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1

Complete Genome Sequence of Geobacillus sp. Strain GHH01, a Thermophilic Lipase-Secreting Bacterium  

PubMed Central

Geobacillus sp. strain GHH01 was isolated during a screening for producers of extracellular thermostable lipases. The completely sequenced and annotated 3.6-Mb genome encodes 3,478 proteins. The strain is genetically equipped to utilize a broad range of different substrates and might develop natural competence.

Wiegand, Sandra; Rabausch, Ulrich; Chow, Jennifer; Daniel, Rolf; Streit, Wolfgang R.

2013-01-01

2

Draft Genome Sequence of Lignocellulose-Degrading Thermophilic Bacterium Geobacillus sp. Strain WSUCF1.  

PubMed

Geobacillus sp. strain WSUCF1 is a thermophilic spore-forming member of the phylum Firmicutes, isolated from a soil sample collected from the compost facility. We report the draft genome sequence of this isolate with an estimated genome size of 3.4 Mb. The genome sequence of this isolate revealed several genes encoding glycoside hydrolases, making it a potential candidate for plant biomass degradation. PMID:23950119

Bhalla, Aditya; Kainth, Amoldeep Singh; Sani, Rajesh K

2013-08-15

3

Catechol 1,2-dioxygenase from ?-naphthol degrading thermophilic Geobacillus sp. strain: purification and properties  

Microsoft Academic Search

The purpose of this study was purification and characterization of catechol 1,2-dioxygenase from Geobacillus sp. G27 strain, which degrades ?-naphthol by the ?-ketoadipate pathway. The catechol 1,2-dioxygenase (C1,2O) was purified\\u000a using four steps of ammonium sulfate precipitation, DEAE-celullose, Sephadex G-150 and hydroxylapatite chromatographies. The\\u000a enzyme was purified about 18-fold with a specific activity of 7.42 U mg of protein?1. The

Gražina Giedraityte; Lilija Kal?dien?

2009-01-01

4

Geobacillus zalihae sp. nov., a thermophilic lipolytic bacterium isolated from palm oil mill effluent in Malaysia  

PubMed Central

Background Thermophilic Bacillus strains of phylogenetic Bacillus rRNA group 5 were described as a new genus Geobacillus. Their geographical distribution included oilfields, hay compost, hydrothermal vent or soils. The members from the genus Geobacillus have a growth temperatures ranging from 35 to 78°C and contained iso-branched saturated fatty acids (iso-15:0, iso-16:0 and iso-17:0) as the major fatty acids. The members of Geobacillus have similarity in their 16S rRNA gene sequences (96.5–99.2%). Thermophiles harboring intrinsically stable enzymes are suitable for industrial applications. The quest for intrinsically thermostable lipases from thermophiles is a prominent task due to the laborious processes via genetic modification. Results Twenty-nine putative lipase producers were screened and isolated from palm oil mill effluent in Malaysia. Of these, isolate T1T was chosen for further study as relatively higher lipase activity was detected quantitatively. The crude T1 lipase showed high optimum temperature of 70°C and was also stable up to 60°C without significant loss of crude enzyme activity. Strain T1T was a Gram-positive, rod-shaped, endospore forming bacterium. On the basic of 16S rDNA analysis, strain T1T was shown to belong to the Bacillus rRNA group 5 related to Geobacillus thermoleovorans (DSM 5366T) and Geobacillus kaustophilus (DSM 7263T). Chemotaxonomic data of cellular fatty acids supported the affiliation of strain T1T to the genus Geobacillus. The results of physiological and biochemical tests, DNA/DNA hybridization, RiboPrint analysis, the length of lipase gene and protein pattern allowed genotypic and phenotypic differentiation of strain T1T from its validly published closest phylogenetic neighbors. Strain T1T therefore represents a novel species, for which the name Geobacillus zalihae sp. nov. is proposed, with the type strain T1T (=DSM 18318T; NBRC 101842T). Conclusion Strain T1T was able to secrete extracellular thermostable lipase into culture medium. The strain T1T was identified as Geobacillus zalihae T1T as it differs from its type strains Geobacillus kaustophilus (DSM 7263T) and Geobacillus thermoleovorans (DSM 5366T) on some physiological studies, cellular fatty acids composition, RiboPrint analysis, length of lipase gene and protein profile.

Rahman, Raja Noor Zaliha Raja Abd; Leow, Thean Chor; Salleh, Abu Bakar; Basri, Mahiran

2007-01-01

5

Classification of isolates from locations in Austria and Yellowstone National Park as Geobacillus tepidamans sp. nov.  

PubMed

Two moderately thermophilic, Gram-positive, spore-forming bacteria were isolated from different geographical locations and sources; strain GS5-97(T) from a beet sugar factory in Leopoldsdorf, Lower Austria, and strain YNP10 from a geothermally heated soil, Yellowstone National Park, USA. The sequences of their 16S rRNA genes were found to be 99.8% identical, and DNA-DNA hybridization experiments revealed that strains GS5-97(T) and YNP10 share 89.9 mol% similarity to each other, but only 34.3 and 39.2 mol% similarity, respectively, to Geobacillus caldoxylosilyticus DSM 12041(T), which is their closest related type strain. A polyphasic analysis showed that these two isolates were more similar to each other than to other characterized geobacilli. Their DNA G+C content was 43.2 and 42.4 mol%, respectively, and they were identical with respect to many phenotypic features (e.g. T(opt) 55 degrees C; pH(opt) 7.0). Both strains clearly displayed best growth when cultured aerobically. They differed slightly in their cellular fatty acid profiles and polar lipid pattern, and genotypically they could also be distinguished based on randomly amplified polymorphic DNA fingerprints and internal transcribed spacer analysis. Freeze-etching experiments revealed oblique surface layer (S-layer) lattices in both strains, and biochemical analyses of the purified S-layer proteins indicated the occurrence of glycosylation. Based on the properties of these organisms relative to those currently documented for the genus Geobacillus and for the various sister genera in the Bacillus radiation, a novel species is proposed, Geobacillus tepidamans sp. nov., with GS5-97(T) (=ATCC BAA-942(T)=DSM 16325(T)) as the type strain. Strain YNP10 has been deposited in the American Type Culture Collection as ATCC BAA-943. PMID:15545484

Schäffer, Christina; Franck, William L; Scheberl, Andrea; Kosma, Paul; McDermott, Timothy R; Messner, Paul

2004-11-01

6

Characterization of thermostable ?-glucosidases from newly isolated Geobacillus sp. A333 and thermophilic bacterium A343  

Microsoft Academic Search

We have partially purified and characterized two new thermostable exo-?-1,4-glucosidases (E.C.3.2.1.20) isolated from Geobacillus sp. A333 and thermophilic bacterium A343 strains. A333 ?-glucosidase showed optimum activity at 60°C, pH 6.8 and had a value\\u000a of 1.38 K\\u000a m for the pNPG substrate, whereas these results were found to be 65°C, 7.0 and 0.85, respectively for A343 enzyme. Specificity for 20\\u000a different

Arzu Coleri Cihan; Birgul Ozcan; Cumhur Cokmus

2009-01-01

7

Purification and characterization of a thermostable phytate resistant alpha-amylase from Geobacillus sp. LH8.  

PubMed

A thermophilic and amylolytic bacterium (LH8) was isolated from the hot spring of Larijan in Iran at 65 degrees C. Identification of strain LH8 by 16S rDNA sequence analysis showed that LH8 strain belongs to the Geobacillus sp. with 99% sequence similarity with the 16S rDNA of Geobacillus thermodenitrificans. A new alpha-amylase (GA) was extracted from this strain and purified by ion-exchange chromatography. SDS-PAGE showed a single band with an apparent molecular mass of 52kDa. The optimum temperature and pH were 80 degrees C and 5-7, respectively. In the presence of Mn2+, Ca2+, K+, Cr3+ and Al3+, the enzyme activity was stimulated while Mg2+, Ba2+, Ni2+, Zn2+, Fe3+, Cu2+ and EDTA reduced the activity. The K(m) and V(max) values for starch were 3 mg ml(-1) and 6.5 micromol min(-1), respectively. The gene encoding alpha-amylase was isolated and the amino acid sequence was deduced. Comparison of GA and other alpha-amylase amino acid sequences suggested that GA has conserved regions that were previously identified in alpha-amylase family but GA exhibited some substitutions in the sequence. Its phytate resistant is an important property of this enzyme. 5 and 10 mM phytic acid did not inhibit this enzyme. Therefore, features of phytate resistant alpha-amylase from Geobacillus sp. LH8 are discussed. PMID:19874846

Mollania, Nasrin; Khajeh, Khosro; Hosseinkhani, Saman; Dabirmanesh, Bahareh

2009-10-27

8

Characterization of hyperthermostable alpha-amylase from Geobacillus sp. IIPTN.  

PubMed

A newly isolated Geobacillus sp. IIPTN (MTCC 5319) from the hot spring of Uttarakhand's Himalayan region produced a hyperthermostable alpha-amylase. The microorganism was characterized by biochemical tests and 16S rRNA gene sequencing. The optimal temperature and pH were 60 degrees C and 6.5, respectively, for growth and enzyme production. Although it was able to grow in temperature ranges from 50 to 80 degrees C and pH 5.5-8.5. Maximum enzyme production was in exponential phase with activity 135 U ml(-1) at 60 degrees C. Assayed with cassava as substrate, the enzyme displayed optimal activity 192 U ml(-1) at pH 5.0 and 80 degrees C. The enzyme was purified to homogeneity with purification fold 82 and specific activity 1,200 U mg(-1) protein. The molecular mass of the purified enzyme was 97 KDa. The values of K(m) and V(max) were 36 mg ml(-1) and 222 micromol mg(-1) protein min(-1), respectively. The amylase was stable over a broad range of temperature from 40 degrees C to 120 degrees C and pH ranges from 5 to 10. The enzyme was stimulated with Mn(2+), whereas it was inhibited by Hg(2+), Cu(2+), Zn(2+), Mg(2+), and EDTA, suggesting that it is a metalloenzyme. Besides hyperthermostability, the novelty of this enzyme is resistance against protease. PMID:20094713

Dheeran, Pratibha; Kumar, Sachin; Jaiswal, Yogesh K; Adhikari, Dilip K

2010-01-22

9

Isolation and Characterization of a Bacteriocin-Like Substance Produced by Geobacillus toebii Strain HBB-247.  

PubMed

A total of 201 thermophilic bacteria isolated from various thermal spring, mud and soil were tested for their antibacterial activity. Among the mostly active isolates, Geobacillus toebii HBB-247 was further examined. Bacteriocin-like inhibitory substance (BLIS) produced by strain HBB-247 was found to be stable up to 60°C, sensitive to proteolytic enzymes and effective against Enterococcus faecalis, Listeria sp., E. avium, Clostridium pasteurianum, Cellulomonas fimi and some thermophilic strains isolated and identified in this study. As a result of Tricine-SDS-PAGE molecular weight of BLIS was estimated about 38 kDa. Production studies showed that G. toebii HBB-247 starts to produce antibacterial substance at early logarithmic phase of growth and maximum production was detected at the end of the logarithmic phase. PMID:23448995

Ba?bülbül Özdemir, Gamze; Biyik, Haci Halil

2011-09-14

10

Characterization of a recombinant thermostable xylanase from hot spring thermophilic Geobacillus sp. TC-W7.  

PubMed

A xylanase-producing thermophilic strain, Geobacillus sp. TC-W7, was isolated from a hot spring in Yongtai (Fuzhou, China). Subsequently, the xylanase gene that encoded 407 amino acids was cloned and expressed. The recombinant xylanase was purified by GST affinity chromatography and exhibited maximum activity at 75 degrees C and a pH of 8.2. The enzyme was active up to 95 degrees C and showed activity over a wide pH range of 5.2 to 10.2. Additionally, the recombinant xylanase showed high thermostability and pH stability. More than 85% of the enzyme's activity was retained after incubation at 70 degrees C for 90 min at a pH of 8.2. The activity of the recombinant xylanase was enhanced by treatment with 10 mM enzyme inhibitors (DDT, Tween-20, 2-Me, or TritonX-100) and was inhibited by EDTA or PMSF. Its functionality was stable in the presence of Li+, Na+, and K+, but inhibited by Hg2+, Ni2+, Co2+, Cu2+, Zn2+, Pb2+, Fe3+, and Al3+. The functionality of the crude xylanase had similar properties to the recombinant xylanase except for when it was treated with Al2+ or Fe2+. The enzyme might be a promising candidate for various industrial applications such as the biofuel, food, and paper and pulp industries. PMID:23075790

Liu, Bin; Zhang, Ningning; Zhao, Chao; Lin, Baixue; Xie, Lianhui; Huang, Yifan

2012-10-01

11

Molecular cloning, over expression and characterization of thermoalkalophilic esterases isolated from Geobacillus sp  

Microsoft Academic Search

Due to potential use for variety of biotechnological applications, genes encoding thermoalkalophilic esterase from three different\\u000a Geobacillus strains isolated from thermal environmental samples in Balçova (Agamemnon) geothermal site were cloned and respective proteins\\u000a were expressed in Escherichia coli (E.coli) and characterized in detail. Three esterases (Est1, Est2, Est3) were cloned directly by PCR amplification using consensus\\u000a degenerate primers from genomic

Hasan Cihad Tekedar; Gül?ah ?anl?-Mohamed

2011-01-01

12

Isolation of lipase producing thermophilic bacteria: optimization of production and reaction conditions for lipase from Geobacillus sp.  

PubMed

Lipases catalyze the hydrolysis and the synthesis of esters formed from glycerol and long chain fatty acids. Lipases occur widely in nature, but only microbial lipases are commercially significant. In the present study, thirty-two bacterial strains, isolated from soil sample of a hot spring were screened for lipase production. The strain TS-4, which gave maximum activity, was identified as Geobacillus sp. at MTCC, IMTECH, Chandigarh. The isolated lipase producing bacteria were grown on minimal salt medium containing olive oil. Maximal quantities of lipase were produced when 30 h old inoculum was used at 10% (v/v) in production medium and incubated in shaking conditions (150 rpm) for 72 h. The optimal temperature and pH for the bacterial growth and lipase production were found to be 60°C and 9.5, respectively. Maximal enzyme production resulted when mustard oil was used as carbon source and yeast extract as sole nitrogen source at a concentration of 1% (v/v) and 0.15% (w/v), respectively. The different optimized reaction parameters were temperature 65°C, pH 8.5, incubation time 10 min and substrate p-nitrophenyl palmitate. The Km and Vmax values of enzyme were found to be 14 mM and 17.86 ?mol ml-1min-1, respectively, with p-nitrophenyl palmitate as substrate. All metal ions studied (1 mM) increased the lipase activity. PMID:23195552

Mehta, Akshita; Kumar, Rakesh; Gupta, Reena

2012-12-01

13

Isolation and identification of lipase producing thermophilic Geobacillus sp. SBS-4S: cloning and characterization of the lipase.  

PubMed

A thermophilic microorganism, SBS-4S, was isolated from a hot spring located in Gilgit, Northern Areas of Pakistan. It was found to be an aerobic, gram-positive, rod-shaped, thermophilic bacterium that grew on various sugars, carboxylic acids and hydrocarbons at temperatures between 45°C and 75°C. Complete 16S rRNA gene sequence of the microorganism exhibited homology to various species of genus Geobacillus. A highest homology of 99.8% was found with Geobacillus kaustophilus. A partial (0.7 kbp) chaperonin gene sequence also showed a highest homology of 99.4% to that of G. kaustophilus whereas biochemical characteristics of the microorganism were similar to Geobacillus uzenensis. Based on biochemical characterization, 16S rRNA and chaperonin gene sequences, we identified SBS-4S as a strain of genus Geobacillus. Strain SBS-4S produced several extracellular enzymes including amylase, protease and lipase. The lipase encoding gene was cloned, expressed in Escherichia coli and the gene product was characterized. The recombinant lipase was optimally active at 60°C with stability at wide pH range (6-12). The enzyme activity was enhanced remarkably in the presence of Ca(+2). The K(m) and the V(max) for the hydrolysis of p-nitrophenyl acetate were 3.8mM and 2273 ?mol min(-1)mg(-1), respectively. The ability of the recombinant enzyme to be stable at a wide pH range makes it a potential candidate for use in industry. PMID:21185780

Tayyab, Muhammad; Rashid, Naeem; Akhtar, Muhammad

2010-12-24

14

Effectiveness of inoculation with isolated Geobacillus strains in the thermophilic stage of vegetable waste composting.  

PubMed

An inoculum containing two amylolytic and three cellulolytic thermophilic bacteria, isolated from a preceding compost pile and identified as Geobacillus species by 16S rRNA gene sequencing, was applied to a mixture of market waste, rice straw and cow dung (5:1:0.2) so that the initial cell density was 2 x 10(8) colony forming unit (CFU) per gram dry weight at 55 degrees Celsius. The inoculation increased the total cell count particularly in the thermophilic stage as determined by flow cytometry. Concomitantly, there was a significant rise in microbial metabolism in the compost pile as reflected by the dehydrogenase activity. As a result, the C/N ratio dropped more rapidly in the inoculated mixture than that in the control without inoculum. The study, therefore, suggested that inoculation by thermophilic bacteria would be effective in the composting process at least in the thermophilic stage. PMID:20036532

Sarkar, Sutripta; Banerjee, Rajdeep; Chanda, Sunanda; Das, Pradeep; Ganguly, Sandipan; Pal, Subrata

2009-12-29

15

Complete Genome Sequences of Methylophaga sp. Strain JAM1 and Methylophaga sp. Strain JAM7  

PubMed Central

Methylophaga sp. strains JAM1 and JAM7 have been isolated from a denitrification system. Strain JAM1 was the first Methylophaga strain reported to be able to grow under denitrifying conditions. Here, we report the complete genome sequences of the two strains, which allowed prediction of gene clusters involved in denitrification in strain JAM1.

Villeneuve, Celine; Martineau, Christine; Mauffrey, Florian

2012-01-01

16

Purification and characterization of intracellular and extracellular ?-glucosidases from Geobacillus toebii strain E134.  

PubMed

Two different ?-glucosidase-producing thermophilic E134 strains were isolated from a hot spring in Kozakli, Turkey. Based on the phenotypic, phylogenetic and chemotaxonomic evidence, the strain was proposed to be a species of G. toebii. Its thermostable exo-?-1,4-glucosidases also were characterized and compared, which were purified from the intracellular and extracellular fractions with estimated molecular weights of 65 and 45?kDa. The intracellular and extracellular ?-glucosidases showed optimal activity at 65?°C, pH 7·0, and at 70?°C, pH 6·8, with 3·65 and 0·83?K(m) values for the pNPG substrate, respectively. Both enzymes remained active over temperature and pH ranges of 35-70?°C and 4·5-11·0. They retained 82 and 84% of their activities when incubated at 60?°C for 5?h. Their relative activities were 45-75% and 45-60% at pH 4·5 and 11·0 values for 15?h at 35?°C. They could hydrolyse the ?-1,3 and ?-1,4 bonds on substrates in addition to a high transglycosylation activity, although the intracellular enzyme had more affinity to the substrates both in hydrolysis and transglycosylation reactions. Furthermore, although sodium dodecyl sulfate behaved as an activator for both of them at 60?°C, urea and ethanol only increased the activity of the extracellular ?-glucosidase. By this study, G. toebii E134 strain was introduced, which might have a potential in biotechnological processes when the conformational stability of its enzymes to heat, pH and denaturants were considered. Copyright © 2011 John Wiley & Sons, Ltd. PMID:22028281

Cihan, Arzu Coleri; Benli, Mehlika; Cokmus, Cumhur

2011-10-26

17

A novel endoglucanase from the thermophilic bacterium Geobacillus sp. 70PC53 with high activity and stability over a broad range of temperatures  

Microsoft Academic Search

A thermophilic Geobacillus bacterium secreting high activity of endo-glucanase (EC 3.2.1.4) was isolated from rice straw compost supplemented with pig\\u000a manure. A full-length gene of 1,104 bp, celA, encoding this glycosyl hydrolase family 5 endo-glucanase of 368 amino acids was isolated. No related gene from Geobacillus has been reported previously. The recombinant CelA expressed in Escherichia coli had an optimal activity

I-Son Ng; Chen-Wei Li; Yi-Fang Yeh; Po Ting Chen; Jiun-Ly Chir; Chin-Hua Ma; Su-May Yu; Tuan-hua David Ho; Chii-Gong Tong

2009-01-01

18

Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain  

SciTech Connect

A recently discovered thermophilic bacterium, Geobacillus thermoglucosidasius M10EXG, ferments a range of C5 (e.g., xylose) and C6 sugars (e.g., glucose) and istolerant to high ethanol concentrations (10percent, v/v). We have investigated the central metabolism of this bacterium using both in vitro enzyme assays and 13C-based flux analysis to provide insights into the physiological properties of this extremophile and explore its metabolism for bio-ethanol or other bioprocess applications. Our findings show that glucose metabolism in G. thermoglucosidasius M10EXG proceeds via glycolysis, the pentose phosphate pathway, and the TCA cycle; the Entner?Doudoroff pathway and transhydrogenase activity were not detected. Anaplerotic reactions (including the glyoxylate shunt, pyruvate carboxylase, and phosphoenolpyruvate carboxykinase) were active, but fluxes through those pathways could not be accuratelydetermined using amino acid labeling. When growth conditions were switched from aerobic to micro-aerobic conditions, fluxes (based on a normalized glucose uptake rate of 100 units (g DCW)-1 h-1) through the TCA cycle and oxidative pentose phosphate pathway were reduced from 64+-3 to 25+-2 and from 30+-2 to 19+-2, respectively. The carbon flux under micro-aerobic growth was directed formate. Under fully anerobic conditions, G. thermoglucosidasius M10EXG used a mixed acid fermentation process and exhibited a maximum ethanol yield of 0.38+-0.07 mol mol-1 glucose. In silico flux balance modeling demonstrates that lactate and acetate production from G. thermoglucosidasius M10EXG reduces the maximum ethanol yieldby approximately threefold, thus indicating that both pathways should be modified to maximize ethanol production.

Tang, Yinjie J.; Sapra, Rajat; Joyner, Dominique; Hazen, Terry C.; Myers, Samuel; Reichmuth, David; Blanch, Harvey; Keasling, Jay D.

2009-01-20

19

Cadmium Ion Biosorption by the Thermophilic Bacteria Geobacillus stearothermophilus and G. thermocatenulatus  

PubMed Central

This study reports surface complexation models (SCMs) for quantifying metal ion adsorption by thermophilic microorganisms. In initial cadmium ion toxicity tests, members of the genus Geobacillus displayed the highest tolerance to CdCl2 (as high as 400 to 3,200 ?M). The thermophilic, gram-positive bacteria Geobacillus stearothermophilus and G. thermocatenulatus were selected for further electrophoretic mobility, potentiometric titration, and Cd2+ adsorption experiments to characterize Cd2+ complexation by functional groups within and on the cell wall. Distinct one-site SCMs described the extent of cadmium ion adsorption by both studied Geobacillus sp. strains over a range of pH values and metal/bacteria concentration ratios. The results indicate that a functional group with a deprotonation constant pK value of approximately 3.8 accounts for 66% and 80% of all titratable sites for G. thermocatenulatus and G. stearothermophilus, respectively, and is dominant in Cd2+ adsorption reactions. The results suggest a different type of functional group may be involved in cadmium biosorption for both thermophilic strains investigated here, compared to previous reports for mesophilic bacteria.

Hetzer, Adrian; Daughney, Christopher J.; Morgan, Hugh W.

2006-01-01

20

Thioglucosidase activity from Sphingobacterium sp. strain OTG1  

Microsoft Academic Search

Screening for novel thioglucoside hydrolase activity resulted in the isolation of Sphingobacterium sp. strain OTG1 from enrichment cultures containing octylthioglucoside (OTG). OTG was hydrolysed into octanethiol and glucose by cell free extracts. Besides thioglucoside hydrolysis, several other glucoside hydrolase activities were detected in the Sphingobacterium sp. strain OTG1 cell free extract. By adding #-glucosidase inhibitors it was possible to discriminate

G. H. Meulenbeld; S. Hartmans

2001-01-01

21

Genome Sequence of Pectobacterium sp. Strain SCC3193  

PubMed Central

We report the complete and annotated genome sequence of the plant-pathogenic enterobacterium Pectobacterium sp. strain SCC3193, a model strain isolated from potato in Finland. The Pectobacterium sp. SCC3193 genome consists of a 516,411-bp chromosome, with no plasmids.

Koskinen, J. Patrik; Laine, Pia; Niemi, Outi; Nykyri, Johanna; Harjunpaa, Heidi; Auvinen, Petri; Paulin, Lars; Pirhonen, Minna; Palva, Tapio

2012-01-01

22

Genome Sequence of the Marine Janibacter Sp. Strain HTCC2649 ?  

PubMed Central

Janibacter sp. strain HTCC2649 is a novel marine member of the Actinobacteria, family Intrasporangiaceae, and is closely related to Janibacter melonis CM2104T and Knoellia sinensis HKI 0119T. The organism was isolated from a sample collected at Hydrostation S south of Bermuda by using high-throughput culturing techniques. Here we present the genome sequence of Janibacter sp. strain HTCC2649.

Thrash, J. Cameron; Cho, Jang-Cheon; Bertagnolli, Anthony D.; Ferriera, Steve; Johnson, Justin; Vergin, Kevin L.; Giovannoni, Stephen J.

2011-01-01

23

Steroid biotransformation by different strains of Micrococcus sp.  

PubMed

A strain of Micrococcus sp. was isolated for its capability of side chain degradation of cholesterol. This strain was characterized and identified as Micrococcus roseus. It was found to be the best strain for the production of androsta-1,4-diene-3,17-dione and androst-4-ene-3,17-dione compared with other Micrococcus strains. PMID:11501468

Dogra, N; Qazi, G N

2001-01-01

24

Genome Sequence of Sphingomonas sp. Strain PAMC 26605, Isolated from Arctic Lichen (Ochrolechia sp.)  

PubMed Central

The endosymbiotic bacterium Sphingomonas sp. strain PAMC 26605 was isolated from Arctic lichens (Ochrolechia sp.) on the Svalbard Islands. Here we report the draft genome sequence of this strain, which could provide further insights into the symbiotic mechanism of lichens in extreme environments.

Shin, Seung Chul; Ahn, Do Hwan; Lee, Jong Kyu; Kim, Su Jin; Hong, Soon Gyu; Kim, Eun Hye

2012-01-01

25

Isolation and Characterization of a Geobacillus thermoleovorans Strain from an Ultra-Deep South African Gold Mine  

SciTech Connect

A thermophilic, facultative bacterium was isolated from a depth of 3.1 km below ground surface in an ultradeep gold mine in South Africa. This isolate, designated GE-7, was cultivated from pH 8.0, 600C fissure water. GE-7 grows optimally at 650C, pH 6.5 on a wide range of carbon substrates including GE-7 is a long rod-shaped bacterium (4-6 µm long x 0.5 wide) with terminal endospores and flagella, in addition to O2, can also utilize nitrate as an electron acceptor. Phylogenetic analysis of GE-7 16S rDNA sequence revealed high sequence similarity with G. thermoleovorans DSM 5366T (99.6%), however, certain phenotypic characteristics of GE-7 were distinct from this and other strains of G. thermoleovorans previously described.

Deflaun, Mary F.; Fredrickson, Jim K.; Dong, Hailiang; Pfiffner, Susan M.; Onstott, T. C.; Balkwill, David L.; Streger, Sheryl H.; Stackebrandt, E.; Knoessen, S.; van Heerden, E.

2007-03-08

26

Steroid biotransformation by different strains of Micrococcus sp  

Microsoft Academic Search

A strain ofMicrococcus sp. was isolated for its capability of side chain degradation of cholesterol. This strain was characterized and identified\\u000a asMicrococcus roseus. It was found to be the best strain for the production of androsta-1,4-diene-3, 17-dione and androst-4-ene-3, 17-dione compared\\u000a with otherMicrococcus strains.

N. Dogra; G. N. Qazi

2001-01-01

27

Complete Genome Sequence of Antarctic Bacterium Psychrobacter sp. Strain G.  

PubMed

Here, we report the complete genome sequence of Psychrobacter sp. strain G, isolated from King George Island, Antarctica, which can produce lipolytic enzymes at low temperatures. The genomics information of this strain will facilitate the study of the physiology, cold adaptation properties, and evolution of this genus. PMID:24051316

Che, Shuai; Song, Lai; Song, Weizhi; Yang, Meng; Liu, Guiming; Lin, Xuezheng

2013-09-19

28

Heptaketides with antiviral activity from three endolichenic fungal strains Nigrospora sp., Alternaria sp. and Phialophora sp.  

PubMed

Two new heptaketides, (+)-(2S,3S,4aS)-altenuene (1a) and (-)-(2S,3S,4aR)-isoaltenuene (2a), together with six known compounds, (-)-(2R,3R,4aR)-altenuene (1b), (+)-(2R,3R,4aS)-isoaltenuene (2b), 5'-methoxy-6-methyl-biphenyl-3,4,3'-triol (3), alternariol (4), alternariol-9-methyl ether (5), and 4-hydroxyalternariol-9-methyl ether (6) were isolated from the EtOAc extract of an endolichenic fungal strain Nigrospora sphaerica (No.83-1-1-2). Compounds 1a and 1b were separated from enantiomers 1 by chiral HPLC, and so were 2a and 2b from enantiomers 2. Interestingly, 1-6 were also obtained from other two endolichenic fungal strains Alternaria alternata (No.58-8-4-1) and Phialophora sp. (No.96-1-8-1). The structures of 1-6 were elucidated by means of MS, HR-MS, NMR, and X-ray diffraction. Furthermore, the absolute configurations of 1a-2b were determined by CD experiments and CD calculation. Of these compounds, 4 and 5 showed antiviral activity against herpes simplex virus (HSV) in vitro, with IC(50) values of 13.5 and 21.3 ?M, and with selective index (SI) values of 26.5 and 17.1, respectively. PMID:22613072

He, Jun-Wei; Chen, Guo-Dong; Gao, Hao; Yang, Fan; Li, Xiao-Xia; Peng, Tao; Guo, Liang-Dong; Yao, Xin-Sheng

2012-05-14

29

Genome sequence of Enterobacter sp. strain SP1, an endophytic nitrogen-fixing bacterium isolated from sugarcane.  

PubMed

Enterobacter sp. strain SP1 is an endophytic nitrogen-fixing bacterium isolated from a sugarcane stem and can promote plant growth. The draft genome sequence of strain SP1 presented here will promote comparative genomic studies to determine the genetic background of interactions between endophytic enterobacteria and plants. PMID:23209221

Zhu, Bo; Chen, Mingyue; Lin, Li; Yang, Litao; Li, Yangrui; An, Qianli

2012-12-01

30

Genome Sequence of Alcaligenes sp. Strain HPC1271  

PubMed Central

We report a draft genome sequence of Alcaligenes sp. strain HPC1271, which demonstrates antimicrobial activity against multidrug-resistant bacteria. Antibiotic production by Alcaligenes has not been frequently reported, and hence, the availability of the genome sequence should enable us to explore new antibiotic-producing gene clusters.

Sagarkar, Sneha; Tanksale, Himgouri; Sharma, Nandita; Qureshi, Asifa; Khardenavis, Anshuman; Purohit, Hemant J.

2013-01-01

31

Metabolism of 2-, 3- and 4-hydroxybenzoates by soil isolates Alcaligenes sp. strain PPH and Pseudomonas sp. strain PPD.  

