Li-Xia; Qiu, Feng

2017-02-01

A novel withanolide, aromaphysalin A (1), possessing an exceptional C(11)-C(15) bond and an unprecedented 4,9-cyclized aromatic ring (ring A), is isolated from stems and leaves of Physalis angulata L. Its structure was determined by a combination of HRESIMS, 2D NMR spectra, and theoretical calculations. Compound 1 exhibited inhibitory activity on NO production with an IC 50 value of 51.64 μM. A plausible biosynthetic pathway for 1 is also discussed.

MORPHOLOGICAL TRANSFORMATION AND DNA ADDUCT FORMATION BY BENZ[J]ACEANTHRYLENE AND ITS METABOLITES IN C3H1OT1/2CL8 CELLS: EVIDENCE FOR BOTH CYCLOPENTA-RING AND BAY REGION METABOLIC ACTIVATION PATHWAYS

EPA Science Inventory

Benz[j]aceanthrylene (B[j]A), a cyclopenta-fused polycyclic aromatic hydrocarbon (CP-PAH) related to 3-methylcholanthrene, has been studied to identify the major routes of metabolic activation in transformable C3H1OT1/2CLB (C3H1OT1/2) mouse embryo fibroblasts in culture. he morph...

Polycyclovorans algicola gen. nov., sp. nov., an aromatic-hydrocarbon-degrading marine bacterium found associated with laboratory cultures of marine phytoplankton.

PubMed

Gutierrez, Tony; Green, David H; Nichols, Peter D; Whitman, William B; Semple, Kirk T; Aitken, Michael D

2013-01-01

A strictly aerobic, halotolerant, rod-shaped bacterium, designated strain TG408, was isolated from a laboratory culture of the marine diatom Skeletonema costatum (CCAP1077/1C) by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. 16S rRNA gene sequence analysis placed this organism within the order Xanthomonadales of the class Gammaproteobacteria. Its closest relatives included representatives of the Hydrocarboniphaga-Nevskia-Sinobacter clade (<92% sequence similarity) in the family Sinobacteraceae. The strain exhibited a narrow nutritional spectrum, preferring to utilize aliphatic and aromatic hydrocarbon compounds and small organic acids. Notably, it displayed versatility in degrading two- and three-ring PAHs. Moreover, catechol 2,3-dioxygenase activity was detected in lysates, indicating that this strain utilizes the meta-cleavage pathway for aromatic compound degradation. Cells produced surface blebs and contained a single polar flagellum. The predominant isoprenoid quinone of strain TG408 was Q-8, and the dominant fatty acids were C(16:0), C(16:1) ω7c, and C(18:1) ω7c. The G+C content of the isolate's DNA was 64.3 mol% ± 0.34 mol%. On the basis of distinct phenotypic and genotypic characteristics, strain TG408 represents a novel genus and species in the class Gammaproteobacteria for which the name Polycyclovorans algicola gen. nov., sp. nov., is proposed. Quantitative PCR primers targeting the 16S rRNA gene of this strain were developed and used to show that this organism is found associated with other species of marine phytoplankton. Phytoplankton may be a natural biotope in the ocean where new species of hydrocarbon-degrading bacteria await discovery and which contribute significantly to natural remediation processes.

Studies on the Simultaneous Formation of Aroma-Active and Toxicologically Relevant Vinyl Aromatics from Free Phenolic Acids during Wheat Beer Brewing.

PubMed

Langos, Daniel; Granvogl, Michael

2016-03-23

During the brewing process of wheat beer, the desired aroma-active vinyl aromatics 2-methoxy-4-vinylphenol and 4-vinylphenol as well as the undesired and toxicologically relevant styrene are formed from their respective precursors, free ferulic acid, p-coumaric acid, and cinnamic acid, deriving from the malts. Analysis of eight commercial wheat beers revealed high concentrations of 2-methoxy-4-vinylphenol and 4-vinylphenol always in parallel with high concentrations of styrene or low concentrations of the odorants in parallel with low styrene concentrations, suggesting a similar pathway. To better understand the formation of these vinyl aromatics, each process step of wheat beer brewing and the use of different strains of Saccharomyces cerevisiae were evaluated. During wort boiling, only a moderate decarboxylation of free phenolic acids and formation of desired and undesired vinyl aromatics were monitored due to the thermal treatment. In contrast, this reaction mainly occurred enzymatically catalyzed during fermentation with S. cerevisiae strain W68 with normal Pof(+) activity (phenolic off-flavor) resulting in a wheat beer eliciting the typical aroma requested by consumers due to high concentrations of 2-methoxy-4-vinylphenol (1790 μg/L) and 4-vinylphenol (937 μg/L). Unfortunately, also a high concentration of undesired styrene (28.3 μg/L) was observed. Using a special S. cerevisiae strain without Pof(+) activity resulted in a significant styrene reduction (

Enhanced formation of aromatic amino acids increases fragrance without affecting flower longevity or pigmentation in Petunia × hybrida.

PubMed

Oliva, Moran; Ovadia, Rinat; Perl, Avichai; Bar, Einat; Lewinsohn, Efraim; Galili, Gad; Oren-Shamir, Michal

2015-01-01

Purple Petunia × hybrida V26 plants accumulate fragrant benzenoid-phenylpropanoid molecules and anthocyanin pigments in their petals. These specialized metabolites are synthesized mainly from the aromatic amino acids phenylalanine. Here, we studied the profile of secondary metabolites of petunia plants, expressing a feedback-insensitive bacterial form of 3-deoxy-di-arabino-heptulosonate 7-phosphate synthase enzyme (AroG*) of the shikimate pathway, as a tool to stimulate the conversion of primary to secondary metabolism via the aromatic amino acids. We focused on specialized metabolites contributing to flower showy traits. The presence of AroG* protein led to increased aromatic amino acid levels in the leaves and high phenylalanine levels in the petals. In addition, the AroG* petals accumulated significantly higher levels of fragrant benzenoid-phenylpropanoid volatiles, without affecting the flowers' lifetime. In contrast, AroG* abundance had no effect on flavonoids and anthocyanins levels. The metabolic profile of all five AroG* lines was comparable, even though two lines produced the transgene in the leaves, but not in the petals. This implies that phenylalanine produced in leaves can be transported through the stem to the flowers and serve as a precursor for formation of fragrant metabolites. Dipping cut petunia stems in labelled phenylalanine solution resulted in production of labelled fragrant volatiles in the flowers. This study emphasizes further the potential of this metabolic engineering approach to stimulate the production of specialized metabolites and enhance the quality of various plant organs. Furthermore, transformation of vegetative tissues with AroG* is sufficient for induced production of specialized metabolites in organs such as the flowers. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Organ specificity of the bladder carcinogen 4-aminobiphenyl in inducing DNA damage and mutation in mice.

PubMed

Yoon, Jae-In; Kim, Sang-In; Tommasi, Stella; Besaratinia, Ahmad

2012-02-01

Aromatic amines are a widespread class of environmental contaminants present in various occupational settings and tobacco smoke. Exposure to aromatic amines is a major risk factor for bladder cancer development. The etiologic involvement of aromatic amines in the genesis of bladder cancer is attributable to their ability to form DNA adducts, which upon eluding repair and causing mispairing during replication, may initiate mutagenesis. We have investigated the induction of DNA adducts in relation to mutagenesis in bladder and various nontarget organs of transgenic Big Blue mice treated weekly (i.p.) with a representative aromatic amine compound, 4-aminobiphenyl (4-ABP), for six weeks, followed by a six-week recovery period. We show an organ-specificity of 4-ABP in inducing repair-resistant DNA adducts in bladder, kidney, and liver of carcinogen-treated animals, which accords with the bioactivation pathway of this chemical in the respective organs. In confirmation, we show a predominant and sustained mutagenic effect of 4-ABP in bladder, and much weaker but significant mutagenicity of 4-ABP in the kidney and liver of carcinogen-treated mice, as reflected by the elevation of background cII mutant frequency in the respective organs. The spectrum of mutations produced in bladder of 4-ABP-treated mice matches the known mutagenic properties of 4-ABP-DNA adducts, as verified by the preponderance of induced mutations occurring at G:C base pairs (82.9%), with the vast majority being G:C→T:A transversions (47.1%). Our data support a possible etiologic role of 4-ABP in bladder carcinogenesis and provide a mechanistic view on how DNA adduct-driven mutagenesis, specifically targeted to bladder urothelium, may account for organ-specific tumorigenicity of this chemical. ©2011 AACR.

Novel Scheme for Biosynthesis of Aryl Metabolites from l-Phenylalanine in the Fungus Bjerkandera adusta

PubMed Central

Lapadatescu, Carmen; Giniès, Christian; Le Quéré, Jean-Luc; Bonnarme, Pascal

2000-01-01

Aryl metabolite biosynthesis was studied in the white rot fungus Bjerkandera adusta cultivated in a liquid medium supplemented with l-phenylalanine. Aromatic compounds were analyzed by gas chromatography-mass spectrometry following addition of labelled precursors (14C- and 13C-labelled l-phenylalanine), which did not interfere with fungal metabolism. The major aromatic compounds identified were benzyl alcohol, benzaldehyde (bitter almond aroma), and benzoic acid. Hydroxy- and methoxybenzylic compounds (alcohols, aldehydes, and acids) were also found in fungal cultures. Intracellular enzymatic activities (phenylalanine ammonia lyase, aryl-alcohol oxidase, aryl-alcohol dehydrogenase, aryl-aldehyde dehydrogenase, lignin peroxidase) and extracellular enzymatic activities (aryl-alcohol oxidase, lignin peroxidase), as well as aromatic compounds, were detected in B. adusta cultures. Metabolite formation required de novo protein biosynthesis. Our results show that l-phenylalanine was deaminated to trans-cinnamic acid by a phenylalanine ammonia lyase and trans-cinnamic acid was in turn converted to aromatic acids (phenylpyruvic, phenylacetic, mandelic, and benzoylformic acids); benzaldehyde was a metabolic intermediate. These acids were transformed into benzaldehyde, benzyl alcohol, and benzoic acid. Our findings support the hypothesis that all of these compounds are intermediates in the biosynthetic pathway from l-phenylalanine to aryl metabolites. Additionally, trans-cinnamic acid can also be transformed via β-oxidation to benzoic acid. This was confirmed by the presence of acetophenone as a β-oxidation degradation intermediate. To our knowledge, this is the first time that a β-oxidation sequence leading to benzoic acid synthesis has been found in a white rot fungus. A novel metabolic scheme for biosynthesis of aryl metabolites from l-phenylalanine is proposed. PMID:10742235

Effect of experimental diabetes on the levels of aromatic and branched-chain amino acids in rat blood and brain.

PubMed

Crandall, E A; Fernstrom, J D

1983-03-01

Male rats treated 3 wk earlier with streptozotocin showed abnormally high blood levels of leucine, isoleucine, and valine throughout the 24-h period. Serum phenylalanine levels were slightly increased, while those of tryptophan and tyrosine were occasionally reduced. In brain, the level of each branched-chain amino acid was significantly increased above normal at all times. The brain concentration of each aromatic amino acid was always below normal. These changes were restored almost to normal by exogenous insulin therapy. Since the ingestion of protein is normally a major factor influencing blood amino acid levels, the effect of ingesting single, protein-containing meals on the blood and brain levels of these amino acids was also studied. After an overnight fast, the ingestion of a protein-containing meal by diabetic rats increased substantially both blood and brain levels of each branched-chain amino acid. No such increases occurred in normal rats. Ingestion of this meal produced only small changes in the brain and blood levels of the aromatic amino acids in both diabetic and normal rats. The changes in the brain level of each large neutral amino acid in some cases paralleled those in its blood level. More often, they paralleled the changes in the blood ratio of each amino acid to the sum of the other aromatic and branched-chain amino acids. This ratio is often a good predictor of the competitive transport of these amino acids into brain (Fernstrom and Faller, 1978). The observed changes in the brain levels of these amino acids in diabetes may influence the rates at which they are consumed in metabolic pathways within this organ.

Hydrous pyrolysis of polycyclic aromatic hydrocarbons and implications for the origin of PAH in hydrothermal petroleum

NASA Technical Reports Server (NTRS)

McCollom, T. M.; Simoneit, B. R.; Shock, E. L.

1999-01-01

Polycyclic aromatic hydrocarbons (PAH) are found at high concentrations in thermally altered organic matter and hydrothermally generated petroleum from sediment-covered seafloor hydro-thermal systems. To better understand the factors controlling the occurrence of PAH in thermally altered environments, the reactivities of two PAH, phenanthrene and anthracene, were investigated in hydrothermal experiments. The compounds were heated with water at 330 degrees C in sealed reaction vessels for durations ranging from 1 to 17 days. Iron oxide and sulfide minerals, formic acid, or sodium for-mate were included in some experiments to vary conditions within the reaction vessel. Phenanthrene was unreactive both in water alone and in the presence of minerals for up to 17 days, while anthracene was partially hydrogenated (5-10%) to di- and tetrahydroanthracene. In the presence of 6-21 vol % formic acid, both phenanthrene and anthracene reacted extensively to form hydrogenated and minor methylated derivatives, with the degree of hydrogenation and methylation increasing with the amount of formic acid. Phenanthrene was slightly hydrogenated in sodium formate solutions. The hydrogenation reactions could be readily reversed; heating a mixture of polysaturated phenanthrenes resulted in extensive dehydrogenation (aromatization) after 3 days at 330 degrees C. While the experiments demonstrate that reaction pathways for the hydrogenation of PAH under hydrothermal conditions exist, the reactions apparently require higher concentrations of H2 than are typical of geologic settings. The experiments provide additional evidence that PAH may be generated in hydrothermal systems from progressive aromatization and dealkylation of biologically derived polycyclic precursors such as steroids and terpenoids. Furthermore, the results indicate that PAH initially present in sediments or formed within hydrothermal systems are resistant to further thermal degradation during hydrothermal alteration.