PubMed

Pseudomonas sp. strain PPD and Alcaligenes sp. strain PPH isolated from soil by enrichment culture technique utilize 2-, 3- and 4-hydroxybenzoates as the sole source of carbon and energy. The degradation pathways were elucidated by performing whole-cell O(2) uptake, enzyme activity and induction studies. Depending on the mixture of carbon source and the preculture condition, strain PPH was found to degrade 2-hydroxybenzoate either via the catechol or gentisate route and has both salicylate 1-hydroxylase and salicylate 5-hydroxylase. Strain PPD utilizes 2-hydroxybenzoate via gentisate. Both strains degrade 3- and 4-hydroxybenzoate via gentisate and protocatechuate, respectively. Enzymes were induced by respective hydroxybenzoate. Growth pattern, O(2) uptake and enzyme activity profiles on the mixture of three hydroxybenzoates as a carbon source suggest coutilization by both strains. When 3- or 4-hydroxybenzoate grown culture was used as an inoculum, strain PPH failed to utilize 2-hydroxybenzoate via catechol, indicating the modulation of the metabolic pathways, thus generating metabolic diversity. PMID:17169001

Deveryshetty, Jaigeeth; Suvekbala, V; Varadamshetty, Gautham; Phale, Prashant S

2006-12-13

32

Characterization of isofenphos hydrolases from Arthrobacter sp. strain B5  

Microsoft Academic Search

Two organophosphorus compound hydrolases constitutively expressed in Arthrobacter sp. strain B-5 that was capable of degrading various organophosphorus insecticides were purified from the cells' cytosol. The enzymes were similarly composed of a single subunit with a molecular weight of 45,000 Da, but had different isoelectric points of 3.6 and 3.9. In addition, the hydrolases were found to possess identical N-terminal

Kazufumi Ohshiro; Tsuyoshi Ono; Tsutomu Hoshino; Takeo Uchiyama

1997-01-01

33

The first protein map of Synechococcus sp. strain PCC 7942  

Microsoft Academic Search

The first protein map was developed of Synechococcus sp. strain PCC 7942, a model organism for studies of photosynthesis, prokaryotic circadian rhythms, cell division, carbon-concentrating\\u000a mechanisms, and adaptive responses to a variety of stresses. The proteome was analyzed by two-dimensional gel electrophoresis\\u000a with subsequent MALDI-TOF mass spectroscopy and database analysis. Of the 140 analyzed protein spots, 110 were successfully\\u000a identified

O. A. Koksharova; Johan Klint; Ulla Rasmussen

2006-01-01

34

Genome Sequence of Sphingomonas sp. Strain PAMC 26621, an Arctic-Lichen-Associated Bacterium Isolated from a Cetraria sp.  

PubMed Central

The lichen-associated bacterial strain Sphingomonas sp. PAMC 26621 was isolated from an Arctic lichen Cetraria sp. on Svalbard Islands. Here we report the draft genome sequence of this strain, which could provide novel insights into the molecular principles of lichen-microbe interactions.

Lee, Hyoungseok; Shin, Seung Chul; Lee, Jungeun; Kim, Su Jin; Kim, Bum-Keun; Hong, Soon Gyu; Kim, Eun Hye

2012-01-01

35

Desulfurization of dibenzothiophene by Corynebacterium sp. strain SY1  

SciTech Connect

Strain SY1, identified as a Corynebacterium sp., was isolated on the basis of the ability to utilize dibenzothiophene (DBT) as a sole source of sulfur. Strain SY1 could utilize a wide range of organic and inorganic sulfur compounds, such as DBT sulfone, dimethyl sulfide, dimethyl sulfoxide, dimethyl sulfone, CS{sub 2}, FeS{sub 2}, and even elemental sulfur. Strain SY1 metabolized DBT to dibenzothiophene-5-oxide, DBT sulfone, and 2-hydroxybiphenyl, which was subsequently nitrated to produce at least two different hydroxynitrobiphenyls during cultivation. These metabolites were separated by silica gel column chromatography and identified by nuclear magnetic resonance, UV, and mass spectral techniques. Resting cells of SY1 desulfurized toluenesulfonic acid and released sulfite anion. On the basis of these results, a new DBT degradation pathway is proposed.

Omori, Toshio; Monna, L.; Saiki, Yuko; Kodama, Tohru (Univ. of Tokyo (Japan))

1992-03-01

36

Complete genome sequence of Paenibacillus sp. strain JDR-2  

PubMed Central

Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by the identification of genes and characterization of encoded enzymes and has been further defined by the sequencing and annotation of the complete genome, which we describe. In addition to genes implicated in the utilization of ?-1,4-xylan, genes have also been identified for the utilization of other hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources.

Chow, Virginia; Nong, Guang; St. John, Franz J.; Rice, John D.; Dickstein, Ellen; Chertkov, Olga; Bruce, David; Detter, Chris; Brettin, Thomas; Han, James; Woyke, Tanja; Pitluck, Sam; Nolan, Matt; Pati, Amrita; Martin, Joel; Copeland, Alex; Land, Miriam L.; Goodwin, Lynne; Jones, Jeffrey B.; Ingram, Lonnie O.; Shanmugam, Keelnathan T.; Preston, James F.

2012-01-01

37

Complete genome sequence of Paenibacillus sp. strain JDR-2  

SciTech Connect

Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by the identification of genes and characterization of encoded enzymes and has been further defined by the sequencing and annotation of the complete genome, which we describe. In addition to genes implicated in the utilization of -1,4-xylan, genes have also been identified for the utilization of other hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources.

Chow, Virginia [University of Florida; Nong, Guang [University of Florida; St. John, Franz J. [US Forest Service, Forest Products Laboratory, Madison, Wisconsin, USA; Dickstein, Ellen [University of Florida; Chertkov, Olga [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Brettin, Thomas S [ORNL; Han, James [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Martin, Joel [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Jones, Jeffrey B. [University of Florida; Ingram, Lonnie O. [University of Florida; Shanmugam, Keelnathan T. [University of Florida; Preston, James F. [University of Florida

2012-01-01

38

Chlorpyrifos degradation by the cyanobacterium Synechocystis sp. strain PUPCCC 64  

Microsoft Academic Search

Background, aim, and scope  Indiscriminate use of insecticides leads to environmental problems and poses a great threat to beneficial microorganisms.\\u000a The aim of the present work was to study chlorpyrifos degradation by a rice field cyanobacterium Synechocystis sp. strain PUPCCC 64 so that the organism is able to reduce insecticide pollution in situ.\\u000a \\u000a \\u000a \\u000a \\u000a Material and methods  The unicellular cyanobacterium isolated and purified

D. P. Singh; J. I. S. Khattar; J. Nadda; Y. Singh; A. Garg; N. Kaur; A. Gulati

39

Biodegradation of Ether Pollutants by Pseudonocardia sp. Strain ENV478  

PubMed Central

A bacterium designated Pseudonocardia sp. strain ENV478 was isolated by enrichment culturing on tetrahydrofuran (THF) and was screened to determine its ability to degrade a range of ether pollutants. After growth on THF, strain ENV478 degraded THF (63 mg/h/g total suspended solids [TSS]), 1,4-dioxane (21 mg/h/g TSS), 1,3-dioxolane (19 mg/h/g TSS), bis-2-chloroethylether (BCEE) (12 mg/h/g TSS), and methyl tert-butyl ether (MTBE) (9.1 mg/h/g TSS). Although the highest rates of 1,4-dioxane degradation occurred after growth on THF, strain ENV478 also degraded 1,4-dioxane after growth on sucrose, lactate, yeast extract, 2-propanol, and propane, indicating that there was some level of constitutive degradative activity. The BCEE degradation rates were about threefold higher after growth on propane (32 mg/h/g TSS) than after growth on THF, and MTBE degradation resulted in accumulation of tert-butyl alcohol. Degradation of 1,4-dioxane resulted in accumulation of 2-hydroxyethoxyacetic acid (2HEAA). Despite its inability to grow on 1,4-dioxane, strain ENV478 degraded this compound for >80 days in aquifer microcosms. Our results suggest that the inability of strain ENV478 and possibly other THF-degrading bacteria to grow on 1,4-dioxane is related to their inability to efficiently metabolize the 1,4-dioxane degradation product 2HEAA but that strain ENV478 may nonetheless be useful as a biocatalyst for remediating 1,4-dioxane-contaminated aquifers.

Vainberg, Simon; McClay, Kevin; Masuda, Hisako; Root, Duane; Condee, Charles; Zylstra, Gerben J.; Steffan, Robert J.

2006-01-01

40

Monocyclic Aromatic Hydrocarbon Degradation by Rhodococcus sp. Strain DK17  

PubMed Central

Rhodococcus sp. strain DK17 was isolated from soil and analyzed for the ability to grow on o-xylene as the sole carbon and energy source. Although DK17 cannot grow on m- and p-xylene, it is capable of growth on benzene, phenol, toluene, ethylbenzene, isopropylbenzene, and other alkylbenzene isomers. One UV-generated mutant strain, DK176, simultaneously lost the ability to grow on o-xylene, ethylbenzene, isopropylbenzene, toluene, and benzene, although it could still grow on phenol. The mutant strain was also unable to oxidize indole to indigo following growth in the presence of o-xylene. This observation suggests the loss of an oxygenase that is involved in the initial oxidation of the (alkyl)benzenes tested. Another mutant strain, DK180, isolated for the inability to grow on o-xylene, retained the ability to grow on benzene but was unable to grow on alkylbenzenes due to loss of a meta-cleavage dioxygenase needed for metabolism of methyl-substituted catechols. Further experiments showed that DK180 as well as the wild-type strain DK17 have an ortho-cleavage pathway which is specifically induced by benzene but not by o-xylene. These results indicate that DK17 possesses two different ring-cleavage pathways for the degradation of aromatic compounds, although the initial oxidation reactions may be catalyzed by a common oxygenase. Gas chromatography-mass spectrometry and 300-MHz proton nuclear magnetic resonance spectrometry clearly show that DK180 accumulates 3,4-dimethylcatechol from o-xylene and both 3- and 4-methylcatechol from toluene. This means that there are two initial routes of oxidation of toluene by the strain. Pulsed-field gel electrophoresis analysis demonstrated the presence of two large megaplasmids in the wild-type strain DK17, one of which (pDK2) was lost in the mutant strain DK176. Since several other independently derived mutant strains unable to grow on alkylbenzenes are also missing pDK2, the genes encoding the initial steps in alkylbenzene metabolism (but not phenol metabolism) appear to be present on this approximately 330-kb plasmid.

Kim, Dockyu; Kim, Young-Soo; Kim, Seong-Ki; Kim, Si Wouk; Zylstra, Gerben J.; Kim, Young Min; Kim, Eungbin

2002-01-01

41

Biodegradation of malathion by Brevibacillus sp. strain KB2 and Bacillus cereus strain PU.  

PubMed

We report here the degradation of a pesticide, malathion, by Brevibacillus sp. strain KB2 and Bacillus cereus strain PU, isolated from soil samples collected from malathion contaminated field and an army firing range respectively. Both the strains were cultured in the presence of malathion under aerobic and energy-limiting conditions. Both strains grew well in the medium having malathion concentration up to 0.15%. Reverse phase HPLC-UV analysis indicated that Strain KB2 was able to degrade 72.20% of malaoxon (an analogue of malathion) and 36.22% of malathion, while strain PU degraded 87.40% of malaoxon and 49.31% of malathion, after 7 days of incubation. The metabolites mal-monocarboxylic acid and mal-dicarboxylic acid were identified by Gas chromatography/mass spectrometry. The factors affecting biodegradation efficiency were investigated and effect of malathion concentration on degradation rate was also determined. The strain was analyzed for carboxylesterase activity and maximum activity 210 ± 2.5 U ml(-1) and 270 U ± 2.7 ml(-1) was observed for strains KB2 and PU, respectively. Cloning and sequencing of putative malathion degrading carboxylesterase gene was done using primers based PCR approach. PMID:22805834

Singh, Baljinder; Kaur, Jagdeep; Singh, Kashmir

2011-10-13

42

Complete Genome Sequence of Acidovorax sp. Strain KKS102, a Polychlorinated-Biphenyl Degrader  

PubMed Central

We report the complete genome sequence of Acidovorax sp. strain KKS102, a polychlorinated-biphenyl-degrading strain isolated from a soil sample in Tokyo. The genome contains a single circular 5,196,935-bp chromosome and no plasmids.

Maruyama, Fumito; Mitsui, Hisayuki; Nagata, Yuji; Tsuda, Masataka

2012-01-01

43

Leucobacter chromiiresistens sp. nov., a chromate-resistant strain.  

PubMed

A Gram-positive, irregular rod-shaped, non-motile, yellow-pigmented bacterium, strain JG 31(T), was isolated in the course of identifying chromium-resistant soil bacteria. 16S rRNA gene sequence analysis of the isolated bacterium indicated its phylogenetic position within the genus Leucobacter. Binary 16S rRNA gene sequence alignments of the isolated bacterium with the 11 species of the genus recognized at the time of writing revealed sequence similarities of more than 97?% with Leucobacter alluvii (GenBank accession no: AM072820; 99.4?%), Leucobacter iarius (AM040493; 98.2?%), Leucobacter aridicollis (AJ781047; 97.8?%), Leucobacter komagatae (AB007419; 97.4?%), Leucobacter chironomi (EU346911; 97.1?%) and Leucobacter luti (AM072819; 97.1?%). In contrast, DNA-DNA hybridization experiments showed similarity values below 28?% for DNA samples from the most closely related type strains of L. alluvii, L. aridicollis and L. iarius. Protein analysis by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and automated RiboPrinting using the restriction enzyme PvuII differentiated strain JG 31(T) from all type strains of the genus Leucobacter. The dominant fatty acids of the novel isolate were anteiso-C(15?:?0), anteiso-C(17?:?0) and iso-C(16?:?0), while the quinone system consisted of menaquinones MK-11, MK-10, MK-9 and MK-8. In a B-type cross-linked peptidoglycan, the cell-wall amino acids were alanine, glycine, threonine, glutamic acid and 2,4-diaminobutyric acid. Strain JG 31(T) was able to grow in a medium containing up to 300 mM K(2)CrO(4) and showed cellular aggregation in response to chromate stress. From biochemical and genomic analyses, the new strain is considered to represent a novel species of the genus Leucobacter, for which the name Leucobacter chromiiresistens sp. nov. is proposed. The type strain is strain JG 31(T) (?=?DSM 22788(T) ?=?CCOS 200(T)). PMID:20511468

Sturm, Gunnar; Jacobs, Johanna; Spröer, Cathrin; Schumann, Peter; Gescher, Johannes

2010-05-28

44

Degradation of alkylphenol ethoxylates by Pseudomonas sp. strain TR01.  

PubMed Central

An alkylphenol ethoxylate-degrading bacterium was isolated from activated sludge of a municipal sewage treatment plant by enrichment culture. This organism was found to belong to the genus Pseudomonas; since no corresponding species was identified, we designated it as Pseudomonas sp. strain TR01. This strain had an optimal temperature and pH of 30 degrees C and 7, respectively, for both growth and the degradation of Triton N-101 (a nonylphenol ethoxylate in which the average number of ethylene oxide [EO] units is 9.5). The strain was unable to mineralize Triton N-101 but was able to degrade its EO chain exclusively. The resulting dominant intermediate was identified by normal-phase high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry as a nonylphenol ethoxylate with 2 mol of EO units. A carboxylated metabolite, [(nonylphenoxy)ethoxy]acetic acid, was detected by gas chromatography-mass spectrometry. This bacterium also metabolized alcohol ethoxylates with various numbers of EO units but not polyethylene glycols whatever their degree of polymerization. By oxygen consumption assay, the alkyl group or arene corresponding to the hydrophobic part of alcohol ethoxylates or alkylphenol ethoxylates was shown to contribute to the induction of the metabolic system of the EO chain of Triton N-101, instead of the EO chain itself, which corresponds to its hydrophilic part. Thus, the isolated pseudomonad bacterium has unique substrate assimilability: it metabolizes the EO chain only when the chain linked to bulky hydrophobic groups.

Maki, H; Masuda, N; Fujiwara, Y; Ike, M; Fujita, M

1994-01-01

45

Draft Genome Sequence of Brevibacillus sp. Strain BAB-2500, a Strain That Might Play an Important Role in Agriculture.  

PubMed

A Gram-positive bacterium, Brevibacillus sp. strain BAB-2500, was isolated as a lab contaminant in Gandhinagar, Gujarat, India. The draft genome (5.3 Mb) of the strain possesses genes for the reduction of arsenate and aluminum. These findings might provide insights into the utilization of this strain for improving crop production. PMID:23472223

Joshi, M N; Sharma, A; Pandit, A S; Pandya, R V; Saxena, A K; Bagatharia, S B

2013-02-28

46

Draft Genome Sequence of Brevibacillus sp. Strain BAB-2500, a Strain That Might Play an Important Role in Agriculture  

PubMed Central

A Gram-positive bacterium, Brevibacillus sp. strain BAB-2500, was isolated as a lab contaminant in Gandhinagar, Gujarat, India. The draft genome (5.3 Mb) of the strain possesses genes for the reduction of arsenate and aluminum. These findings might provide insights into the utilization of this strain for improving crop production.

Joshi, M. N.; Sharma, A.; Pandit, A. S.; Pandya, R. V.; Saxena, A. K.

2013-01-01

47

Complete genome sequence of the fenitrothion-degrading Burkholderia sp. strain YI23.  

PubMed

Burkholderia species are ubiquitous in soil environments. Many Burkholderia species isolated from various environments have the potential to biodegrade man-made chemicals. Burkholderia sp. strain YI23 was isolated from a golf course soil and identified as a fenitrothion-degrading bacterium. In this study, we report the complete genome sequence of Burkholderia sp. strain YI23. PMID:22275096

Lim, Jong Sung; Choi, Beom Soon; Choi, Ah Young; Kim, Kyung Duk; Kim, Dong In; Choi, Ik Young; Ka, Jong-Ok

2012-02-01

48

Draft Genome Sequence of Ralstonia sp. Strain GA3-3, Isolated from Australian Suburban Soil.  

PubMed

Ralstonia sp. strain GA3-3 is a hexachlorocyclohexane (HCH)-degrading bacterial strain isolated from suburban soil in Canberra, Australia. The genome of strain GA3-3 was sequenced to investigate its ability to degrade ?-HCH. Here, we report the annotated genome sequence of this strain. PMID:23833131

Pearce, Stephen L; Pushiri, Hafizah; Oakeshott, John G; Russell, Robyn J; Pandey, Gunjan

2013-07-05

49

Genome Sequence of Rhodococcus sp. Strain R04, a Polychlorinated-Biphenyl Biodegrader ?  

PubMed Central

The genus Rhodococcus has proved to be a promising option for the cleanup of polluted sites and application of a microbial biocatalyst. Rhodococcus sp. strain R04, isolated from oil-contaminated soil, can biodegrade polychlorinated biphenyls. Here we report the draft genome sequence of Rhodococcus sp. strain R04, which could be used to predict genes for xenobiotic biodegradation and provide important insights into the applications of this strain.

Yang, Xiuqing; Xue, Rui; Shen, Chong; Li, Shuren; Gao, Chong; Wang, Qi; Zhao, Xiaoxia

2011-01-01

50

Dynamics of genome architecture in Rhizobium sp. strain NGR234.  

PubMed

Bacterial genomes are usually partitioned in several replicons, which are dynamic structures prone to mutation and genomic rearrangements, thus contributing to genome evolution. Nevertheless, much remains to be learned about the origins and dynamics of the formation of bacterial alternative genomic states and their possible biological consequences. To address these issues, we have studied the dynamics of the genome architecture in Rhizobium sp. strain NGR234 and analyzed its biological significance. NGR234 genome consists of three replicons: the symbiotic plasmid pNGR234a (536,165 bp), the megaplasmid pNGR234b (>2,000 kb), and the chromosome (>3,700 kb). Here we report that genome analyses of cell siblings showed the occurrence of large-scale DNA rearrangements consisting of cointegrations and excisions between the three replicons. As a result, four new genomic architectures have emerged. Three consisted of the cointegrates between two replicons: chromosome-pNGR234a, chromosome-pNGR234b, and pNGR234a-pNGR234b. The other consisted of a cointegrate of the three replicons (chromosome-pNGR234a-pNGR234b). Cointegration and excision of pNGR234a with either the chromosome or pNGR234b were studied and found to proceed via a Campbell-type mechanism, mediated by insertion sequence elements. We provide evidence showing that changes in the genome architecture did not alter the growth and symbiotic proficiency of Rhizobium derivatives. PMID:11741857

Mavingui, Patrick; Flores, Margarita; Guo, Xianwu; Dávila, Guillermo; Perret, Xavier; Broughton, William J; Palacios, Rafael

2002-01-01

51

Dichloromethane dehalogenase of Hyphomicrobium sp. strain DM2.  

PubMed

Dichloromethane dehalogenase, a highly inducible glutathione-dependent enzyme catalyzing the conversion of dichloromethane into formaldehyde and inorganic chloride, was purified fivefold with 60% yield from Hyphomicrobium sp. strain DM2. The electrophoretically homogeneous purified enzyme exhibited a specific activity of 17.3 mkat/kg of protein. Its pH optimum was 8.5. The enzyme was stable at -20 degrees C for at least 6 months. A subunit molecular weight of 33,000 was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Gel filtration of native dichloromethane dehalogenase yielded a molecular weight of 195,000. Subunit cross-linking with dimethyl suberimidate confirmed the hexameric tertiary structure of the enzyme. Dichloromethane dehalogenase was highly specific for dihalomethanes. Its apparent Km values were 30 microM for CH2Cl2, 15 microM for CH2BrCl, 13 microM for CH2Br2, 5 microM for CH2I2, and 320 microM for glutathione. Several chlorinated aliphatic compounds inhibited the dichloromethane dehalogenase activity of the pure enzyme. The Ki values of the competitive inhibitors 1,2-dichloroethane and 1-chloropropane were 3 and 56 microM, respectively. PMID:3988708

Kohler-Staub, D; Leisinger, T

1985-05-01

52

Dichloromethane dehalogenase of Hyphomicrobium sp. strain DM2.  

PubMed Central

Dichloromethane dehalogenase, a highly inducible glutathione-dependent enzyme catalyzing the conversion of dichloromethane into formaldehyde and inorganic chloride, was purified fivefold with 60% yield from Hyphomicrobium sp. strain DM2. The electrophoretically homogeneous purified enzyme exhibited a specific activity of 17.3 mkat/kg of protein. Its pH optimum was 8.5. The enzyme was stable at -20 degrees C for at least 6 months. A subunit molecular weight of 33,000 was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Gel filtration of native dichloromethane dehalogenase yielded a molecular weight of 195,000. Subunit cross-linking with dimethyl suberimidate confirmed the hexameric tertiary structure of the enzyme. Dichloromethane dehalogenase was highly specific for dihalomethanes. Its apparent Km values were 30 microM for CH2Cl2, 15 microM for CH2BrCl, 13 microM for CH2Br2, 5 microM for CH2I2, and 320 microM for glutathione. Several chlorinated aliphatic compounds inhibited the dichloromethane dehalogenase activity of the pure enzyme. The Ki values of the competitive inhibitors 1,2-dichloroethane and 1-chloropropane were 3 and 56 microM, respectively. Images

Kohler-Staub, D; Leisinger, T

1985-01-01

53

Genome Sequence of Herbaspirillum sp. Strain GW103, a Plant Growth-Promoting Bacterium  

PubMed Central

Herbaspirillum sp. strain GW103 was isolated from rhizosphere soil of the reed Phragmites australis on reclaimed land. Here we report the 5.05-Mb draft genome sequence of the strain, providing bioinformation about the agronomic benefits of this strain, such as multiple traits relevant to plant root colonization and plant growth promotion.

Lee, Gun Woong; Lee, Kui-Jae

2012-01-01

54

Genome sequence of Herbaspirillum sp. strain GW103, a plant growth-promoting bacterium.  

PubMed

Herbaspirillum sp. strain GW103 was isolated from rhizosphere soil of the reed Phragmites australis on reclaimed land. Here we report the 5.05-Mb draft genome sequence of the strain, providing bioinformation about the agronomic benefits of this strain, such as multiple traits relevant to plant root colonization and plant growth promotion. PMID:22815460

Lee, Gun Woong; Lee, Kui-Jae; Chae, Jong-Chan

2012-08-01

55

Complete Genome Sequence of a Thermophilic Hydrogenotrophic Methanogen, Methanothermobacter sp. Strain CaT2  

PubMed Central

We isolated a thermophilic hydrogenotrophic methanogen, Methanothermobacter sp. strain CaT2, which is able to aggregate and utilize formate. Here, we report the complete genome sequence of this organism.

Toh, Hidehiro; Toyoda, Atsushi

2013-01-01

56

Studies on Nitrobenzene Metabolism by a Comamonas sp. Strain JS7651.  

National Technical Information Service (NTIS)

Funded studies focused on the biodegradation of nitrobenzene by Comamonas sp. strain JS765, which was isolated in Dr. Jim C. Spain's laboratory, Tyndall AFB. The genes encoding the nitrobenzene dioxygenase system were cloned and sequenced from JS765. The ...

D. T. Gibson D. J. Lessner

2000-01-01

57

Guidance of Cytophaga sp. strain U67 gliding on the sheaths of Oscillatoria princeps.  

PubMed Central

Individual cells of Cytophaga sp. strain U67 glided in helical patterns on the surface of sheaths deposited by the cyanobacterium Oscillatoria princeps. Possible bases for the helical substructure of the sheath are discussed. Images

McGrath, C F; Burchard, R P

1985-01-01

58

Genome sequence of Pantoea sp. strain Sc 1, an opportunistic cotton pathogen.  

PubMed

Pantoea is comprised of a broad spectrum of species, including plant pathogens. Here, we provide an annotated genome sequence of Pantoea sp. strain Sc 1, which was isolated from a diseased cotton boll. This research provides the first genome sequence of a bona fide Pantoea sp. insect-vectored cotton pathogen. PMID:22582377

Medrano, Enrique G; Bell, Alois A

2012-06-01

59

Genome Sequence of Pantoea sp. Strain Sc 1, an Opportunistic Cotton Pathogen  

PubMed Central

Pantoea is comprised of a broad spectrum of species, including plant pathogens. Here, we provide an annotated genome sequence of Pantoea sp. strain Sc 1, which was isolated from a diseased cotton boll. This research provides the first genome sequence of a bona fide Pantoea sp. insect-vectored cotton pathogen.

Bell, Alois A.

2012-01-01

60

Gliding motility of Cytophaga sp. strain U67.  

PubMed Central

Video techniques were used to analyze the motion of the gliding bacterium Cytophaga sp. strain U67. Cells moved singly on glass along the long axis at a speed of about 2 micrometers/s, advancing, retreating, stopping, pivoting about a pole, or flipping over. They did not flex or roll. Cells of different lengths moved at about the same speed. Cells sometimes spun continuously about a pole at a frequency of about 2 HZ, the body moving in a plane parallel to that of the glass or on the surface of a cone having either a large or a small solid angle. Polystyrene latex spheres moved to and fro on the surfaces of cells, also at a speed of about 2 micrometers/s. They moved in the same fashion whether a cell was in suspension, gliding, or at rest on the glass. Two spheres on the same cell often moved in opposite directions, passing by one another in close proximity. Small and large spheres and aggregates of spheres all moved at about the same speed. An aggregate moved down the side of a cell with a fixed orientation, even when only one sphere was in contact with the cell. Spheres occasionally left one cell and were picked up by another. Cell pretreated with small spheres did not adhere to glass. When the cells were deprived of oxygen, they stopped gliding, and the spheres stopped moving on their surfaces. The spheres became completely immobilized; they no longer moved from cell to cell or exhibited Brownian movement. Cytophaga spp. are known to have a typical gram-negative cell envelope: an inner (cytoplasmic) membrane, a thin peptidoglycan layer, and an outer (lipopolysaccharide) membrane. Our data are consistent with a model for gliding in which sites to which glass and polystyrene strongly adsorb move within the fluid outer membrane along tracks fixed to the rigid peptidoglycan framework. Images

Lapidus, I R; Berg, H C

1982-01-01

61

Genome Sequence of Rhodococcus sp. Strain BCP1, a Biodegrader of Alkanes and Chlorinated Compounds  

PubMed Central

Rhodococcus sp. strain BCP1 cometabolizes chlorinated compounds and mineralizes a broad range of alkanes, as it is highly tolerant to them. The high-quality draft genome sequence of Rhodococcus sp. strain BCP1, consisting of 6,231,823 bp, with a G+C content of 70.4%, 5,902 protein-coding genes, and 58 RNA genes, is presented here.

Cappelletti, M.; Di Gennaro, P.; D'Ursi, P.; Orro, A.; Mezzelani, A.; Landini, M.; Fedi, S.; Frascari, D.; Presentato, A.; Milanesi, L.

2013-01-01

62

Whole-genome sequence of Enterobacter sp. strain SST3, an endophyte isolated from Jamaican sugarcane (Saccharum sp.) stalk tissue.  

PubMed

Enterobacter sp. strain SST3 is an endophytic bacterium isolated from Saccharum spp. Here we present its annotated draft genome that may shed light on its role as a bacterial endophyte of sugarcane. To our knowledge, this is the first genome announcement of a sugarcane-associated bacterium from the genus Enterobacter. PMID:23045495

Gan, Han Ming; McGroty, Sean E; Chew, Teong Han; Chan, Kok Gan; Buckley, Larry J; Savka, Michael A; Hudson, André O

2012-11-01

63

Molecular Identification of Two Strains of Phellinus sp. by Internal Transcribed Spacer Sequence Analysis.  

PubMed

Two species of cultivated Phellinus sp. were identified as P. baumii by internal transcribed spacer (ITS) sequence analysis. The fruit bodies of the examined strains were similar to those of naturally occurring strains, having a bracket-like form, yellow-to-orange color, and poroid hymenial surfaces. The DNA sequences of ITS region of both strains showed a homology of 99% with ITS1 to ITS2 sequences of P. (Inonotus) baumii strain PB0806. PMID:22783119

Shin, Kwang-Soo

2011-12-07

64

Heterologous exopolysaccharide production in Rhizobium sp. strain NGR234 and consequences for nodule development.  

PubMed Central

Rhizobium sp. strain NGR234 produces large amounts of acidic exopolysaccharide. Mutants that fail to synthesize this exopolysaccharide are also unable to nodulate the host plant Leucaena leucocephala. A hybrid strain of Rhizobium sp. strain NGR234 containing exo genes from Rhizobium meliloti was constructed. The background genetics and nod genes of Rhizobium sp. strain NGR234 are retained, but the cluster of genes involved in exopolysaccharide biosynthesis was deleted. These exo genes were replaced with genes required for the synthesis of succinoglycan exopolysaccharide from R. meliloti. As a result of the genetic manipulation, the ability of these hybrids to synthesize exopolysaccharide was restored, but the structure was that of succinoglycan and not that of Rhizobium sp. strain NGR234. The replacement genes were contained on a cosmid which encoded the entire known R. meliloti exo gene cluster, with the exception of exoB. Cosmids containing smaller portions of this exo gene cluster did not restore exopolysaccharide production. The presence of succinoglycan was indicated by staining with the fluorescent dye Calcofluor, proton nuclear magnetic resonance spectroscopy, and monosaccharide analysis. Although an NGR234 exoY mutant containing the R. meliloti exo genes produced multimers of the succinoglycan repeat unit, as does the wild-type R. meliloti, the deletion mutant of Rhizobium sp. strain NGR234 containing the R. meliloti exo genes produced only the monomer. The deletion mutant therefore appeared to lack a function that affects the multiplicity of succinoglycan produced in the Rhizobium sp. strain NGR234 background. Although these hybrid strains produced succinoglycan, they were still able to induce the development of an organized nodule structure on L. leucocephala. The resulting nodules did not fix nitrogen, but they did contain infection threads and bacteroids within plant cells. This clearly demonstrated that a heterologous acidic exopolysaccharide structure was sufficient to enable nodule development to proceed beyond the developmental barrier imposed on mutants of Rhizobium sp. strain NGR234 that are unable to synthesize any acidic exopolysaccharide. Images

Gray, J X; Zhan, H J; Levery, S B; Battisti, L; Rolfe, B G; Leigh, J A

1991-01-01

65

Improvement of Strain Penicillium sp. EZ-ZH190 for Tannase Production by Induced Mutation.  