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

Energy profile of maltooligosaccharide permeation through maltoporin as derived from the structure and from a statistical analysis of saccharide-protein interactions.

PubMed Central

Meyer, J. E.; Schulz, G. E.

1997-01-01

The crystal structure of the maltodextrin-specific porin from Salmonella typhimurium ligated with a maltotrioside at the pore eyelet is known at 2.4 A resolution. The three glucose units assume a conformation close to the natural amylose helix. The pore eyelet fits exactly the cross-section of a maltooligosaccharide chain and thus functions as a constraining orifice. The oligomer permeates the membrane by screwing along the amylose helix through this orifice. Because each glucose glides along the given helix, its interactions can be sampled at any point along the pathway. The interactions are mostly hydrogen bonds, but also contacts to aromatic rings at one side of the pore. We have derived the energy profile of a gliding maltooligosaccharide by following formation and breakage of hydrogen bonds and by assessing the saccharide-aromatics interactions from a statistical analysis of saccharide binding sites in proteins. The resulting profile indicates smooth permeation despite extensive hydrogen bonding at the orifice. PMID:9144780

Ionic liquid [OMIm][OAc] directly inducing oxidation cleavage of the β-O-4 bond of lignin model compounds.

PubMed

Yang, Yingying; Fan, Honglei; Meng, Qinglei; Zhang, Zhaofu; Yang, Guanying; Han, Buxing

2017-08-03

We explored the oxidation reactions of lignin model compounds directly induced by ionic liquids under metal-free conditions. In this work, it was found that ionic liquid 1-octyl-3-methylimidazolium acetate as a solvent could promote the aerobic oxidation of lignin model compound 2-phenoxyacetophenone (1) and the yields of phenol and benzoic acid from 1 could be as high as 96% and 86%, respectively. A possible reaction pathway was proposed based on a series of control experiments. An acetate anion from the ionic liquid attacked the hydrogen from the β-carbon thereby inducing the cleavage of the C-O bond of the aromatic ether. Furthermore, it was found that 2-(2-methoxyphenoxy)-1-phenylethanone (4) with a methoxyl group could also be transformed into aromatic products in this simple reaction system and the yields of phenol and benzoic acid from 4 could be as high as 98% and 85%, respectively. This work provides a simple way for efficient transformation of lignin model compounds.

Anaerobic biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by a facultative anaerobe Pseudomonas sp. JP1.

PubMed

Liang, Lei; Song, Xiaohui; Kong, Jing; Shen, Chenghui; Huang, Tongwang; Hu, Zhong

2014-11-01

Polycyclic aromatic hydrocarbons (PAHs) are harmful persistent organic pollutants, while the high-molecular-weight (HMW) PAHs are even more detrimental to the environment and human health. However, microbial anaerobic degradation of HMW PAHs has rarely been reported. One facultative anaerobe Pseudomonas sp. JP1 was isolated from Shantou Bay, Shantou, China, which could degrade a variety of HMW PAHs. After 40 days cultivation with strain JP1, anaerobic biodegradation rate of benzo[a]pyrene (BaP), fluoranthene, and phenanthrene was 30, 47, and 5 %, respectively. Consumption of nitrate as the electron acceptor was confirmed by N-(1-naphthyl) ethylenediamine spectrophotometry. Supplementation of sodium sulfite, maltose, or glycine, and in a salinity of 0-20 ‰ significantly stimulated anaerobic degradation of BaP. Lastly, the anaerobic degradation metabolites of BaP by strain JP1 were investigated using GC/MS, and the degradation pathway was proposed. This study is helpful for further studies on the mechanism of anaerobic biodegradation of PAHs.

Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network

PubMed Central

Widhalm, Joshua R.; Gutensohn, Michael; Yoo, Heejin; Adebesin, Funmilayo; Qian, Yichun; Guo, Longyun; Jaini, Rohit; Lynch, Joseph H.; McCoy, Rachel M.; Shreve, Jacob T.; Thimmapuram, Jyothi; Rhodes, David; Morgan, John A.; Dudareva, Natalia

2015-01-01

In addition to proteins, L-phenylalanine is a versatile precursor for thousands of plant metabolites. Production of phenylalanine-derived compounds is a complex multi-compartmental process using phenylalanine synthesized predominantly in plastids as precursor. The transporter(s) exporting phenylalanine from plastids, however, remains unknown. Here, a gene encoding a Petunia hybrida plastidial cationic amino-acid transporter (PhpCAT) functioning in plastidial phenylalanine export is identified based on homology to an Escherichia coli phenylalanine transporter and co-expression with phenylalanine metabolic genes. Radiolabel transport assays show that PhpCAT exports all three aromatic amino acids. PhpCAT downregulation and overexpression result in decreased and increased levels, respectively, of phenylalanine-derived volatiles, as well as phenylalanine, tyrosine and their biosynthetic intermediates. Metabolic flux analysis reveals that flux through the plastidial phenylalanine biosynthetic pathway is reduced in PhpCAT RNAi lines, suggesting that the rate of phenylalanine export from plastids contributes to regulating flux through the aromatic amino-acid network. PMID:26356302

Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network

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

Widhalm, Joshua R.; Gutensohn, Michael; Yoo, Heejin

In addition to proteins, L-phenylalanine is a versatile precursor for thousands of plant metabolites. Production of phenylalanine-derived compounds is a complex multi-compartmental process using phenylalanine synthesized predominantly in plastids as precursor. The transporter(s) exporting phenylalanine from plastids, however, remains unknown. Here, a gene encoding a Petunia hybrida plastidial cationic amino-acid transporter (PhpCAT) functioning in plastidial phenylalanine export is identified based on homology to an Escherichia coli phenylalanine transporter and co-expression with phenylalanine metabolic genes. Radiolabel transport assays show that PhpCAT exports all three aromatic amino acids. PhpCAT downregulation and overexpression result in decreased and increased levels, respectively, of phenylalanine-derived volatiles,more » as well as phenylalanine, tyrosine and their biosynthetic intermediates. Metabolic flux analysis reveals that flux through the plastidial phenylalanine biosynthetic pathway is reduced in PhpCAT RNAi lines, suggesting that the rate of phenylalanine export from plastids contributes to regulating flux through the aromatic amino-acid network.« less

Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network

DOE PAGES

Widhalm, Joshua R.; Gutensohn, Michael; Yoo, Heejin; ...

2015-09-10

In addition to proteins, L-phenylalanine is a versatile precursor for thousands of plant metabolites. Production of phenylalanine-derived compounds is a complex multi-compartmental process using phenylalanine synthesized predominantly in plastids as precursor. The transporter(s) exporting phenylalanine from plastids, however, remains unknown. Here, a gene encoding a Petunia hybrida plastidial cationic amino-acid transporter (PhpCAT) functioning in plastidial phenylalanine export is identified based on homology to an Escherichia coli phenylalanine transporter and co-expression with phenylalanine metabolic genes. Radiolabel transport assays show that PhpCAT exports all three aromatic amino acids. PhpCAT downregulation and overexpression result in decreased and increased levels, respectively, of phenylalanine-derived volatiles,more » as well as phenylalanine, tyrosine and their biosynthetic intermediates. Metabolic flux analysis reveals that flux through the plastidial phenylalanine biosynthetic pathway is reduced in PhpCAT RNAi lines, suggesting that the rate of phenylalanine export from plastids contributes to regulating flux through the aromatic amino-acid network.« less

Arenium ions are not obligatory intermediates in electrophilic aromatic substitution

PubMed Central

Galabov, Boris; Koleva, Gergana; Simova, Svetlana; Hadjieva, Boriana; Schaefer, Henry F.; Schleyer, Paul von Ragué

2014-01-01

Our computational and experimental investigation of the reaction of anisole with Cl2 in nonpolar CCl4 solution challenges two fundamental tenets of the traditional SEAr (arenium ion) mechanism of aromatic electrophilic substitution. Instead of this direct substitution process, the alternative addition–elimination (AE) pathway is favored energetically. This AE mechanism rationalizes the preferred ortho and para substitution orientation of anisole easily. Moreover, neither the SEAr nor the AE mechanisms involve the formation of a σ-complex (Wheland-type) intermediate in the rate-controlling stage. Contrary to the conventional interpretations, the substitution (SEAr) mechanism proceeds concertedly via a single transition state. Experimental NMR investigations of the anisole chlorination reaction course at various temperatures reveal the formation of tetrachloro addition by-products and thus support the computed addition–elimination mechanism of anisole chlorination in nonpolar media. The important autocatalytic effect of the HCl reaction product was confirmed by spectroscopic (UV-visible) investigations and by HCl-augmented computational modeling. PMID:24972792

Control of peptide nanotube diameter by chemical modifications of an aromatic residue involved in a single close contact

PubMed Central

Tarabout, Christophe; Roux, Stéphane; Gobeaux, Frédéric; Fay, Nicolas; Pouget, Emilie; Meriadec, Cristelle; Ligeti, Melinda; Thomas, Daniel; IJsselstijn, Maarten; Besselievre, François; Buisson, David-Alexandre; Verbavatz, Jean-Marc; Petitjean, Michel; Valéry, Céline; Perrin, Lionel; Rousseau, Bernard; Artzner, Franck; Paternostre, Maité; Cintrat, Jean-Christophe

2011-01-01

Supramolecular self-assembly is an attractive pathway for bottom-up synthesis of novel nanomaterials. In particular, this approach allows the spontaneous formation of structures of well-defined shapes and monodisperse characteristic sizes. Because nanotechnology mainly relies on size-dependent physical phenomena, the control of monodispersity is required, but the possibility of tuning the size is also essential. For self-assembling systems, shape, size, and monodispersity are mainly settled by the chemical structure of the building block. Attempts to change the size notably by chemical modification usually end up with the loss of self-assembly. Here, we generated a library of 17 peptides forming nanotubes of monodisperse diameter ranging from 10 to 36 nm. A structural model taking into account close contacts explains how a modification of a few Å of a single aromatic residue induces a fourfold increase in nanotube diameter. The application of such a strategy is demonstrated by the formation of silica nanotubes of various diameters. PMID:21518895

Inferring sources of polycyclic aromatic hydrocarbons (PAHs) in sediments from the western Taiwan Strait through end-member mixing analysis.

PubMed

Li, Tao; Sun, Guihua; Ma, Shengzhong; Liang, Kai; Yang, Chupeng; Li, Bo; Luo, Weidong

2016-11-15

Concentration, spatial distribution, composition and sources of polycyclic aromatic hydrocarbons (PAHs) were investigated based on measurements of 16 PAH compounds in surface sediments of the western Taiwan Strait. Total PAH concentrations ranged from 2.41 to 218.54ngg -1 . Cluster analysis identified three site clusters representing the northern, central and southern regions. Sedimentary PAHs mainly originated from a mixture of pyrolytic and petrogenic in the north, from pyrolytic in the central, and from petrogenic in the south. An end-member mixing model was performed using PAH compound data to estimate mixing proportions for unknown end-members (i.e., extreme-value sample points) proposed by principal component analysis (PCA). The results showed that the analyzed samples can be expressed as mixtures of three end-members, and the mixing of different end-members was strongly related to the transport pathway controlled by two currents, which alternately prevail in the Taiwan Strait during different seasons. Copyright © 2016. Published by Elsevier Ltd.

Slow pyrolysis polygeneration of bamboo (Phyllostachys pubescens): Product yield prediction and biochar formation mechanism.

PubMed

Wang, Huihui; Wang, Xin; Cui, Yanshan; Xue, Zhongcai; Ba, Yuxin

2018-05-11

Slow pyrolysis of bamboo was conducted at 400-600 °C and pyrolysis products were characterized with FTIR, BET, XRD, SEM, EDS and GC to establish a pyrolysis product yield prediction model and biochar formation mechanism. Pyrolysis biochar yield was predicted based on content of cellulose, hemicellulose and lignin in biomass with their carbonization index of 0.20, 0.35 and 0.45. The formation mechanism of porous structure in pyrolysis biochar was established based on its physicochemical property evolution and emission characteristics of pyrolysis gas. The main components (cellulose, hemicellulose and lignin) had different pyrolysis or chemical reaction pathways to biochar. Lignin had higher aromatic structure, which resulted higher biochar yield. It was the main biochar precursor during biomass pyrolysis. Cellulose was likely to improve porous structure of pyrolysis biochar due to its high mass loss percentage. Higher pyrolysis temperatures (600 °C) promoted inter- and intra-molecular condensation reactions and aromaticity in biochar. Copyright © 2018 Elsevier Ltd. All rights reserved.

Geochemistry of polycyclic aromatic hydrocarbons in the bottom sediments of the eastern Arctic shelf

NASA Astrophysics Data System (ADS)

Petrova, V. I.; Batova, G. I.; Kursheva, A. V.; Litvinenko, I. V.; Savinov, V. M.; Savinova, T. N.

2008-04-01

Sources and pathways of supply of polycyclic aromatic hydrocarbons (PAH) in the surface sediments of the Laptev and East Siberian seas were identified based on an analysis of the lithological-geochemical characteristics and distribution of organic matter (OM). The distribution of organic carbon, humic acids, bitumoids, and hydrocarbons demonstrates the determining role of the riverine runoff in the formation of the recent sediments. The total average content of PAH in the sediments of this region approximates 37 ng/g, not exceeding 80 ng/g of dry sediment. The biogenic components of the PAH (alkylphenanthrenes, alkylchrysenes, perylene) dominate in the estuarine-shelf and coastal-shelf sediments enriched with plant detritus and significantly decrease in the pelagic zone. The anthropogenic influence is observed in sediments of the port of Tiksi, where the total content of PAH with dominant pyrogenic components is two orders of magnitude higher as compared with the background values in the study region.

Cross-benzoin and Stetter-type reactions mediated by KOtBu-DMF via an electron-transfer process.

PubMed

Ragno, Daniele; Zaghi, Anna; Di Carmine, Graziano; Giovannini, Pier Paolo; Bortolini, Olga; Fogagnolo, Marco; Molinari, Alessandra; Venturini, Alessandro; Massi, Alessandro

2016-10-18

The condensation of aromatic α-diketones (benzils) with aromatic aldehydes (benzoin-type reaction) and chalcones (Stetter-type reaction) in DMF in the presence of catalytic (25 mol%) KOtBu is reported. Both types of umpolung processes proceed with good efficiency and complete chemoselectivity. On the basis of spectroscopic evidence (MS analysis) of plausible intermediates and literature reports, the occurrence of different ionic pathways have been evaluated to elucidate the mechanism of a model cross-benzoin-like reaction along with a radical route initiated by an electron-transfer process to benzil from the carbamoyl anion derived from DMF. This mechanistic investigation has culminated in a different proposal, supported by calculations and a trapping experiment, based on double electron-transfer to benzil with formation of the corresponding enediolate anion as the key reactive intermediate. A mechanistic comparison between the activation modes of benzils in KOtBu-DMF and KOtBu-DMSO systems is also described.

Bacterial oxidation of the polycyclic aromatic hydrocarbons acenaphthene and acenaphthylene.

PubMed Central

Schocken, M J; Gibson, D T

1984-01-01

A Beijerinckia sp. and a mutant strain, Beijerinckia sp. strain B8/36, were shown to cooxidize the polycyclic aromatic hydrocarbons acenaphthene and acenaphthylene. Both organisms oxidized acenaphthene to the same spectrum of metabolites, which included 1-acenaphthenol, 1-acenaphthenone, 1,2-acenaphthenediol, acenaphthenequinone, and a compound that was tentatively identified as 1,2-dihydroxyacenaphthylene. In contrast, acenaphthylene was oxidized to acenaphthenequinone and the compound tentatively identified as 1,2-dihydroxyacenaphthylene by the wild-type strain of Beijerinckia. Both of these products were also formed when the organism was incubated with synthetic cis-1,2-acenaphthenediol. A metabolite identified as cis-1,2-acenaphthenediol was formed from acenaphthylene by the mutant Beijerinckia sp. strain B8/36. Cell extracts prepared from the wild-type Beijerinckia strain contain a constitutive pyridine nucleotide-dependent dehydrogenase which can oxidize 1-acenaphthenol and 9-fluorenol. The results indicate that although acenaphthene and acenaphthylene are both oxidized to acenaphthenequinone, the pathways leading to the formation of this end product are different. PMID:6089663

Environmental Electrophiles: Protein Adducts, Modulation of Redox Signaling, and Interaction with Persulfides/Polysulfides.

PubMed

Kumagai, Yoshito; Abiko, Yumi

2017-01-17

Included among the many environmental electrophiles are aromatic hydrocarbon quinones formed during combustion of gasoline, crotonaldehyde in tobacco smoke, methylmercury accumulated in fish, cadmium contaminated in rice, and acrylamide in baked foods. These electrophiles can modify nucleophilic functions such as cysteine residues in proteins forming adducts and in the process activate cellular redox signal transduction pathways such as kinases and transcription factors. However, higher concentrations of electrophiles disrupt such signaling by nonselective covalent modification of cellular proteins. Persulfide/polysulfides produced by various enzymes appear to capture environmental electrophiles because of the formation of their sulfur adducts without electrophilicity. We therefore speculate that persulfide/polysulfides are candidates for the regulation of redox signal transduction pathways (e.g., cell survival, cell proliferation, and adaptive response) and toxicity during exposure to environmental electrophiles.

Modification of aniline containing proteins using an oxidative coupling strategy.

PubMed

Hooker, Jacob M; Esser-Kahn, Aaron P; Francis, Matthew B

2006-12-13

A new bioconjugation reaction has been developed based on the chemoselective modification of anilines through an oxidative coupling pathway. Aryl amines were installed on the surface of protein substrates through lysine acylation reactions or through the use of native chemical ligation techniques. Upon exposure to NaIO4 in aqueous buffer, the anilines coupled rapidly to the aromatic rings of N,N-dialkyl-N'-acyl-p-phenylenediamines. The identities of the reaction products were confirmed using ESI-MS and through comparison to small molecule analogs. Control experiments indicated that none of the native amino acids participated in the reaction. The resulting bioconjugates were found to be stable toward hydrolysis from pH 4 to pH 11 and in the presence of many commonly used oxidants, reductants, and nucleophiles. A fluorescent phenylenediamine reagent was synthesized for the selective detection of aniline labeled proteins in mixtures, and the reaction was used to append the C-terminus of the green fluorescent protein with a single PEG chain. When combined with techniques for the incorporation of unnatural amino acids into proteins, this bioorthogonal coupling method should prove useful for a number of applications requiring a high degree of labeling specificity.

Androgens and bone health.

PubMed

Hansen, K A; Tho, S P

1998-01-01

Osteoporosis is one of the most common metabolic bone diseases in the adult population and its prevalence will continue to rise as our population grows older. In both sexes, hypogonadism is associated with accelerated loss of bone and development of osteoporosis. Adrenal and gonadal androgen levels decline with advancing age in both sexes. Androgens act by either directly binding to androgen receptors, or by aromatization of androgens to estrogens and subsequently interacting with estrogen receptors. Both pathways are important for skeletal health. Direct androgen binding to an androgen receptor may play a more important role in early skeletal development and determination of sexual dimorphic traits. While bone remodeling, which is important in maintaining healthy bone through life, is primarily stimulated by estrogen, studies in the rat and human support the complex action of androgens and estrogens in bone modeling and remodeling, and hence the development and maintenance of healthy bone. In postmenopausal females, the addition of androgens to hormone replacement therapy results in significant additional improvement in bone mineral density compared to estrogen replacement alone. Accumulating evidence indicate that androgens play an important role in the health of bone and the potential benefit of adding these agents to hormone replacement regimens.

Androgens and osteoporosis.

PubMed

Ebeling, Peter R

2010-06-01

The review is timely given recent advances regarding mechanisms of androgen action on bone cells and in humans. Osteoporosis in men is an important public health problem. An improved understanding of the role of androgens in the pathophysiology of bone loss will lead to new treatments. Androgen receptors are present in most bone cells. Testosterone acts on bone both directly via the androgen receptor and indirectly, following aromatization, via the oestrogen receptor. During skeletal modelling, ERalpha is critical for longitudinal bone growth. For periosteal growth and bone expansion, androgen receptor activation has a positive effect, whereas ERalpha activation is inhibitory. During skeletal remodelling, both receptor pathways generate similar and additive effects on bone.Androgen deficiency is a common secondary cause of osteoporosis in men and should be treated with testosterone, particularly in symptomatic men. However, lack of efficacy data for testosterone in osteoporosis means it is less useful as a first-line treatment in men with age-related declines in testosterone and osteoporosis, when other agents such as bisphosphonates and parathyroid hormone are effective. Randomized, placebo-controlled trials of testosterone therapy in men with age-related declines in testosterone and osteoporosis are needed, and should carefully evaluate potential risks, as well as its efficacy in reducing fractures and other health benefits.

Degradation of ampicillin antibiotic by electrochemical processes: evaluation of antimicrobial activity of treated water.

PubMed

Vidal, Jorge; Huiliñir, Cesar; Santander, Rocío; Silva-Agredo, Javier; Torres-Palma, Ricardo A; Salazar, Ricardo

2018-05-17

Ampicillin (AMP) is an antibiotic widely used in hospitals and veterinary clinics around the world for treating infections caused by bacteria. Therefore, it is common to find traces of this antibiotic in wastewater from these entities. In this work, we studied the mineralization of this antibiotic in solution as well as the elimination of its antimicrobial activity by comparing different electrochemical advanced oxidation processes (EAOPs), namely electro-oxidation with hydrogen peroxide (EO-H 2 O 2 ), electro-Fenton (EF), and photo electro-Fenton (PEF). With PEF process, a high degradation, mineralization, and complete elimination of antimicrobial activity were achieved in 120-min electrolysis with high efficiency. In the PEF process, fast mineralization rate is caused by hydroxyl radicals (·OH) that are generated in the bulk, on the anode surface, by UV radiation, and most importantly, by the direct photolysis of complexes formed between Fe 3+ and some organic intermediates. Moreover, some products and intermediates formed during the degradation of the antibiotic Ampicillin, such as inorganic ions, carboxylic acids, and aromatic compounds, were determined by photometric and chromatographic methods. An oxidation pathway is proposed for the complete conversion to CO 2 .

Structure-related clustering of gene expression fingerprints of thp-1 cells exposed to smaller polycyclic aromatic hydrocarbons.

PubMed

Wan, B; Yarbrough, J W; Schultz, T W

2008-01-01

This study was undertaken to test the hypothesis that structurally similar PAHs induce similar gene expression profiles. THP-1 cells were exposed to a series of 12 selected PAHs at 50 microM for 24 hours and gene expressions profiles were analyzed using both unsupervised and supervised methods. Clustering analysis of gene expression profiles revealed that the 12 tested chemicals were grouped into five clusters. Within each cluster, the gene expression profiles are more similar to each other than to the ones outside the cluster. One-methylanthracene and 1-methylfluorene were found to have the most similar profiles; dibenzothiophene and dibenzofuran were found to share common profiles with fluorine. As expression pattern comparisons were expanded, similarity in genomic fingerprint dropped off dramatically. Prediction analysis of microarrays (PAM) based on the clustering pattern generated 49 predictor genes that can be used for sample discrimination. Moreover, a significant analysis of Microarrays (SAM) identified 598 genes being modulated by tested chemicals with a variety of biological processes, such as cell cycle, metabolism, and protein binding and KEGG pathways being significantly (p < 0.05) affected. It is feasible to distinguish structurally different PAHs based on their genomic fingerprints, which are mechanism based.

Microbial Diversity in Natural Asphalts of the Rancho La Brea Tar Pits▿

PubMed Central

Kim, Jong-Shik; Crowley, David E.

2007-01-01

Bacteria commonly inhabit subsurface oil reservoirs, but almost nothing is known yet about microorganisms that live in naturally occurring terrestrial oil seeps and natural asphalts that are comprised of highly recalcitrant petroleum hydrocarbons. Here we report the first survey of microbial diversity in ca. 28,000-year-old samples of natural asphalts from the Rancho La Brea Tar Pits in Los Angeles, CA. Microbiological studies included analyses of 16S rRNA gene sequences and DNA encoding aromatic ring-hydroxylating dioxygenases from two tar pits differing in chemical composition. Our results revealed a wide range of phylogenetic groups within the Archaea and Bacteria domains, in which individual taxonomic clusters were comprised of sets of closely related species within novel genera and families. Fluorescent staining of asphalt-soil particles using phylogenetic probes for Archaea, Bacteria, and Pseudomonas showed coexistence of mixed microbial communities at high cell densities. Genes encoding dioxygenases included three novel clusters of enzymes. The discovery of life in the tar pits provides an avenue for further studies of the evolution of enzymes and catabolic pathways for bacteria that have been exposed to complex hydrocarbons for millennia. These bacteria also should have application for industrial microbiology and bioremediation. PMID:17416692

Use of REMPI-TOFMS for real-time measurement of trace aromatics during operation of aircraft ground equipment

NASA Astrophysics Data System (ADS)

Gullett, Brian; Touati, Abderrahmane; Oudejans, Lukas

Emissions of aromatic air toxics from aircraft ground equipment (AGE) were measured with a resonance enhanced multiphoton ionization-time of flight mass spectrometry (REMPI-TOFMS) system consisting of a pulsed solid state laser for photoionization and a TOFMS for mass discrimination. This instrument was capable of characterizing turbine emissions and the effect of varying load operations on pollutant production. REMPI-TOFMS is capable of high selectivity and low detection limits (part per trillion to part per billion) in real time (1 s resolution). Hazardous air pollutants and criteria pollutants were measured during startups and idle and full load operations. Measurements of compounds such as benzene, toluene, ethylbenzene, xylenes, styrene, and polycyclic aromatic hydrocarbons compared well with standard methods. Startup emissions from the AGE data showed persistent concentrations of pollutants, unlike those from a diesel generator, where a sharp spike in emissions rapidly declined to steady state levels. The time-resolved responses of air toxics concentrations varied significantly by source, complicating efforts to minimize these emissions with common operating prescriptions. The time-resolved measurements showed that pollutant concentrations decline (up to 5×) in a species-specific manner over the course of multiple hours of operation, complicating determination of accurate and precise emission factors via standard extractive sampling. Correlations of air toxic concentrations with more commonly measured pollutants such as CO or PM were poor due to the relatively greater changes in the measured toxics' concentrations.

Tyrosine biosynthesis, metabolism, and catabolism in plants.