PubMed

In the search for an efficient producer of tannase, Penicillium sp. EZ-ZH190 was subjected to mutagenesis using heat treatment and strain EZ-ZH290 was isolated. The maximum tannase in this mutant strain was 4.32 U/mL with an incubation period of 84 h as compared to wild strain EZ-ZH190 where the incubation period was 96 h with a maximum enzyme activity of 4.33 U/mL. Also, the Penicillium sp. EZ-ZH290 tannase had a maximum activity at 40 °C and pH 5.5. Then, the spores of strain EZ-ZH290 were subjected to ? irradiation mutagenesis and strain EZ-ZH390 was isolated. Strain EZ-ZH390 exhibited higher tannase activity (7.66 U/mL) than the parent strain EZ-ZH290. It was also found that Penicillium sp. EZ-ZH390 tannase had an optimum activity at 35 °C and a broad pH profile with an optimum at pH 5.5. The tannase pH stability of Penicillium sp. EZ-ZH390 and its maximum production of tannase followed the same trend for five generations confirming the occurrence of stable mutant. This paper is shown that ? irradiation can mutate the Penicillium sp. leading to increase the tannase production. PMID:23955297

Zakipour-Molkabadi, E; Hamidi-Esfahani, Z; Sahari, M A; Azizi, M H

2013-08-17

66

Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria).  

PubMed

Here we present the draft genome of Leucobacter sp. strain UCD-THU. The genome contains 3,317,267 bp in 11 scaffolds. This strain was isolated from a residential toilet as part of an undergraduate project to sequence reference genomes of microbes from the built environment. PMID:23792744

Holland-Moritz, Hannah E; Bevans, Dakota R; Lang, Jenna M; Darling, Aaron E; Eisen, Jonathan A; Coil, David A

2013-06-27

67

Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria).  

PubMed

Here, we present the draft genome sequence of Microbacterium sp. strain UCD-TDU, a member of the phylum Actinobacteria. The assembly contains 3,746,321 bp (in 8 scaffolds). This strain was isolated from a residential toilet as part of an undergraduate student research project to sequence reference genomes of microbes from the built environment. PMID:23516225

Bendiks, Zachary A; Lang, Jenna M; Darling, Aaron E; Eisen, Jonathan A; Coil, David A

2013-03-21

68

Complete Genome Sequence of Clostridium sp. Strain BNL1100, a Cellulolytic Mesophile Isolated from Corn Stover  

PubMed Central

We present the full genome sequence of Clostridium sp. strain BNL1100, a Gram-positive, endospore-forming, lignocellulolytic bacterium isolated from a corn stover enrichment culture. The 4,613,747-bp genome of strain BNL1100 contains 4,025 putative protein-coding genes, of which 103 are glycoside hydrolases, the highest detected number in cluster III clostridia.

Li, Luen-Luen; Taghavi, Safiyh; Izquierdo, Javier A.

2012-01-01

69

Draft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium Arthrobacter sp. Strain SJCon  

PubMed Central

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.

Vikram, Surendra; Kumar, Shailesh; Vaidya, Bhumika; Pinnaka, Anil Kumar

2013-01-01

70

Genome Sequence of Janthinobacterium sp. Strain PAMC 25724, Isolated from Alpine Glacier Cryoconite  

PubMed Central

The draft genome of Janthinobacterium sp. strain PAMC 25724, which is a violacein-producing psychrotolerant bacterium, was determined. The strain was isolated from glacier cryoconite of the Alps mountain permafrost region. The sequence will allow identification and characterization of the genetic determination of its cold-adaptive properties.

Kim, Su Jin; Shin, Seung Chul; Hong, Soon Gyu; Lee, Yung Mi; Lee, Hyoungseok; Lee, Jungeun

2012-01-01

71

Functional genomic approaches for understanding the mode of action of Bacillus sp biocontrol strains  

Technology Transfer Automated Retrieval System (TEKTRAN)

Complete genome sequencing of several Bacillus sp. strains has shed new light on the mode of action of these antagonists of plant pathogens. The use of genomic data mining tools provided the ability to quickly determine the potential of these strains to produce bioactive secondary metabolites. Our B...

72

Taxol from Tubercularia sp. strain TF5, an endophytic fungus of Taxus mairei  

Microsoft Academic Search

The diterpenoid taxol is an important anticancer agent used widely in the clinic. The purpose of this work was to identify a taxol-producing endophytic fungus (strain TF5) isolated from Taxus mairei and study its anticancer activities. Strain TF5 was identified as a Tubercularia sp. according to the morphology of the fungal culture, the mechanism of spore production and the characteristics

Jianfeng Wang; Guiling Li; Huaying Lu; Zhonghui Zheng; Yaojian Huang; Wenjin Su

2000-01-01

73

Complete Biodegradation of 4-Fluorocinnamic Acid by a Consortium Comprising Arthrobacter sp. Strain G1 and Ralstonia sp. Strain H1 ? †  

PubMed Central

A consortium of the newly isolated bacterial strains Arthrobacter sp. strain G1 and Ralstonia sp. strain H1 utilized 4-fluorocinnamic acid for growth under aerobic conditions. Strain G1 converted 4-fluorocinnamic acid into 4-fluorobenzoic acid and used the two-carbon side chain for growth, with some formation of 4-fluoroacetophenone as a dead-end side product. In the presence of strain H1, complete mineralization of 4-fluorocinnamic acid and release of fluoride were obtained. Degradation of 4-fluorocinnamic acid by strain G1 occurred through a ?-oxidation mechanism and started with the formation of 4-fluorocinnamoyl-coenzyme A (CoA), as indicated by the presence of 4-fluorocinnamoyl-CoA ligase. Enzymes for further transformation were detected in cell extract, i.e., 4-fluorocinnamoyl-CoA hydratase, 4-fluorophenyl-?-hydroxy propionyl-CoA dehydrogenase, and 4-fluorophenyl-?-keto propionyl-CoA thiolase. Degradation of 4-fluorobenzoic acid by strain H1 proceeded via 4-fluorocatechol, which was converted by an ortho-cleavage pathway.

Hasan, Syed A.; Ferreira, Maria Isabel M.; Koetsier, Martijn J.; Arif, Muhammad I.; Janssen, Dick B.

2011-01-01

74

Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains.  

PubMed

In silico, physiological and in planta analyses were used to characterize pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1, and assess its potential ecological function under free-living and symbiotic growth conditions. Sequence analysis revealed the presence of an uptake hydrogenase system, a repABC family plasmid replication module and open reading frames encoding type IV secretion system, TraI and TraR autoinducer proteins and several copper resistance-related proteins. Bradyrhizobium sp. BTAi1 was capable of growing in 200 mg l(-1) CuCl2. In contrast, the closely related, plasmid-free Bradyrhizobium sp. strain ORS278 could not grow at copper concentrations exceeding 100 mg l(-1). The plasmid-localized hydrogenase genes were phylogenetically distinct from those typically found in other rhizobial species, and were most related to hup genes from Thiobacillus denitrificans. The induction of the plasmid-borne hydrogenase genes during symbiosis was significantly lower than the two chromosomal-borne hydrogenase clusters. CHEF-pulsed-field gel electrophoresis was used for a comprehensive analysis of the diversity, abundance and genetic composition of accessory plasmids in other Bradyrhizobium strains. Plasmids were detected in 11 of 46 (23.9%) geographically diverse Bradyrhizobium japonicum and Bradyrhizobium elkanii strains, isolated from the United States, China and Thailand. Plasmid size was heterogeneous, ranging from 75 to 330 kb, with only two strains (DASA01244 and DASA01265) harboring plasmids with identical (240 kb) size. None of the plasmids harbored nodulation or hydrogenase genes. Taken together, our results indicate that while plasmids having ecologically significant functions may be detected in Bradyrhizobium sp. strains, they lack genes necessary for symbioses with legumes. PMID:18219284

Cytryn, Eddie J; Jitacksorn, Siriluck; Giraud, Eric; Sadowsky, Michael J

2008-01-24

75

Membrane fatty acids adaptive profile in the simultaneous presence of arsenic and toluene in Bacillus sp. ORAs2 and Pseudomonas sp. ORAs5 strains  

Microsoft Academic Search

Bacillus sp. ORAs2 and Pseudomonas sp. ORAs5, two arsenic-resistant bacterial strains previously isolated from sediments of the Orbetello Lagoon, Italy, were\\u000a tested for their adaptation to mixed contaminants on the level of membrane fatty acid composition. The two bacterial strains\\u000a were characterized by high levels of arsenic resistance, and Pseudomonas sp. ORAs5 was also shown to be solvent-tolerant. The bacterial

Milva Pepi; Hermann J. Heipieper; Janett Fischer; Marcella Ruta; Margherita Volterrani; Silvano E. Focardi

2008-01-01

76

Study of cellulases from a newly isolated thermophilic and cellulolytic Brevibacillus sp. strain JXL  

Microsoft Academic Search

A potentially novel aerobic, thermophilic, and cellulolytic bacterium designated as Brevibacillus sp. strain JXL was isolated from swine waste. Strain JXL can utilize a broad range of carbohydrates including: cellulose,\\u000a carboxymethylcellulose (CMC), xylan, cellobiose, glucose, and xylose. In two different media supplemented with crystalline\\u000a cellulose and CMC at 57°C under aeration, strain JXL produced a basal level of cellulases as

Yanna Liang; Jemil Yesuf; Steve Schmitt; Kelly Bender; John Bozzola

2009-01-01

77

Isolation and characterization of polycyclic aromatic hydrocarbons-degrading Sphingomonas sp. strain ZL5  

Microsoft Academic Search

A bacterial strain ZL5, capable of growing on phenanthrene as a sole carbon and energy source but not naphthalene, was isolated by selective enrichment from crude-oil-contaminated soil of Liaohe Oil Field in China. The isolate was identified as a Sphingomonas sp. strain on the basis of 16S ribosomal DNA analysis. Strain ZL5 grown on phenanthrene exhibited catechol 2,3-dioxygenase (C23O) activity

Yongsheng Liu; Jie Zhang; Zhongze Zhang

2004-01-01

78

Geobacillus thermodenitrificans subsp. calidus, subsp. nov., a thermophilic and ?-glucosidase producing bacterium isolated from Kizilcahamam, Turkey.  

PubMed

An ?-glucosidase producing, thermophilic, facultatively anaerobic, and endospore-forming, motile, rod-shaped bacterial strain F84b(T) was isolated from a high temperature well-pipeline sediment sample in Kizilcahamam, Turkey. The growth occurred at temperatures, pH and salinities ranging from 45 to 69ºC (optimum 60ºC), 7.0 to 8.5 (optimum 8.0) and 0 to 5% (w/v) (optimum 3.5%), respectively. Strain F84b(T) was able to grow on a wide range of carbon sources. Starch and tyrosine utilization, amylase, catalase and oxidase activities, nitrate reduction, and gas production from nitrate were all positive. The G+C content of the genomic DNA was 49.6 mol%. The menaquinone content was MK-7. The dominant cellular fatty acids were iso-C17:0, iso-C15:0, and C16:0. In phylogenetic analysis of 16S rRNA gene sequence, strain F84b(T) showed high sequence similarity to Geobacillus thermodenitrificans (99.8%) and to Geobacillus subterraneus (99.3%) with DNA hybridization values of 74.3% and 29.1%, respectively. In addition, the Rep-PCR and the intergenic 16S-23S rRNA gene fingerprinting profiles differentiated strain F84b(T) from the Geobacillus species studied. The results obtained from the physiological and biochemical characters, the menaquinone contents, the borderline DNA-DNA hybridization homology, and the genomic fingerprinting patterns had allowed phenotypic, chemotaxonomic and genotypic differentiation of strain F84b(T) from G. thermodenitrificans. Therefore, strain F84b(T) is assigned to be a new subspecies of G. thermodenitrificans, for which the name Geobacillus thermodenitrificans subsp. calidus, subsp. nov. is proposed (The type strain F84b(T) = DSM 22629(T) = NCIMB 14582(T)). PMID:21606609

Cihan, Arzu Coleri; Ozcan, Birgul; Tekin, Nilgun; Cokmus, Cumhur

2011-01-01

79

Plasmid-Borne Genes Code for an Angular Dioxygenase Involved in Dibenzofuran Degradation by Terrabacter sp. Strain YK3  

Microsoft Academic Search

The genes responsible for angular dioxygenation of dibenzofuran in actinomycetes were cloned by using a degenerate set of PCR primers designed by using conserved sequences of the dioxygenase alpha subunit genes. One sequence of alpha subunit genes was commonly amplified from four dibenzofuran-utilizing actinomycetes: Terrabacter sp. strains YK1 and YK3, Rhodococcus sp. strain YK2, and Microbacterium sp. strain YK18. A

Toshiya Iida; Yuki Mukouzaka; Kaoru Nakamura; Toshiaki Kudo

2002-01-01

80

Marine diatom, Navicula sp. strain JPCC DA0580 and marine green alga, Chlorella sp. strain NKG400014 as potential sources for biodiesel production.  

PubMed

Marine diatom, strain JPCC DA0580, and marine green microalga strain NKG400014 were selected as high neutral lipid-producers from marine microalgal culture collection toward biodiesel production. These strains were tentatively identified as Navicula sp. and Chlorella sp., respectively, by 18S rDNA analysis. Growth and lipid accumulation conditions of both strains were analyzed by changing nutrient concentrations in growth media and initial illuminance intensity. The highest productivity of fatty acid methyl ester (FAME) reached to 154 mg/L/week for NKG400014 and 185 mg/L/week for JPCC DA0580. Gas chromatography/mass spectrometry analysis indicates that FAME fraction from NKG400014 mainly contained 9-12-15-octadecatrienoate (C18:3) and that from JPCC DA0580 mainly contained methyl palmitate (C16:0) and methyl palmitoleate (C16:1). Furthermore, calorimetric analysis revealed that the energy content of strain was 4,233 +/- 55 kcal/kg (i.e., 15.9 +/- 0.2 MJ/kg) for NKG400014 and 6,423 +/- 139 kcal/mg (i.e., 26.9 +/- 0.6 MJ/kg) for JPCC DA0580, respectively. The value from JPCC DA0580 was equivalent to that of coal. The strains NKG400014 and JPCC DA0580 will become a promising resource that can grow as dominant species in the open ocean toward production of both liquid and solid biofuels. PMID:19756412

Matsumoto, Mitsufumi; Sugiyama, Hiroshi; Maeda, Yoshiaki; Sato, Reiko; Tanaka, Tsuyoshi; Matsunaga, Tadashi

2009-09-08

81

Characterization of phenanthrene degradation by strain polyporus sp. S133.  

PubMed

Polyporus sp. S133, a fungus collected from contaminated soil, was used to degrade phenanthrene, a polycyclic aromatic hydrocarbon, in a mineral salt broth liquid culture. A maximal degradation rate (92%) was obtained when Polyporus sp. S133 was cultured for 30 days with agitation at 120 r/min, as compared to 44% degradation in non-agitated cultures. Furthermore, the degradation was affected by the addition of surfactants. Tween 80 was the most suitable surfactant for the degradation of phenanthrene by Polyporus sp. S133. The degradation rate increased as the amount of Tween 80 added increased. The rate in agitated cultures was about 2 times that in non-agitated cultures. The mechanism of degradation was determined through the identification of metabolites; 9,10-phenanthrenequinone, 2,2'-diphenic acid, phthalic acid, and protocatechuic acid. Several enzymes (manganese peroxidase, lignin peroxidase, laccase, 1,2-dioxygenase and 2,3-dioxygenase) produced by Polyporus sp. S133 were detected during the incubation. The highest level of activity was shown by 1,2-dioxygenase (187.4 U/L) after 20 days of culture. PMID:20397398

Hadibarata, Tony; Tachibana, Sanro

2010-01-01

82

Genome Sequence of Marine Bacterium Idiomarina sp. Strain 28-8, Isolated from Korean Ark Shells  

PubMed Central

Idiomarina sp. strain 28-8 is an aerobic, Gram-negative, flagellar bacterium isolated from the bodies of ark shells (Scapharca broughtonii) collected from underwater sediments in Gangjin Bay, South Korea. Here, we present the draft genome sequence of Idiomarina sp. 28-8 (2,971,606 bp, with a G+C content of 46.9%), containing 2,795 putative coding sequences.

Kim, Woo-Jin; Kim, Young-Ok; Kim, Dong-Gyun; Nam, Bo-Hye; Kong, Hee Jeong; Jung, Hyungtaek; Lee, Sang-Jun; Kim, Dong-Wook

2013-01-01

83

Genome Sequence of Marine Bacterium Idiomarina sp. Strain 28-8, Isolated from Korean Ark Shells.  

PubMed

Idiomarina sp. strain 28-8 is an aerobic, Gram-negative, flagellar bacterium isolated from the bodies of ark shells (Scapharca broughtonii) collected from underwater sediments in Gangjin Bay, South Korea. Here, we present the draft genome sequence of Idiomarina sp. 28-8 (2,971,606 bp, with a G+C content of 46.9%), containing 2,795 putative coding sequences. PMID:24092779

Kim, Woo-Jin; Kim, Young-Ok; Kim, Dong-Gyun; Nam, Bo-Hye; Kong, Hee Jeong; Jung, Hyungtaek; Lee, Sang-Jun; Kim, Dong-Wook; Kim, Dae-Soo; Chae, Sung-Hwa

2013-10-03

84

Biodegradation of Bis(2-Chloroethyl) Ether by Xanthobacter sp. Strain ENV481?  

PubMed Central

Degradation of bis(2-chloroethyl) ether (BCEE) was observed to occur in two bacterial strains. Strain ENV481, a Xanthobacter sp. strain, was isolated by enrichment culturing of samples from a Superfund site located in the northeastern United States. The strain was able to grow on BCEE or 2-chloroethylethyl ether as the sole source of carbon and energy. BCEE degradation in strain ENV481 was facilitated by sequential dehalogenation reactions resulting in the formation of 2-(2-chloroethoxy)ethanol and diethylene glycol (DEG), respectively. 2-Hydroxyethoxyacetic acid was detected as a product of DEG catabolism by the strain. Degradation of BCEE by strain ENV481 was independent of oxygen, and the strain was not able to grow on a mixture of benzene, ethylbenzene, toluene, and xylenes, other prevalent contaminants at the site. Another bacterial isolate, Pseudonocardia sp. strain ENV478 (S. Vainberg et al., Appl. Environ. Microbiol. 72:5218-5224, 2006), degraded BCEE after growth on tetrahydrofuran or propane but was not able to grow on BCEE as a sole carbon source. BCEE degradation by strain ENV478 appeared to be facilitated by a monooxygenase-mediated O-dealkylation mechanism, and it resulted in the accumulation of 2-chloroacetic acid that was not readily degraded by the strain.

McClay, Kevin; Schaefer, Charles E.; Vainberg, Simon; Steffan, Robert J.

2007-01-01

85

Isolation of Acetobacterium sp. Strain AG, Which Reductively Debrominates Octa- and Pentabrominated Diphenyl Ether Technical Mixtures  

PubMed Central

Polybrominated diphenyl ethers (PBDEs) are a class of environmental pollutants that have been classified as persistent organic pollutants since 2009. In this study, a sediment-free enrichment culture (culture G) was found to reductively debrominate octa- and penta-BDE technical mixtures to less-brominated congeners (tetra-, tri-, and di-BDEs) via a para-dominant debromination pattern for the former and a strict para debromination pattern for the latter. Culture G could debrominate 96% of 280 nM PBDEs in an octa-BDE mixture to primarily tetra-BDEs in 21 weeks. Continuous transferring of culture G with octa-/penta-BDEs dissolved in n-nonane or trichloroethene (TCE) yielded two strains (Acetobacterium sp. strain AG and Dehalococcoides sp. strain DG) that retained debromination capabilities. In the presence of lactate but without TCE, strain AG could cometabolically debrominate 75% of 275 nM PBDEs in a penta-BDE mixture in 33 days. Strain AG shows 99% identity to its closest relative, Acetobacterium malicum. In contrast to strain AG, strain DG debrominated PBDEs only in the presence of TCE. In addition, 18 out of 19 unknown PBDE debromination products were successfully identified from octa- and penta-BDE mixtures and revealed, for the first time, a comprehensive microbial PBDE debromination pathway. As an acetogenic autotroph that rapidly debrominates octa- and penta-BDE technical mixtures, Acetobacterium sp. strain AG adds to the still-limited understanding of PBDE debromination by microorganisms.

Ding, Chang; Chow, Wai Ling

2013-01-01

86

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.  

PubMed

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N(2)-fixing root nodules on diverse and globally distributed angiosperms in the "actinorhizal" symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%-98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses. PMID:17151343

Normand, Philippe; Lapierre, Pascal; Tisa, Louis S; Gogarten, Johann Peter; Alloisio, Nicole; Bagnarol, Emilie; Bassi, Carla A; Berry, Alison M; Bickhart, Derek M; Choisne, Nathalie; Couloux, Arnaud; Cournoyer, Benoit; Cruveiller, Stephane; Daubin, Vincent; Demange, Nadia; Francino, Maria Pilar; Goltsman, Eugene; Huang, Ying; Kopp, Olga R; Labarre, Laurent; Lapidus, Alla; Lavire, Celine; Marechal, Joelle; Martinez, Michele; Mastronunzio, Juliana E; Mullin, Beth C; Niemann, James; Pujic, Pierre; Rawnsley, Tania; Rouy, Zoe; Schenowitz, Chantal; Sellstedt, Anita; Tavares, Fernando; Tomkins, Jeffrey P; Vallenet, David; Valverde, Claudio; Wall, Luis G; Wang, Ying; Medigue, Claudine; Benson, David R

2006-12-06

87

Identification of metabolites from the degradation of fluoranthene by Mycobacterium sp. strain PYR-1  

SciTech Connect

Polycyclic aromatic hydrocarbons (PAHs) such as flouranthene are widespread environmental pollutants shown to be cytotoxic, mutagenic, and carcinogenic. Mycobacterium sp. strain PYR-1 substancially mineralizes fluoranthene in pure culture and in sediments. In this report, additional metabolites of fluoranthene are identified and its possible modes of degradation by Mycobacterium sp. strain PYR-1 are discussed. The experimental results identify metabolites with the intact fluorene configuration and an initial oxygenated metabolite in which the single benzene ring has been attacked. Several metabolic pathways, operating simultaneously, are involved in the degradation of fluoranthen by Mycobacterium sp. strain PYR-1. The low concentrations of metabolites, the rapid evolution of carbon dioxide, and the rapid disappearance of fluoranthene from the medium provide concrete evidence of the usefulness of this Mycobacterium for bioremediation of some PAHs.

Kelley, I.; Freeman, J.P.; Evans, F.E.; Cerniglia, C.E. (Food and Drug Administration, Jefferson, AR (United States))

1993-03-01

88

Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains  

Microsoft Academic Search

In silico, physiological and in planta analyses were used to characterize pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1, and assess its potential ecological function under free-living and symbiotic growth conditions. Sequence analysis revealed the presence of an uptake hydrogenase system, a repABC family plasmid replication module and open reading frames encoding type IV secretion system, TraI and

Eddie J Cytryn; Siriluck Jitacksorn; Eric Giraud; Michael J Sadowsky

2008-01-01

89

Complete detoxification of tris(1,3-dichloro-2-propyl) phosphate by mixed two bacteria, Sphingobium sp. strain TCM1 and Arthrobacter sp. strain PY1.  

PubMed

Tris(1,3-dichloro-2-propyl) phosphate (TDCPP), a flame retardant, is regarded as a potentially toxic and persistent environmental contaminant. We previously isolated a TDCPP-degrading bacterium, Sphingobium sp. strain TCM1, which, however, produced a toxic metabolite: 1,3-dichloro-2-propanol (1,3-DCP). This study was undertaken to develop a technique for complete TDCPP detoxification using strain TCM1 with a 1,3-DCP-degrading bacterium, Arthrobacter sp. strain PY1. For efficient detoxification, we designed a resting cell system and examined the effect of freezing and lyophilization treatments for preparation of their resting cells. Results show that treatments had no marked adverse effect on their activities. The TDCPP dephosphorylation by TCM1 resting cells was optimal at 30°C and pH 8.5. Also, 1,3-DCP dehalogenation by strain PY1 resting cells was optimal at 35°C and pH 9.5. Under those respective conditions, the activities were 2.48 ?mol h?¹·OD????¹ for TDCPP and 0.95 ?mol h?¹·OD????¹ for 1,3-DCP. Based on these results, we set the reaction temperature to 30°C and pH to 9.0. Then we examined the detoxification of 50 ?M TDCPP using mixed resting cells at a final OD(660) of 0.05 for strain TCM1 and 0.2 for strain PY1. In these conditions, TDCPP was eliminated after 1h, but some of the resulting 1,3-DCP remained at a constant level. The increase in strain PY1 cells to a final OD??? of 4.0 decreased the TDCPP dephosphorylation rate of strain TCM1 cells but achieved complete detoxification of TDCPP during 12 h of reaction. PMID:21956155

Takahashi, Shouji; Obana, Yuki; Okada, Shohei; Abe, Katsumasa; Kera, Yoshio

2011-09-28

90

Improved method for the isolation of biosurfactant glycolipids from Rhodococcus sp. Strain H13A  

SciTech Connect

Rhodococcus sp. strain H13A (previously name Arthrobacter sp. strain H13A) degrades haxadecane and produces exocellular glycolipids, one or more of which are biosurfactants. An improved method for the isolation of the biosurfactant glycolipids by using XM 50 diafiltration and isopropanol precipitation was devised. This procedure was advantageous since it removes protein coisolated when the glycolipids are obtained by organic extraction and silicic acid chromatography. The protein apparently does not contribute any biosurfactant characteristics to the glycolipids. The deacylated glycolipid backbone included only a disaccharide.

Bryant, F.O. (Univ. of Georgia, Athens (USA))

1990-05-01

91

Cytotoxic Potential of Industrial Strains of Bacillus sp  

Microsoft Academic Search

The cytotoxic potential of selected strains of Bacillus licheniformis, Bacillus amyloliquefaciens, and Bacillus subtilis, used in the production of industrial enzyme products, has been assessed. Cytotoxicity was determined in Chinese hamster ovary (CHO-K1) cells by measuring total cellular metabolic activity using the tetrazolium salt 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). Initially the MTT assay was validated against toxigenic strains of Bacillus cereus, to

P. B. Pedersen; M. E. Bjørnvad; M. D. Rasmussen; J. N. Petersen

2002-01-01

92

Complete genome sequence of the denitrifying and N(2)O-reducing bacterium Pseudogulbenkiania sp. strain NH8B.  

PubMed

Pseudogulbenkiania sp. strain NH8B is a Neisseriales bacterium isolated from an agricultural field. This strain has strong denitrification and N(2)O reduction activities. Here, we report the finished and annotated genome sequence of this organism. PMID:22038961

Ishii, Satoshi; Tago, Kanako; Nishizawa, Tomoyasu; Oshima, Kenshiro; Hattori, Masahira; Senoo, Keishi

2011-11-01

93

Complete Genome Sequence of the Denitrifying and N2O-Reducing Bacterium Pseudogulbenkiania sp. Strain NH8B  

PubMed Central

Pseudogulbenkiania sp. strain NH8B is a Neisseriales bacterium isolated from an agricultural field. This strain has strong denitrification and N2O reduction activities. Here, we report the finished and annotated genome sequence of this organism.

Ishii, Satoshi; Tago, Kanako; Nishizawa, Tomoyasu; Oshima, Kenshiro; Hattori, Masahira; Senoo, Keishi

2011-01-01

94

Polyhydroxyalkanoate (PHA) production using waste vegetable oil by Pseudomonas sp. strain DR2.  

PubMed

To produce polyhydroxyalkanoate (PHA) from inexpensive substrates by bacteria, vegetable-oil-degrading bacteria were isolated from a rice field using enrichment cultivation. The isolated Pseudomonas sp. strain DR2 showed clear orange or red spots of accumulated PHA granules when grown on phosphate and nitrogen limited medium containing vegetable oil as the sole carbon source and stained with Nile blue A. Up to 37.34% (w/w) of intracellular PHA was produced from corn oil, which consisted of three major 3-hydroxyalkanoates; octanoic (C8:0, 37.75% of the total 3-hydroxyalkanoate content of PHA), decanoic (C10:0, 36.74%), and dodecanoic (C12:0, 11.36%). Pseudomonas sp. strain DR2 accumulated up to 23.52% (w/w) of PHAMCL from waste vegetable oil. The proportion of 3- hydroxyalkanoate of the waste vegetable-oil-derived PHA [hexanoic (5.86%), octanoic (45.67%), decanoic (34.88%), tetradecanoic (8.35%), and hexadecanoic (5.24%)] showed a composition ratio different from that of the corn-oil-derived PHA. Strain DR2 used three major fatty acids in the same ratio, and linoleic acid was the major source of PHA production. Interestingly, the production of PHA in Pseudomonas sp. strain DR2 could not occur in either acetate- or butyrate-amended media. Pseudomonas sp. strain DR2 accumulated a greater amount of PHA than other well-studied strains (Chromobacterium violaceum and Ralstonia eutropha H16) when grown on vegetable oil. The data showed that Pseudomonas sp. strain DR2 was capable of producing PHA from waste vegetable oil. PMID:18756101

Song, Jin Hwan; Jeon, Che Ok; Choi, Mun Hwan; Yoon, Sung Chul; Park, Woojun

2008-08-01

95

CpcM Posttranslationally Methylates Asparagine-71/72 of Phycobiliprotein Beta Subunits in Synechococcus sp. Strain PCC 7002 and Synechocystis sp. Strain PCC 6803? †  

PubMed Central

Cyanobacteria produce phycobilisomes, which are macromolecular light-harvesting complexes mostly assembled from phycobiliproteins. Phycobiliprotein beta subunits contain a highly conserved ?-N-methylasparagine residue, which results from the posttranslational modification of Asn71/72. Through comparative genomic analyses, we identified a gene, denoted cpcM, that (i) encodes a protein with sequence similarity to other S-adenosylmethionine-dependent methyltransferases, (ii) is found in all sequenced cyanobacterial genomes, and (iii) often occurs near genes encoding phycobiliproteins in cyanobacterial genomes. The cpcM genes of Synechococcus sp. strain PCC 7002 and Synechocystis sp. strain PCC 6803 were insertionally inactivated. Mass spectrometric analyses of phycobiliproteins isolated from the mutants confirmed that the CpcB, ApcB, and ApcF were 14 Da lighter than their wild-type counterparts. Trypsin digestion and mass analyses of phycobiliproteins isolated from the mutants showed that tryptic peptides from phycocyanin that included Asn72 were also 14 Da lighter than the equivalent peptides from wild-type strains. Thus, CpcM is the methyltransferase that modifies the amide nitrogen of Asn71/72 of CpcB, ApcB, and ApcF. When cells were grown at low light intensity, the cpcM mutants were phenotypically similar to the wild-type strains. However, the mutants were sensitive to high-light stress, and the cpcM mutant of Synechocystis sp. strain PCC 6803 was unable to grow at moderately high light intensities. Fluorescence emission measurements showed that the ability to perform state transitions was impaired in the cpcM mutants and suggested that energy transfer from phycobiliproteins to the photosystems was also less efficient. The possible functions of asparagine N methylation of phycobiliproteins are discussed.