PubMed

Schenck, Craig A; Maeda, Hiroshi A

2018-05-01

L-Tyrosine (Tyr) is an aromatic amino acid (AAA) required for protein synthesis in all organisms, but synthesized de novo only in plants and microorganisms. In plants, Tyr also serves as a precursor of numerous specialized metabolites that have diverse physiological roles as electron carriers, antioxidants, attractants, and defense compounds. Some of these Tyr-derived plant natural products are also used in human medicine and nutrition (e.g. morphine and vitamin E). While the Tyr biosynthesis and catabolic pathways have been extensively studied in microbes and animals, respectively, those of plants have received much less attention until recently. Accumulating evidence suggest that the Tyr biosynthetic pathways differ between microbes and plants and even within the plant kingdom, likely to support the production of lineage-specific plant specialized metabolites derived from Tyr. The interspecies variations of plant Tyr pathway enzymes can now be used to enhance the production of Tyr and Tyr-derived compounds in plants and other synthetic biology platforms. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Polycyclic aromatic hydrocarbons and molecular hydrogen in oxygen-rich planetary nebulae: the case of NGC 6720

PubMed Central

Cox, N. L. J.; Pilleri, P.; Berné, O.; Cernicharo, J.; Joblin, C.

2015-01-01

Evolved stars are primary sources for the formation of polycyclic aromatic hydrocarbons (PAHs) and dust grains. Their circumstellar chemistry is usually designated as either oxygen-rich or carbon-rich, although dual-dust chemistry objects, whose infrared spectra reveal both silicate- and carbon-dust features, are also known. The exact origin and nature of this dual-dust chemistry is not yet understood. Spitzer-IRS mid-infrared spectroscopic imaging of the nearby, oxygen-rich planetary nebula NGC 6720 reveals the presence of the 11.3 μm aromatic (PAH) emission band. It is attributed to emission from neutral PAHs, since no band is observed in the 7–8 μm range. The spatial distribution of PAHs is found to closely follow that of the warm clumpy molecular hydrogen emission. Emission from both neutral PAHs and warm H2 is likely to arise from photo-dissociation regions associated with dense knots that are located within the main ring. The presence of PAHs together with the previously derived high abundance of free carbon (relative to CO) suggest that the local conditions in an oxygen-rich environment can also become conducive to in-situ formation of large carbonaceous molecules, such as PAHs, via a bottom-up chemical pathway. In this scenario, the same stellar source can enrich the interstellar medium with both oxygen-rich dust and large carbonaceous molecules. PMID:26924856

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

Howard, J. B.; Richter, H.

This project is concerned with the kinetics and mechanisms of aromatics oxidation and the growth process to polycyclic aromatic hydrocarbons (PAH) of increasing size, soot and fullerenes formation in flames. The overall objective of the experimental aromatics oxidation work is to extend the set of available data by measuring concentration profiles for decomposition intermediates such as phenyl, cyclopentadienyl, phenoxy or indenyl radicals which could not be measured with molecular-beam mass spectrometry to permit further refinement and testing of benzene oxidation mechanisms. The focus includes PAH radicals which are thought to play a major role in the soot formation process whilemore » their concentrations are in many cases too low to permit measurement with conventional mass spectrometry. The radical species measurements are used in critical testing and improvement of a kinetic model describing benzene oxidation and PAH growth. Thermodynamic property data of selected species are determined computationally, for instance using density functional theory (DFT). Potential energy surfaces are explored in order to identify additional reaction pathways. The ultimate goal is to understand the conversion of high molecular weight compounds to nascent soot particles, to assess the roles of planar and curved PAH and relationships between soot and fullerenes formation. The specific aims are to characterize both the high molecular weight compounds involved in the nucleation of soot particles and the structure of soot including internal nanoscale features indicative of contributions of planar and/or curved PAH to particle inception.« less

EFFECTS OF ULTRAVIOLET-B LIGHT AND POLYAROMATIC HYDROCARBON EXPOSURE ON SEA URCHIN DEVELOPMENT AND BACTERIAL BIOLUMINESCENCE

EPA Science Inventory

Polycyclic aromatic hydrocarbons (PAHs) are relatively common contaminants of the Gulf of Mexico and may be activated to more toxic metabolites by ultraviolet-B (UV-B) light. A marine bacterial bioassay system (Vibrio fischeri) which focused on the reduction of luciferase-mediate...

IN VITRO CYTOTOXICITY OF AROMATIC AEROBIC BIOTRANSFORMATION PRODUCTS IN BLUEGILL SUNFISH BF-2 CELLS

EPA Science Inventory

Toluene (methylbenzene) is a common environmental pollutant that is found in many hazardous waste sites and it is an aquifer contaminant. A concern is the potential risk to human and ecosystem health due to exposure to toluene and its major biotransformation products. The cytotox...

Mechanism, kinetics, and pathways of self-sensitized sunlight photodegradation of phenylarsonic compounds.

PubMed

Xie, Xiande; Hu, Yuanan; Cheng, Hefa

2016-06-01

Being highly water-soluble, phenylarsonic feed additives discharged in animal wastes can easily accumulate in surface water bodies. The photodegradation mechanism, kinetics, and pathways of p-arsanilic acid (p-ASA), 4-hydrophenylarsonic acid (4-HPAA), and phenylarsonic acid (PAA) in water under simulated and natural sunlight irradiation were investigated. The -AsO(OH)2 group was cleaved from the aromatic ring during photodegradation, and p-benzoquinone and p-hydroquinone were formed as the major organic degradation intermediates. Experimental results did not indicate any significant direct photolysis of the phenylarsonic compounds under simulated and natural sunlight irradiation, but consistently showed that they sensitized the formation of singlet oxygen, which was responsible for their photodegradation and oxidation of the As(III) released. A simple (1)O2-based "heterogeneous" model was developed, which could well describe the kinetics of (1)O2 formation and phenylarsonic compound photodegradation under various conditions. Indirect photolysis caused by inorganic ions commonly present in natural waters was negligible, while natural organic matter could significantly inhibit their photodegradation. The half-lives of p-ASA, 4-HPAA, and PAA photodegradation under simulated sunlight irradiation (765 W m(-2), 25 °C) were 11.82 ± 0.19, 20.06 ± 0.10, and 135 ± 6.0 min, respectively, while their degradation rates under natural sunlight in the Pearl River Delta of southern China were 5 times slower due to lower irradiation intensity and water temperatures (19-23 °C). Copyright © 2016 Elsevier Ltd. All rights reserved.

S-glutathionyl-(chloro)hydroquinone reductases: a new class of glutathione transferases functioning as oxidoreductases

PubMed Central

Belchik, Sara M.; Xun, Luying

2011-01-01

Glutathione transferases (GSTs) are best known for transferring glutathione (GSH) to hydrophobic organic compounds, making the conjugates more soluble. However, the omega-class GSTs of animals and the lambda-class GSTs and dehydroascorbate reductases (DHARs) of plants have little or no activity for GSH transfer. Instead, they catalyze GSH-dependent oxidoreductions. The lambda-class GSTs reduce disulfide bonds, the DHARs reduce the disulfide bonds and dehydroascorbate, and the omega-class GSTs can reduce more substrates, including disulfide bonds, dehydroascorbate, and dimethylarsinate. Glutathionyl-(chloro)hydroquinone reductases (GS-HQRs) are the newest class of GSTs that mainly catalyze oxidoreductions. Besides the activities of the other three classes, GS-HQRs also reduce GS-hydroquinones, including GS-trichloro-p-hydroquinone, GS-dichloro-p-hydroquinone, GS-2-hydroxy-p-hydroquinone, and GS-p-hydroquinone. They are conserved and widely distributed in bacteria, fungi, protozoa, and plants, but not in animals. The four classes are phylogenetically more related to each other than to other GSTs, and they share a Cys-Pro motif at the GSH-binding site. Hydroquinones are metabolic intermediates of certain aromatic compounds. They can be auto-oxidized by O2 to benzoquinones, which spontaneously react with GSH to form GS-hydroquinones via Michael’s addition. GS-HQRs are expected to channel GS-hydroquinones, formed spontaneously or enzymatically, back to hydroquinones. When the released hydroquinones are intermediates of metabolic pathways, GS-HQRs play a maintenance role for the pathways. Further, the common presence of GS-HQRs in plants, green algae, cyanobacteria, and halobacteria suggest a beneficial role in the light-using organisms. PMID:21425927

Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers

PubMed Central

Kerou, Melina; Offre, Pierre; Valledor, Luis; Abby, Sophie S.; Melcher, Michael; Nagler, Matthias; Weckwerth, Wolfram; Schleper, Christa

2016-01-01

Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distribution and adaptions, growth requirements, and genome contents. We report here the genome and proteome of Nitrososphaera viennensis EN76, the type species of the archaeal class Nitrososphaeria of the phylum Thaumarchaeota encompassing all known AOA. N. viennensis is a soil organism with a 2.52-Mb genome and 3,123 predicted protein-coding genes. Proteomic analysis revealed that nearly 50% of the predicted genes were translated under standard laboratory growth conditions. Comparison with genomes of closely related species of the predominantly terrestrial Nitrososphaerales as well as the more streamlined marine Nitrosopumilales [Candidatus (Ca.) order] and the acidophile “Ca. Nitrosotalea devanaterra” revealed a core genome of AOA comprising 860 genes, which allowed for the reconstruction of central metabolic pathways common to all known AOA and expressed in the N. viennensis and “Ca. Nitrosopelagicus brevis” proteomes. Concomitantly, we were able to identify candidate proteins for as yet unidentified crucial steps in central metabolisms. In addition to unraveling aspects of core AOA metabolism, we identified specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu, including the capacity for biofilm formation, cell surface modifications and cell adhesion, and carbohydrate conversions as well as detoxification of aromatic compounds and drugs. PMID:27864514

Geochemical interpretation of distribution of aromatic hydrocarbons in components of geologic environment of Pechora, Barents and Kara seas.

NASA Astrophysics Data System (ADS)

Kursheva, Anna; Petrova, Vera; Litvinenko, Ivan; Morgunova, Inna

2017-04-01

Information about the hydrocarbons content (including aromatic ones) in components of geologic environment allows to define common factors in distribution and correlation both nature and technogenic component, and also to reveal the sources of contamination. At that, it should be noted, that hydrocarbons are widely spread in lithosphere and create steady geochemical background, variations are caused here by specifics of initial organic matter, conditions of its accumulation and transformation. The basis of the study are the samples of sea water and deep sea sediments (more than 600 stations), collected in western sector of Arctic region (Pechora, Barents and Kara seas) during the scientific-research expeditions of FSBI "VNIIOkeangeologia" for the period 2000-2010. Total content of aromatic hydrocarbons was defined by spectrofluorometric method using analyzer «FLUORAT-Panorama-02». Certification of data was performed on representative samples based on contents and molecule structure of polycyclic aromatic hydrocarbons using GC-MS (Agilent 5973/6850 GC-MS System). Results of spectrofluorometric analysis of lipid fraction of organic matter of bottom sediments allowed to define specific parameters, which characterize various lithofacies groups of sediments. Thus, sandy residues are characterized by low level of aromatic hydrocarbons (ca. 4.3 μg/g) with prevalence of bi- and tri-aromatic compounds (λmax 270-310 nm). This correlates with low sorption capacity of coarse-grained sediments and absence of organic-mineral component, containing the breakdown products of initial organic matter. Tetra- and penta- aromatic structures prevail in clay sediments (ca. 13.0 μg/g), which are typical components of lipid fraction of organic matter of post sedimentation and early diagenetic stages of transformation. At that, changes of spectral characteristic of sediments in stratigraphic sequence completely reflect processes of diagenetic transformation of organic matter, including aromatization and new formation of number of compounds, for example perylene (λmax 405,435 nm). The presence in sediments of highly transformed (post-diagenetic) organic material forms special (for naphthides) type of spectrum (λmax 370-380 nm), which interface is fundamentally different from recent marine sediments. Similar type of spectrum in combination with anomalously high content of aromatic hydrocarbons (ca. 349.1 μg/g) is typical, in particular, for shelf of Spitsbergen archipelago, whose erosion and redeposition of carboniferous rocks play important role in deposits formation. Similar content of aromatic hydrocarbons was noted in sediments of shelf of the Island Kolguev, where exogenous anomaly is caused mainly by anthropogenic factors. This assumption correlates with the results of aromatic hydrocarbons examination where pyrogenic components dominate. The influence of endogenous processes (seepage of hydrocarbons) also may lead to substantial deformation of background spectrum due to formation of intensive peak in short-wave region (λmax max 240-260 nm). Credibility of collected results is proven by significant correlation of quantitative estimation of aromatic hydrocarbons contents conducted using both dispersed organic matter extraction and fractionation and spectrofluorimetry methods. Results, received during GC-MS analysis also prove spectrofluorometric information.

Identification of benzothiazole derivatives and polycyclic aromatic hydrocarbons as aryl hydrocarbon receptor agonists present in tire extracts.

PubMed

He, Guochun; Zhao, Bin; Denison, Michael S

2011-08-01

Leachate from rubber tire material contains a complex mixture of chemicals previously shown to produce toxic and biological effects in aquatic organisms. The ability of these leachates to induce Ah receptor (AhR)-dependent cytochrome P4501A1 expression in fish indicated the presence of AhR active chemicals, but the responsible chemicals and their direct interaction with the AhR signaling pathway were not examined. Using a combination of AhR-based bioassays, we have demonstrated the ability of tire extract to stimulate both AhR DNA binding and AhR-dependent gene expression and confirmed that the responsible chemicals were metabolically labile. The application of CALUX (chemical-activated luciferase gene expression) cell bioassay-driven toxicant identification evaluation not only revealed that tire extract contained a variety of known AhR-active polycyclic aromatic hydrocarbons but also identified 2-methylthiobenzothiazole and 2-mercaptobenzothiazole as AhR agonists. Analysis of a structurally diverse series of benzothiazoles identified many that could directly stimulate AhR DNA binding and transiently activate the AhR signaling pathway and identified benzothiazoles as a new class of AhR agonists. In addition to these compounds, the relatively high AhR agonist activity of a large number of fractions strongly suggests that tire extract contains a large number of physiochemically diverse AhR agonists whose identities and toxicological/biological significances are unknown. Copyright © 2011 SETAC.

Evaluation of coal-related model compounds using a tandem mass spectrometry.

PubMed

Li, Guo-Sheng; Dong, Xueming; Fan, Xing; You, Chun-Yan; Wu, Ge; Zhao, Yun-Peng; Lu, Yao; Wei, Xian-Yong; Ma, Feng-Yun

2018-05-08

Gas chromotography/mass spectrometry (GC/MS) is a routine and basic instrumental method for the analysis of complex coal conversion products in chemical industry. To further enhance practical potentials of GC/MS in chemical industry, a tandem MS method for the selection of ion pair applied in monitoring coal conversions was established by using GC/quadrupole time-of-flight MS (GC/Q-TOF MS). The corresponding fragmentation pathways were explored and suitable ion pairs were screened. Fourteen coal-related model compounds (CRMCs) were analyzed using a GC/Q-TOF MS with different collision induced dissociation (CID) energies (5-20 eV). The fragmentation pathways can offer a better understanding of chemical bond breaking, hydrogen transfer, rearrangement reactions and elimination of neutral fragments for CRMCs during the CID process. The precursor ions of aromatic hydrocarbons without alkyl chain were hard to fragment with a CID energy of 20 eV. But aromatic hydrocarbons with branched chains were prone to fragment via the loss of alkyl chains and further fragmented through ring-open reactions. Compared to C alk -C ar bond, C ar -C ar bond was hard to fragment duo to its high bond dissociation energy. The existence of heteroatoms facilitated fragmentation that was conducive to screening ion pair. The CID technique of GC/Q-TOF MS will contribute to the studies on the organic composition of coals and building monitoring methods for coal conversions via fragmentation and ion pair selection. This article is protected by copyright. All rights reserved.

Potential Metabolic Activation of a Representative C2-Alkylated Polycyclic Aromatic Hydrocarbon 6-Ethylchrysene Associated with the Deepwater Horizon Oil Spill in Human Hepatoma (HepG2) Cells

PubMed Central

2016-01-01

Exposure to polycyclic aromatic hydrocarbons (PAHs) is the major human health hazard associated with the Deepwater Horizon oil spill. C2-Chrysenes are representative PAHs present in crude oil and could contaminate the food chain. We describe the metabolism of a C2-chrysene regioisomer, 6-ethylchrysene (6-EC), in human HepG2 cells. The structures of the metabolites were identified by HPLC-UV-fluorescence detection and LC-MS/MS. 6-EC-tetraol isomers were identified as signature metabolites of the diol-epoxide pathway. O-Monomethyl-O-monosulfonated-6-EC-catechol, its monohydroxy products, and N-acetyl-l-cysteine(NAC)-6-EC-ortho-quinone were discovered as signature metabolites of the ortho-quinone pathway. Potential dual metabolic activation of 6-EC involving the formation of bis-electrophiles, i.e., a mono-diol-epoxide and a mono-ortho-quinone within the same structure, bis-diol-epoxides, and bis-ortho-quinones was observed as well. The identification of 6-EC-tetraol, O-monomethyl-O-monosulfonated-6-EC-catechol, its monohydroxy products, and NAC-6-EC-ortho-quinone supports potential metabolic activation of 6-EC by P450 and AKR enzymes followed by metabolic detoxification of the ortho-quinone through interception of its redox cycling capability by catechol-O-methyltransferase and sulfotransferase enzymes. The tetraols and catechol conjugates could be used as biomarkers of human exposure to 6-EC resulting from oil spills. PMID:27054409

Identification of Benzothiazole Derivatives and Polycyclic Aromatic Hydrocarbons as Aryl Hydrocarbon Receptor Agonists Present in Tire Extracts

PubMed Central

He, Guochun; Zhao, Bin; Denison, Michael S.

2012-01-01

Leachate from rubber tire material contains a complex mixture of chemicals previously shown to produce toxic and biological effects in aquatic organisms. While the ability of these leachates to induce Ah receptor (AhR)-dependent cytochrome P4501A1 expression in fish indicated the presence of AhR active chemicals, the responsible chemical(s) and their direct interaction with the AhR signaling pathway were not examined. Using a combination of AhR-based bioassays, we have demonstrated the ability of tire extract to stimulate both AhR DNA binding and AhR-dependent gene expression and confirmed that the responsible chemical(s) was metabolically labile. The application of CALUX (Chemical-Activated LUciferase gene eXpression) cell bioassay-driven toxicant identification evaluation not only revealed that tire extract contained a variety of known AhR-active polycyclic aromatic hydrocarbons, but also identified 2-methylthiobenzothiazole and 2-mercaptobenzothiazole as AhR agonists. Analysis of a structurally diverse series of benzothiazoles identified many that could directly stimulate AhR DNA binding and transiently activate the AhR signaling pathway and identified benzothiazoles as a new class of AhR agonists. In addition to these compounds, the relatively high AhR agonist activity of a large number of fractions strongly suggests that tire extract contains a large number of physiochemically diverse AhR agonists whose identities and toxicological/biological significances are unknown. PMID:21590714

Structural basis of stereospecificity in the bacterial enzymatic cleavage of β-aryl ether bonds in lignin

DOE PAGES

Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.; ...

2015-12-04

Here, lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, wemore » present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.« less

A Novel Method to Identify Differential Pathways in Hippocampus Alzheimer's Disease.

PubMed

Liu, Chun-Han; Liu, Lian

2017-05-08

BACKGROUND Alzheimer's disease (AD) is the most common type of dementia. The objective of this paper is to propose a novel method to identify differential pathways in hippocampus AD. MATERIAL AND METHODS We proposed a combined method by merging existed methods. Firstly, pathways were identified by four known methods (DAVID, the neaGUI package, the pathway-based co-expressed method, and the pathway network approach), and differential pathways were evaluated through setting weight thresholds. Subsequently, we combined all pathways by a rank-based algorithm and called the method the combined method. Finally, common differential pathways across two or more of five methods were selected. RESULTS Pathways obtained from different methods were also different. The combined method obtained 1639 pathways and 596 differential pathways, which included all pathways gained from the four existing methods; hence, the novel method solved the problem of inconsistent results. Besides, a total of 13 common pathways were identified, such as metabolism, immune system, and cell cycle. CONCLUSIONS We have proposed a novel method by combining four existing methods based on a rank product algorithm, and identified 13 significant differential pathways based on it. These differential pathways might provide insight into treatment and diagnosis of hippocampus AD.

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

Zeng, Xiaofei; Collins, Maya; Borole, Abhijeet P.

Phenolic compounds in hydrolysate/pyrolysate and wastewater streams produced during the pretreatment of lignocellulosic biomass for biofuel production present a significant challenge in downstream processes. Bioelectrochemical systems are increasingly recognized as an alternative technology to handle biomass-derived streams and to promote water reuse in biofuel production. Thus, a thorough understanding of the fate of phenolic compounds in bioanodes is urgently needed. The present study investigated the biotransformation of three structurally similar phenolic compounds (syringic acid, SA; vanillic acid, VA; 4-hydroxybenzoic acid, HBA), and their individual contribution to exoelectrogenesis in a microbial electrolysis cell (MEC) bioanode. Fermentation of SA resulted in themore » highest exoelectrogenic activity among the three compounds tested, with 50% of the electron equivalents converted to current, compared to 12 and 9% for VA and HBA, respectively. The biotransformation of SA, VA and HBA was initiated by demethylation and decarboxylation reactions common to all three compounds, resulting in their corresponding hydroxylated analogs. SA was transformed to pyrogallol (1,2,3-trihydroxybenzene), whose aromatic ring was then cleaved via a phloroglucinol pathway, resulting in acetate production, which was then used in exoelectrogenesis. In contrast, more than 80% of VA and HBA was converted to catechol (1,2-dihydroxybenzene) and phenol (hydroxybenzene) as their respective dead-end products. The persistence of catechol and phenol is explained by the fact that the phloroglucinol pathway does not apply to di- or mono-hydroxylated benzenes. Previously reported, alternative ring-cleaving pathways were either absent in the bioanode microbial community or unfavorable due to high energy-demand reactions. With the exception of acetate oxidation, all biotransformation steps in the bioanode occurred via fermentation, independently of exoelectrogenesis. Therefore, the observed exoelectrogenic activity in batch runs conducted with SA, VA and HBA was controlled by the extent of fermentative transformation of the three phenolic compounds in the bioanode, which is related to the number and position of the methoxy and hydroxyl substituents.« less

The Extent of Fermentative Transformation of Phenolic Compounds in the Bioanode Controls Exoelectrogenic Activity in a Microbial Electrolysis Cell

DOE PAGES

Zeng, Xiaofei; Collins, Maya; Borole, Abhijeet P.; ...

2016-11-27

Phenolic compounds in hydrolysate/pyrolysate and wastewater streams produced during the pretreatment of lignocellulosic biomass for biofuel production present a significant challenge in downstream processes. Bioelectrochemical systems are increasingly recognized as an alternative technology to handle biomass-derived streams and to promote water reuse in biofuel production. Thus, a thorough understanding of the fate of phenolic compounds in bioanodes is urgently needed. The present study investigated the biotransformation of three structurally similar phenolic compounds (syringic acid, SA; vanillic acid, VA; 4-hydroxybenzoic acid, HBA), and their individual contribution to exoelectrogenesis in a microbial electrolysis cell (MEC) bioanode. Fermentation of SA resulted in themore » highest exoelectrogenic activity among the three compounds tested, with 50% of the electron equivalents converted to current, compared to 12 and 9% for VA and HBA, respectively. The biotransformation of SA, VA and HBA was initiated by demethylation and decarboxylation reactions common to all three compounds, resulting in their corresponding hydroxylated analogs. SA was transformed to pyrogallol (1,2,3-trihydroxybenzene), whose aromatic ring was then cleaved via a phloroglucinol pathway, resulting in acetate production, which was then used in exoelectrogenesis. In contrast, more than 80% of VA and HBA was converted to catechol (1,2-dihydroxybenzene) and phenol (hydroxybenzene) as their respective dead-end products. The persistence of catechol and phenol is explained by the fact that the phloroglucinol pathway does not apply to di- or mono-hydroxylated benzenes. Previously reported, alternative ring-cleaving pathways were either absent in the bioanode microbial community or unfavorable due to high energy-demand reactions. With the exception of acetate oxidation, all biotransformation steps in the bioanode occurred via fermentation, independently of exoelectrogenesis. Therefore, the observed exoelectrogenic activity in batch runs conducted with SA, VA and HBA was controlled by the extent of fermentative transformation of the three phenolic compounds in the bioanode, which is related to the number and position of the methoxy and hydroxyl substituents.« less

Biodegradation of Aliphatic-Aromatic Copolyesters by Thermomonospora fusca and Other Thermophilic Compost Isolates

PubMed Central

Kleeberg, Ilona; Hetz, Claudia; Kroppenstedt, Reiner Michael; Müller, Rolf-Joachim; Deckwer, Wolf-Dieter

1998-01-01

Random aliphatic-aromatic copolyesters synthesized from 1,4-butanediol, adipic acid, and terephthalic acid (BTA) have excellent thermal and mechanical properties and are biodegradable by mixed cultures (e.g., in compost). Over 20 BTA-degrading strains were isolated by using compost as a microbial source. Among these microorganisms, thermophilic actinomycetes obviously play an outstanding role and appear to dominate the initial degradation step. Two actinomycete strains exhibited about 20-fold higher BTA degradation rates than usually observed in a common compost test. These isolates were identified as Thermomonospora fusca strains. They appeared to be particularly suitable for establishment of rapid degradation tests and were used in comparative studies on the biodegradation of various polyesters. PMID:9572944

Impact of gas chromatography and mass spectrometry combined with gas chromatography and olfactometry for the sex differentiation of Baccharis articulata by the analysis of volatile compounds.

PubMed

Minteguiaga, Manuel; Umpiérrez, Noelia; Fariña, Laura; Falcão, Manuel A; Xavier, Vanessa B; Cassel, Eduardo; Dellacassa, Eduardo

2015-09-01

The Baccharis genus has more than 400 species of aromatic plants. However, only approximately 50 species have been studied in oil composition to date. From these studies, very few take into consideration differences between male and female plants, which is a significant and distinctive factor in Baccharis in the Asteraceae family. Baccharis articulata is a common shrub that grows wild in south Brazil, northern and central Argentina, Bolivia, Paraguay and Uruguay. It is considered to be a medicinal plant and is employed in traditional medicine. We report B. articulata male and female volatile composition obtained by simultaneous distillation-extraction technique and analyzed by gas chromatography with mass spectrometry. Also, an assessment of aromatic differences between volatile extracts was evaluated by gas chromatography with olfactometry. The results show a very similar chemical composition between male and female extracts, with a high proportion of terpene compounds of which β-pinene, limonene and germacrene D are the main components. Despite the chemical similarity, great differences in aromatic profile were found: male plant samples exhibited the strongest odorants in number and intensity of aromatic attributes. These differences explain field observations which indicate differences between male and female flower aroma, and might be of ecological significance in the attraction of pollinating insects. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Removal of Intermediate Aromatic Halogenated DBPs by Activated Carbon Adsorption: A New Approach to Controlling Halogenated DBPs in Chlorinated Drinking Water.