Shen, Gaozhong; Leonard, Heidi S.; Schluchter, Wendy M.; Bryant, Donald A.

2008-01-01

96

Improved Eco-Friendly Recombinant Anabaena sp. Strain PCC7120 with Enhanced Nitrogen Biofertilizer Potential?  

PubMed Central

Photosynthetic, nitrogen-fixing Anabaena strains are native to tropical paddy fields and contribute to the carbon and nitrogen economy of such soils. Genetic engineering was employed to improve the nitrogen biofertilizer potential of Anabaena sp. strain PCC7120. Constitutive enhanced expression of an additional integrated copy of the hetR gene from a light-inducible promoter elevated HetR protein expression and enhanced functional heterocyst frequency in the recombinant strain. The recombinant strain displayed consistently higher nitrogenase activity than the wild-type strain and appeared to be in homeostasis with compatible modulation of photosynthesis and respiration. The enhanced combined nitrogen availability from the recombinant strain positively catered to the nitrogen demand of rice seedlings in short-term hydroponic experiments and supported better growth. The engineered strain is stable, eco-friendly, and useful for environmental application as nitrogen biofertilizer in paddy fields.

Chaurasia, Akhilesh Kumar; Apte, Shree Kumar

2011-01-01

97

Bio sorption of strontium from aqueous solution by New Strain Bacillus sp. GTG-83  

SciTech Connect

Attempt was made to isolate bacterial strains capable of removing Sr biologically. In this study we collected ten different water samples from naturally radioactive spring Neydasht in Iran and bacterial strains samples isolated. Initial screening of a total of 50 bacterial isolates resulted in selection of one strain. The strain showed maximum adsorption capacity with 55 mg Sr/g dry wt. It was tentatively identified as Bacillus sp. according to morphological and biochemical properties and called strain GTG-83. Studies indicated that Bacillus sp. GTG-83 was able to grow aerobically in the presence of 50 mM SrCl{sub 2} but showed severe growth inhibition at levels above that concentration. The bio-sorption capacity of Bacillus sp. GTG-83 strongly depends on solution pH, and the maximum Sr sorption capacity of Bacillus sp. GTG-83 were obtained at pH 10 independent of the absence or the presence of increasing concentrations of salt (MgCl{sub 2}). Sr-salt bio-sorption studies were also performed at this pH values. Equilibrium uptakes of Sr increased with increasing Sr concentrations up to 250 mg/l for Bacillus sp. GTG-83. Maximum bio-sorption of Sr was obtained at temperatures in the range of 30-35 deg. C. Bacillus sp. GTG-83 bio-sorbed 97 mg Sr/g dry wt at 100 mg/l initial Sr concentration without salt medium (MgCl{sub 2}). When salt concentration (MgCl{sub 2}) increased to 15% (w/v), these values dropped to 23.6 mg Sr/g dry wt at the same conditions. Uptake of Sr within 5 min of incubation was relatively rapid and the absorption continued slowly thereafter. (authors)

Tajer Mohammad Ghazvini, P.; Ghorbanzadeh Mashkani, S.; Ghafourian, H. [Nuclear Research Center, Atomic Energy, Organization of Iran, Dept. of Nuclear Biotechnology, North Karegar St., Tehran (Iran, Islamic Republic of)

2007-07-01

98

Identification and nitrogen regulation of the cyanase gene from the cyanobacteria Synechocystis sp. strain PCC 6803 and Synechococcus sp. strain PCC 7942.  

PubMed Central

An open reading frame (slr0899) on the genome of Synechocystis sp. strain PCC 6803 encodes a polypeptide of 149 amino acid residues, the sequence of which is 40% identical to that of cyanase from Escherichia coli. Introduction into a cyanase-deficient E. coli strain of a plasmid-borne slr0899 resulted in expression of low but significant activity of cyanase. Targeted interruption of a homolog of slr0899 from Synechococcus sp. strain PCC 7942, encoding a protein 77% identical to that encoded by slr0899, resulted in loss of cellular cyanase activity. These results indicated that slr0899 and its homolog in the strain PCC 7942 represent the cyanobacterial cyanase gene (designated cynS). While cynS of strain PCC 6803 is tightly clustered with the four putative molybdenum cofactor biosynthesis genes located downstream, cynS of strain PCC 7942 was found to be tightly clustered with the two genes located upstream, which encode proteins similar to the subunits of the cyanobacterial nitrate-nitrite transporter. In both strains, cynS was transcribed as a part of a large transcription unit and the transcription was negatively regulated by ammonium. Cyanase activity was low in ammonium-grown cells and was induced 7- to 13-fold by inhibition of ammonium fixation or by transfer of the cells to ammonium-free media. These findings indicated that cyanase is an ammonium-repressible enzyme in cyanobacteria, the expression of which is regulated at the level of transcription. Similar to other ammonium-repressible genes in cyanobacteria, expression of cynS required NtcA, a global nitrogen regulator of cyanobacteria.

Harano, Y; Suzuki, I; Maeda, S; Kaneko, T; Tabata, S; Omata, T

1997-01-01

99

Phenotypic and physiological changes in Acinetobacter sp. strain DR1 with exogenous plasmid.  

PubMed

The genus Acinetobacter has been recognized to take up exogenous DNA from the environment. In this study, we conducted natural transformation with a novel diesel-degrading Acinetobacter sp. strain, designated strain DR1, using the broad host range plasmid pRK415. Many factors, including temperature, quantities of DNA, and aeration have proven critically important for efficient natural transformation. Interestingly, the Acinetobacter sp. strain DR1 (pRK415) differed both phenotypically and physiologically from the wild-type strain in several regards, including motility, biofilm formation ability, and responses to oxidative stress: the transformed cells were rendered more sensitive to hydrogen peroxide and cumene hydroperoxide, and their motilities and biofilm formation activity were also attenuated. Our data demonstrated that caution should be exercised when conducting genetic manipulation with plasmids, due to the possibility that phenotypic and physiological changes in the host might occur along with the uptake of plasmids. PMID:20607540

Park, Jungsoon; Park, Woojun

2010-07-07

100

Description of the erythromycin-producing bacterium Arthrobacter sp. strain NRRL B-3381 as Aeromicrobium erythreum gen. nov., sp. nov.  

PubMed

Arthrobacter sp. strain NRRL B-3381T (T = type strain) is a nonmycelial, nonsporulating actinomycete that produces the macrolide antibiotic erythromycin. This bacterium differs in many ways from the type species of the genus Arthrobacter (Arthrobacter globiformis), suggesting that a taxonomic revision is appropriate. The G + C content of strain NRRL B-3381T DNA is 71 to 73 mol%, and the peptidoglycan of this organism contains LL-diaminopimelic acid. Evolutionary distance data obtained from 16S rRNA sequences identified NRRL B-3381T as the deepest branching member of the Nocardioides group of actinomycetes. The principal long-chain fatty acids which we identified that distinguished strain NRRL B-3381T from related G + C-rich bacteria were 10-methyloctadecanoic (tuberculosteric), octadecenoic, and hexadecanoic acids. These characteristics, together with phage typing and biochemical characteristics, form the basis for our recommendation that strain NRRL B-3381 should be the type strain of a new taxon, for which we propose the name Aeromicrobium erythreum. PMID:1883712

Miller, E S; Woese, C R; Brenner, S

1991-07-01

101

Complete genome sequence of Geobacillus thermoglucosidans TNO-09.020, a thermophilic sporeformer associated with a dairy-processing environment.  

PubMed

Thermophilic spore-forming bacteria are a common cause of contamination in dairy products. We isolated the thermophilic strain Geobacillus thermoglucosidans TNO-09.020 from a milk processing plant and report the complete genome of a dairy plant isolate consisting of a single chromosome of 3.75 Mb. PMID:22815439

Zhao, Yu; Caspers, Martien P; Abee, Tjakko; Siezen, Roland J; Kort, Remco

2012-08-01

102

A Novel Nitrate\\/Nitrite Permease in the Marine Cyanobacterium Synechococcus sp. Strain PCC 7002  

Microsoft Academic Search

The nrtP and narB genes, encoding nitrate\\/nitrite permease and nitrate reductase, respectively, were isolated from the marine cyanobacterium Synechococcus sp. strain PCC 7002 and characterized. NrtP is a member of the major facilitator superfamily and is unrelated to the ATP-binding cassette-type nitrate transporters that previously have been described for freshwater strains of cyanobacteria. However, NrtP is similar to the NRT2-

TOSHIO SAKAMOTO; KAORI INOUE-SAKAMOTO; DONALD A. BRYANT

1999-01-01

103

Genome Sequence of the Methanotrophic Alphaproteobacterium Methylocystis sp. Strain Rockwell (ATCC 49242) ?  

PubMed Central

Methylocystis sp. strain Rockwell (ATCC 49242) is an aerobic methane-oxidizing alphaproteobacterium isolated from an aquifer in southern California. Unlike most methanotrophs in the Methylocystaceae family, this strain has a single pmo operon encoding particulate methane monooxygenase but no evidence of the genes encoding soluble methane monooxygenase. This is the first reported genome sequence of a member of the Methylocystis species of the Methylocystaceae family in the order Rhizobiales.

Stein, Lisa Y.; Bringel, Francoise; DiSpirito, Alan A.; Han, Sukkyun; Jetten, Mike S. M.; Kalyuzhnaya, Marina G.; Kits, K. Dimitri; Klotz, Martin G.; Op den Camp, Huub J. M.; Semrau, Jeremy D.; Vuilleumier, Stephane; Bruce, David C.; Cheng, Jan-Fang; Davenport, Karen W.; Goodwin, Lynne; Han, Shunsheng; Hauser, Loren; Lajus, Aurelie; Land, Miriam L.; Lapidus, Alla; Lucas, Susan; Medigue, Claudine; Pitluck, Sam; Woyke, Tanja

2011-01-01

104

Reduction of Selenite to Elemental Red Selenium by Pseudomonas sp. Strain CA5  

Microsoft Academic Search

A Pseudomonas sp. that may be useful in bioremediation projects was isolated from soil. The strain is of potential value because it reduces\\u000a selenite to elemental red selenium and is unusual in that it was resistant to high concentrations of both selenate and selenite.\\u000a Exposure of the strain to 50, 100, and 150 mM selenite reduced growth by 28, 57, and

William J. Hunter; Daniel K. Manter

2009-01-01

105

Kinetics of d-lactic acid production by Sporolactobacillus sp. strain CASD using repeated batch fermentation  

Microsoft Academic Search

d-Lactic acid was produced by Sporolactobacillus sp. strain CASD in repeated batch fermentation with one- and two-reactor systems. The strain showed relatively high energy consumption in its growth-related metabolism in comparison with other lactic acid producers. When the fermentation was repeated with 10% (v\\/v) of previous culture to start a new batch, d-lactic acid production shifted from being cell-maintenance-dependent to

Bo Zhao; Limin Wang; Fengsong Li; Dongliang Hua; Cuiqing Ma; Yanhe Ma; Ping Xu

2010-01-01

106

Genome Sequence of the Pyrene- and Fluoranthene-Degrading Bacterium Cycloclasticus sp. Strain PY97M.  

PubMed

Cycloclasticus sp. strain PY97M was isolated from a phenanthrene-degrading consortium, enriched from Yellow Sea sediment of China. Here, we present the draft genome sequence of strain PY97M, which contains 2,359,509 bp with a G+C content of 41.92% and contains 2, 264 protein-coding genes and 40 tRNAs. PMID:23908283

Cui, Zhisong; Xu, Guangsu; Li, Qian; Gao, Wei; Zheng, Li

2013-08-01

107

Optimization of manganese peroxidase production by the white rot fungus Bjerkandera sp. strain BOS55  

Microsoft Academic Search

Manganese dependent peroxidase (MnP) is the most ubiquitous peroxidase produced by white rot fungi. MnP is known to be involved in lignin degradation, biobleaching and in the oxidation of hazardous organopollutants. Bjerkandera sp. strain BOS55 is a nitrogen-unregulated white rot fungus which produces high amounts of MnP in the excess of N-nutrients due to increased biomass yield. Therefore, the strain

T. Mester; J. A. Field

1997-01-01

108

Draft genome sequence of Serratia sp. strain M24T3, isolated from pinewood disease nematode Bursaphelenchus xylophilus.  

PubMed

Here we report the draft genome sequence of Serratia sp. strain M24T3, which is associated with pinewood nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease. Serratia sp. strain M24T3 has been identified as a bionematocide for B. xylophilus in vitro, and multiple genes potentially involved in virulence and nematotoxity were identified. PMID:22740681

Proença, Diogo Neves; Espírito Santo, Christophe; Grass, Gregor; Morais, Paula V

2012-07-01

109

Draft genome sequence of Pseudomonas sp. strain M47T1, carried by Bursaphelenchus xylophilus isolated from Pinus pinaster.  

PubMed

The draft genome sequence of Pseudomonas sp. strain M47T1, carried by the Bursaphelenchus xylophilus pinewood nematode, the causative agent of pine wilt disease, is presented. In Pseudomonas sp. strain M47T1, genes that make this a plant growth-promoting bacterium, as well as genes potentially involved in nematotoxicity, were identified. PMID:22887683

Proença, Diogo Neves; Espírito Santo, Christophe; Grass, Gregor; Morais, Paula V

2012-09-01

110

Draft Genome Sequence of Pseudomonas sp. Strain M47T1, Carried by Bursaphelenchus xylophilus Isolated from Pinus pinaster  

PubMed Central

The draft genome sequence of Pseudomonas sp. strain M47T1, carried by the Bursaphelenchus xylophilus pinewood nematode, the causative agent of pine wilt disease, is presented. In Pseudomonas sp. strain M47T1, genes that make this a plant growth-promoting bacterium, as well as genes potentially involved in nematotoxicity, were identified.

Proenca, Diogo Neves; Espirito Santo, Christophe; Grass, Gregor

2012-01-01

111

Genome Sequence of Paenibacillus sp. Strain Aloe-11, an Endophytic Bacterium with Broad Antimicrobial Activity and Intestinal Colonization Ability  

PubMed Central

Paenibacillus sp. strain Aloe-11, a Gram-positive, spore-forming, facultatively anaerobic bacterium isolated from the root of Aloe chinensis in the southwest region of China, has excellent antibiotic activity and intestine colonization ability. Here, we present the 5.8-Mb draft genome sequence of Paenibacillus sp. strain Aloe-11.

Li, Neng-Zhang; Xia, Tian; Xu, Ya-Li; Qiu, Rong-Rong; Xiang, Heng; He, Dan

2012-01-01

112

Survey of 150 strains belonging to the Mycobacterium terrae complex and description of Mycobacterium engbaekii sp. nov., Mycobacterium heraklionense sp. nov. and Mycobacterium longobardum sp. nov.  

PubMed

A thorough phenotypic and genotypic analysis of 150 strains belonging to the Mycobacterium terrae complex resulted in the identification of a number of previously unreported sequevars (sqvs) within the species known to belong to the complex. For the species Mycobacterium arupense, three sqvs were detected in the 16S rRNA gene, six sqvs in the hsp65 gene and 15 sqvs in the rpoB gene; in Mycobacterium senuense two sqvs were present in each of the three genetic regions; in Mycobacterium kumamotonense four, two and nine sqvs were found, respectively, and in M. terrae three, four and six sqvs were found, respectively. The inappropriate inclusion of Mycobacterium triviale within the M. terrae complex was confirmed. The limited utility of biochemical tests and of mycolic acid analyses for the differentiation of the members of M. terrae complex was also confirmed. The survey allowed the recognition of three previously undescribed species that were characterized by unique sequences in the 16S rRNA, hsp65 and rpoB genes. Mycobacterium engbaekii sp. nov. (proposed previously 40 years ago but never validly published) was characterized by pink photochromogenic pigmentation and rapid growth; phylogenetically it was related to Mycobacterium hiberniae. The type strain of this species, of which eight strains were investigated, is ATCC 27353(T) (?=?DSM 45694(T)). A cluster of 24 strains was the basis for the description of Mycobacterium heraklionense sp. nov., which has an intermediate growth rate and is unpigmented; nitrate reductase activity is typically strong. Closely related to M. arupense with respect to the 16S rRNA gene, M. heraklionense sp. nov. could be clearly differentiated from the latter species in the other genetic regions investigated. The type strain is NCTC 13432(T) (?=?LMG 24735(T)?=?CECT 7509(T)). Mycobacterium longobardum sp. nov., represented in the study by seven strains, was characterized by a unique phylogenetic location within the M. terrae complex, clearly divergent from any other species. The type strain is DSM 45394(T) (?=?CCUG 58460(T)). PMID:22447702

Tortoli, Enrico; Gitti, Zoe; Klenk, Hans-Peter; Lauria, Stefania; Mannino, Roberta; Mantegani, Paola; Mariottini, Alessandro; Neonakis, Ioannis

2012-03-23

113

Genome Sequence of the Agar-Degrading Marine Bacterium Alteromonadaceae sp. Strain G7  

PubMed Central

Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases.

Kwak, Min-Jung; Song, Ju Yeon; Kim, Byung Kwon; Chi, Won-Jae; Kwon, Soon-Kyeong; Choi, Soobeom; Chang, Yong-Keun

2012-01-01

114

Favolon B, a new triterpenoid isolated from the Chilean Mycena sp. strain 96180.  

PubMed

A new biologically active triterpenoid, favolon B (1), was isolated from fermentation broths of Mycena sp. strain 96180. Favolon B showed antifungal activities towards Botrytis cinerea, Mucor miehei, Paecilomyces variotii and Penicillium notatum. No activities were observed against bacteria and yeasts. The structure of favolon B was elucidated by spectroscopic techniques. PMID:15813182

Aqueveque, Pedro; Anke, Timm; Anke, Heidrun; Sterner, Olov; Becerra, José; Silva, Mario

2005-01-01

115

Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria).  

PubMed

Here, we present the draft genome sequence of an actinobacterium, Dietzia sp. strain UCD-THP, isolated from a residential toilet handle. The assembly contains 3,915,613 bp. The genome sequences of only two other Dietzia species have been published, those of Dietzia alimentaria and Dietzia cinnamea. PMID:23661480

Diep, Amanda L; Lang, Jenna M; Darling, Aaron E; Eisen, Jonathan A; Coil, David A

2013-05-09

116

Substrate Preferences in Biodesulfurization of Diesel Range Fuels by Rhodococcus sp. Strain ECRD-1  

Microsoft Academic Search

The range of sulfur compounds in fuel oil and the substrate range and preference of the biocatalytic system determine the maximum extent to which sulfur can be removed by biodesulfurization. We show that the biodesulfurization apparatus in Rhodococcus sp. strain ECRD-1 is able to attack all isomers of dibenzothio- phene including those with at least four pendant carbons, with a

Roger C. Prince; Matthew J. Grossman

2003-01-01

117

Genome Sequence of the Welan Gum-Producing Strain Sphingomonas sp. ATCC 31555  

PubMed Central

Sphingomonas sp. strain ATCC 31555 can produce an anionic heteropolysaccharide, welan gum, which shows excellent stability and viscosity retention even at high temperatures. Here we present a 4.0-Mb assembly of its genome sequence. We have annotated 10 coding sequences (CDSs) responsible for the welan gum biosynthesis and 55 CDSs related to monosaccharide metabolism.

Wang, Xiaoyu; Tao, Fei; Gai, Zhonghui; Tang, Hongzhi

2012-01-01

118

Genome Sequence of Amycolatopsis sp Strain ATCC 39116, a Plant Biomass-Degrading Actinomycete  

SciTech Connect

We announce the availability of a high-quality draft of the genome sequence of Amycolatopsis sp. strain 39116, one of few bacterial species that are known to consume the lignin component of plant biomass. This genome sequence will further ongoing efforts to use microorganisms for the conversion of plant biomass into fuels and high-value chemicals.

Davis, Jennifer R. [Brown University; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Shunsheng [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Sello, Jason K. [Brown University

2012-01-01

119

Genome Sequence of the Plant Growth-Promoting Rhizobacterium Bacillus sp. Strain JS  

PubMed Central

Volatile and nonvolatile compounds emitted from the plant growth-promoting rhizobacterium Bacillus sp. strain JS enhance the growth of tobacco and lettuce. Here, we report the high-quality genome sequence of this bacterium. Its 4.1-Mb genome reveals a number of genes whose products are possibly involved in promotion of plant growth or antibiosis.

Song, Ju Yeon; Kim, Hyun A; Kim, Ji-Seoung; Kim, Seon-Young; Jeong, Haeyoung; Kang, Sung Gyun; Kim, Byung Kwon; Kwon, Soon-Kyeong; Lee, Choong Hoon; Yu, Dong Su; Kim, Beom Seok; Kim, Sun-Hyung

2012-01-01

120

Deep Desulfurization of Extensively Hydrodesulfurized Middle Distillate Oil by Rhodococcus sp. Strain ECRD-1  

PubMed Central

Dibenzothiophene (DBT), and in particular substituted DBTs, are resistant to hydrodesulfurization (HDS) and can persist in fuels even after aggressive HDS treatment. Treatment by Rhodococcus sp. strain ECRD-1 of a middle distillate oil whose sulfur content was virtually all substituted DBTs produced extensive desulfurization and a sulfur level of 56 ppm.

Grossman, M. J.; Lee, M. K.; Prince, R. C.; Minak-Bernero, V.; George, G. N.; Pickering, I. J.

2001-01-01

121

Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria)  

PubMed Central

Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum Actinobacteria, isolated from a restaurant chair cushion. The assembly contains 3,791,485 bp (G+C content of 73%) and is contained in 68 scaffolds.

Coil, David A.; Doctor, Jessica I.; Lang, Jenna M.; Darling, Aaron E.

2013-01-01

122

Genome Sequence of the Marine Photoheterotrophic Bacterium Erythrobacter sp. Strain NAP1  

PubMed Central

Here we report the full genome sequence of marine phototrophic bacterium Erythrobacter sp. strain NAP1. The 3.3-Mb genome contains a full set of photosynthetic genes organized in one 38.9-kb cluster; however, it does not contain genes for CO2 or N2 fixation, thereby confirming that the organism is a photoheterotroph.

Koblizek, Michal; Janouskovec, Jan; Obornik, Miroslav; Johnson, Justin H.; Ferriera, Steven; Falkowski, Paul G.

2011-01-01

123

Draft Genome Sequence of the Nitrate- and Phosphate-Accumulating Bacillus sp. Strain MCC0008  

PubMed Central

Here, we report the draft genome sequence of the nitrate- and phosphate-accumulating Bacillus sp. strain MCC0008, isolated from a consortium enriched from municipal sewage in nitrate broth (HiMedia M439). The total size of the genome is 5,609,456 bp, with a G+C content of 35.1%.

DebRoy, Shreya; Bhattacharjee, Amrita; Thakur, Ashoke Ranjan

2013-01-01

124

OXIDATION OF BIPHENYL BY A MULTICOMPONENT ENZYME SYSTEM FROM PSEUDOMONAS SP. STRAIN LB400  

EPA Science Inventory

Pseudomonas sp. strain LB400 grows on biphenyl as the sole carbon and energy source. his organism also cooxidizes several chlorinated biphenyl congeners. iphenyl dioxygenase activity in cell extract required addition of NAD(P)H as an electron donor for the conversion of biphenyl ...

125

OXIDATION OF BIPHENYL BY A MULTICOMPONENT ENZYME SYSTEM FROM PSEUDOMONAS SP. STRAIN LB400  

EPA Science Inventory

Pseudomonas sp. strain LB400 grows on biphenyl as the sole carbon and energy source. This organism also cooxidizes several chlorinated biphenyl congeners. Biphenyl dioxygenase activity in cell extract required addition of NAD(P)H as an electron donor for the conversion of bipheny...

126

Identification of a Chlorobenzene Reductive Dehalogenase in Dehalococcoides sp. Strain CBDB1  

Microsoft Academic Search

Received 19 July 2007\\/Accepted 1 October 2007 A chlorobenzene reductive dehalogenase of the anaerobic dehalorespiring bacterium Dehalococcoides sp. strain CBDB1 was identified. Due to poor biomass yields, standard protein isolation procedures were not applicable. Therefore, cell extracts from cultures grown on trichlorobenzenes were separated by native poly- acrylamide gel electrophoresis and analyzed directly for chlorobenzene reductive dehalogenase activity within gel

Lorenz Adrian; Jan Rahnenfuhrer; Johan Gobom; Tina Holscher

2007-01-01

127

Characterization of the Arsenate Respiratory Reductase from Shewanella sp. Strain ANA3  

Microsoft Academic Search

Microbial arsenate respiration contributes to the mobilization of arsenic from the solid to the soluble phase in various locales worldwide. To begin to predict the extent to which As(V) respiration impacts arsenic geochemical cycling, we characterized the expression and activity of the Shewanella sp. strain ANA-3 arsenate respiratory reductase (ARR), the key enzyme involved in this metabolism. ARR is expressed

Davin Malasarn; Jennifer R. Keeffe; Dianne K. Newman

2008-01-01

128

Respiration of 2,4,6-trinitrotoluene by Pseudomonas sp. strain JLR11.  

PubMed

Under anoxic conditions Pseudomonas sp. strain JLR11 can use 2,4, 6-trinitrotoluene (TNT) as the sole N source, releasing nitrite from the aromatic ring and subsequently reducing it to ammonium and incorporating it into C skeletons. This study shows that TNT can also be used as a terminal electron acceptor in respiratory chains under anoxic conditions by Pseudomonas sp. strain JLR11. TNT-dependent proton translocation coupled to the reduction of TNT to aminonitrotoluenes has been observed in TNT-grown cells. This extrusion did not occur in nitrate-grown cells or in anaerobic TNT-grown cells treated with cyanide, a respiratory chain inhibitor. We have shown that in a membrane fraction prepared from Pseudomonas sp. strain JLR11 grown on TNT under anaerobic conditions, the synthesis of ATP was coupled to the oxidation of molecular hydrogen and to the reduction of TNT. This phosphorylation was uncoupled by gramicidin. Respiration by Pseudomonas sp. strain JLR11 is potentially useful for the biotreatment of TNT in polluted waters and soils, particularly in phytorhizoremediation, in which bacterial cells are transported to the deepest root zones, which are poor in oxygen. PMID:10671458

Esteve-Nuñez, A; Lucchesi, G; Philipp, B; Schink, B; Ramos, J L

2000-03-01

129

Respiration of 2,4,6-Trinitrotoluene by Pseudomonas sp. Strain JLR11  

PubMed Central

Under anoxic conditions Pseudomonas sp. strain JLR11 can use 2,4,6-trinitrotoluene (TNT) as the sole N source, releasing nitrite from the aromatic ring and subsequently reducing it to ammonium and incorporating it into C skeletons. This study shows that TNT can also be used as a terminal electron acceptor in respiratory chains under anoxic conditions by Pseudomonas sp. strain JLR11. TNT-dependent proton translocation coupled to the reduction of TNT to aminonitrotoluenes has been observed in TNT-grown cells. This extrusion did not occur in nitrate-grown cells or in anaerobic TNT-grown cells treated with cyanide, a respiratory chain inhibitor. We have shown that in a membrane fraction prepared from Pseudomonas sp. strain JLR11 grown on TNT under anaerobic conditions, the synthesis of ATP was coupled to the oxidation of molecular hydrogen and to the reduction of TNT. This phosphorylation was uncoupled by gramicidin. Respiration by Pseudomonas sp. strain JLR11 is potentially useful for the biotreatment of TNT in polluted waters and soils, particularly in phytorhizoremediation, in which bacterial cells are transported to the deepest root zones, which are poor in oxygen.

Esteve-Nunez, Abraham; Lucchesi, Gloria; Philipp, Bodo; Schink, Bernhard; Ramos, Juan L.

2000-01-01

130

Gene Structures and Regulation of the Alkane Hydroxylase Complex in Acinetobacter sp. Strain M-1  

PubMed Central

In the long-chain n-alkane degrader Acinetobacter sp. strain M-1, two alkane hydroxylase complexes are switched by controlling the expression of two n-alkane hydroxylase-encoding genes in response to the chain length of n-alkanes, while rubredoxin and rubredoxin ruductase are encoded by a single gene and expressed constitutively.

Tani, Akio; Ishige, Takeru; Sakai, Yasuyoshi; Kato, Nobuo

2001-01-01

131

New metabolites in the degradation of fluorene by Arthrobacter sp. strain F101  

Microsoft Academic Search

Fluorene is a major component of fossil fuels, is commonly identified in atmosphere, fresh water, and river and marine sediments. Fluorene is highly toxic to fish and aquantic algae and has carcinogenic potential. The Chemical structure of fluorene offers a variety of possibilities for biodegradation. Arthrobacter sp. strain F101 has been shown to grow on fluorene as a sole source

MERCE CASELLAS; MAGDALENA GRIFOLL; A. M. Solanas

1997-01-01

132

Screening of mutant strain Streptomyces mediolani sp. AC37 for (-)-8-O-methyltetrangomycin production enhancement.  

PubMed

Streptomyces mediolani sp. AC37 was isolated from the root system of higher plant Taxus baccata and produced metabolite identified as (-)-8-O-methyltetrangomycin according to LC/MS/MS analysis. In our screening program for improvements of bioactive secondary metabolites from plant associate streptomycetes, mutation was used as a tool for the induction of genetic variations for selection of higher (-)-8-O-methyltetrangomycin producers of isolates. S. mediolani sp. AC37 was treated with UV irradiation and chemical mutagenic treatment (N-nitroso-N-methyl-urea). The radical scavenging and antioxidant capacity of (-)-8-O-methyltetrangomycin and extracts isolated from mutants were tested using EPR spin trapping technique and ABTS(·+) assay. Comparison of electron microscopic images of Streptomyces sp. AC37 and mutant strains of Streptomyces sp. AC37 revealed substantial differences in morphology and ultrastructure. PMID:23274989

Jiménez, Jakeline Trejos; Sturdíková, Maria; Brezová, Vlasta; Svajdlenka, Emil; Novotová, Marta

2012-12-30

133

The role of extracellular polysaccharides produced by the terrestrial cyanobacterium Nostoc sp. strain HK-01 in NaCl tolerance  

Microsoft Academic Search

The terrestrial cyanobacterium Nostoc sp. HK-01 was more tolerant to NaCl stress than the aquatic cyanobacterium Anabaena sp. PCC 7120 (also called Nostoc sp. PCC 7120) which is similar to Nostoc sp. HK-01 in phylogeny. We determined the amount of extracellular polysaccharides (capsular and released polysaccharides)\\u000a from the cells of both strains cultured with or without 200 mM NaCl. The amount

Hidehisa Yoshimura; Toshihisa Kotake; Tsutomu Aohara; Yoichi Tsumuraya; Masahiko Ikeuchi; Masayuki Ohmori

134

Insertional inactivation of genes to isolate mutants of Synechococcus sp. strain PCC 7942: isolation of filamentous strains.  