PubMed

Jiang, Jingyi; Zhang, Xiangru; Zhu, Xiaohu; Li, Yu

2017-03-21

During chlorine disinfection of drinking water, chlorine may react with natural organic matter (NOM) and bromide ion in raw water to generate halogenated disinfection byproducts (DBPs). To mitigate adverse effects from DBP exposure, granular activated carbon (GAC) adsorption has been considered as one of the best available technologies for removing NOM (DBP precursor) in drinking water treatment. Recently, we have found that many aromatic halogenated DBPs form in chlorination, and they act as intermediate DBPs to decompose and form commonly known DBPs including trihalomethanes and haloacetic acids. In this work, we proposed a new approach to controlling drinking water halogenated DBPs by GAC adsorption of intermediate aromatic halogenated DBPs during chlorination, rather than by GAC adsorption of NOM prior to chlorination (i.e., traditional approach). Rapid small-scale column tests were used to simulate GAC adsorption in the new and traditional approaches. Significant reductions of aromatic halogenated DBPs were observed in the effluents with the new approach; the removals of total organic halogen, trihalomethanes, and haloacetic acids by the new approach always exceeded those by the traditional approach; and the effluents with the new approach were considerably less developmentally toxic than those with the traditional approach. Our findings indicate that the new approach is substantially more effective in controlling halogenated DBPs than the traditional approach.

Molecular mechanisms in the pyrolysis of unsaturated chlorinated hydrocarbons: formation of benzene rings. 1. Quantum chemical studies.

PubMed

McIntosh, Grant J; Russell, Douglas K

2013-05-23

Analogues of important aromatic growth mechanisms in hydrocarbon pyrolysis and combustion systems are extended to chlorinated systems. We consider the addition of C2Cl2 to both C4Cl3 and C4Cl5 radicals at the M06-2X/6-311+G(3df,3p)//B3LYP/6-31G(d) level of theory, and we demonstrate that these reaction systems have much in common with those of nonchlorinated species. In particular, we find that these radicals appear to lead preferentially to fulvenes, and not to the observed aromatic products, as is found in nonchlorinated systems. We have therefore also considered nonradical C4/C2 channels by way of Diels-Alder cyclization of C4Cl4/C2Cl2 and C4H2Cl2/C2HCl pairs to describe aromatic formation. While the latter pair readily leads to the formation of partially chlorinated benzenes, the fully chlorinated congeners are sterically prohibited from ring closing directly; this leads to a series of novel rearrangement processes which predict the formation of hexachloro-1,5-diene-3-yne, in addition to hexachlorobenzene, in good agreement with experiment. This suggests, for the first time, that facile nonradical routes to aromatic formation are operative in partially and fully chlorinated pyrolysis and combustion systems.

[Transmission and development of foreign medicinal materials in the Tang and Song Dynasties].

PubMed

Wu, Meng-Hua; Zhao, Zhong-Zhen; Cao, Hui

2016-11-01

Many foreign medicinal materials that were imported to China via the Silk Road and maritime trade have enriched Chinese medicine. Imported foreign medicines reached a high point by the Tang and Song Dynasties, particularly in the case of aromatic medicines, which supplemented domestic Chinese aromatics and were widely employed in official dispensaries in the Song Dynasty. This study investigated historical records related to imported Chinese medicines in the Tang and Song periods, focusing on their varieties, quantity, use, and localization trends. Foreign medicines were assimilated as Chinese medical theory was applied to interpret their effects, and aromatics such as frankincense that were extremely expensive in the Tang Dynasty became accessible to common people by the Song Dynasty. By the Song Dynasty, some foreign medicines began to be domestically cultivated and the boundary between foreign and traditional Chinese medicines became blurred; foreign medicines gradually transformed into Chinese medicines. The importation of foreign medicines during the Tang and Song Dynasties was a historical turning point that contributed greatly to the development of traditional Chinese medicine. Copyright© by the Chinese Pharmaceutical Association.

The structure of dimethylallyl tryptophan synthase reveals a common architecture of aromatic prenyltransferases in fungi and bacteria

PubMed Central

Metzger, Ute; Schall, Christoph; Zocher, Georg; Unsöld, Inge; Stec, Edyta; Li, Shu-Ming; Heide, Lutz; Stehle, Thilo

2009-01-01

Ergot alkaloids are toxins and important pharmaceuticals that are produced biotechnologically on an industrial scale. The first committed step of ergot alkaloid biosynthesis is catalyzed by dimethylallyl tryptophan synthase (DMATS; EC 2.5.1.34). Orthologs of DMATS are found in many fungal genomes. We report here the x-ray structure of DMATS, determined at a resolution of 1.76 Å. A complex of DMATS from Aspergillus fumigatus with its aromatic substrate L-tryptophan and with an analogue of its isoprenoid substrate dimethylallyl diphosphate reveals the structural basis of this enzyme-catalyzed Friedel-Crafts reaction, which shows strict regiospecificity for position 4 of the indole nucleus of tryptophan as well as unusual independence of the presence of Mg2+ ions. The 3D structure of DMATS belongs to a rare β/α barrel fold, called prenyltransferase barrel, that was recently discovered in a small group of bacterial enzymes with no sequence similarity to DMATS. These bacterial enzymes catalyze the prenylation of aromatic substrates in the biosynthesis of secondary metabolites (i.e., a reaction similar to that of DMATS). PMID:19706516

Electronic distributions within protein phenylalanine aromatic rings are reflected by the three-dimensional oxygen atom environments.

PubMed Central

Thomas, K A; Smith, G M; Thomas, T B; Feldmann, R J

1982-01-01

The atomic environments of 170 phenylalanine-residue aromatic rings from 28 protein crystal structures are transformed into a common orientation and combined to calculate an average three-dimensional environment. The spatial distribution of atom types in this environment reveals a preferred interaction between oxygen atoms and the edge of the planar aromatic rings. From the difference in frequency of interaction of oxygen atoms with the edge and the top of the ring, an apparent net free energy difference of interaction favoring the edge of the ring is estimated to be about -1 kcal/mol (1 cal = 4.184 J). Ab initio quantum mechanical calculations, performed on a model consisting of benzene and formamide, indicate that the observed geometry is stabilized by a favorable enthalpic interaction. Although benzene rings are considered to be nonpolar, the electron distribution is a complex multipole with no net dipole moment. The observed interaction orientation frequencies demonstrate that these multipolar electron distributions, when occurring at the short distances encountered in densely packed protein molecules, are significant determinants of internal packing geometries. PMID:6956896

Characterization of organic nitrogen in aerosols at a forest site in the southern Appalachian Mountains

NASA Astrophysics Data System (ADS)

Chen, Xi; Xie, Mingjie; Hays, Michael D.; Edgerton, Eric; Schwede, Donna; Walker, John T.

2018-05-01

This study investigates the composition of organic particulate matter in PM2.5 in a remote montane forest in the southeastern US, focusing on the role of organic nitrogen (N) in sulfur-containing secondary organic aerosol (nitrooxy-organosulfates) and aerosols associated with biomass burning (nitro-aromatics). Bulk water-soluble organic N (WSON) represented ˜ 14 % w/w of water-soluble total N (WSTN) in PM2.5 on average across seasonal measurement campaigns conducted in the spring, summer, and fall of 2015. The largest contributions of WSON to WSTN were observed in spring ( ˜ 18 % w/w) and the lowest in the fall ( ˜ 10 % w/w). On average, identified nitro-aromatic and nitrooxy-organosulfate compounds accounted for a small fraction of WSON, ranging from ˜ 1 % in spring to ˜ 4 % in fall, though were observed to contribute as much as 28 % w/w of WSON in individual samples that were impacted by local biomass burning. The highest concentrations of oxidized organic N species occurred during summer (average of 0.65 ng N m-3) along with a greater relative abundance of higher-generation oxygenated terpenoic acids, indicating an association with more aged aerosol. The highest concentrations of nitro-aromatics (e.g., nitrocatechol and methyl-nitrocatechol), levoglucosan, and aged SOA tracers were observed during fall, associated with aged biomass burning plumes. Nighttime nitrate radical chemistry is the most likely formation pathway for nitrooxy-organosulfates observed at this low NOx site (generally < 1 ppb). Isoprene-derived organosulfate (MW216, 2-methyltetrol derived), which is formed from isoprene epoxydiols (IEPOX) under low NOx conditions, was the most abundant individual organosulfate. Concentration-weighted average WSON / WSOC ratios for nitro-aromatics + organosulfates + terpenoic acids were 1 order of magnitude lower than the overall aerosol WSON / WSOC ratio, indicating the presence of other uncharacterized higher-N-content species. Although nitrooxy-organosulfates and nitro-aromatics contributed a small fraction of WSON, our results provide new insight into the atmospheric formation processes and sources of these largely uncharacterized components of atmospheric organic N, which also helps to advance the atmospheric models to better understand the chemistry and deposition of reactive N.

Stimulation of aryl metabolite production in the basidiomycete Bjerkandera sp. strain BOS55 with biosynthetic precursors and lignin degradation products.

PubMed Central

Mester, T; Swarts, H J; Romero i Sole, S; de Bont, J A; Field, J A

1997-01-01

Aryl metabolites are known to have an important role in the ligninolytic system of white rot fungi. The addition of known precursors and aromatic acids representing lignin degradation products stimulated the production of aryl metabolites (veratryl alcohol, veratraldehyde, p-anisaldehyde, and 3-chloro-p-anisaldehyde) in the white rot fungus Bjerkandera sp. strain BOS55. The presence of manganese (Mn) is known to inhibit the biosynthesis of veratryl alcohol (T. Mester, E. de Jong, and J.A. Field, Appl. Environ. Microbiol. 61:1881-1887, 1995). A new finding of this study was that the production of the other aryl metabolites, p-anisaldehyde and 3-chloro-p-anisaldehyde, was also inhibited by Mn. We attempted to bypass the Mn-inhibited step in the biosynthesis of aryl metabolites by the addition of known and suspected precursors. Most of these compounds were not able to bypass the inhibiting effect of Mn. Only the fully methylated precursors (veratrate, p-anisate, and 3-chloro-p-anisate) provided similar concentrations of aryl metabolites in the presence and absence of Mn, indicating that Mn does not influence the reduction of the benzylic acid group. The addition of deuterated benzoate and 4-hydroxybenzoate resulted in the formation of deuterated aryl metabolites, indicating that these aromatic acids entered into the biosynthetic pathway and were common intermediates to all aryl metabolites. Only deuterated chlorinated anisyl metabolites were produced when the cultures were supplemented with deuterated 3-chloro-4-hydroxybenzoate. This observation combined with the fact that 3-chloro-4-hydroxybenzoate is a natural product of Bjerkandera spp. (H. J. Swarts, F. J. M. Verhagen, J. A. Field, and J. B. P. A. Wijnberg, Phytochemistry 42:1699-1701, 1996) suggest that it is a possible intermediate in chlorinated anisyl metabolite biosynthesis. PMID:9143129

The effect of geometrical presentation of multimodal cation-exchange ligands on selective recognition of hydrophobic regions on protein surfaces.

PubMed

Woo, James; Parimal, Siddharth; Brown, Matthew R; Heden, Ryan; Cramer, Steven M

2015-09-18

The effects of spatial organization of hydrophobic and charged moieties on multimodal (MM) cation-exchange ligands were examined by studying protein retention behavior on two commercial chromatographic media, Capto™ MMC and Nuvia™ cPrime™. Proteins with extended regions of surface-exposed aliphatic residues were found to have enhanced retention on the Capto MMC system as compared to the Nuvia cPrime resin. The results further indicated that while the Nuvia cPrime ligand had a strong preference for interactions with aromatic groups, the Capto MMC ligand appeared to interact with both aliphatic and aromatic clusters on the protein surfaces. These observations were formalized into a new set of protein surface property descriptors, which quantified the local distribution of electrostatic and hydrophobic potentials as well as distinguishing between aromatic and aliphatic properties. Using these descriptors, high-performing quantitative structure-activity relationship (QSAR) models (R(2)>0.88) were generated for both the Capto MMC and Nuvia cPrime datasets at pH 5 and pH 6. Descriptors of electrostatic properties were generally common across the four models; however both Capto MMC models included descriptors that quantified regions of aliphatic-based hydrophobicity in addition to aromatic descriptors. Retention was generally reduced by lowering the ligand densities on both MM resins. Notably, elution order was largely unaffected by the change in surface density, but smaller and more aliphatic proteins tended to be more affected by this drop in ligand density. This suggests that modulating the exposure, shape and density of the hydrophobic moieties in multimodal chromatographic systems can alter the preference for surface exposed aliphatic or aromatic residues, thus providing an additional dimension for modulating the selectivity of MM protein separation systems. Copyright © 2015 Elsevier B.V. All rights reserved.

Interactive effects of Cd and PAHs on contaminants removal from co-contaminated soil planted with hyperaccumulator plant Sedum alfredii

USDA-ARS?s Scientific Manuscript database

Soil contamination by multiple organic and inorganic contaminants is common but its remediation by hyperaccumulator plants is rarely reported. The growth of a cadmium (Cd) hyperaccumulator Sedum alfredii and removal of contaminants from Cd and polycyclic aromatic hydrocarbons(PAHs) co-contaminated s...

TESTING FOR ADDITIVITY IN THE LOW DOSE REGION OF AN ENVIRONMENTALLY RELEVANT MIXTURE OF 18 OLYHALOGENATED AROMATIC HYDROCARBONS.

EPA Science Inventory

A common default assumption in risk assessment of chemical mixtures is that the chemicals combine additively in the low dose region. Under additivity, with information from single chemical dose-response data, the risk associated with the mixture can be estimated. The objective ...