PubMed Central

We have developed a simple procedure for generating mutants of the cyanobacterium Synechococcus sp. strain PCC 7942 in which the site of the lesion can be readily identified. This procedure involves transforming Synechococcus sp. strain PCC 7942 with a library of its own DNA that was fully digested with Sau3A and ligated into the plasmid vector pUC8. The homologous integration of the recombinant plasmid into the genome will often result in the disruption of a gene and the loss of gene function. We have used this method to generate many mutants of Synechococcus sp. strain PCC 7942 which grow as multicellular filaments rather than as unicells. Since the gene harboring the lesion was tagged with pUC8, it was easily isolated. In this paper, we discuss the usefulness of this procedure for the generation of mutants, and we characterize one mutant in which the lesion may be in an operon involved in the assembly of lipopolysaccharides. Images

Dolganov, N; Grossman, A R

1993-01-01

135

Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1.  

PubMed

A Gram-positive bacterial strain capable of aerobic biodegradation of 4-fluorophenol (4-FP) as the sole source of carbon and energy was isolated by selective enrichment from soil samples collected near an industrial site. The organism, designated strain IF1, was identified as a member of the genus Arthrobacter on the basis of 16S ribosomal RNA gene sequence analysis. Arthrobacter strain IF1 was able to mineralize 4-FP up to concentrations of 5 mM in batch culture. Stoichiometric release of fluoride ions was observed, suggesting that there is no formation of halogenated dead-end products during 4-FP metabolism. The degradative pathway of 4-FP was investigated using enzyme assays and identification of intermediates by gas chromatography (GC), GC-mass spectrometry (MS), high-performance liquid chromatography, and liquid chromatography-MS. Cell-free extracts of 4-FP-grown cells contained no activity for catechol 1,2-dioxygenase or catechol 2,3-dioxygenase, which indicates that the pathway does not proceed through a catechol intermediate. Cells grown on 4-FP oxidized 4-FP, hydroquinone, and hydroxyquinol but not 4-fluorocatechol. During 4-FP metabolism, hydroquinone accumulated as a product. Hydroquinone could be converted to hydroxyquinol, which was further transformed into maleylacetic acid and beta-ketoadipic acid. These results indicate that the biodegradation of 4-FP starts with a 4-FP monooxygenase reaction that yields benzoquinone, which is reduced to hydroquinone and further metabolized via the beta-ketoadipic acid pathway. PMID:18228015

Ferreira, Maria Isabel M; Marchesi, Julian R; Janssen, Dick B

2008-01-29

136

Polyphasic taxonomic study of strain CCM 2783 resulting in the description of Arthrobacter stackebrandtii sp. nov.  

PubMed

Strain CCM 2783, previously classified as representing Arthrobacter aurescens, was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis and chemotaxonomic characteristics such as peptidoglycan type A3alpha Lys-Ala(2), major menaquinone MK-9(H(2)) and fatty acid composition confirmed assignment of the strain to the genus Arthrobacter. The results of phylogenetic analysis, DNA-DNA relatedness experiments and physiological and chemotaxonomic characteristics indicate that CCM 2783 differs from its nearest phylogenetic relative Arthrobacter psychrolactophilus and from other recognized Arthrobacter species. Therefore, a novel species, Arthrobacter stackebrandtii sp. nov., is proposed with the type strain CCM 2783(T) (=DSM 16005(T)). PMID:15774666

Tvrzová, Ludmila; Schumann, Peter; Spröer, Cathrin; Sedlácek, Ivo; Verbarg, Susanne; Kroppenstedt, Reiner M; Pácová, Zdena

2005-03-01

137

TNT and nitroaromatic compounds are chemoattractants for Burkholderia cepacia R34 and Burkholderia sp. strain DNT  

Microsoft Academic Search

Nitroaromatic compounds are toxic and potential carcinogens. In this study, a drop assay was used to detect chemotaxis toward nitroaromatic compounds for wild-type Burkholderia cepacia R34, wild-type Burkholderia sp. strain DNT, and a 2,4-dinitrotoluene (2,4-DNT) dioxygenase mutant strain (S5). The three strains are chemotactic toward 2,4,6-trinitrotoluene (TNT), 2,3-DNT, 2,4-DNT, 2,5-DNT, 2-nitrotoluene (NT), 4NT, and 4-methyl-5-nitrocatechol (4M5NC), but not toward 2,6-DNT.

Thammajun Leungsakul; Brendan G. Keenan; Barth F. Smets; Thomas K. Wood

2005-01-01

138

Isolation and Characterization of Novosphingobium sp. Strain MT1, a Dominant Polychlorophenol-Degrading Strain in a Groundwater Bioremediation System  

PubMed Central

A high-rate fluidized-bed bioreactor has been treating polychlorophenol-contaminated groundwater in southern Finland at 5 to 8°C for over 6 years. We examined the microbial diversity of the bioreactor using three 16S ribosomal DNA (rDNA)-based methods: denaturing gradient gel electrophoresis, length heterogeneity-PCR analysis, and restriction fragment length polymorphism analysis. The molecular study revealed that the process was dependent on a stable bacterial community with low species diversity. The dominant organism, Novosphingobium sp. strain MT1, was isolated and characterized. Novosphingobium sp. strain MT1 degraded the main contaminants of the groundwater, 2,4,6-trichlorophenol, 2,3,4,6-tetrachlorophenol, and pentachlorophenol, at 8°C. The strain carried a homolog of the pcpB gene, coding for the pentachlorophenol-4-monooxygenase in Sphingobium chlorophenolicum. Spontaneous deletion of the pcpB gene homolog resulted in the loss of degradation ability. Phenotypic dimorphism (planktonic and sessile phenotypes), low growth rate (0.14 to 0.15 h?1), and low-copy-number 16S rDNA genes (single copy) were characteristic of strain MT1 and other MT1-like organisms isolated from the bioreactor.

Tiirola, Marja A.; Mannisto, Minna K.; Puhakka, Jaakko A.; Kulomaa, Markku S.

2002-01-01

139

Dissimilatory Iodate Reduction by Marine Pseudomonas sp. Strain SCT?  

PubMed Central

Bacterial iodate (IO3?) reduction is poorly understood largely due to the limited number of available isolates as well as the paucity of information about key enzymes involved in the reaction. In this study, an iodate-reducing bacterium, designated strain SCT, was newly isolated from marine sediment slurry. SCT is phylogenetically closely related to the denitrifying bacterium Pseudomonas stutzeri and reduced 200 ?M iodate to iodide (I?) within 12 h in an anaerobic culture containing 10 mM nitrate. The strain did not reduce iodate under the aerobic conditions. An anaerobic washed cell suspension of SCT reduced iodate when the cells were pregrown anaerobically with 10 mM nitrate and 200 ?M iodate. However, cells pregrown without iodate did not reduce it. The cells in the former category showed methyl viologen-dependent iodate reductase activity (0.31 U mg?1), which was located predominantly in the periplasmic space. Furthermore, SCT was capable of anaerobic growth with 3 mM iodate as the sole electron acceptor, and the cells showed enhanced activity with respect to iodate reductase (2.46 U mg?1). These results suggest that SCT is a dissimilatory iodate-reducing bacterium and that its iodate reductase is induced by iodate under anaerobic growth conditions.

Amachi, Seigo; Kawaguchi, Nahito; Muramatsu, Yasuyuki; Tsuchiya, Satoshi; Watanabe, Yuko; Shinoyama, Hirofumi; Fujii, Takaaki

2007-01-01

140

New metabolites in the degradation of fluorene by Arthrobacter sp. strain F101  

SciTech Connect

Fluorene is a major component of fossil fuels, is commonly identified in atmosphere, fresh water, and river and marine sediments. Fluorene is highly toxic to fish and aquantic algae and has carcinogenic potential. The Chemical structure of fluorene offers a variety of possibilities for biodegradation. Arthrobacter sp. strain F101 has been shown to grow on fluorene as a sole source of carbon and energy. This study identifies new metabolites and key enzymatic activities that support and extend the pathways previously proposed for the metabolism of fluorene by Arthrobacter sp. 41 refs., 3 figs., 2 tabs.

Casellas, M.; Grifoll, M.; Solanas, A.M. [Universitat de Barcelona (Spain)] [and others

1997-03-01

141

Oxidation of arsenite by Thiomonas strains and characterization of Thiomonas arsenivorans sp. nov.  

PubMed

A novel bacterium, strain b6(T) (T=type strain), was isolated from a disused mine site by growth using arsenite [As(III)] as energy source in a simple mineral medium. Cells of strain b6(T) were rod-shaped, Gram-negative, non-sporulating and motile. Optimum growth occurred at temperatures between 20 and 30 degrees C, and at pH between 4.0 and 7.5. Strain b6(T) grew chemoautotrophically on As(III), sulphur and thiosulphate, and also heterotrophically on yeast extract and a variety of defined organic compounds. Several other Thiomonas strains, including the type species Thiomonas (Tm.) intermedia, were able to oxidize As(III), though only strain b6(T) and strain NO115 could grow using As(III) as sole energy source in the absence of any organic compound. The G+C content of the DNA of strain b6(T) was 65.1 mol %. Comparative small subunit (SSU) ribosomal RNA (rRNA) analysis indicated that strain b6(T) belongs to the genus Thiomonas in the beta-subdivision of the Proteobacteria. It was closely related to an unnamed Thiomonas strain (NO115) isolated from a Norwegian mining site, though sequence identities between strain b6(T) and characterized Thiomonas species were less than 95%. DNA-DNA hybridization between strain b6(T) and the type species of the genus Tm. intermedia showed less than 50% homology. On the basis of phylogenetic and phenotypic characteristics, strain b6(T) (DSM 16361(T), LMG 22795(T)) is proposed as the type strain of the new species Thiomonas arsenivorans, sp. nov. PMID:16341463

Battaglia-Brunet, Fabienne; Joulian, Catherine; Garrido, Francis; Dictor, Marie-Christine; Morin, Dominique; Coupland, Kris; Barrie Johnson, D; Hallberg, Kevin B; Baranger, Philippe

2005-12-08

142

Reclassification of Rhizobium tropici type A strains as Rhizobium leucaenae sp. nov.  

PubMed

Rhizobium tropici is a well-studied legume symbiont characterized by high genetic stability of the symbiotic plasmid and tolerance to tropical environmental stresses such as high temperature and low soil pH. However, high phenetic and genetic variabilities among R. tropici strains have been largely reported, with two subgroups, designated type A and B, already defined within the species. A polyphasic study comprising multilocus sequence analysis, phenotypic and genotypic characterizations, including DNA-DNA hybridization, strongly supported the reclassification of R. tropici type A strains as a novel species. Type A strains formed a well-differentiated clade that grouped with R. tropici, Rhizobium multihospitium, Rhizobium miluonense, Rhizobium lusitanum and Rhizobium rhizogenes in the phylogenies of the 16S rRNA, recA, gltA, rpoA, glnII and rpoB genes. Several phenotypic traits differentiated type A strains from all related taxa. The novel species, for which the name Rhizobium leucaenae sp. nov. is proposed, is a broad host range rhizobium being able to establish effective root-nodule symbioses with Leucaena leucocephala, Leucaena esculenta, common beans (Phaseolus vulgaris) and Gliricidia sepium. Strain CFN 299(T) (?=?USDA 9039(T)?=?LMG 9517(T)?=?CECT 4844(T)?=?JCM 21088(T)?=?IAM 14230(T)?=?SEMIA 4083(T)?=?CENA 183(T)?=?UMR1026(T)?=?CNPSo 141(T)) is designated the type strain of Rhizobium leucaenae sp. nov. PMID:21742822

Ribeiro, Renan Augusto; Rogel, Marco A; López-López, Aline; Ormeño-Orrillo, Ernesto; Barcellos, Fernando Gomes; Martínez, Julio; Thompson, Fabiano Lopes; Martínez-Romero, Esperanza; Hungria, Mariangela

2011-07-08

143

Isolation and characterization of polycyclic aromatic hydrocarbons-degrading Sphingomonas sp. strain ZL5.  

PubMed

A bacterial strain ZL5, capable of growing on phenanthrene as a sole carbon and energy source but not naphthalene, was isolated by selective enrichment from crude-oil-contaminated soil of Liaohe Oil Field in China. The isolate was identified as a Sphingomonas sp. strain on the basis of 16S ribosomal DNA analysis. Strain ZL5 grown on phenanthrene exhibited catechol 2,3-dioxygenase (C23O) activity but no catechol 1,2-dioxygenase, gentisate 1,2-dioxygenase, protocatechuate 3,4-dioxygenase and protocatechuate 4,5-dioxygenase activities. This suggests that the mode of cleavage of phenanthrene by strain ZL5 could be meta via the intermediate catechol, which is different from the protocatechuate way of other two bacteria, Alcaligenes faecelis AFK2 and Nocardioides sp. strain KP7, also capable of growing on phenanthrene but not naphthalene. A resident plasmid (approximately 60 kb in size), designated as pZL, was detected from strain ZL5. Curing the plasmid with mitomycin C and transferring the plasmid to E. coli revealed that pZL was responsible for polycyclic aromatic hydrocarbons degradation. The C23O gene located on plasmid pZL was cloned and overexpressed in E. coli JM109(DE3). The ring-fission activity of the purified C23O from the recombinant E. coli on dihydroxylated aromatics was in order of catechol > 4-methylcatechol > 3-methylcatechol > 4-chlorocatechol > 3,4-dihydroxyphenanthrene > 3-chlorocatechol. PMID:15228078

Liu, Yongsheng; Zhang, Jie; Zhang, Zhongze

2004-06-01

144

Actinobacillus succinogenes sp. nov., a novel succinic-acid-producing strain from the bovine rumen.  

PubMed

Strain 130ZT was isolated from the bovine rumen. It is a facultatively anaerobic, pleomorphic, Gram-negative rod. It exhibits a 'Morse code' form of morphology, which is characteristic of the genus Actinobacillus. Strain 130ZT is a capnophilic, osmotolerant succinogen that utilizes a broad range of sugars. It accumulates high concentrations of succinic acid (> 70 g l-1). Strain 130ZT is positive for catalase, oxidase, alkaline phosphatase and beta-galactosidase, but does not produce indole or urease. Acid but no gas is produced from D-glucose and D-fructose. 16S rRNA sequence analysis places strain 130ZT within the family Pasteurellaceae; the most closely related members of the family Pasteurellaceae have 16S rRNA similarities of 95.5% or less with strain 130ZT. Strain 130ZT was compared with Actinobacillus lignieresii and the related Bisgaard Taxa 6 and 10. Based upon morphological and biochemical properties, strain 130ZT is most similar to members of the genus Actinobacillus within the family Pasteurellaceae. It is proposed that strain 130ZT be classified as a new species, Actinobacillus succinogenes. The type strain of Actinobacillus succinogenes sp. nov. is ATCC 55618T. PMID:10028265

Guettler, M V; Rumler, D; Jain, M K

1999-01-01

145

Carotenoid-containing outer membrane of Synechocystis sp. strain PCC6714.  

PubMed Central

Outer membranes, free of cytoplasmic or thylakoid membranes and peptidoglycan components, were obtained from Synechocystis sp. strain PCC6714. Electron microscope studies revealed double-track outer membrane vesicles with a smooth-appearing exoplasmic surface, an exoplasmic fracture face covered by closely packed particles and a corresponding plasmic fracture face with regularly distributed holes. Lipopolysaccharide, proteins, lipids, and carotenoids were the constituents of the outer membrane of Synechocystis sp. PCC6714. Twelve polypeptides were found in outer membrane fractions, among them two dominant outer membrane proteins (Mrs, 67,000 and 61,000). Lipopolysaccharide-specific components were GlcN and an unidentified heptose. Outer membrane lipid extracts contained phosphatidylglycerol, sulfolipid, phosphatidylcholine, and unknown lipids. The carotenoids, myxoxanthophyll, related carotenoid-glycosides, zeaxanthin, echinenone, and beta-carotene were found to be true constituents of the outer membrane of Synechocystis sp. PCC6714. Images

Jurgens, U J; Weckesser, J

1985-01-01

146

Genome Sequence of the Multiple-?-Lactam-Antibiotic-Resistant Bacterium Acidovorax sp. Strain MR-S7.  

PubMed

Acidovorax sp. strain MR-S7 was isolated from activated sludge in a treatment system for wastewater containing ?-lactam antibiotic pollutants. Strain MR-S7 demonstrates multidrug resistance for various types of ?-lactam antibiotics at high levels of MIC. The draft genome sequence clarified that strain MR-S7 harbors unique ?-lactamase genes. PMID:23814112

Miura, Takamasa; Kusada, Hiroyuki; Kamagata, Yoichi; Hanada, Satoshi; Kimura, Nobutada

2013-06-27

147

Physiological characteristics of Thiomicrospira sp. strain L-12 isolated from deep-sea hydrothermal vents  

SciTech Connect

Growth of the obligately chemolithotrophic Thiomicrospira sp. strain L-12, isolated from a hydrothermal vent at a depth of 2,550 m in the Galapagos Rift region, was optimal at pH 8 and required 200 mM Na/sup +/ and divalent ions (Ca/sup 2 +/ and Mg/sup 2 +/). The organism was microaerophilic and tolerated 300 ..mu..M sulfide without a decrease in the rate of CO/sub 2/ incorporation. Growth and CO/sub 2/ incorporation occurred within the temperature range of 10 to 35/sup 0/C, with both optimal at 25/sup 0/C. At the in situ pressure of 250 atm, the rate of CO/sub 2/ incorporation was reduced by 25% relative to that measured at 1 atm; it was entirely suppressed at 500 atm. The results of this physiological characterization suggest that Thiomicrospira sp. strain L-12 can be an active autotroph in the hydrothermal environment.

Ruby, E.G.; Jannasch, H.W.

1982-01-01

148

Novel amidases of two Aminobacter sp. strains: Biotransformation experiments and elucidation of gene sequences.  

PubMed

The amidase activities of two Aminobacter sp. strains (DSM24754 and DSM24755) towards the aryl-substituted substrates phenylhydantoin, indolylmethyl hydantoin, D,L-6-phenyl-5,6-dihydrouracil (PheDU) and para-chloro-D,L-6-phenyl-5,6-dihydrouracil were compared. Both strains showed hydantoinase and dihydropyrimidinase activity by hydrolyzing all substrates to the corresponding N-carbamoyl-?- or N-carbamoyl-?-amino acids. However, carbamoylase activity and thus a further degradation of these products to ?- and ?-amino acids was not detected. Additionally, the genes coding for a dihydropyrimidinase and a carbamoylase of Aminobacter sp. DSM24754 were elucidated. For Aminobacter sp. DSM24755 a dihydropyrimidinase gene flanked by two genes coding for putative ABC transporter proteins was detected. The deduced amino acid sequences of both dihydropyrimidinases are highly similar to the well-studied dihydropyrimidinase of Sinorhizobium meliloti CECT4114. The latter enzyme is reported to accept substituted hydantoins and dihydropyrimidines as substrates. The deduced amino acid sequence of the carbamoylase gene shows a high similarity to the very thermostable enzyme of Pseudomonas sp. KNK003A. PMID:22738219

Engel, Ulrike; Syldatk, Christoph; Rudat, Jens

2012-06-27

149

Nocardiopsis yanglingensis sp. nov., a thermophilic strain isolated from a compost of button mushrooms.  

PubMed

A strain named A18 was recovered from a compost of button mushrooms. It was characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence comparison, it belonged to the genus Nocardiopsis and was most closely related to the type strains of Nocardiopsis flavescens (sequence similarity 98.0%), Nocardiopsis prasina (97.5%), Nocardiopsis metallicus (97.4%), Nocardiopsis alba (97.3%). The combination of phylogenetic analysis, DNA-DNA hybridization, phenotypic characteristics and chemotaxonomic data supported the proposal that strain A18 represents a new species of the genus Nocardiopsis, for which the name Nocardiopsis yanglingensis sp. nov. was proposed (type strain A18(T) = KCTC 19723(T) = CCTCC 209063(T)). PMID:21671196

Yan, Xia; Yan, Hua; Liu, Zenan; Liu, Xiaodong; Mo, Haiping; Zhang, Liping

2011-06-14

150

Cometabolic Degradation of Dibenzofuran and Dibenzothiophene by a Newly Isolated Carbazole-Degrading Sphingomonas sp. Strain  

Microsoft Academic Search

A carbazole-utilizing bacterium was isolated by enrichment from petroleum-contaminated soil. The isolate, designated Sphingomonas sp. strain XLDN2-5, could utilize carbazole (CA) as the sole source of carbon, nitrogen, and energy. Washed cells of strain XLDN2-5 were shown to be capable of degrading dibenzofuran (DBF) and dibenzothiophene (DBT). Examination of metabolites suggested that XLDN2-5 degraded DBF to 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienic acid and subsequently

Zhonghui Gai; B. Yu; L. Li; Y. Wang; C. Ma; J. Feng; Z. Deng; P. Xu

2007-01-01

151

Molecular identification of a novel ?-1,3-glucanase from alkaliphilic Nocardiopsis sp. strain F96  

Microsoft Academic Search

Alkaliphilic Nocardiopsis sp. strain F96 produced three -1,3-glucanase isozymes of different molecular masses (BglF1, BglF2 and BglF3). The N-terminal amino acid sequences of BglFs indicated that these isozymes were the products of a single gene. The -1,3-glucanase gene (bglF) was cloned from the chromosomal DNA of strain F96. The bglF gene encoded a polypeptide of 270 amino acids including a

Sumiko Masuda; Kimiko Endo; Naoya Koizumi; Tokusuke Hayami; Tetsuya Fukazawa; Rie Yatsunami; Toshiaki Fukui; Satoshi Nakamura

2006-01-01

152

Transformation of substituted fluorenes and fluorene analogs by pseudomonas sp. strain F274  

SciTech Connect

Pseudomonas sp. strain F274, previously shown to catabolize fluorene via fluorenone and its angular dioxygenation, 2`, 3`-dihydroxy-2-carboxybiphenyl, phthalate, and protocatechuate, was examined for its ability to transform substituted fluorenes and S- and N-heterocyclic analogs. Halogen- and methyl-substituted fluorenes were metabolized to correspondingly substituted phthalates via attack on the unsubstituted ring. In the case of 1-methylfluorene, initial oxidation of the methyl group to carboxyl prevented all other transformations but 9-monooxygenation. This strain also oxidized the S-heteroatoms and benzylic methylenic groups of fluorene analogs. No angular dioxygenation of S- and N-heterocycles was observed. 24 refs., 2 figs., 1 tab.

Grifoll, M. [Univ. of Barcelon (Spain); Selifonov, S.A. [Univ. of West Florida, Pensacola, FL (United States)]|[Univ. of Minnesota, St. Paul, MN (United States); Chapman, P.J.

1995-09-01

153

Toluene and ethylbenzene oxidation by purified naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4  

SciTech Connect

Naphthalene dioxygenase (NDO) catalyzes the first reaction in the aerobic catabolism of naphthalene by Pseudomonas sp strain NCIB 9816-4. Studies suggest that the enzyme may oxidize aromatic hydrocarbons such as toluene and ethylbenzene at the alkyl substituents rather than the aromatic nucleus. This paper reports on multiple pathways for the oxidation of the methyl and thyl groups of toluene and ethylbenzene by NDO. 47 refs., 6 figs., 3 tabs.

Lee, K.; Gibson, D.T. [Univ. of Iowa, Iowa City, IA (United States)

1996-09-01

154

Purification and characterization of hydroquinone dioxygenase from Sphingomonas sp. strain TTNP3  

Microsoft Academic Search

Hydroquinone-1,2-dioxygenase, an enzyme involved in the degradation of alkylphenols in Sphingomonas sp. strain TTNP3 was purified to apparent homogeneity. The extradiol dioxygenase catalyzed the ring fission of hydroquinone\\u000a to 4-hydroxymuconic semialdehyde and the degradation of chlorinated and several alkylated hydroquinones. The activity of 1\\u000a mg of the purified enzyme with unsubstituted hydroquinone was 6.1 ?mol per minute, the apparent Km

Boris A Kolvenbach; Markus Lenz; Dirk Benndorf; Erdmann Rapp; Jan Fousek; Cestmir Vlcek; Andreas Schäffer; Frédéric LP Gabriel; Hans-Peter E Kohler; Philippe FX Corvini

2011-01-01

155

Microbial desulfurization of alkylated dibenzothiophene and alkylated benzothiophene by recombinant Rhodococcus sp. strain T09  

Microsoft Academic Search

The dibenzothiophene (DBT) desulfurizing operon, dsz, was introduced into various benzothiophene (BT)-desulfurizing bacteria using a Rhodococcus-E. coli shuttle vector. Of the tested recombinant bacteria, only those from Rhodococcus sp. strain T09 grew with both DBT and BT as the sole sulfur source. These recombinant cells desulfurized not only alkylated BTs, but also various alkylated DBTs, producing alkylated hydroxybiphenyls as the

T. Matsui; K. Hirasawa; J. Konishi; Y. Tanaka; K. Maruhashi; R. Kurane

2001-01-01

156

Effect of dsz D gene expression on benzothiophene degradation of Rhodococcus sp. strain T09  

Microsoft Academic Search

In order to enhance benzothiophene (BT) degradation, a flavin–oxidoreductase gene, dsz D from dibenzothiophene (DBT) desulphurizing Rhodococcuserythropolis KA2-5-1 was expressed in BT desulphurizing Rhodococcus sp. strain T09 using a Rhodococcus–E. coli shuttle vector. The BT degradation rate was increased about threefold with BT grown recombinant cell, suggesting that the flavin–oxidoreductase is involved in BT degradation and the dsz D gene

Toru Matsui; Kazuaki Hirasawa; Ken-ichi Koizumi; Kenji Maruhashi; Ryuichiro Kurane

2001-01-01

157

Polycyclic aromatic hydrocarbon degradation by the white rot fungus Bjerkandera sp. strain BOS55  

Microsoft Academic Search

Outline of this thesis<\\/strong>In this thesis the conditions for optimal PAH oxidation by the white rot fungus Bjerkandera sp. strain BOS55 were evaluated. In Chapter 2, culture conditions like aeration and cosubstrate concentrations, which influenced the oxidation of the PAH compound anthracene and the ligninolytic indicator dye Poly R-478 by the white rot fungus, were studied. Two parameters were identified

M. J. J. Kotterman

1998-01-01

158

Three Replicons of Rhizobium sp. Strain NGR234 Harbor Symbiotic Gene Sequences  

PubMed Central

Rhizobium sp. strain NGR234 contains three replicons: the symbiotic plasmid or pNGR234a, a megaplasmid (pNGR234b), and the chromosome. Symbiotic gene sequences not present in pNGR234a were analyzed by hybridization. DNA sequences homologous to the genes fixLJKNOPQGHIS were found on the chromosome, while sequences homologous to nodPQ and exoBDFLK were found on pNGR234b.

Flores, Margarita; Mavingui, Patrick; Girard, Lourdes; Perret, Xavier; Broughton, William J.; Martinez-Romero, Esperanza; Davila, Guillermo; Palacios, Rafael

1998-01-01

159

Five naturally bioactive molecules including two rhamnopyranoside derivatives isolated from the Streptomyces sp. strain TN58  

Microsoft Academic Search

Extraction of 25 L fermentation broth of the newly isolated Streptomyces sp. strain TN58 and various separation and purification steps led to the isolation of five bioactive metabolites, namely brevianamide F (C1), reported from a streptomycete for the first time, N -acetyltryptamine (C2), thiazolidomycin (C3), and two rhamnopyranosides (C4 and C5). These two rhamnopyranosides were produced directly, without precursor addition.

Raoudha Ben Ameur Mehdi; Khaled A. Shaaban; Ines Karray Rebai; Slim Smaoui; Samir Bejar; Lotfi Mellouli

2009-01-01

160

Isolation of Regulated Genes of the Cyanobacterium Synechocystis sp. Strain PCC 6803 by Differential Display†  

PubMed Central

Global identification of differentially regulated genes in prokaryotes is constrained because the mRNA does not have a 3? polyadenylation extension; this precludes specific separation of mRNA from rRNA and tRNA and synthesis of cDNAs from the entire mRNA population. Knowledge of the entire genome sequence of Synechocystis sp. strain PCC 6803 has enabled us to develop a differential display procedure that takes advantage of a short palindromic sequence that is dispersed throughout the Synechocystis sp. strain PCC 6803 genome. This sequence, designated the HIP (highly iterated palindrome) element, occurs in approximately half of the Synechocystis sp. strain PCC 6803 genes but is absent in rRNA and tRNA genes. To determine the feasibility of exploiting the HIP element, alone or in combination with specific primer subsets, for analyzing differential gene expression, we used HIP-based primers to identify light intensity-regulated genes. Several gene fragments, including those encoding ribosomal proteins and phycobiliprotein subunits, were differentially amplified from RNA templates derived from cells grown in low light or exposed to high light for 3 h. One novel finding was that expression of certain genes of the pho regulon, which are under the control of environmental phosphate levels, were markedly elevated in high light. High-light activation of pho regulon genes correlated with elevated growth rates that occur when the cells are transferred from low to high light. These results suggest that in high light, the rate of growth of Synechocystis sp. strain PCC 6803 exceeds its capacity to assimilate phosphate, which, in turn, may trigger a phosphate starvation response and activation of the pho regulon.

Bhaya, Devaki; Vaulot, Daniel; Amin, Pinky; Takahashi, Akiko Watanabe; Grossman, Arthur R.

2000-01-01

161

High-level chromate resistance in Arthrobacter sp. strain FB24 requires previously uncharacterized accessory genes  

Microsoft Academic Search

BACKGROUND: The genome of Arthrobacter sp. strain FB24 contains a chromate resistance determinant (CRD), consisting of a cluster of 8 genes located on a 10.6 kb fragment of a 96 kb plasmid. The CRD includes chrA, which encodes a putative chromate efflux protein, and three genes with amino acid similarities to the amino and carboxy termini of ChrB, a putative

Kristene L. Henne; Cindy N. Nakatsu; Dorothea K. Thompson; Allan E Konopka

2009-01-01

162

Dichloromethane as the sole carbon source for Hyphomicrobium sp. strain DM2 under denitrification conditions  

Microsoft Academic Search

Hyphomicrobium sp. strain DM2 was found to grow anaerobically in the presence of nitrate with methanol, formaldehyde, formate or dichloromethane. The estimated growth rate constants with methanol and dichloromethane under denitrification conditions were 0.04 h-1 and 0.015 h-1, respectively, which is twofold and fourfold lower than the rates of aerobic growth with these substrates. Slight accumulation of nitrite was observed

Doris Kohler-Staub; Simone Frank; Thomas Leisinger

1995-01-01

163

Four new citrinin derivatives from a marine-derived Penicillium sp. fungal strain.  

PubMed

Four new citrinin derivatives, including two citrinin dimers and two citrinin monomer derivatives, were isolated and identified from a marine-derived fungal strain Penicillium sp. ML226 along with six known related compounds. Their structures were elucidated by spectroscopic and chemical methods. The new compounds showed modest cytotoxic activity against HepG-2 cell line and weak antimicrobial activity against Staphylococcus aureus. PMID:23681057

Wang, Mei Ling; Lu, Chun Hua; Xu, Qing Yan; Song, Si Yang; Hu, Zhi Yu; Zheng, Zhong Hui

2013-05-16

164

Novel Psychrophilic and Thermolabile L-Threonine Dehydrogenase from Psychrophilic Cytophaga sp. Strain KUC-1  

Microsoft Academic Search

A psychrophilic bacterium, Cytophaga sp. strain KUC-1, that abundantly produces a NAD-dependent L-threonine dehydrogenase was isolated from Antarctic seawater, and the enzyme was purified. The molecular weight of the enzyme was estimated to be 139,000, and that of the subunit was determined to be 35,000. The enzyme is a homotetramer. Atomic absorption analysis showed that the enzyme contains no metals.

Takayuki Kazuoka; Shouhei Takigawa; Noriaki Arakawa; Yoshiyuki Hizukuri; Ikuo Muraoka; Tadao Oikawa; Kenji Soda

2003-01-01

165

Stabilization of a truncated Bacillus sp. strain TS23 ? -amylase by replacing histidine-436 with aspartate  

Microsoft Academic Search

Summary Histidine-436 of a truncated Bacillus sp. strain TS-23 ?-amylase (His6-tagged ?NC) has been known to be responsible for thermostability of the enzyme. To understand further the structural role of this residue, site-directed mutagenesis was conducted to replace His-436 of His6-tagged ?NC with aspartate, lysine, tyrosine or threonine. Starch-plate assay showed that all Escherichia coli M15 transformants conferring the mutated

Huei-Fen Lo; Ya-Hui Chen; Nai-Wan Hsiao; Hsiang-Ling Chen; Hui-Yu Hu; Wen-Hwei Hsu; Long-Liu Lin

2005-01-01

166

Purification and Characterization of Allophanate Hydrolase (AtzF) from Pseudomonas sp. Strain ADP  

Microsoft Academic Search

AtzF, allophanate hydrolase, is a recently discovered member of the amidase signature family that catalyzes the terminal reaction during metabolism of s-triazine ring compounds by bacteria. In the present study, the atzF gene from Pseudomonas sp. strain ADP was cloned and expressed as a His-tagged protein, and the protein was purified and characterized. AtzF had a deduced subunit molecular mass

Nir Shapir; Michael J. Sadowsky; Lawrence P. Wackett

2005-01-01

167

Xylose metabolism in the anaerobic fungus Piromyces sp. strain E2 follows the bacterial pathway  

Microsoft Academic Search

The anaerobic fungus Piromyces sp. strain E2 metabolizes xylose via xylose isomerase and d-xylulokinase as was shown by enzymatic and molecular analyses. This resembles the situation in bacteria. The clones encoding the two enzymes were obtained from a cDNA library. The xylose isomerase gene sequence is the first gene of this type reported for a fungus. Northern blot analysis revealed

Harry R. Harhangi; Anna S. Akhmanova; Roul Emmens; Chris van der Drift; Johannes P. van Dijken; Mike S. M. Jetten; Jack T. Pronk

2003-01-01

168

Production of amylase by newly isolated moderate halophile, Halobacillus sp. strain MA2  

Microsoft Academic Search

Production of extracellular amylase was demonstrated under stress conditions of high temperature and high salinity in aerobically cultivated culture of a newly isolated moderately halophilic bacterium of spore-forming Halobacillus sp. strain MA-2 in medium containing starch, peptone, beef extract, and NaCl. The maximum amylase production was secreted in the presence of 15% (w\\/v) Na2SO4 (3.2 U ml?1). The isolate was

M. A Amoozegar; F Malekzadeh; Khursheed A Malik

2003-01-01

169

Diverse reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp strain NCIB 9816  

Microsoft Academic Search

Naphthalene dioxygenase (NDO) fromPseudomonas sp strain NCIB 9816 is a multicomponent enzyme system which initiates naphthalene catabolism by catalyzing the addition of both atoms of molecular oxygen and two hydrogen atoms to the substrate to yield enantiomerically pure (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. NDO has a relaxed substrate specificity and catalyzes the dioxygenation of many related 2- and 3-ring aromatic and hydroaromatic (benzocyclic) compounds

SM Resnick; K Lee; DT Gibson

1996-01-01

170

Transcriptomic Analysis Reveals a Bifurcated Terephthalate Degradation Pathway in Rhodococcus sp. Strain RHA1  

Microsoft Academic Search

Phthalate isomers and their esters are important pollutants whose biodegradation is not well understood. Rhodococcus sp. strain RHA1 is notable for its ability to degrade a wide range of aromatic compounds. RHA1 was previously shown to degrade phthalate (PTH) and to have genes putatively encoding terephthalate (TPA) degradation. Transcriptomic analysis of 8,213 genes indicated that 150 were up-regulated during growth

Hirofumi Hara; Lindsay D. Eltis; Julian E. Davies; William W. Mohn

2007-01-01

171

Active site residues controlling substrate specificity in 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42  

Microsoft Academic Search

Acidovorax (formerly Pseudomonas) sp. strain JS42 utilizes 2-nitrotoluene as sole carbon, nitrogen, and energy source. 2-Nitrotoluene 2,3-dioxygenase (2NTDO)\\u000a catalyzes the initial step in 2-nitrotoluene degradation by converting 2-nitrotoluene to 3-methylcatechol. In this study,\\u000a we identified specific amino acids at the active site that control specificity. The residue at position 350 was found to be\\u000a critical in determining both the enantiospecificity

Kyung-Seon Lee; Juanito V. Parales; Rosmarie Friemann; Rebecca E. Parales

2005-01-01

172

Type II Isopentenyl Diphosphate Isomerase from Synechocystis sp. Strain PCC 6803  

PubMed Central

Open reading frame sll1556 in the cyanobacterium Synechocystis sp. strain 6803 encodes a putative type II isopentenyl diphosphate (IPP) isomerase. The His6-tagged protein was produced in Escherichia coli and purified by Ni2+ chromatography. The homotetrameric enzyme required NADPH, flavin mononucleotide, and Mg2+ for activity; KmIPP was 52 ?M, and kcatIPP was 0.23 s?1.

Barkley, Sam J.; Desai, Shrivallabh B.; Poulter, C. Dale

2004-01-01

173

Type II isopentenyl diphosphate isomerase from Synechocystis sp. strain PCC 6803.  

PubMed

Open reading frame sll1556 in the cyanobacterium Synechocystis sp. strain 6803 encodes a putative type II isopentenyl diphosphate (IPP) isomerase. The His(6)-tagged protein was produced in Escherichia coli and purified by Ni(2+) chromatography. The homotetrameric enzyme required NADPH, flavin mononucleotide, and Mg(2+) for activity; K(m)(IPP) was 52 microM, and k(cat)(IPP) was 0.23 s(-1). PMID:15547291

Barkley, Sam J; Desai, Shrivallabh B; Poulter, C Dale

2004-12-01

174

Whole-Genome Sequence of Cupriavidus sp. Strain BIS7, a Heavy-Metal-Resistant Bacterium  

PubMed Central

Cupriavidus sp. strain BIS7 is a Malaysian tropical soil bacterium that exhibits broad heavy-metal resistance [Co(II), Zn(II), Ni(II), Se(IV), Cu(II), chromate, Co(III), Fe(II), and Fe(III)]. It is particularly resistant to Fe(II), Fe(III), and Zn(II). Here we present the assembly and annotation of its genome.

Hong, Kar Wai; Thinagaran, Dinaiz a/l; Gan, Han Ming; Yin, Wai-Fong

2012-01-01

175

Anabaena sp. Strain PCC 7120 hetY Gene Influences Heterocyst Development  

Microsoft Academic Search

The filamentous cyanobacterium Anabaena (Nostoc) sp. strain PCC 7120 responds to starvation for fixed nitrogen by producing a semiregular pattern of nitrogen-fixing cells called heterocysts. Overexpression of the hetY gene partially suppressed heterocyst formation, resulting in an abnormal heterocyst pattern. Inactivation of hetY increased the time required for heterocyst maturation and caused defects in heterocyst morphology. The 489-bp hetY gene

Ho-Sung Yoon; Martin H. Lee; Jin Xiong; James W. Golden

2003-01-01

176

patS Minigenes Inhibit Heterocyst Development of Anabaena sp. Strain PCC 7120  

Microsoft Academic Search

The patS gene encodes a small peptide that is required for normal heterocyst pattern formation in the cyanobacterium Anabaena sp. strain PCC 7120. PatS is proposed to control the heterocyst pattern by lateral inhibition. patS minigenes were constructed and expressed by different developmentally regulated promoters to gain further insight into PatS signaling. patS minigenes patS4 to patS8 encode PatS C-terminal

Xiaoqiang Wu; Duan Liu; Martin H. Lee; James W. Golden

2004-01-01

177

Abenquines A–D: aminoquinone derivatives produced by Streptomyces sp. strain DB634  

Microsoft Academic Search

New bioactive secondary metabolites, called abenquines, were found in the fermentation broth of Streptomyces sp. strain DB634, which was isolated from the soils of the Chilean highland of the Atacama Desert. They are composed of an amino acid linked to an N-acetyl-aminobenzoquinone. Isolation of the abenquines (1–4), their structure elucidation by NMR analysis and MS, as well as the kinetics

Dirk Schulz; Pascal Beese; Birgit Ohlendorf; Arlette Erhard; Heidi Zinecker; Cristina Dorador; Johannes F Imhoff

2011-01-01

178

Transformation of nitroaromatic compounds by a methanogenic bacterium, Methanococcus sp. (strain B)  

Microsoft Academic Search

The transformation of several nitroaromatic compounds by a newly isolated methanogenic bacterium, Methanococcus sp. (strain B) was studied. The presence of nitroaromatic compounds (0.5 mM) viz., nitrobenzene, 2,4-dinitrobenzene, 2,4,6-trinitrobenzene, 2,4-dinitrophenol, 2,4-dinitrobenzene, and 2,6-dinitrotoluene in the culture medium did not inhibit growth of the isolate. The bacteria grew rapidly and reached stationary phase within seven days of incubation. All the nitroaromatic

Ramaraj Boopathy

1994-01-01

179

Transformation of nitroaromatic compounds by a methanogenic bacterium, Methanococcus sp. (strain B)  

Microsoft Academic Search

?????The transformation of several nitroaromatic compounds by a newly isolated methanogenic bacterium, Methanococcus sp. (strain B) was studied. The presence of nitroaromatic compounds (0.5?mM) viz., nitrobenzene, 2,4-dinitrobenzene, 2,4,6-trinitrobenzene, 2,4-dinitrophenol, 2,4-dinitrotoluene, and 2,6-dinitrotoluene in the culture medium did not inhibit growth of the isolate. The bacteria grew rapidly and reached stationary phase within seven days of incubation. All the nitroaromatic compounds

Ramaraj Boopathy

1994-01-01

180

Preliminary characterization of the probiotic properties of Candida famata and Geobacillus thermoleovorans  

PubMed Central

Background and Objective Probiotics are live microbial feed supplements which beneficially affect the host animal by improving its intestinal microbial balance, producing metabolites which inhibit the colonization or growth of other microorganisms or by competing with them for resources such as nutrients or space. The aim of this study was to investigate the probiotic properties of Candida famata and Geobacillus thermoleovorans. Material and Methods In this study, yeast and bacterial strains isolated from pure oil waste were identified using Api 50 CHB and Api Candida Systems and their probiotic properties were studied through antimicrobial activity, biofilm production, adherence assay and enzymatic characterization. Results and Conclusion According to biochemical analyses, these strains corresponded to Geobacillus thermoleovorans and Candida famata. Antagonism assay results showed that the tested strains have an inhibitory effect against tested pathogenic bacteria. The yeast Candida famata was unable to produce biofilm on Congo Red Agar (CRA), while the bacterial strain was a slime producer. Adherence assays to abiotic surfaces revealed that the investigated strains were fairly adhesive to polystyrene with values ranging from 0.18 to 0.34 at 595 nm. The enzymatic characterization revealed that the tested strains expressed enzymes such as phosphatase alkaline, esterase lipase (C8), amylase, lipase, lecitenase and caseinase. The obtained results may allow the isolated strains to be considered as having the potential to be candidate probiotics.

Mahdhi, A; Hmila, Z; Behi, A; Bakhrouf, A

2011-01-01

181

An insertion element prevents phycobilisome synthesis in N2-fixing Synechocystis sp. strain BO 8402.  

PubMed Central

The unicellular diazotrophic cyanobacterium Synechocystis sp. strain BO 8402, isolated from Lake Constance, contains a novel insertion sequence, IS8402, in the apcA gene encoding a pigmented protein of phycobilisomes. IS8402 comprises 1,322 bp, flanked by two inverted repeats of 15 bp. Upon insertion in the target DNA, direct duplications of 8 nucleotides were generated. One open reading frame, potentially coding for a protein of 399 amino acids, was found. The deduced amino acid sequence shows homology to putative transposases of the IS4 family. Precise excision of the insertion element resulted in a spontaneous revertant, Synechocystis sp. strain BO 9201, that had regained the ability to form hemidiscoidal phycobilisomes. Apart from the unique insertion of IS8402 into apcA in strain BO 8402 both strains contain at least 12 further homologous insertion elements at corresponding sites in the genomes. The unique insertion in strain BO 8402 prevents the expression of apcABC operon and hence abolishes the formation of intact phycobilisomes. This decreases the quantum efficiency of photosystem II and promotes anaerobic N2 fixation in a unicellular cyanobacterium with a highly oxygen-sensitive nitrogenase.

Brass, S; Ernst, A; Boger, P

1996-01-01

182

The cylindrospermopsin gene cluster of Aphanizomenon sp. strain 10E6: organization and recombination.  

PubMed

Cylindrospermopsin (CYN), a potent hepatoxin, occurs in freshwaters worldwide. Several cyanobacterial species produce the toxin, but the producing species vary between geographical regions. Aphanizomenon flos-aquae, a common algae species in temperate fresh and brackish waters, is one of the three well-documented CYN producers in European waters. So far, no genetic information on the CYN genes of this species has been available. Here, we describe the complete CYN gene cluster, including flanking regions from the German Aphanizomenon sp. strain 10E6 using a full genome sequencing approach by 454 pyrosequencing and bioinformatic identification of the gene cluster. In addition, we have sequenced a approximately 7 kb fragment covering the genes cyrC (partially), cyrA and cyrB (partially) of the same gene cluster in the CYN-producing Aphanizomenon sp. strains 10E9 and 22D11. Comparisons with the orthologous gene clusters of the Australian Cylindrospermopsis raciborskii strains AWT205 and CS505 and the partial gene cluster of the Israeli Aphanizomenon ovalisporum strain ILC-146 revealed a high gene sequence similarity, but also extensive rearrangements of gene order. The high sequence similarity (generally higher than that of 16S rRNA gene fragments from the same strains), atypical GC-content and signs of transposase activities support the suggestion that the CYN genes have been horizontally transferred. PMID:20430808

Stüken, Anke; Jakobsen, Kjetill S

2010-04-29

183

Plant compounds that induce polychlorinated biphenyl biodegradation by Arthrobacter sp. strain B1B.  

PubMed Central

Plant compounds that induced Arthrobacter sp. strain B1B to cometabolize polychlorinated biphenyls (PCBs) were identified by a screening assay based on the formation of a 4,4'-dichlorobiphenyl ring fission product. A chemical component of spearmint (Mentha spicata), l-carvone, induced Arthrobacter sp. strain B1B to cometabolize Aroclor 1242, resulting in significant degradation of 26 peaks in the mixture, including selected tetra- and pentachlorobiphenyls. Evidence for PCB biodegradation included peak disappearance, formation of a phenylhexdienoate ring fission product, and chlorobenzoate accumulation in the culture supernatant. Carvone was not utilized as a growth substrate and was toxic at concentrations of greater than 500 mg liter-1. Several compounds structurally related to l-carvone, including limonene, p-cymene, and isoprene, also induced cometabolism of PCBs by Arthrobacter sp. strain B1B. A structure-activity analysis showed that chemicals with an unsaturated p-menthane structural motif promoted the strongest cometabolism activity. These data suggest that certain plant-derived terpenoids may be useful for promoting enhanced rates of PCB biodegradation by soil bacteria.

Gilbert, E S; Crowley, D E

1997-01-01

184

The bzd Gene Cluster, Coding for Anaerobic Benzoate Catabolism, in Azoarcus sp. Strain CIB  

PubMed Central

We report here that the bzd genes for anaerobic benzoate degradation in Azoarcus sp. strain CIB are organized as two transcriptional units, i.e., a benzoate-inducible catabolic operon, bzdNOPQMSTUVWXYZA, and a gene, bzdR, encoding a putative transcriptional regulator. The last gene of the catabolic operon, bzdA, has been expressed in Escherichia coli and encodes the benzoate-coenzyme A (CoA) ligase that catalyzes the first step in the benzoate degradation pathway. The BzdA enzyme is able to activate a wider range of aromatic compounds than that reported for other previously characterized benzoate-CoA ligases. The reduction of benzoyl-CoA to a nonaromatic cyclic intermediate is carried out by a benzoyl-CoA reductase (bzdNOPQ gene products) detected in Azoarcus sp. strain CIB extracts. The bzdW, bzdX, and bzdY gene products show significant similarity to the hydratase, dehydrogenase, and ring-cleavage hydrolase that act sequentially on the product of the benzoyl-CoA reductase in the benzoate catabolic pathway of Thauera aromatica. Benzoate-CoA ligase assays and transcriptional analyses based on lacZ-reporter fusions revealed that benzoate degradation in Azoarcus sp. strain CIB is subject to carbon catabolite repression by some organic acids, indicating the existence of a physiological control that connects the expression of the bzd genes to the metabolic status of the cell.

Barragan, Maria J. Lopez; Carmona, Manuel; Zamarro, Maria T.; Thiele, Barbel; Boll, Matthias; Fuchs, Georg; Garcia, Jose L.; Diaz, Eduardo

2004-01-01

185

Effects of Deficiency and Overdose of Group 2 Sigma Factors in Triple Inactivation Strains of Synechocystis sp. Strain PCC 6803? †  

PubMed Central

Acclimation of cyanobacteria to environmental changes includes major changes in the gene expression patterns partly orchestrated by the replacement of a particular ? subunit with another in the RNA polymerase holoenzyme. The cyanobacterium Synechocystis sp. strain PCC 6803 encodes nine ? factors, all belonging to the ?70 family. Cyanobacteria typically encode many group 2 ? factors that closely resemble the principal ? factor. We inactivated three out of the four group 2 ? factors of Synechocystis simultaneously in all possible combinations and found that all triple inactivation strains grow well under standard conditions. Unlike the other strains, the ?sigBCD strain, which contains SigE as the only functional group 2 ? factor, did not grow faster under mixotrophic than under autotrophic conditions. The SigB and SigD factors were important in low-temperature acclimation, especially under diurnal light rhythm. The ?sigBCD, ?sigBCE, and ?sigBDE strains were sensitive to high-light-induced photoinhibition, indicating a central role of the SigB factor in high-light tolerance. Furthermore, the ?sigBCE strain (SigD is the only functional group 2 ? factor) appeared to be locked in the high-fluorescence state (state 1) and grew slowly in blue but not in orange or white light. Our results suggest that features of the triple inactivation strains can be categorized as (i) direct consequences of the inactivation of a particular ? factor(s) and (ii) effects resulting from the higher probability that the remaining group 2 ? factors associate with the RNA polymerase core.

Pollari, Maija; Rantamaki, Susanne; Huokko, Tuomas; Karlund-Marttila, Anna; Virjamo, Virpi; Tyystjarvi, Esa; Tyystjarvi, Taina

2011-01-01

186

Isolation and characterization of a thermophilic bacterium, Geobacillus thermocatenulatus, degrading nylon 12 and nylon 66.  

PubMed

A thermophilic bacterium, identified as a neighboring species to Geobacillus thermocatenulatus, having a growth optimum at 55 degrees C and, capable of degrading nylon 12, was isolated from soil by enrichment culture technique at 60 degrees C. At this temperature, the strain grew on 5 g nylon 12 l(-1) with a decrease in its molecular weight from 41000 to 11000 over 20 d. The degradation was assumed to be due to endogenous hydrolysis of amide bond in nylon 12. The strain degraded also nylon 66 with a decrease in its molecular weight from 43000 to 17000 in 20 d at 60 degrees C. Nylon 6 was not degraded. PMID:14626419

Tomita, Kosuke; Ikeda, Noritoshi; Ueno, Ayumi

2003-10-01

187

Genome sequences of Burkholderia sp. strains CCGE1002 and H160, isolated from legume nodules in Mexico and Brazil.  

PubMed

The genome sequences of Burkholderia sp. strains CCGE1002 from Mexico and H160 from Brazil, isolated from legume nodules, are reported. Their gene contents in relation to plant-microbe interactions and xenobiotic degradation are discussed. PMID:23209196

Ormeño-Orrillo, Ernesto; Rogel, Marco A; Chueire, Ligia Maria Oliveira; Tiedje, James M; Martínez-Romero, Esperanza; Hungria, Mariangela

2012-12-01

188

Anabaena sp. strain PCC 7120 responds to nitrogen deprivation with a cascade-like sequence of transcriptional activations.  

PubMed Central

Anabaena sp. strain PCC 7120 adapts to deprivation of fixed nitrogen by undergoing physiological and genetic changes that include formation of N2-fixing heterocysts. Whether or not certain of the genes involved are interdependently expressed has been studied.

Cai, Y; Wolk, C P

1997-01-01

189

Photoacclimation of Prochlorococcus sp. (Prochlorophyta) Strains Isolated from the North Atlantic and the Mediterranean Sea.  

PubMed Central

Two Atlantic (SARG and NATL1) strains and one Mediterranean (MED) strain of Prochlorococcus sp., a recently discovered marine, free-living prochlorophyte, were grown over a range of "white" irradiances (lg) and under low blue light to examine their photoacclimation capacity. All three strains contained divinyl (DV) chlorophylls (Chl) a and b, both distinguishable from "normal" Chls by their red-shifted blue absorption maximum, a Chl c-like pigment at low concentration, zeaxanthin, and [alpha]-carotene. The presence of two phaeophytin b peaks in acidified extracts from both Atlantic strains grown at high lg suggests that these strains also had a normal Chl b-like pigment. In these strains, the total Chl b to DV-Chl a molar ratio decreased from about 1 at 7.5 [mu]mol quanta m-2 s-1 to 0.4 to 0.5 at 133 [mu]mol quanta m-2 s-1. In contrast, the MED strain always had a low DV-Chl b to DV-Chl a molar ratio, ranging between 0.13 at low lg and 0.08 at high lg. The discrepancies between the Atlantic and MED strains could result from differences either in the number of light-harvesting complexes (LHC) II per photosystem II or in the Chl b-binding capacity of the apoproteins constituting LHC II. Photosynthesis was saturated at approximately 5 fg C(fg Chl)-1 h-1 or 6 fg C cell-1 h-1, and growth was saturated at approximately 0.45 d-1 for both MED and SARG strains at 18[deg]C, but saturating irradiances differed between strains. Atlantic strains exhibited increased light-saturated rates and quantum yield for carbon fixation under blue light.

Partensky, F.; Hoepffner, N.; Li, WKW.; Ulloa, O.; Vaulot, D.

1993-01-01

190

Draft Genome Sequence of Paenisporosarcina sp. Strain TG-20, a Psychrophilic Bacterium Isolated from the Basal Ice of Taylor Glacier  

PubMed Central

We report the draft genome sequence of Paenisporosarcina sp. strain TG-20, which is 4.12 Mb in size and consists of 4,071 protein-coding genes and 76 RNA genes. The genome sequence of Paenisporosarcina sp. TG-20 may provide useful information about molecular adaptations that enhance survival in icy subsurface environments.

Lee, Jun Hyuck; Koh, Hye Yeon; Lee, Sung Gu; Doyle, Shawn; Christner, Brent C.

2012-01-01

191

The capacity to comigrate with Lyophyllum sp strain Karsten through different soils is spread among several phylogenetic groups within the genus Burkholderia  

Microsoft Academic Search

Recently, two strains related to Burkholderia terrae, denoted BS001 and BS110, were shown to be strongly interactive with the soil fungus Lyophyllum sp. strain Karsten, forming a biofilm around the L. sp. strain Karsten hyphae and migrating along growing hyphae in soil. Here, we extend the findings obtained with strains BS001 and BS110 and show that the migratory ability with

R. Nazir; M. Z. Zhang; W. De Boer; J. D. Van Elsas

2012-01-01

192

Soluble methane monooxygenase gene clusters from trichloroethylene-degrading Methylomonas sp. strains and detection of methanotrophs during in situ bioremediation  

Microsoft Academic Search

The soluble MMO (sMMO) gene clusters from group 1 methanotrophs were characterized. An 9.1-kb KpmI fragment from Methylomonas sp. strain KSWIII and a 7.5-kb SalI fragment from methylomonas sp. strain KSPIII which contained the sMMO gene clusters were cloned and sequenced. The sequences of these two fragments were almost identical. The sMMO gene clusters in the fragment consisted of six

Toru Shigematsu; Satoshi Hanada; Masahiro Eguchi; Yoichi Kamagata; Takahiro Kanagawa; RYUICHIRO KURANE; Ryuichiro

1999-01-01

193

Initial Reactions in Anaerobic Oxidation of m-Xylene by the Denitrifying Bacterium Azoarcus sp. Strain T  

Microsoft Academic Search

The initial enzymatic steps in anaerobic m-xylene oxidation were studied in Azoarcus sp. strain T, a denitrifying bacterium capable of mineralizing m-xylene via 3-methylbenzoate. Permeabilized cells of m-xylene- grown Azoarcus sp. strain T catalyzed the addition of m-xylene to fumarate to form (3-methylbenzyl)succinate. In the presence of succinyl coenzyme A (CoA) and nitrate, (3-methylbenzyl)succinate was oxidized to E-(3- methylphenyl)itaconate (or

CYNTHIA J. KRIEGER; HARRY R. BELLER; MARTIN REINHARD; ALFRED M. SPORMANN

1999-01-01

194

Toxicological Effects of Selective Herbicides on Plant Growth Promoting Activities of Phosphate Solubilizing Klebsiella sp . Strain PS19  

Microsoft Academic Search

This study examines the effect of four herbicides, quizalafop-p-ethyl, clodinafop, metribuzin and glyphosate, on plant growth promoting activities like phosphate solubilization, siderophores,\\u000a indole acetic acid, exo-polysaccharides, hydrogen cyanide and ammonia production by herbicide tolerant Klebsiella sp. strain PS19. The strain was isolated from mustard rhizosphere. The selected herbicides were applied two to three times\\u000a at the recommended rates. Klebsiella sp.

Munees Ahemad

2011-01-01

195

Extracellular Signal Molecule(s) Involved in the Carbon Starvation Response of Marine Vibrio sp. Strain S14  

Microsoft Academic Search

The role of exogenous metabolites as putative signal molecules mediating and\\/or regulating the carbon starvation adaptation program in Vibrio sp. strain S14 was investigated. Addition of the stationary-phase supernatant extract (SSE) of Vibrio sp. strain S14 to logarithmic-phase cells resulted in a significant number of carbon starvation-induced proteins being up-regulated. Halogenated furanones, putative antagonists of acylated homoserine lactones (AHLs), inhibited

SUJATHA SRINIVASAN; JORGEN OSTLING; TIMOTHY CHARLTON; ROCKY DE NYS; KATHY TAKAYAMA; STAFFAN KJELLEBERG

1998-01-01

196

Purification and characterization of hydroquinone dioxygenase from Sphingomonas sp. strain TTNP3  

PubMed Central

Hydroquinone-1,2-dioxygenase, an enzyme involved in the degradation of alkylphenols in Sphingomonas sp. strain TTNP3 was purified to apparent homogeneity. The extradiol dioxygenase catalyzed the ring fission of hydroquinone to 4-hydroxymuconic semialdehyde and the degradation of chlorinated and several alkylated hydroquinones. The activity of 1 mg of the purified enzyme with unsubstituted hydroquinone was 6.1 ?mol per minute, the apparent Km 2.2 ?M. ICP-MS analysis revealed an iron content of 1.4 moles per mole enzyme. The enzyme lost activity upon exposure to oxygen, but could be reactivated by Fe(II) in presence of ascorbate. SDS-PAGE analysis of the purified enzyme yielded two bands of an apparent size of 38 kDa and 19 kDa, respectively. Data from MALDI-TOF analyses of peptides of the respective bands matched with the deduced amino acid sequences of two neighboring open reading frames found in genomic DNA of Sphingomonas sp strain TTNP3. The deduced amino acid sequences showed 62% and 47% identity to the large and small subunit of hydroquinone dioxygenase from Pseudomonas fluorescens strain ACB, respectively. This heterotetrameric enzyme is the first of its kind found in a strain of the genus Sphingomonas sensu latu.

2011-01-01

197

Purification and characterization of hydroquinone dioxygenase from Sphingomonas sp. strain TTNP3.  

PubMed

Hydroquinone-1,2-dioxygenase, an enzyme involved in the degradation of alkylphenols in Sphingomonas sp. strain TTNP3 was purified to apparent homogeneity. The extradiol dioxygenase catalyzed the ring fission of hydroquinone to 4-hydroxymuconic semialdehyde and the degradation of chlorinated and several alkylated hydroquinones. The activity of 1 mg of the purified enzyme with unsubstituted hydroquinone was 6.1 ?mol per minute, the apparent Km 2.2 ?M. ICP-MS analysis revealed an iron content of 1.4 moles per mole enzyme. The enzyme lost activity upon exposure to oxygen, but could be reactivated by Fe(II) in presence of ascorbate. SDS-PAGE analysis of the purified enzyme yielded two bands of an apparent size of 38 kDa and 19 kDa, respectively. Data from MALDI-TOF analyses of peptides of the respective bands matched with the deduced amino acid sequences of two neighboring open reading frames found in genomic DNA of Sphingomonas sp strain TTNP3. The deduced amino acid sequences showed 62% and 47% identity to the large and small subunit of hydroquinone dioxygenase from Pseudomonas fluorescens strain ACB, respectively. This heterotetrameric enzyme is the first of its kind found in a strain of the genus Sphingomonas sensu latu. PMID:21906340

Kolvenbach, Boris A; Lenz, Markus; Benndorf, Dirk; Rapp, Erdmann; Fousek, Jan; Vlcek, Cestmir; Schäffer, Andreas; Gabriel, Frédéric Lp; Kohler, Hans-Peter E; Corvini, Philippe Fx

2011-05-27

198

Identification, Purification and Characterization of Laterosporulin, a Novel Bacteriocin Produced by Brevibacillus sp. Strain GI-9  

PubMed Central

Background Bacteriocins are antimicrobial peptides that are produced by bacteria as a defense mechanism in complex environments. Identification and characterization of novel bacteriocins in novel strains of bacteria is one of the important fields in bacteriology. Methodology/Findings The strain GI-9 was identified as Brevibacillus sp. by 16 S rRNA gene sequence analysis. The bacteriocin produced by strain GI-9, namely, laterosporulin was purified from supernatant of the culture grown under optimal conditions using hydrophobic interaction chromatography and reverse-phase HPLC. The bacteriocin was active against a wide range of Gram-positive and Gram-negative bacteria. MALDI-TOF experiments determined the precise molecular mass of the peptide to be of 5.6 kDa and N-terminal sequencing of the thermo-stable peptide revealed low similarity with existing antimicrobial peptides. The putative open reading frame (ORF) encoding laterosporulin and its surrounding genomic region was fished out from the draft genome sequence of GI-9. Sequence analysis of the putative bacteriocin gene did not show significant similarity to any reported bacteriocin producing genes in database. Conclusions We have identified a bacteriocin producing strain GI-9, belonging to the genus Brevibacillus sp. Biochemical and genomic characterization of laterosporulin suggests it as a novel bacteriocin with broad spectrum antibacterial activity.