Ascorbic Acid Enhances the Accumulation of Polycyclic Aromatic Hydrocarbons (PAHs) in Roots of Tall Fescue (Festuca arundinacea Schreb.)

PubMed Central

Gao, Yanzheng; Li, Hui; Gong, Shuaishuai

2012-01-01

Plant contamination by polycyclic aromatic hydrocarbons (PAHs) is crucial to food safety and human health. Enzyme inhibitors are commonly utilized in agriculture to control plant metabolism of organic components. This study revealed that the enzyme inhibitor ascorbic acid (AA) significantly reduced the activities of peroxidase (POD) and polyphenol oxidase (PPO), thus enhancing the potential risks of PAH contamination in tall fescue (Festuca arundinacea Schreb.). POD and PPO enzymes in vitro effectively decomposed naphthalene (NAP), phenanthrene (PHE) and anthracene (ANT). The presence of AA reduced POD and PPO activities in plants, and thus was likely responsible for enhanced PAH accumulation in tall fescue. This conclusion is supported by the significantly enhanced uptake of PHE in plants in the presence of AA, and the positive correlation between enzyme inhibition efficiencies and the rates of metabolism of PHE in tall fescue roots. This study provides a new perspective, that the common application of enzyme inhibitors in agricultural production could increase the accumulation of organic contaminants in plants, hence enhancing risks to food safety and quality. PMID:23185628

Inhibitors of calling behavior of Plodia interpunctella.

PubMed

Hirashima, Akinori; Shigeta, Yoko; Eiraku, Tomohiko; Kuwano, Eiichi

2003-01-01

Some octopamine agonists were found to suppress the calling behavior of the stored product Indian meal moth, Plodia interpunctella. Compounds were screened using a calling behavior bioassay using female P. interpunctella. Four active derivatives, with inhibitory activity at the nanomolar range, were identified in order of decreasing activity: 2-(1-phenylethylamino)-2-oxazoline > 2-(2-ethyl,6-methylanilino)oxazolidine > 2-(2-methyl benzylamino)-2-thiazoline > 2-(2,6-diethylanilino)thiazolidine. Three-dimensional pharmacophore hypotheses were built from a set of 15 compounds. Among the ten common-featured models generated by the program Catalyst/HipHop, a hypothesis including a hydrogen-bond acceptor lipid, a hydrophobic aromatic and two hydrophobic aliphatic features was considered to be essential for inhibitory activity in the calling behavior. Active compounds mapped well onto all the hydrogen-bond acceptor lipid, hydrophobic aromatic and hydrophobic aliphatic features of the hypothesis. On the other hand, less active compounds were shown not to achieve the energetically favorable conformation that is found in the active molecules in order to fit the 3D common-feature pharmacophore models. The present studies demonstrate that inhibition of calling behavior is via an octopamine receptor.

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.

Characterization of gossypol biosynthetic pathway

PubMed Central

Tian, Xiu; Ruan, Ju-Xin; Huang, Jin-Quan; Fang, Xin; Chen, Zhi-Wen; Hong, Hui; Wang, Ling-Jian; Mao, Ying-Bo; Lu, Shan; Zhang, Tian-Zhen; Chen, Xiao-Ya

2018-01-01

Gossypol and related sesquiterpene aldehydes in cotton function as defense compounds but are antinutritional in cottonseed products. By transcriptome comparison and coexpression analyses, we identified 146 candidates linked to gossypol biosynthesis. Analysis of metabolites accumulated in plants subjected to virus-induced gene silencing (VIGS) led to the identification of four enzymes and their supposed substrates. In vitro enzymatic assay and reconstitution in tobacco leaves elucidated a series of oxidative reactions of the gossypol biosynthesis pathway. The four functionally characterized enzymes, together with (+)-δ-cadinene synthase and the P450 involved in 7-hydroxy-(+)-δ-cadinene formation, convert farnesyl diphosphate (FPP) to hemigossypol, with two gaps left that each involves aromatization. Of six intermediates identified from the VIGS-treated leaves, 8-hydroxy-7-keto-δ-cadinene exerted a deleterious effect in dampening plant disease resistance if accumulated. Notably, CYP71BE79, the enzyme responsible for converting this phytotoxic intermediate, exhibited the highest catalytic activity among the five enzymes of the pathway assayed. In addition, despite their dispersed distribution in the cotton genome, all of the enzyme genes identified show a tight correlation of expression. Our data suggest that the enzymatic steps in the gossypol pathway are highly coordinated to ensure efficient substrate conversion. PMID:29784821

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

Gut Microbiota Regulation of Tryptophan Metabolism in Health and Disease.

PubMed

Agus, Allison; Planchais, Julien; Sokol, Harry

2018-06-13

The gut microbiota is a crucial actor in human physiology. Many of these effects are mediated by metabolites that are either produced by the microbes or derived from the transformation of environmental or host molecules. Among the array of metabolites at the interface between these microorganisms and the host is the essential aromatic amino acid tryptophan (Trp). In the gut, the three major Trp metabolism pathways leading to serotonin (5-hydroxytryptamine), kynurenine (Kyn), and indole derivatives are under the direct or indirect control of the microbiota. In this review, we gather the most recent advances concerning the central role of Trp metabolism in microbiota-host crosstalk in health and disease. Deciphering the complex equilibrium between these pathways will facilitate a better understanding of the pathogenesis of human diseases and open therapeutic opportunities. Copyright © 2018 Elsevier Inc. All rights reserved.

A competing, dual mechanism for catalytic direct benzene hydroxylation from combined experimental-DFT studies.

PubMed

Vilella, Laia; Conde, Ana; Balcells, David; Díaz-Requejo, M Mar; Lledós, Agustí; Pérez, Pedro J

2017-12-01

A dual mechanism for direct benzene catalytic hydroxylation is described. Experimental studies and DFT calculations have provided a mechanistic explanation for the acid-free, Tp x Cu-catalyzed hydroxylation of benzene with hydrogen peroxide (Tp x = hydrotrispyrazolylborate ligand). In contrast with other catalytic systems that promote this transformation through Fenton-like pathways, this system operates through a copper-oxyl intermediate that may interact with the arene ring following two different, competitive routes: (a) electrophilic aromatic substitution, with the copper-oxyl species acting as the formal electrophile, and (b) the so-called rebound mechanism, in which the hydrogen is abstracted by the Cu-O moiety prior to the C-O bond formation. Both pathways contribute to the global transformation albeit to different extents, the electrophilic substitution route seeming to be largely favoured.

Identification of aldolase and ferredoxin reductase within the dbt operon of Burkholderia fungorum DBT1.

PubMed

Piccoli, Stefano; Andreolli, Marco; Giorgetti, Alejandro; Zordan, Fabio; Lampis, Silvia; Vallini, Giovanni

2014-05-01

Burkholderia fungorum DBT1, first isolated from settling particulate matter of an oil refinery wastewater, is a bacterial strain which has been shown capable of utilizing several polycyclic aromatic hydrocarbons (PAHs) including dibenzothiophene (DBT). In particular, this microbe is able to efficiently degrade DBT through the Kodama pathway. Previous investigations have lead to the identification of six genes, on a total of eight, required for DBT degradation. In the present study, a combined experimental/computational approach was adopted to identify and in silico characterize the two missing genes, namely a ferredoxin reductase and a hydratase-aldolase. Thus, the finding of all enzymatic components of the Kodama pathway in B. fungorum DBT1 makes this bacterial strain amenable for possible exploitation in soil bioremediation protocols. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Overproduction of geraniol by enhanced precursor supply in Saccharomyces cerevisiae.

PubMed

Liu, Jidong; Zhang, Weiping; Du, Guocheng; Chen, Jian; Zhou, Jingwen

2013-12-01

Monoterpene geraniol, a compound obtained from aromatic plants, has wide applications. In this study, geraniol was synthesized in Saccharomyces cerevisiae through the introduction of geraniol synthase. To increase geraniol production, the mevalonate pathway in S. cerevisiae was genetically manipulated to enhance the supply of geranyl diphosphate, a substrate used for the biosynthesis of geraniol. Identification and optimization of the key regulatory points in the mevalonate pathway in S. cerevisiae increased geraniol production to 36.04 mg L(-1). The results obtained revealed that the IDI1-encoded isopentenyl diphosphate isomerase is a rate-limiting enzyme in the biosynthesis of geraniol in S. cerevisiae, and overexpression of MAF1, a negative regulator in tRNA biosynthesis, is another effective method to increase geraniol production in S. cerevisiae. Copyright © 2013 Elsevier B.V. All rights reserved.

Exploring the formation pathways of donor-acceptor catenanes in aqueous dynamic combinatorial libraries.

PubMed

Cougnon, Fabien B L; Au-Yeung, Ho Yu; Pantoş, G Dan; Sanders, Jeremy K M

2011-03-09

The discovery through dynamic combinatorial chemistry (DCC) of a new generation of donor-acceptor [2]catenanes highlights the power of DCC to access unprecedented structures. While conventional thinking has limited the scope of donor-acceptor catenanes to strictly alternating stacks of donor (D) and acceptor (A) aromatic units, DCC is demonstrated in this paper to give access to unusual DAAD, DADD, and ADAA stacks. Each of these catenanes has specific structural requirements, allowing control of their formation. On the basis of these results, and on the observation that the catenanes represent kinetic bottlenecks in the reaction pathway, we propose a mechanism that explains and predicts the structures formed. Furthermore, the spontaneous assembly of catenanes in aqueous dynamic systems gives a fundamental insight into the role played by hydrophobic effect and donor-acceptor interactions when building such complex architectures.

Unprecedented 22,26-seco physalins from Physalis angulata and their anti-inflammatory potential.

PubMed

Sun, Cheng-Peng; Oppong, Mahmood Brobbey; Zhao, Feng; Chen, Li-Xia; Qiu, Feng

2017-10-25

Two novel physalins, including a 22,26-seco physalin, physalin X (1), and a 11,15-cyclo-9(10),14(17),22(26)-triseco physalin with an unprecedented aromatic ring, aromaphysalin B (2), were isolated from Physalis angulata L. Their structures were determined by IR, UV, HRESIMS, and 2D NMR spectra as well as theoretical calculations. Compounds 1 and 2 exhibited inhibitory activities on NO production with IC 50 values of 68.50 and 29.69 μM, respectively. A plausible biosynthetic pathway for 2 is also discussed.

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

NONE

The Taylorville Central Illinois Public Service (CIPS) Company site is located on the south end of Taylorville, Christian County, Illinois. Past industrial activities at this site, 60-100 years ago, have resulted in subsurface soil and groundwater contamination by high levels of polynuclear aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs). Complete pathways at this site include exposure to sediments, surface water, air, and fish in the Seaman Estate Pond. The Illinois Department of Public Health (IDPH) concludes that exposure to site related contaminants to local residents does not pose a health hazard at this time.

Vinylation of nitro-substituted indoles, quinolinones, and anilides with grignard reagents.

PubMed

Egris, Riccardo; Villacampa, Mercedes; Menéndez, J Carlos

2009-10-19

The reaction of vinyl Grignard reagents with o-methoxynitroarenes containing an electron-releasing substituent para to the nitro group proceeds through a pathway that is different from the initially expected Bartoli indole synthesis. Thus, instead of giving fused indole derivatives, these reactions provide a very mild and efficient new procedure for the synthesis of synthetically relevant aromatic systems containing an o-nitrovinyl moiety, such as 5-nitro-4-vinylindoles, 6-nitro-7-vinylindoles, 6-nitro-5-vinyl-2(1H)quinolinones, and 4-nitro-3-vinylanilines.

Initial reactions involved in the dissimilation of mandelate by Rhodotorula graminis.