Singh, Pradip Kumar; Chittpurna; Ashish; Sharma, Vikas; Patil, Prabhu B.; Korpole, Suresh

2012-01-01

199

The cloned 1-aminocyclopropane-1-carboxylate (ACC) deaminase gene from Sinorhizobium sp. strain BL3 in Rhizobium sp. strain TAL1145 promotes nodulation and growth of Leucaena leucocephala.  

PubMed

The objective of this study was to determine the role of 1-aminocyclopropane-1-carboxylate (ACC) deaminase of symbionts in nodulation and growth of Leucaena leucocephala. The acdS genes encoding ACC deaminase were cloned from Rhizobium sp. strain TAL1145 and Sinorhizobium sp. BL3 in multicopy plasmids, and transferred to TAL1145. The BL3-acdS gene greatly enhanced ACC deaminase activity in TAL1145 compared to the native acdS gene. The transconjugants of TAL1145 containing the native or BL3 acdS gene could grow in minimal media containing 1.5mM ACC, whereas BL3 could tolerate up to 3mM ACC. The TAL1145 acdS gene was inducible by mimosine and not by ACC, while the BL3 acdS gene was highly inducible by ACC and not by mimosine. The transconjugants of TAL1145 containing the native- and BL3-acdS genes formed nodules with greater number and sizes, and produced higher root mass on L. leucocephala than by TAL1145. This study shows that the introduction of multiple copies of the acdS gene increased ACC deaminase activities of TAL1145 and enhanced its symbiotic efficiency on L. leucocephala. PMID:18406559

Tittabutr, Panlada; Awaya, Jonathan D; Li, Qing X; Borthakur, Dulal

2008-04-11

200

Biodegradation of phenanthrene with biosurfactant production by a new strain of Brevibacillus sp.  

PubMed

In this work, a phenanthrene-degrading bacterial strain was isolated by enrichment method from hydrocarbon contaminated sludge samples and identified as Brevibacillus sp. PDM-3 based on morphological, biochemical, chemotaxonomic (FAMEs analysis) and molecular (16S rDNA sequencing) analysis. Growth parameters for efficient degradation of phenanthrene such as nutrient medium, pH, temperature, rpm and inoculum size were standardized and 93% of phenanthrene was degraded in 6 days as analysed by HPLC. The bacterial strain PDM-3 also has the ability to produce biosurfactant during phenanthrene degradation as detected by the surface tension measurements of the culture supernatant and the emulsification index (EI??). The biosurfactant was identified by its functional groups through FT-IR spectroscopy. Phenanthrene degradation and biosurfactant production are associated with each other and can be used in environmental biotechnology. Further, the strain has the ability to degrade other PAHs such as anthracene and fluorene by utilizing them as sole carbon and energy source. PMID:20627713

Reddy, M Srikanth; Naresh, B; Leela, T; Prashanthi, M; Madhusudhan, N Ch; Dhanasri, G; Devi, Prathibha

2010-06-02

201

Microbial desulfurization of alkylated dibenzothiophene and alkylated benzothiophene by recombinant Rhodococcus sp. strain T09.  

PubMed

The dibenzothiophene (DBT) desulfurizing operon, dsz, was introduced into various benzothiophene (BT)-desulfurizing bacteria using a Rhodococcus-E. coli shuttle vector. Of the tested recombinant bacteria, only those from Rhodococcus sp. strain T09 grew with both DBT and BT as the sole sulfur source. These recombinant cells desulfurized not only alkylated BTs, but also various alkylated DBTs, producing alkylated hydroxybiphenyls as the desulfurized products. Recombinant strain T09 also desulfurized alkylated DBT in an oil-water, two-phase resting-cell reaction. The dsz operon had the same desulfurizing activity when inserted into the vector in either orientation, indicating that the promoter region of the operon was functional in strain T09. PMID:11499930

Matsui, T; Hirasawa, K; Konishi, J; Tanaka, Y; Maruhashi, K; Kurane, R

2001-07-01

202

Effects of Modified Phycobilin Biosynthesis in the Cyanobacterium Synechococcus sp. Strain PCC 7002?  

PubMed Central

The pathway for phycocyanobilin biosynthesis in Synechococcus sp. strain PCC 7002 comprises two enzymes: heme oxygenase and phycocyanobilin synthase (PcyA). The phycobilin content of cells can be modified by overexpressing genes encoding alternative enzymes for biliverdin reduction. Overexpression of the pebAB and HY2 genes, encoding alternative ferredoxin-dependent biliverdin reductases, caused unique effects due to the overproduction of phycoerythrobilin and phytochromobilin, respectively. Colonies overexpressing pebAB became reddish brown and visually resembled strains that naturally produce phycoerythrin. This was almost exclusively due to the replacement of phycocyanobilin by phycoerythrobilin on the phycocyanin ?-subunit. This phenotype was unstable, and such strains rapidly reverted to the wild-type appearance, presumably due to strong selective pressure to inactivate pebAB expression. Overproduction of phytochromobilin, synthesized by the Arabidopsis thaliana HY2 product, was tolerated much better. Cells overexpressing HY2 were only slightly less pigmented and blue-green than the wild type. Although the pcyA gene could not be inactivated in the wild type, pcyA was easily inactivated when cells expressed HY2. These results indicate that phytochromobilin can functionally substitute for phycocyanobilin in Synechococcus sp. strain PCC 7002. Although functional phycobilisomes were assembled in this strain, the overall phycobiliprotein content of cells was lower, the efficiency of energy transfer by these phycobilisomes was lower than for wild-type phycobilisomes, and the absorption cross-section of the cells was reduced relative to that of the wild type because of an increased spectral overlap of the modified phycobiliproteins with chlorophyll a. As a result, the strain producing phycobiliproteins carrying phytochromobilin grew much more slowly at low light intensity.

Alvey, Richard M.; Biswas, Avijit; Schluchter, Wendy M.; Bryant, Donald A.

2011-01-01

203

Oxidation of elemental sulfur by Fusarium solani strain THIF01 harboring endobacterium Bradyrhizobium sp.  

PubMed

Nineteen fungal strains having an ability to oxidize elemental sulfur in mineral salts medium were isolated from deteriorated sandstones of Angkor monuments. These fungi formed clearing zone on agar medium supplemented with powder sulfur due to the dissolution of sulfur. Representative of the isolates, strain THIF01, was identified as Fusarium solani on the basis of morphological characteristics and phylogenetic analyses. PCR amplification targeting 16S rRNA gene and analyses of full 16S rRNA gene sequence indicated strain THIF01 harbors an endobacterium Bradyrhizobium sp.; however, involvement of the bacterium in the sulfur oxidation is still unclear. Strain THIF01 oxidized elemental sulfur to thiosulfate and then sulfate. Germination of the spores of strain THIF01 was observed in a liquid medium containing mineral salts supplemented with elemental sulfur (rate of germinated spores against total spores was 60.2%), and the culture pH decreased from pH 4.8 to 4.0. On the contrary, neither germination (rate of germinated spores against total spores was 1.0%) nor pH decrease was observed without the supplement of elemental sulfur. Strain THIF01 could also degrade 30 ppmv and ambient level (approximate 500 pptv) of carbonyl sulfide. PMID:20571793

Li, Xian Shu; Sato, Tsutomu; Ooiwa, Yuji; Kusumi, Asako; Gu, Ji-Dong; Katayama, Yoko

2010-06-23

204

Biodegradation of polycyclic aromatic hydrocarbons by a halotolerant bacterial strain Ochrobactrum sp. VA1.  

PubMed

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants in the environment and are derived from both man-made and natural resources. The present study is focused on the degradation of PAHs by a halotolerant bacterial strain under saline conditions. The bacterial strain VA1 was isolated from a PAH-degrading consortium that was enriched from marine water samples that were collected from different sites at Chennai, India. In the present study, a clearing zone formed on PAH-amended mineral salt agar media confirmed the utilization of PAH by the bacterial strain VA1. The results show that the strain VA1 was able to degrade anthracene (88%), phenanthrene (98%), naphthalene (90%), fluorene (97%), pyrene (84%), benzo(k)fluoranthene (57%) and benzo(e)pyrene (50%) at a 30 g/L NaCl concentration. The present study reveals that the VA1 strain was able to degrade PAHs in petroleum wastewater under saline conditions. The promising PAH-degrading halotolerant bacterial strain, VA1, was identified as Ochrobactrum sp. using biochemical and molecular techniques. PMID:20934193

Arulazhagan, P; Vasudevan, N

2010-10-12

205

Biodegradation of 3-nitrotoluene by Rhodococcus sp. strain ZWL3NT.  

PubMed

A pure bacterial culture was isolated by its ability to utilize 3-nitrotoluene (3NT) as the sole source of carbon, nitrogen, and energy for growth. Analysis of its 16S rRNA gene showed that the organism (strain ZWL3NT) belongs to the genus Rhodococcus. A rapid disappearance of 3NT with concomitant release of nitrite was observed when strain ZWL3NT was grown on 3NT. The isolate also grew on 2-nitrotoluene, 3-methylcatechol and catechol. Two metabolites, 3-methylcatechol and 2-methyl-cis,cis-muconate, in the reaction mixture were detected after incubation of cells of strain ZWL3NT with 3NT. Enzyme assays showed the presence of both catechol 1,2-dioxygenase and catechol 2,3-dioxygenase in strain ZWL3NT. In addition, a catechol degradation gene cluster (catRABC cluster) for catechol ortho-cleavage pathway was cloned from this strain and cell extracts of Escherichia coli expressing CatA and CatB exhibited catechol 1,2-dioxygenase activity and cis,cis-muconate cycloisomerase activity, respectively. These experimental evidences suggest a novel pathway for 3NT degradation with 3-methylcatechol as a key metabolite by Rhodococcus sp. strain ZWL3NT. PMID:23250222

Tian, Xiao-Jun; Liu, Xiao-Yang; Liu, Hong; Wang, Shu-Jun; Zhou, Ning-Yi

2012-12-19

206

Corynebacterium freneyi sp. nov., alpha-glucosidase-positive strains related to Corynebacterium xerosis.  

PubMed

Three coryneform strains from clinical specimens were studied. They belonged to the genus Corynebacterium, since they had type IV cell walls containing corynemycolic acids. They had phenotypic characteristics that included alpha-glucosidase, pyrazinamidase and alkaline phosphatase activities and fermentation of glucose, ribose, maltose and sucrose. These are the characteristics of Corynebacterium xerosis. Since this species is very rare in human pathology, the strains were studied in more detail by comparing the 16S-23S intergenic spacers, rDNA sequences and levels of DNA similarity of these three strains and those of the reference strains C. xerosis ATCC 373T and Corynebacterium amycolatum CIP 103452T. According to DNA-DNA hybridization data, the three novel strains are members of the same species (level of DNA similarity >72%). Phylogenetic analysis revealed that these strains are closely related to C. xerosis and C. amycolatum, but DNA-relatedness experiments showed clearly that they constitute a distinct new species, with levels of DNA relatedness of less than 23% to C. xerosis ATCC 373T and less than 5% to C. amycolatum CIP 103452T. Two other alpha-glucosidase-positive strains presenting the same biochemical characteristics were included in the study and proved to be C. amycolatum. This new species can be differentiated from C. xerosis and C. amycolatum strains by carbon source utilization, intergenic spacer region length profiles and some biochemical characteristics such as glucose fermentation at 42 degrees C and growth at 20 degrees C. The name Corynebacterium freneyi sp. nov. is proposed with the type strain ISPB 6695110T (= CIP 106767T = DSM 44506T). PMID:11594602

Renaud, F N; Aubel, D; Riegel, P; Meugnier, H; Bollet, C

2001-09-01

207

Short Chain N-acyl Homoserine Lactone Production by Soil Isolate Burkholderia sp. Strain A9.  

PubMed

In the bacteria kingdom, quorum sensing (QS) is a cell-to-cell communication that relies on the production of and response to specific signaling molecules. In proteobacteria, N-acylhomoserine lactones (AHLs) are the well-studied signaling molecules. The present study aimed to characterize the production of AHL of a bacterial strain A9 isolated from a Malaysian tropical soil. Strain A9 was identified as Burkholderia sp. using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry and 16S rDNA nucleotide sequence analysis. AHL production by A9 was detected with two biosensors, namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Thin layer chromatography results showed N-hexanoylhomoserine lactone (C6-HSL) and N-octanoylhomoserine lactone (C8-HSL) production. Unequivocal identification of C6-HSL and C8-HSL was achieved by high resolution triple quadrupole liquid chromatography-mass spectrometry analysis. We have demonstrated that Burkholderia sp. strain A9 produces AHLs that are known to be produced by other Burkholderia spp. with CepI/CepR homologs. PMID:24084115

Chen, Jian Woon; Koh, Chong-Lek; Sam, Choon-Kook; Yin, Wai-Fong; Chan, Kok-Gan

2013-09-30

208

Minimal Streptomyces sp. strain C5 daunorubicin polyketide biosynthesis genes required for aklanonic acid biosynthesis.  

PubMed Central

The structure of the Streptomyces sp. strain C5 daunorubicin type II polyketide synthase (PKS) gene region is different from that of other known type II PKS gene clusters. Directly downstream of the genes encoding ketoacylsynthase alpha and beta (KS alpha, KS beta) are two genes (dpsC, dpsD) encoding proteins of unproven function, both absent from other type II PKS gene clusters. Also in contrast to other type II PKS clusters, the gene encoding the acyl carrier protein (ACP), dpsG, is located about 6.8 kbp upstream of the genes encoding the daunorubicin KS alpha and KS beta. In this work, we demonstrate that the minimal genes required to produce aklanonic acid in heterologous hosts are dpsG (ACP), dauI (regulatory activator), dpsA (KS alpha), dpsB (KS beta), dpsF (aromatase), dpsE (polyketide reductase), and dauG (putative deoxyaklanonic acid oxygenase). The two unusual open reading frames, dpsC (KASIII homolog lacking a known active site) and dpsD (acyltransferase homolog), are not required to synthesize aklanonic acid. Additionally, replacement of dpsD or dpsCD in Streptomyces sp. strain C5 with a neomycin resistance gene (aphI) results in mutant strains that still produced anthracyclines.

Rajgarhia, V B; Strohl, W R

1997-01-01

209

Amino acid transport systems required for diazotrophic growth in the cyanobacterium Anabaena sp. strain PCC 7120.  

PubMed Central

Uptake of 16 amino acids by the filamentous, heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 was characterized with regard to kinetic parameters of transport, intracellular accumulation of the transported amino acids, and sensitivity of the transport process to energy metabolism inhibitors. Mutants resistant to certain toxic analogs of some amino acids were isolated that were impaired in amino acid transport. Results obtained in this study, together with those reported previously (A. Herrero and E. Flores, J. Biol. Chem. 265:3931-3935, 1990), suggest that there are at least five amino acid transport systems in strain PCC 7120: one high-affinity, active system for basic amino acids; one low-affinity, passive system for basic amino acids; two high-affinity, active systems with overlapping, but not identical, specificities for neutral amino acids; and one putative system for acidic amino acids. Some of the amino acid transport mutants were impaired in diazotrophic growth. These mutants were unable to develop a normal percentage of heterocysts and normal nitrogenase activity in response to nitrogen stepdown. Putative roles for the amino acid transport systems in uptake of extracellular amino acids, recapture of amino acids that have leaked from the cells, and intercellular transfer of amino acids in the filaments of Anabaena sp. strain PCC 7120 are discussed.

Montesinos, M L; Herrero, A; Flores, E

1995-01-01

210

Plasmid dependence of Pseudomonas sp. strain NK87 enzymes that degrade 6-aminohexanoate-cyclic dimer.  

PubMed Central

A bacterial strain, Pseudomonas sp. strain NK87, that can use 6-aminohexanoate-cyclic dimer as the sole source of carbon and nitrogen was newly isolated from wastewater of a factory which produces nylon-6. Two responsible enzymes, 6-aminohexanoate-cyclic-dimer hydrolase (P-EI) and 6-aminohexanoate-dimer hydrolase (P-EII), were found in the NK87 strain, as is the case with Flavobacterium sp. strain KI72, another 6-aminohexanoate-cyclic-dimer-metabolizing bacterium (H. Okada, S. Negoro, H. Kimura, and S. Nakamura, Nature [London] 306:203-206, 1983). The P-EI enzyme is immunologically identical to the 6-aminohexanoate-cyclic-dimer hydrolase of KI72 (F-EI). However, antiserum against the 6-aminohexanoate-dimer hydrolase purified from KI72 (F-EII) did not react with cell extracts of NK87, indicating that the F-EII and P-EII enzymes are immunologically different. Restriction endonuclease analyses show that the NK87 strain harbors at least six plasmids ranging in size from 20 to 80 kilobase pairs (kbp). The P-EI and P-EII genes were cloned in Escherichia coli. Both the P-EI and F-EI probes strongly hybridized with a 23-kbp plasmid in Southern hybridization analyses. The P-EII probe hybridized specifically with an 80-kbp plasmid, but the F-EII probe hybridized with none of the plasmids harbored in NK87. These results indicate that the P-EI gene and P-EII gene are encoded on the 23-kbp and 80-kbp plasmids, respectively. Images

Kanagawa, K; Negoro, S; Takada, N; Okada, H

1989-01-01

211

Draft Genome Sequence of the Actinomycete Rhodococcus sp. Strain AW25M09, Isolated from the Hadsel Fjord, Northern Norway  

PubMed Central

The cold-adapted Rhodococcus sp. strain AW25M09 was isolated from an Atlantic hagfish caught off the shore of northern Norway as part of an ongoing bioprospecting project that aims to identify novel bacteria with biotechnological potential. Here, we present the 5.8-Mb draft genome sequence, together with details regarding the origin of the strain and its sequence assembly.

Hjerde, Erik; Pierechod, Marcin M.; Williamson, Adele K.; Bjerga, Gro E. K.; Willassen, Nils P.; Smalas, Arne O.

2013-01-01

212

Genome Sequence of Methylobacterium sp. Strain GXF4, a Xylem-Associated Bacterium Isolated from Vitis vinifera L. Grapevine  

PubMed Central

Methylobacterium sp. strain GXF4 is an isolate from grapevine. Here we present the sequence, assembly, and annotation of its genome, which may shed light on its role as a grapevine xylem inhabitant. To our knowledge, this is the first genome announcement of a plant xylem-associated strain of the genus Methylobacterium.

Gan, Han Ming; Chew, Teong Han; Hudson, Andre O.

2012-01-01

213

Genome Sequence of Acinetobacter sp. Strain HA, Isolated from the Gut of the Polyphagous Insect Pest Helicoverpa armigera  

PubMed Central

In this study, Acinetobacter sp. strain HA was isolated from the midgut of a fifth-instar larva of Helicoverpa armigera. Here, we report the draft genome sequence (3,125,085 bp) of this strain that consists of 102 contigs, 2,911 predicted coding sequences, and a G+C content of 41%.

Malhotra, Jaya; Dua, Ankita; Saxena, Anjali; Sangwan, Naseer; Mukherjee, Udita; Pandey, Neeti; Rajagopal, Raman; Khurana, Paramjit; Khurana, Jitendra P.

2012-01-01

214

The Draft Genome Sequence of Nocardioides sp. Strain CF8 Reveals the Scope of Its Metabolic Capabilities.  

PubMed

Nocardioides sp. strain CF8 was isolated from a soil sample collected at the Hanford Department of Energy site, Richland, WA. The strain was identified in microcosms based on its ability to grow on butane and has been characterized for its potential applications in the biodegradation of halogenated hydrocarbons. Here, the draft genome sequence is reported. PMID:23833136

Kimbrel, Jeffrey A; Chang, Jeff; Arp, Daniel J; Sayavedra-Soto, Luis A

2013-07-05

215

Whole-genome sequence of N-acylhomoserine lactone-synthesizing and -degrading Acinetobacter sp. strain GG2.  

PubMed

Acinetobacter sp. strain GG2 is a quorum-sensing and quorum-quenching bacterium isolated from the ginger rhizosphere. It degrades a broad range of N-acylhomoserine lactone molecules via lactonase. The genome sequence of strain GG2 may provide insights on the regulation of quorum-sensing and quorum-quenching mechanisms in this bacterium. PMID:23105061

Hong, Kar-Wai; Koh, Chong-Lek; Sam, Choon-Kook; Yin, Wai-Fong; Chan, Kok-Gan

2012-11-01

216

Draft Genome Sequence of Streptomyces sp. Strain Wigar10, Isolated from a Surface-Sterilized Garlic Bulb  

PubMed Central

Streptomyces sp. strain Wigar10 was isolated from a surface-sterilized garlic bulb (Allium sativum var. Purple Stripe). Its genome encodes several novel secondary metabolite biosynthetic gene clusters and provides a genetic basis for further investigation of this strain's chemical biology and potential for interaction with its garlic host.

Klassen, Jonathan L.; Adams, Sandye M.; Bramhacharya, Shanti; Giles, Steven S.; Goodwin, Lynne A.; Woyke, Tanja; Currie, Cameron R.

2011-01-01

217

Complete Genome Sequence of Methylocystis sp. Strain SC2, an Aerobic Methanotroph with High-Affinity Methane Oxidation Potential  

PubMed Central

Methylocystis sp. strain SC2 is an aerobic type II methanotroph isolated from a highly polluted aquifer in Germany. A specific trait of the SC2 strain is the expression of two isozymes of particulate methane monooxygenase with different methane oxidation kinetics. Here we report the complete genome sequence of this methanotroph that contains not only a circular chromosome but also two large plasmids.

Dam, Bomba; Dam, Somasri; Kube, Michael; Reinhardt, Richard

2012-01-01

218

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

SciTech Connect

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.

Sikkema, J.; Bont, J.A.M. de (Wageningen Agricultural Univ. (Netherlands))

1993-02-01

219

Genome Sequence of the Ethene- and Vinyl Chloride-Oxidizing Actinomycete Nocardioides sp. Strain JS614?  

PubMed Central

Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium.

Coleman, Nicholas V.; Wilson, Neil L.; Barry, Kerrie; Brettin, Thomas S.; Bruce, David C.; Copeland, Alex; Dalin, Eileen; Detter, John C.; del Rio, Tijana Glavina; Goodwin, Lynne A.; Hammon, Nancy M.; Han, Shunsheng; Hauser, Loren J.; Israni, Sanjay; Kim, Edwin; Kyrpides, Nikolaos; Land, Miriam L.; Lapidus, Alla; Larimer, Frank W.; Lucas, Susan; Pitluck, Sam; Richardson, Paul; Schmutz, Jeremy; Tapia, Roxanne; Thompson, Sue; Tice, Hope N.; Spain, Jim C.; Gossett, James G.; Mattes, Timothy E.

2011-01-01

220

Substrate Preferences in Biodesulfurization of Diesel Range Fuels by Rhodococcus sp. Strain ECRD-1  

PubMed Central

The range of sulfur compounds in fuel oil and the substrate range and preference of the biocatalytic system determine the maximum extent to which sulfur can be removed by biodesulfurization. We show that the biodesulfurization apparatus in Rhodococcus sp. strain ECRD-1 is able to attack all isomers of dibenzothiophene including those with at least four pendant carbons, with a slight preference for those substituted in the ?-position. With somewhat less avidity, this apparatus is also able to attack substituted benzothiophenes with between two and seven pendant carbons. Some compounds containing sulfidic sulfur are also susceptible to desulfurization, although we have not yet been able to determine their molecular identities.

Prince, Roger C.; Grossman, Matthew J.

2003-01-01

221

Roseovarius sp. strain 217: aerobic taurine dissimilation via acetate kinase and acetate-CoA ligase.  

PubMed

The genome sequence of Roseovarius sp. strain 217 indicated that many pathway enzymes found in other organisms for the degradation of taurine are represented, but that a novel, apparently energy-dependent pathway is involved in the conversion of acetyl phosphate to acetyl CoA. Thus, an ABC transporter for taurine could be postulated, while inducible taurine: pyruvate aminotransferase, alanine dehydrogenase, sulfoacetaldehyde acetyltransferase and sulfite dehydrogenase could be assayed. Whereas phosphate acetyltransferase has been found in other organisms, none was indicated in the genome sequence and no activity was found in cell-free extracts. Instead, acetate kinase was active as was acetate-CoA ligase. PMID:17425660

Baldock, Marijke I; Denger, Karin; Smits, Theo H M; Cook, Alasdair M

2007-04-10

222

Genome Sequence of the Ethene- and Vinyl Chloride-Oxidizing Actinomycete Nocardioides sp Strain JS614  

SciTech Connect

Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium.

Coleman, Nicholas V [University of Sydney, Australia; Wilson, Neil L [University of Sydney, Australia; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Han, Shunsheng [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Israni, Sanjay [U.S. Department of Energy, Joint Genome Institute; Kim, Edwin [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Larimer, Frank W [ORNL; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Richardson, Paul [U.S. Department of Energy, Joint Genome Institute; Schmutz, Jeremy [Stanford University; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Thompson, Sue [Los Alamos National Laboratory (LANL); Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Spain, Jim C [Georgia Institute of Technology; Gossett, James G [Cornell University; Mattes, Timothy E [University of Iowa

2011-01-01

223

Derivatization of bioactive carbazoles by the biphenyl-degrading bacterium Ralstonia sp. strain SBUG 290  

Microsoft Academic Search

Different 9H-carbazole derivatives have been investigated within the last decades due to their broad range of pharmacological applications.\\u000a While the metabolism of 9H-carbazole has previously been reported, nothing was known about the bacterial transformation of 2,3,4,9-tetrahydro-1H-carbazole and 9-methyl-9H-carbazole. Thus, for the first time, the bacterial biotransformation of 2,3,4,9-tetrahydro-1H-carbazole and 9-methyl-9H-carbazole was analyzed using biphenyl-grown cells of Ralstonia sp. strain SBUG

Doreen Waldau; Annett Mikolasch; Michael Lalk; Frieder Schauer

2009-01-01

224

[Bioflocculant producing capability by two strains of Bacillus sp. in diversified carbon sources].  

PubMed

Two strains of Bacillus sp. F2 and F6 could produce bioflocculants with high flocculating effects by pure culture and mixed culture. Many kinds of carbon sources could be utilized. Organic compound which molecular weight under 200 such as saccharide, alcoholic aldehyde, ester and organic acid were favorable for producing bioflocculant. And some low-cost biomass scrap could be used as good carbon sources for industrialized production of bioflocculants, such as waste beet molasses, cellulose's fermentation residue and sewage of hydrogen producing reactor. PMID:16366489

Zhu, Yan-Bin; Ma, Fang; Ren, Nan-Qi; Huang, Jun-Li; Wang, Ai-Jie

2005-09-01

225

Abenquines A-D: aminoquinone derivatives produced by Streptomyces sp. strain DB634.  

PubMed

New bioactive secondary metabolites, called abenquines, were found in the fermentation broth of Streptomyces sp. strain DB634, which was isolated from the soils of the Chilean highland of the Atacama Desert. They are composed of an amino acid linked to an N-acetyl-aminobenzoquinone. Isolation of the abenquines (1-4), their structure elucidation by NMR analysis and MS, as well as the kinetics of their production are presented. The abenquines show inhibitory activity against bacteria, dermatophytic fungi and phosphodiesterase type 4b. The amino acid attached to the quinone is relevant to the enzyme inhibitory activity. PMID:21952099

Schulz, Dirk; Beese, Pascal; Ohlendorf, Birgit; Erhard, Arlette; Zinecker, Heidi; Dorador, Cristina; Imhoff, Johannes F

2011-09-28

226

Three-dimensional structure of the regularly constructed surface layer from Synechocystis sp. strain CLII.  

PubMed Central

The isolated, outermost cell wall layer from Synechocystis sp. strain CLII is described using electron microscopy and Fourier reconstruction to study the three-dimensional structure of the proteins within the layer to a resolution of ca. 3 nm. This surface layer forms regular hexagonal arrays (a = b = 15.2 nm). The two-dimensional space group is p6. The monomer proteins form hexamers arranged around a central hollow cylinder. The linkers between the hexamers are of the delta type and are located approximately in the central section between the top and bottom of the protein layer. Images

Karlsson, B; Vaara, T; Lounatmaa, K; Gyllenberg, H

1983-01-01

227

Biosynthesis of poly(?- l -lysine)s in two newly isolated strains of Streptomyces sp  

Microsoft Academic Search

The biosynthesis of poly(?-l-lysine) (?-PL) in the two newly isolated strains of Streptomyces\\u000a lydicus USE-11 (USE-11) and Streptomyces sp. USE-51 (USE-51) was studied by a newly developed two-stage culture method of cell growth at pH 6.8 and ?-PL production at pH 4.5. USE-11 synthesized ?-PL consisting of about 28 residues at a high production level, whereas USE-51 did the polymer with 15

Hideo Hirohara; Munenori Takehara; Masayuki Saimura; Atsushi Masayuki; Masahiro Miyamoto

2006-01-01

228

Purification, biochemical characterization and gene sequencing of a thermostable raw starch digesting ?-amylase from Geobacillus thermoleovorans subsp. stromboliensis subsp. nov  

Microsoft Academic Search

This study reports the purification and biochemical characterization of a raw starch-digesting ?-amylase from Geobacillus thermoleovorans subsp. stromboliensis subsp. nov. (strain PizzoT). The molecular weight was estimated to be 58 kDa by SDS–PAGE. The enzyme was highly active over a wide range of pH from\\u000a 4.0–10.0. The optimum temperature of the enzyme was 70°C. It showed extreme thermostability in the presence

Ilaria Finore; Ceyda Kasavi; Annarita Poli; Ida Romano; Ebru Toksoy Oner; Betul Kirdar; Laura Dipasquale; Barbara Nicolaus; Licia Lama

229

Purification and structure elucidation of antifungal and antibacterial activities of newly isolated Streptomyces sp. strain US80  

Microsoft Academic Search

A new actinomycete strain, designated US80 and producing antimicrobial activities against Gram-positive and Gram-negative bacteria and fungi, was isolated from Tunisian oasis soil. Cultural characteristic studies strongly suggested that this strain belongs to the genus Streptomyces. The nucleotide sequence of the 16S rRNA gene (1517 pb) of Streptomyces sp. strain US80 exhibited close similarity (97–98%) with other Streptomyces 16S rRNA

Lilia Fourati-Ben Fguira; Serge Fotso; Raoudha Ben Ameur-Mehdi; Lotfi Mellouli; Hartmut Laatsch

2005-01-01

230

Characterization of Gordonia sp. strain F.5.25.8 capable of dibenzothiophene desulfurization and carbazole utilization  

Microsoft Academic Search

A dibenzothiophene (DBT)-degrading bacterial strain able to utilize carbazole as the only source of nitrogen was identified as Gordonia sp. F.5.25.8 due to its 16S rRNA gene sequence and phenotypic characteristics. Gas chromatography (GC) and GC–mass spectroscopy analyses showed that strain F.5.25.8 transformed DBT into 2-hydroxybiphenyl (2-HBP). This strain was also able to grow using various organic sulfur or nitrogen

S. C. C. Santos; D. S. Alviano; C. S. Alviano; M. Pádula; A. C. Leitão; O. B. Martins; C. M. S. Ribeiro; M. Y. M. Sassaki; C. P. S. Matta; J. Bevilaqua; G. V. Sebastián; L. Seldin

2006-01-01

231

ISOLATION, IDENTIFICATION AND PARTIAL CHARACTERIZATION OF THE PROBIOTIC PROPERTIES OF Lactobacillus sp. STRAINS OBTAINED FROM THE GASTROINTESTINAL TRACT OF BROILERS  

Microsoft Academic Search

Isolation of different strains of Lactobacillus sp. from the gastrointestinal tract (GIT) of broilers was carried out aiming to make a preliminary selection and identification of those strains which could resist the main natural barriers in the digestive flow: acid pH (pH 2) and bile salts (1.5 g L -1 of Ox-biles). As result, 20 strains with probiotic activity potential

TECNOLOGÍA TECNOLOGÍA

2008-01-01

232

Properties of Mutants of Synechocystis sp. Strain PCC 6803 Lacking Inorganic Carbon Sequestration Systems  

SciTech Connect

A mutant ( 5) of Synechocystis sp. strain PCC 6803 constructed by inactivating five inorganic carbon sequestration systems did not take up CO2 or HCO3– and was unable to grow in air with or without glucose. The 4 mutant in which BicA is the only active inorganic carbon sequestration system showed low activity of HCO3– uptake and grew under these conditions but more slowly than the wild-type strain. The 5 mutant required 1.7% CO2 to attain half the maximal growth rate. Electron transport activity of the mutants was strongly inhibited under high light intensities, with the 5 mutant more susceptible to high light than the 4 mutant. The results implicated the significance of carbon sequestration in dissipating excess light energy.