PubMed Central

Durham, D R

1984-01-01

Rhodotorula graminis utilized DL-mandelate, L(+)-mandelate, and D(-)-mandelate as sole sources of carbon and energy. Growth on these aromatic substrates resulted in the induction of an NAD-dependent D(-)-mandelate dehydrogenase and a dye-linked L(+)-mandelate dehydrogenase, each catalyzing the stereospecific conversion of its respective enantiomer of mandelate to benzoylformate. Benzoylformate was oxidized to benzaldehyde, which was dehydrogenated to benzoate by an NAD-dependent benzaldehyde dehydrogenase. Benzoate was further metabolized through p-hydroxybenzoate and the protocatechuate branch of the beta-ketoadipate pathway. PMID:6389497

Growth Substrate- and Phase-Specific Expression of Biphenyl, Benzoate, and C1 Metabolic Pathways in Burkholderia xenovorans LB400

PubMed Central

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

2005-01-01

Recent microarray experiments suggested that Burkholderia xenovorans LB400, a potent polychlorinated biphenyl (PCB)-degrading bacterium, utilizes up to three apparently redundant benzoate pathways and a C1 metabolic pathway during biphenyl and benzoate metabolism. To better characterize the roles of these pathways, we performed quantitative proteome profiling of cells grown on succinate, benzoate, or biphenyl and harvested during either mid-logarithmic growth or the transition between the logarithmic and stationary growth phases. The Bph enzymes, catabolizing biphenyl, were ∼16-fold more abundant in biphenyl- versus succinate-grown cells. Moreover, the upper and lower bph pathways were independently regulated. Expression of each benzoate pathway depended on growth substrate and phase. Proteins specifying catabolism via benzoate dihydroxylation and catechol ortho-cleavage (ben-cat pathway) were approximately an order of magnitude more abundant in benzoate- versus biphenyl-grown cells at the same growth phase. The chromosomal copy of the benzoyl-coenzyme A (CoA) (boxC) pathway was also expressed during growth on biphenyl: BoxC proteins were approximately twice as abundant as Ben and Cat proteins under these conditions. By contrast, proteins of the megaplasmid copy of the benzoyl-CoA (boxM) pathway were only detected in transition-phase benzoate-grown cells. Other proteins detected at increased levels in benzoate- and biphenyl-grown cells included general stress response proteins potentially induced by reactive oxygen species formed during aerobic aromatic catabolism. Finally, C1 metabolic enzymes were present in biphenyl-grown cells during transition phase. This study provides insights into the physiological roles and integration of apparently redundant catabolic pathways in large-genome bacteria and establishes a basis for investigating the PCB-degrading abilities of this strain. PMID:16291673

Shaofu Zhuyu decoction ameliorates obesity-mediated hepatic steatosis and systemic inflammation by regulating metabolic pathways

PubMed Central

Park, Hee-Sook; Lee, So Min; Jeong, Nam-Joo; Kim, Soon-Hee; Lee, Kyoung-Won; Lee, Ju-A

2017-01-01

Shaofu Zhuyu decoction (SFZYD, also known as Sobokchugeo-tang), a classical prescription drug in traditional East Asian medicine, has been used to treat blood stasis syndrome (BSS). Hepatic steatosis is the result of excess caloric intake, and its pathogenesis involves internal retention of phlegm and dampness, blood stasis, and liver Qi stagnation. To evaluate the effects of treatment with SFZYD on obesity-induced inflammation and hepatic steatosis, we fed male C57BL/6N mice a high fat diet (HFD) for 8 weeks and then treated them with SFZYD by oral gavage for an additional 4 weeks. The results of histological and biochemical examinations indicated that SFZYD treatment ameliorates systemic inflammation and hepatic steatosis. A partial least squares-discriminant analysis (PLS-DA) scores plot of serum metabolites showed that HFD mice began to produce metabolites similar to those of normal chow (NC) mice after SFZYD administration. We noted significant alterations in the levels of twenty-seven metabolites, alterations indicating that SFZYD regulates the TCA cycle, the pentose phosphate pathway and aromatic amino acid metabolism. Increases in the levels of TCA cycle intermediate metabolites, such as 2-oxoglutaric acid, isocitric acid, and malic acid, in the serum of obese mice were significantly reversed after SFZYD treatment. In addition to inducing changes in the above metabolites, treatment with SFZYD also recovered the expression of genes related to hepatic mitochondrial dysfunction, including Ucp2, Cpt1α, and Ppargc1α, as well as the expression of genes involved in lipid metabolism and inflammation, without affecting glucose uptake or insulin signaling. Taken together, these findings suggest that treatment with SFZYD ameliorated obesity-induced systemic inflammation and hepatic steatosis by regulating inflammatory cytokine and adipokine levels in the circulation and various tissues. Moreover, treatment with SFZYD also reversed alterations in the levels of metabolites of the TCA cycle, the pentose phosphate pathway and aromatic amino acid metabolism. PMID:28570676

Anaerobic Dehalogenation of Chloroanilines by Dehalococcoides mccartyi Strain CBDB1 and Dehalobacter Strain 14DCB1 via Different Pathways as Related to Molecular Electronic Structure.

PubMed

Zhang, Shangwei; Wondrousch, Dominik; Cooper, Myriel; Zinder, Stephen H; Schüürmann, Gerrit; Adrian, Lorenz

2017-04-04

Dehalococcoides mccartyi strain CBDB1 and Dehalobacter strain 14DCB1 are organohalide-respiring microbes of the phyla Chloroflexi and Firmicutes, respectively. Here, we report the transformation of chloroanilines by these two bacterial strains via dissimilar dehalogenation pathways and discuss the underlying mechanism with quantum chemically calculated net atomic charges of the substrate Cl, H, and C atoms. Strain CBDB1 preferentially removed Cl doubly flanked by two Cl or by one Cl and NH 2 , whereas strain 14DCB1 preferentially dechlorinated Cl that has an ortho H. For the CBDB1-mediated dechlorination, comparative analysis with Hirshfeld charges shows that the least-negative Cl discriminates active from nonactive substrates in 14 out of 15 cases and may represent the preferred site of primary attack through cob(I)alamin. For the latter trend, three of seven active substrates provide strong evidence, with partial support from three of the remaining four substrates. Regarding strain 14DCB1, the most positive carbon-attached H atom discriminates active from nonactive chloroanilines in again 14 out of 15 cases. Here, regioselectivity is governed for 10 of the 11 active substrates by the most positive H attached to the highest-charge (most positive or least negative) aromatic C carrying the Cl to be removed. These findings suggest the aromatic ring H as primary site of attack through the supernucleophile Co(I), converting an initial H bond to a full electron transfer as start of the reductive dehalogenation. For both mechanisms, one- and two-electron transfer to Cl (strain CBDB1) or H (strain 14DCB1) are compatible with the presently available data. Computational chemistry research into reaction intermediates and pathways may further aid in understanding the bacterial reductive dehalogenation at the molecular level.

The phn Genes of Burkholderia sp. Strain RP007 Constitute a Divergent Gene Cluster for Polycyclic Aromatic Hydrocarbon Catabolism

PubMed Central

Laurie, Andrew D.; Lloyd-Jones, Gareth

1999-01-01

Cloning and molecular ecological studies have underestimated the diversity of polycyclic aromatic hydrocarbon (PAH) catabolic genes by emphasizing classical nah-like (nah, ndo, pah, and dox) sequences. Here we report the description of a divergent set of PAH catabolic genes, the phn genes, which although isofunctional to the classical nah-like genes, show very low homology. This phn locus, which contains nine open reading frames (ORFs), was isolated on an 11.5-kb HindIII fragment from phenanthrene-degrading Burkholderia sp. strain RP007. The phn genes are significantly different in sequence and gene order from previously characterized genes for PAH degradation. They are transcribed by RP007 when grown at the expense of either naphthalene or phenanthrene, while in Escherichia coli the recombinant phn enzymes have been shown to be capable of oxidizing both naphthalene and phenanthrene to predicted metabolites. The locus encodes iron sulfur protein α and β subunits of a PAH initial dioxygenase but lacks the ferredoxin and reductase components. The dihydrodiol dehydrogenase of the RP007 pathway, PhnB, shows greater similarity to analogous dehydrogenases from described biphenyl pathways than to those characterized from naphthalene/phenanthrene pathways. An unusual extradiol dioxygenase, PhnC, shows no similarity to other extradiol dioxygenases for naphthalene or biphenyl oxidation but is the first member of the recently proposed class III extradiol dioxygenases that is specific for polycyclic arene diols. Upstream of the phn catabolic genes are two putative regulatory genes, phnR and phnS. Sequence homology suggests that phnS is a LysR-type transcriptional activator and that phnR, which is divergently transcribed with respect to phnSFECDAcAdB, is a member of the ς54-dependent family of positive transcriptional regulators. Reverse transcriptase PCR experiments suggest that this gene cluster is coordinately expressed and is under regulatory control which may involve PhnR and PhnS. PMID:9882667

Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis.

PubMed

Yi, Ming; Mudunuri, Uma; Che, Anney; Stephens, Robert M

2009-06-29

One of the challenges in the analysis of microarray data is to integrate and compare the selected (e.g., differential) gene lists from multiple experiments for common or unique underlying biological themes. A common way to approach this problem is to extract common genes from these gene lists and then subject these genes to enrichment analysis to reveal the underlying biology. However, the capacity of this approach is largely restricted by the limited number of common genes shared by datasets from multiple experiments, which could be caused by the complexity of the biological system itself. We now introduce a new Pathway Pattern Extraction Pipeline (PPEP), which extends the existing WPS application by providing a new pathway-level comparative analysis scheme. To facilitate comparing and correlating results from different studies and sources, PPEP contains new interfaces that allow evaluation of the pathway-level enrichment patterns across multiple gene lists. As an exploratory tool, this analysis pipeline may help reveal the underlying biological themes at both the pathway and gene levels. The analysis scheme provided by PPEP begins with multiple gene lists, which may be derived from different studies in terms of the biological contexts, applied technologies, or methodologies. These lists are then subjected to pathway-level comparative analysis for extraction of pathway-level patterns. This analysis pipeline helps to explore the commonality or uniqueness of these lists at the level of pathways or biological processes from different but relevant biological systems using a combination of statistical enrichment measurements, pathway-level pattern extraction, and graphical display of the relationships of genes and their associated pathways as Gene-Term Association Networks (GTANs) within the WPS platform. As a proof of concept, we have used the new method to analyze many datasets from our collaborators as well as some public microarray datasets. This tool provides a new pathway-level analysis scheme for integrative and comparative analysis of data derived from different but relevant systems. The tool is freely available as a Pathway Pattern Extraction Pipeline implemented in our existing software package WPS, which can be obtained at http://www.abcc.ncifcrf.gov/wps/wps_index.php.

Occupational exposure to gases, polycyclic aromatic hydrocarbons and volatile organic compounds in biomass-fired power plants.

PubMed

Jumpponen, M; Rönkkömäki, H; Pasanen, P; Laitinen, J

2013-01-01

The combustion of fuels produces air pollutants in the form of gases, organic compounds, and particulate matter. However, although the environmental aspect of these agents has been examined, workers' exposure to them is still a neglected issue. The purpose of this study was to measure maintenance and ash removal workers' multiple exposures to gases, volatile organic compounds (VOCs) and polycyclic aromatic hydrocarbons (PAHs) during their work tasks in biomass-fired power plants. Our hygienic measurements revealed that carbon monoxide, nitric oxide, ammonia and sulfur dioxide were the most common gases that the workers were exposed to during their tasks. Their average concentrations were 0.45 ppm, 0.06 ppm, 0.11 ppm and 0.42 ppm, respectively. Phenanthrene and naphthalene were the most prominent PAHs. At the same sampling points, the most commonly found VOCs were aromatic and aliphatic hydrocarbons and turpentines. The calculated total PAH concentrations were less than 7% of benzo[a]pyrene's eight-hour occupational exposure limit, and the total VOC concentrations were below the Finnish reference value for the normal industrial level in all measured work tasks. The most evident health effect caused by multiple exposures to gases was upper respiratory track irritation, followed by the disruption of oxygen transport, and finally central nervous system disorders. We recommend powered air respirators with ABEK+P3 cartridges and carbon monoxide gas detectors as the minimum requirement for those working inside biomass-fired power plant boilers, and compressed air breathing apparatus as the best form of protection. Copyright © 2012 Elsevier Ltd. All rights reserved.

Atomistic simulations of aromatic polyurea and polyamide for capacitive energy storage

NASA Astrophysics Data System (ADS)

Dong, Rui; Ranjan, V.; Buongiorno Nardelli, Marco; Bernholc, J.

2015-07-01

Materials for capacitive energy storage with high energy density and low loss are desired in many fields. We investigate several polymers with urea and amide functional groups using density functional theory and classical molecular dynamics simulations. For aromatic polyurea (APU) and para-aramid (PA), we find several nearly energetically degenerate ordered structures, while meta-aromatic polyurea (mAPU) tends to be rotationally disordered along the polymer chains. Simulated annealing of APU and PA structures results in the formation of hydrogen-bonded sheets, highlighting the importance of dipole-dipole interactions. In contrast, hydrogen bonding does not play a significant role in mAPU, hence the propensity to disorder. We find that the disordered structures with misaligned chains have significantly larger dielectric constants, due to significant increase in the free volume, which leads to easier reorientation of dipolar groups in the presence of an electric field. Large segment motion is still not allowed below the glass transition temperature, which explains the experimentally observed very low loss at high field and elevated temperature. However, the degree of disorder needs to be controlled, because highly entangled structures diminish the free dipoles and decrease permittivity. Among the considered materials, mAPU is the most promising dielectric for capacitive energy storage, but the concept of increasing permittivity while maintaining low loss through disorder-induced free volume increase is generally applicable and provides an alternative pathway for the design of high-performance dielectrics for capacitive energy storage.

Roles of free radicals in type 1 phototherapeutic agents: aromatic amines, sulfenamides, and sulfenates.

PubMed

Lin, Tien-Sung; Rajagopalan, Raghavan; Shen, Yuefei; Park, Sungho; Poreddy, Amruta R; Asmelash, Bethel; Karwa, Amolkumar S; Taylor, John-Stephen A

2013-07-03

Detailed analyses of the electron spin resonance (ESR) spectra, cell viability, and DNA degradation studies are presented for the photolyzed Type I phototherapeutic agents: aromatic amines, sulfenamides, and sulfenates. The ESR studies provided evidence that copious free radicals can be generated from these N-H, N-S, and S-O containing compounds upon photoirradiation with UV/visible light. The analyses of spectral data allowed us to identify the free radical species. The cell viability studies showed that these agents after exposure to light exert cytotoxicity to kill cancer cells (U937 leukemia cell lines HTC11, KB, and HT29 cell lines) in a dosage- and time-dependent manner. We examined a possible pathway of cell death via DNA degradation by a plasmid cleavage assay for several compounds. The effects of photosensitization with benzophenone in the presence of oxygen were examined. The studies indicate that planar tricyclic amines and sulfenamides tend to form π-electron delocalized aminyl radicals, whereas nonplanar ones tend to yield nitroxide radicals resulting from the recombination of aminyl radicals with oxygen. The ESR studies coupled with the results of cell viability measurements and DNA degradation reveal that planar N-centered radicals can provide higher potency in cell death and allow us to provide some insights on the reaction mechanisms. We also found the formation of azatropylium cations possessing high aromaticity derived from azepines can facilitate secondary electron transfer to form toxic O2(•-) radicals, which can further exert oxidative stress and cause cell death.