Xu, Min; Bernat, Gabor; Singh, Abhay K.; Mi, Hualing; Rogner, Matthias; Pakrasi, Himadri B.; Ogawa, Teruo

2008-09-10

233

Global proteomic analysis of the chromate response in Arthrobacter sp strain FB24.  

SciTech Connect

A global proteomic evaluation of the response of Arthrobacter sp. strain FB24 to 5 and 20 mM Cr(VI) was conducted using both two-dimensional gel electrophoresis (2-DGE) and liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS). The changes in protein expression found with 2-DGE indicate alterations in central metabolism and amino acid synthesis. Proteome coverage increased from 22% with 2-DGE to 71% with LC/LC-MS/MS. The proteins exhibiting the highest levels of expression under Cr(VI) stress suggest intracellular sulfur limitation, which could be driven by competition for the sulfate (SO{sub 4}{sup 2-}) transporter by the chromate (CrO{sub 4}{sup 2-}) ion. These results are consistent with the growth defects seen with strain FB24 when Cr(VI) concentrations exceeded 5 mM.

Henne, K. L.; Turse, J. E.; Nicora, C. D.; Lipton, M. S.; Tollaksen, S. L.; Lindberg, C.; Babnigg, G.; Giometti, C. S.; Nakatsu, C. H.; Thompson, D. K.; Konopka, A. E.; Biosciences Division; Purdue Univ.; PNNL

2009-04-01

234

Posttranslational Regulation of Nitrate Assimilation in the Cyanobacterium Synechocystis sp. Strain PCC 6803  

PubMed Central

Posttranslational regulation of nitrate assimilation was studied in the cyanobacterium Synechocystis sp. strain PCC 6803. The ABC-type nitrate and nitrite bispecific transporter encoded by the nrtABCD genes was completely inhibited by ammonium as in Synechococcus elongatus strain PCC 7942. Nitrate reductase was insensitive to ammonium, while it is inhibited in the Synechococcus strain. Nitrite reductase was also insensitive to ammonium. The inhibition of nitrate and nitrite transport required the PII protein (glnB gene product) and the C-terminal domain of NrtC, one of the two ATP-binding subunits of the transporter, as in the Synechococcus strain. Mutants expressing the PII derivatives in which Ala or Glu is substituted for the conserved Ser49, which has been shown to be the phosphorylation site in the Synechococcus strain, showed ammonium-promoted inhibition of nitrate uptake like that of the wild-type strain. The S49A and S49E substitutions in GlnB did not affect the regulation of the nitrate and nitrite transporter in Synechococcus either. These results indicated that the presence or absence of negative electric charge at the 49th position does not affect the activity of the PII protein to regulate the cyanobacterial ABC-type nitrate and nitrite transporter according to the cellular nitrogen status. This finding suggested that the permanent inhibition of nitrate assimilation by an S49A derivative of PII, as was previously reported for Synechococcus elongatus strain PCC 7942, is likely to have resulted from inhibition of nitrate reductase rather than the nitrate and nitrite transporter.

Kobayashi, Masaki; Takatani, Nobuyuki; Tanigawa, Mari; Omata, Tatsuo

2005-01-01

235

Synechocystis sp PCC 6803 strains lacking photosystem I and phycobilisome function.  

PubMed Central

To design an in vivo system allowing detailed analysis of photosystem II (PSII) complexes without significant interference from other pigment complexes, part of the psaAB operon coding for the core proteins of photosystem I (PSI) and part of the apcE gene coding for the anchor protein linking the phycobilisome to the thylakoid membrane were deleted from the genome of the cyanobacterium Synechocystis sp strain PCC 6803. Upon transformation and segregation at low light intensity (5 microE m-2 sec-1), a PSI deletion strain was obtained that is light tolerant and grows reasonably well under photoheterotrophic conditions at 5 microE m-2 sec-1 (doubling time approximately 28 hr). Subsequent inactivation of apcE by an erythromycin resistance marker led to reduction of the phycobilin-to-chlorophyll ratio and to a further decrease in light sensitivity. The resulting PSI-less/apcE- strain grew photoheterotrophically at normal light intensity (50 microE m-2 sec-1) with a doubling time of 18 hr. Deletion of apcE in the wild type resulted in slow photoautotrophic growth. The remaining phycobilins in apcE- strains were inactive in transferring light energy to PSII. Cells of both the PSI-less and PSI-less/apcE- strains had an approximately sixfold enrichment of PSII on a chlorophyll basis and were as active in oxygen evolution (on a per PSII basis) as the wild type at saturating light intensity. Both PSI-less strains described here are highly appropriate both for detailed PSII studies and as background strains to analyze site- and region-directed PSII mutants in vivo.

Shen, G; Boussiba, S; Vermaas, W F

1993-01-01

236

Complete detoxification of tris(2-chloroethyl) phosphate by two bacterial strains: Sphingobium sp. strain TCM1 and Xanthobacter autotrophicus strain GJ10.  

PubMed

Tris(2-chloroethyl) phosphate (TCEP), a flame retardant, is recently regarded as a potentially toxic and persistent environmental contaminant. We previously isolated TCEP-degrading bacterium, Sphingobium sp. strain TCM1, which, however, produced a toxic metabolite: 2-chloroethanol (2-CE). This study was undertaken to develop a detoxification technique of TCEP using strain TCM1 with a 2-CE-degrading bacterium: Xanthobacter autotrophicus strain GJ10. TCEP degradation by strain TCM1-resting cells was thermally stable for 30 min at 30 °C. It was optimal at 30 °C and at pH 8.5. In the optimum condition, TCM1 cells up to a final cell density of 0.8 at OD(660) in the reaction mixture were unable to hydrolyze the phosphotriester bonds of 10 ?M TCEP completely. The addition of 50 ?M Co(2+) to reaction mixture enhanced the hydrolysis and caused the complete hydrolysis at the cell density of 0.8. Strain GJ10 resting cells degraded 2-CE only slightly, which might be attributable to lack of coenzyme regeneration of enzymes involved in the degradation. In contrast, the growing cells degraded approximately 180 ?M of 2-CE within 24 h. Based on these results, we designed a two-step TCEP detoxification reaction consisting of TCEP hydrolysis to 2-CE by strain TCM1-resting cells and the following degradation of the resulting 2-CE by strain GJ10-growing cells. The combined reaction completely detoxified 10 ?M TCEP, and thus opens a way to microbial detoxification of the potential toxic, persistent organophosphorus compound. PMID:22578591

Takahashi, Shouji; Miura, Kaneharu; Abe, Katsumasa; Kera, Yoshio

2012-05-10

237

Purification and Characterization of a Glycoside Hydrolase Family 43 ?-xylosidase from Geobacillus thermoleovorans IT08  

Microsoft Academic Search

The gene encoding a glycoside hydrolase family 43 ?-xylosidase (GbtXyl43A) from the thermophilic bacterium Geobacillus thermoleovorans strain IT-08 was synthesized and cloned with a C-terminal His-tag into a pET29b expression vector. The recombinant gene product\\u000a termed GbtXyl43A was expressed in Escherichia coli and purified to apparent homogeneity. Michaelis–Menten kinetic parameters were obtained for the artificial substrates p-nitrophenyl-?-d-xylopyranose (4NPX) and p-nitrophenyl-?-l-arabinofuranose

Kurt Wagschal; Chamroeun Heng; Charles C. Lee; George H. Robertson; William J. Orts; Dominic W. S. Wong

2009-01-01

238

A Novel Nitrate/Nitrite Permease in the Marine Cyanobacterium Synechococcus sp. Strain PCC 7002  

PubMed Central

The nrtP and narB genes, encoding nitrate/nitrite permease and nitrate reductase, respectively, were isolated from the marine cyanobacterium Synechococcus sp. strain PCC 7002 and characterized. NrtP is a member of the major facilitator superfamily and is unrelated to the ATP-binding cassette-type nitrate transporters that previously have been described for freshwater strains of cyanobacteria. However, NrtP is similar to the NRT2-type nitrate transporters found in diverse organisms. An nrtP mutant strain consumes nitrate at a 4.5-fold-lower rate than the wild type, and this mutant grew exponentially on a medium containing 12 mM nitrate at a rate approximately 2-fold lower than that of the wild type. The nrtP mutant cells could not consume nitrite as rapidly as the wild type at pH 10, suggesting that NrtP also functions in nitrite uptake. A narB mutant was unable to grow on a medium containing nitrate as a nitrogen source, although this mutant could grow on media containing urea or nitrite with rates similar to those of the wild type. Exogenously added nitrite enhanced the in vivo activity of nitrite reductase in the narB mutant; this suggests that nitrite acts as a positive effector of nitrite reductase. Transcripts of the nrtP and narB genes were detected in cells grown on nitrate but were not detected in cells grown on urea or ammonia. Transcription of the nrtP and narB genes is probably controlled by the NtcA transcription factor for global nitrogen control. The discovery of a nitrate/nitrite permease in Synechococcus sp. strain PCC 7002 suggests that significant differences in nutrient transporters may occur in marine and freshwater cyanobacteria.

Sakamoto, Toshio; Inoue-Sakamoto, Kaori; Bryant, Donald A.

1999-01-01

239

Chemotaxis of Burkholderia sp. Strain SJ98 towards chloronitroaromatic compounds that it can metabolise  

PubMed Central

Background Burkholderia sp. strain SJ98 is known for its chemotaxis towards nitroaromatic compounds (NACs) that are either utilized as sole sources of carbon and energy or co-metabolized in the presence of alternative carbon sources. Here we test for the chemotaxis of this strain towards six chloro-nitroaromatic compounds (CNACs), namely 2-chloro-4-nitrophenol (2C4NP), 2-chloro-3-nitrophenol (2C3NP), 4-chloro-2-nitrophenol (4C2NP), 2-chloro-4-nitrobenzoate (2C4NB), 4-chloro-2-nitrobenzoate (4C2NB) and 5-chloro-2-nitrobenzoate (5C2NB), and examine its relationship to the degradation of such compounds. Results Strain SJ98 could mineralize 2C4NP, 4C2NB and 5C2NB, and co-metabolically transform 2C3NP and 2C4NB in the presence of an alternative carbon source, but was unable to transform 4C2NP under these conditions. Positive chemotaxis was only observed towards the five metabolically transformed CNACs. Moreover, the chemotaxis was induced by growth in the presence of the metabolisable CNAC. It was also competitively inhibited by the presence of nitroaromatic compounds (NACs) that it could metabolise but not by succinate or aspartate. Conclusions Burkholderia sp. strain SJ98 exhibits metabolic transformation of, and inducible chemotaxis towards CNACs. Its chemotactic responses towards these compounds are related to its previously demonstrated chemotaxis towards NACs that it can metabolise, but it is independently inducible from its chemotaxis towards succinate or aspartate.

2012-01-01

240

The Biosynthetic Pathway for Myxol-2? Fucoside (Myxoxanthophyll) in the Cyanobacterium Synechococcus sp. Strain PCC 7002? †  

PubMed Central

Synechococcus sp. strain PCC 7002 produces a variety of carotenoids, which comprise predominantly dicylic ?-carotene and two dicyclic xanthophylls, zeaxanthin and synechoxanthin. However, this cyanobacterium also produces a monocyclic myxoxanthophyll, which was identified as myxol-2? fucoside. Compared to the carotenoid glycosides produced by diverse microorganisms, cyanobacterial myxoxanthophyll and closely related compounds are unusual because they are glycosylated on the 2?-OH rather than on the 1?-OH position of the ? end of the molecule. In this study, the genes encoding two enzymes that modify the ? end of myxoxanthophyll in Synechococcus sp. strain PCC 7002 were identified. Mutational and biochemical studies showed that open reading frame SynPCC7002_A2032, renamed cruF, encodes a 1?-hydroxylase and that open reading frame SynPCC7002_A2031, renamed cruG, encodes a 2?-O-glycosyltransferase. The enzymatic activity of CruF was verified by chemical characterization of the carotenoid products synthesized when cruF was expressed in a lycopene-producing strain of Escherichia coli. Database searches showed that homologs of cruF and cruG occur in the genomes of all sequenced cyanobacterial strains that are known to produce myxol or the acylic xanthophyll oscillaxanthin. The genomes of many other bacteria that produce hydroxylated carotenoids but do not contain crtC homologs also contain cruF orthologs. Based upon observable intermediates, a complete biosynthetic pathway for myxoxanthophyll is proposed. This study expands the suite of enzymes available for metabolic engineering of carotenoid biosynthetic pathways for biotechnological applications.

Graham, Joel E.; Bryant, Donald A.

2009-01-01

241

Enhanced degradation of 2-nitrotoluene by immobilized cells of Micrococcus sp. strain SMN-1.  

PubMed

Nitrotoluenes are the toxic pollutants of the environment because of their large scale use in the production of explosives. Biodegradation of such chemicals by microorganisms may provide an effective method for their detoxification. We have studied the degradation of 2-nitrotoluene by cells of Micrococcus sp. strain SMN-1 immobilized in various matrices such as polyurethane foam (PUF), sodium alginate (SA), sodium alginate-polyvinyl alcohol (SA-PVA), agar and polyacrylamide. The rate of degradation of 15 and 30 mM 2-nitrotoluene by freely suspended cells and immobilized cells in batches and fed-batch with shaken cultures were compared. The PUF-immobilized cells achieved higher degradation of 15 and 30 mM 2-nitrotoluene than freely suspended cells and the cells immobilized in SA-PVA, polyacrylamide, SA and agar. The PUF-immobilized cells could be reused more than 24 cycles without loosing their degradation capacity and showed more tolerance to pH and temperature changes than freely suspended cells. These results revealed the enhanced rate of degradation of 2-nitrotoluene by PUF-immobilized cells of Micrococcus sp. strain SMN-1. PMID:23153775

Mulla, Sikandar I; Talwar, Manjunatha P; Bagewadi, Zabin K; Hoskeri, Robertcyril S; Ninnekar, Harichandra Z

2012-11-13

242

Physiological factors affecting carbon tetrachloride dehalogenation by the denitrifying bacterium Pseudomonas sp. strain KC.  

PubMed Central

Pseudomonas sp. strain KC was grown on a medium with a low content of transition metals in order to examine the conditions for carbon tetrachloride (CT) transformation. Several carbon sources, including acetate, glucose, glycerol, and glutamate, were able to support CT transformation. The chelators 2,2'-dipyridyl and 1,10-phenanthroline stimulated CT transformation in a rich medium that otherwise did not support this activity. Low (< 10 microM) additions of dissolved iron(II), iron(III), and cobalt(II), as well as an insoluble iron(III) compound, ferric oxyhydroxide, inhibited CT transformation. The addition of 50 microM iron to actively growing cultures resulted in delayed inhibition of CT transformation. CT transformation was seen in aerobic cultures of KC, but with reduced efficiency compared with denitrifying cultures. Inhibition of CT transformation by iron was also seen in aerobically grown cultures. Optimal conditions were used in searching for effective CT transformation activity among denitrifying enrichments grown from samples of aquifer material. No activity comparable to that of Pseudomonas sp. strain KC was found among 16 samples tested.

Lewis, T A; Crawford, R L

1993-01-01

243

Characterization of a novel long-chain n-alkane-degrading strain, Dietzia sp. E1.  

PubMed

The newly isolated strain E1, identified as a Dietzia sp., proved to have an excellent ability to degrade n-C12 to n-C38 alkane components of crude oil. The preferred substrate was the very long-chain alkane n-eicosane at an optimal temperature of 37 degrees C and an optimal pH of 8 under aerobic conditions. The growth and substrate uptake kinetics were monitored during the n-alkane fermentation process, and Dietzia sp. E1 cells were found to possess three distinct levels of cell-surface hydrophobicity. Gas chromatographic/mass spectrometric analysis revealed that intracellular substrate mineralization occurred through the conversion of n-alkane to the corresponding n-alkanal. The monoterminal oxidation pathway was presumably initiated by AlkB and CYP153 terminal alkane hydroxylases, both of their partial coding sequences were successfully detected in the genome of strain E1, a novel member of the Dietzia genus. PMID:21319712

Bihari, Zoltán; Szabó, Zsolt; Szvetnik, Attila; Balázs, Margit; Bartos, Péter; Tolmacsov, Péter; Zombori, Zoltán; Kiss, István

244

Metabolism of dibenzo-p-dioxin by Sphingomonas sp. strain RW1.  

PubMed Central

In the course of our screening for dibenzo-p-dioxin-utilizing bacteria, a Sphingomonas sp. strain was isolated from enrichment cultures inoculated with water samples from the river Elbe. The isolate grew with both the biaryl ethers dibenzo-p-dioxin and dibenzofuran (DF) as the sole sources of carbon and energy, showing doubling times of about 8 and 5 h, respectively. Biodegradation of the two aromatic compounds initially proceeded after an oxygenolytic attack at the angular position adjacent to the ether bridge, producing 2,2',3-trihydroxydiphenyl ether or 2,2',3-trihydroxybiphenyl from the initially formed dihydrodiols, which represent extremely unstable hemiacetals. Results obtained from determinations of enzyme activities and oxygen consumption suggest meta cleavage of the trihydroxy compounds. During dibenzofuran degradation, hydrolysis of 2-hydroxy-6-oxo-6-(2-hydroxyphenyl)-hexa-2,4-dienoate yielded salicylate, which was branched into the catechol meta cleavage pathway and the gentisate pathway. Catechol obtained from the product of meta ring fission of 2,2',3-trihydroxydiphenyl ether was both ortho and meta cleaved by Sphingomonas sp. strain RW1 when this organism was grown with dibenzo-p-dioxin.

Wittich, R M; Wilkes, H; Sinnwell, V; Francke, W; Fortnagel, P

1992-01-01

245

Oxidative Pathway from Squalene to Geranylacetone in Arthrobacter sp. Strain Y-11  

PubMed Central

The reaction pathway from squalene to trans-geranylacetone in Arthrobacter sp. strain Y-11 was studied. The enzyme or enzymes catalyzing squalene degradation were found to be membrane bound. Stoichiometric analysis of a cell-free system revealed that the ratio of squalene to trans-geranylacetone changed from 1:2 to 1:1 as the reaction proceeded, indicating two steps in geranylacetone formation. The initial step was found to be oxygenase catalyzed, from the absolute requirement for molecular oxygen in geranylacetone formation and the incorporation of 18O into geranylacetone under 18O2 atmosphere. By using [3H]squalene as the substrate, we detected an intermediate in the pathway and identified it as 5,9,13-trimethyltetradeca-4,8,12-trienoic acid by mass spectrometry, infrared spectrometry, nuclear magnetic resonance spectrometry, and chemical synthesis. We deduced that squalene was first oxidatively cleaved to geranylacetone and the intermediate, and that the intermediate was further metabolized to geranylacetone. We also synthesized some of the presumptive metabolites, such as 4,8,12-trimethyltrideca-4,8,12-trien-2-one, and confirmed that they served as active precursors for geranylacetone formation. Based on these lines of evidence, we present here the pathway from squalene to trans-geranylacetone in Arthrobacter sp. strain Y-11.

Ikeguchi, Naoki; Nihira, Takuya; Kishimoto, Atsuko; Yamada, Yasuhiro

1988-01-01

246

Impact of bio-augmentation with Sphingomonas sp. strain TTNP3 in membrane bioreactors degrading nonylphenol.  

PubMed

This study evaluates the potential of bio-augmentation to improve the degradation of recalcitrant nonylphenol during the wastewater treatment in membrane bioreactors (MBR). One MBR containing activated sludge was bio-augmented using multistep inoculation with freeze dried Sphingomonas sp. strain TTNP3, whereas a second control reactor contained activated sludge solely. The (14)C-labeled-nonylphenol isomer (4-[1-ethyl-1,3-dimethylpentyl]phenol) was applied as a single pulse. Bio-augmentation resulted in an immediate increase of dissolved radioactivity in the effluent in comparison to the control reactor (13% and 2% of initially applied radioactivity after 1 day, respectively). After 5 days of operation, the retentate of the bio-augmented reactor contained only 7% of the initial radioactivity in contrast to 50% in the control reactor. The radioactivity associated to the mixed liquor suspended solids, i.e., the suspension of biomass and other solids on the retentate side of the membrane, was mainly found as non-extractable residues that were increasingly formed during prolonged reactor operation, especially for the control MBR. HPLC-LSC and GC-MS(n) analyses revealed that the bio-augmented reactor produced more polar hydroquinone as main degradation intermediate, whereas the control reactor effluent contained a complex mixture of apolar compounds with shortened oxidized alkyl chains. Thus, the apparent differences in the behavior of nonylphenol between the reactors were due to the catabolism of nonylphenol conferred by bio-augmentation with Sphingomonas sp. strain TTNP3. PMID:19495744

Cirja, Magdalena; Hommes, Gregor; Ivashechkin, Pavel; Prell, Jürgen; Schäffer, Andreas; Corvini, Philippe F X; Lenz, Markus

2009-06-04

247

Pyruvate carboxylase is involved in metabolism of mimosine by Rhizobium sp. strain TAL1145.  

PubMed

The objective of this study was to determine the role of midK, which encodes a protein similar to pyruvate carboxylase, in mimosine degradation by Rhizobium sp. strain TAL1145. The midK gene is located downstream of midR in the cluster of genes for mimosine degradation in Rhizobium sp. strain TAL1145. The midK mutants of TAL1145 degraded mimosine slower than the wild-type. These mutants could utilize pyruvate as a source of carbon, indicating that there is another pyruvate carboxylase (pyc) gene in TAL1145. Two classes of clones were isolated from the library of TAL1145 by complementing a pyc mutant of Rhizobium etli, one class contained midK, while the other carried pyc. Both midK and pyc of TAL1145 complemented the midK mutant for mimosine degradation, and also the R. etli pyc mutant for pyruvate utilization. The midK-encoded pyruvate carboxylase was required for an efficient conversion of mimosine into 3-hydroxy-4-pyridone (HP). PMID:18493742

Awaya, Jonathan D; Tittabutr, Panlada; Li, Qing X; Borthakur, Dulal

2008-05-21

248

Continuous degradation of trichloroethylene by Xanthobacter sp. strain Py2 during growth on propene  

SciTech Connect

Propene-grown Xanthobacter sp. strain Py2 cells can degrade trichloroethylene (TCE), but the transformation capacity of such cells was limited and depended on both the TCE concentration and the biomass concentration. Toxic metabolites presumably accumulated extracellularly, because the fermentation of glucose by yeast cells was inhibited by TCE degradation products formed by strain Py2. The affinity of the propene monooxygenase for TCE was low, and this allowed strain Py2 to grow on propene in the presence of TCE. During batch growth with propene and TCE, the TCE was not degraded before most of the propene had been consumed. Continuous degradation of TCE in a chemostat culture of strain Py2 growing with propene was observed with TCE concentrations up to 206 {mu}M in the growth medium without washout of the fermentor occurring. At this TCE concentration the specific degradation rate was 1.5 nmol/min/mg of biomass. The total amount of TCE that could be degraded during simultaneous growth on propene depended on the TCE concentration and ranged from 0.03 to 0.34 g of TCE per g of biomass. The biomass yield on propene was not affected by the cometabolic degradation of TCE. 23 refs., 5 figs., 2 tabs.

Reij, M.W.; Kieboom, J.; De Bont, J.A.M.; Hartmans, S. [Wageningen Agricultural Univ. (Netherlands)

1995-08-01

249

Dominant colonization and inheritance of Methylobacterium sp. strain OR01 on perilla plants.  

PubMed

Pink-pigmented facultative methylotrophs (PPFMs) are major inhabitants of the phyllosphere. In a preceding study, we found that perilla plants harbor a dominant population of PPFMs on their leaves and seeds, and that the closest relative of PPFMs (Methylobacterium sp. strain OR01 as representative strain) isolated from red perilla seeds was M. fujisawaense DSM5686(T). In the present study, the specific interaction between red perilla and Methylobacterium species was investigated. All the PPFMs isolated from red perilla seeds harvested in the Ohara area of Kyoto, Japan in 2009, 2010, and 2011 and the PPFMs isolated from red perilla leaves planted at four geographically different places in Japan had 16S rRNA sequences identical to that of strain OR01. Direct transmission of PPFMs from seeds to leaves and the competitiveness of strain OR01 were confirmed. This report is the first step toward understanding the species-level specificity of the interaction between perilla plants and Methylobacterium species. PMID:23832351

Mizuno, Masayuki; Yurimoto, Hiroya; Iguchi, Hiroyuki; Tani, Akio; Sakai, Yasuyoshi

2013-07-07

250

Metabolism of dibenzofuran by pseudomonas sp. strain HH69 and the mixed culture HH27  

SciTech Connect

A Pseudomonas sp. strain, HH69, and a mixed culture, designated HH27, were isolated by selective enrichment from soil samples. The pure strain and the mixed culture grew aerobically on dibenzofuran as the sole source of carbon and energy. Degradation proceeded via salicylic acid which was branched into the gentisic acid and the catechol pathway. Both salicylic acid and gentisic acid accumulated in the culture medium of strain HH69. The acids were slowly metabolized after growth ceased. The enzymes responsible for their metabolism showed relatively low activities. Besides the above-mentioned acids, 2-hydroxyacetophenone, benzopyran-4-one (chrome), several 2-substituted chroman-4-ones, and traces of the four isomeric monohydroxydibenzofurans were identified in the culture medium. 2,2{prime},3-Trihydroxybiphenyl was isolated from the medium of a dibenzofuran-converting mutant derived from parent strain HH69, which can no longer grow on dibenzofuran. This gives evidence for a novel type of dioxygenases responsible for the attack on the biarylether structure of the dibenzofuran molecule. A meta-fission mechanism for cleavage of the dihydroxylated aromatic nucleus of 2,2{prime},3-trihydroxybiphenyl is suggested as the next enzymatic step in the degradative pathway.

Fortnagel, P.; Harms, H.; Wittich, R.M. (Institut fuer Allgemeine Botanik, Ohnhorststrasse (Germany, F.R.)); Krohn, S.; Meyer, H.; Sinnwell, V.; Wilkes, H.; Francke, W. (Universitaet Hamburg (Germany, F.R.))

1990-04-01

251

Aerobic and Anaerobic Toluene Degradation by a Newly Isolated Denitrifying Bacterium, Thauera sp. Strain DNT-1  

PubMed Central

A newly isolated denitrifying bacterium, Thauera sp. strain DNT-1, grew on toluene as the sole carbon and energy source under both aerobic and anaerobic conditions. When this strain was cultivated under oxygen-limiting conditions with nitrate, first toluene was degraded as oxygen was consumed, while later toluene was degraded as nitrate was reduced. Biochemical observations indicated that initial degradation of toluene occurred through a dioxygenase-mediated pathway and the benzylsuccinate pathway under aerobic and denitrifying conditions, respectively. Homologous genes for toluene dioxygenase (tod) and benzylsuccinate synthase (bss), which are the key enzymes in aerobic and anaerobic toluene degradation, respectively, were cloned from genomic DNA of strain DNT-1. The results of Northern blot analyses and real-time quantitative reverse transcriptase PCR suggested that transcription of both sets of genes was induced by toluene. In addition, the tod genes were induced under aerobic conditions, whereas the bss genes were induced under both aerobic and anaerobic conditions. On the basis of these results, it is concluded that strain DNT-1 modulates the expression of two different initial pathways of toluene degradation according to the availability of oxygen in the environment.

Shinoda, Yoshifumi; Sakai, Yasuyoshi; Uenishi, Hiroshi; Uchihashi, Yasumitsu; Hiraishi, Akira; Yukawa, Hideaki; Yurimoto, Hiroya; Kato, Nobuo

2004-01-01

252

Safety evaluation of a thermolysin enzyme produced from Geobacillus stearothermophilus.  

PubMed

Thermolysin is a zinc metalloprotease that has potential uses in the food industry. The safety of thermolysin has not been demonstrated before, and therefore a series of standard toxicological tests to assess its potential toxicity was undertaken. The thermolysin used in this study was derived from the thermophilic bacterium Geobacillus stearothermophilus, which had undergone chemical mutagenesis to generate strains with increased thermolysin production. Acute toxicity studies in rats and mice showed that thermolysin powder is not acutely toxic with an oral LD50 of more than 18,000 mg/kg (2520 mg/kg thermolysin protein) in rats and more than 24,000 mg/kg (3360 mg/kg protein) in mice. Subchronic feeding studies in rats for 91 days at doses up to 1000 mg/kg (390 mg/kg protein) revealed no significant differences between treated and non-treated groups and a No Observed Effect Level (NOEL) of 1000 mg/kg (390 mg/kg protein) per day was established. Results from genotoxicity tests such as in vitro chromosomal aberration assay and in vivo mouse micronucleus were negative. Allergenicity sequence analysis revealed no evidence suggesting that thermolysin is an allergen. The data presented in this study support the conclusion that thermolysin is safe for use in food production. PMID:23831195

Ke, Qingdong; Chen, Alice; Minoda, Masashi; Yoshida, Hiromichi

2013-07-03

253

High-Level Chromate Resistance in Arthrobacter sp. strain FB24 Requires Previously Uncharacterized Accessory Genes  

SciTech Connect

The annotated genome sequence of Arthrobacter sp. strain FB24 revealed a chromate resistance determinant (CRD): a cluster of 8 genes located on a 10.6 kb fragment of a 96 kb plasmid. The CRD includes chrA, which encodes a putative chromate efflux protein, and three genes with amino acid similarities to the amino and carboxy termini of ChrB, a putative regulatory protein. There are also three novel genes that have not been previously associated with chromate resistance in other bacteria; they encode an oxidoreductase (most similar to malate:quinone oxidoreductase), a functionally unknown protein with a WD40 repeat domain and a lipoprotein. A chromate-sensitive mutant (strain D11) was generated by curing FB24 of its 96-kb plasmid. Elemental analysis indicated that chromate-exposed cells of strain D11 accumulated three times more chromium than strain FB24. Introduction of the CRD into strain D11 conferred chromate resistance comparable to wild-type levels, whereas deletion of specific regions of the CRD led to decreased resistance. Using real-time reverse transcriptase PCR, we show that expression of each gene within the CRD is specifically induced in response to chromate but not by lead, hydrogen peroxide or arsenate. Higher levels of chrA expression were achieved when the chrB orthologs and the WD40 repeat domain genes were present, suggesting their regulatory roles. Collectively, our findings indicate that chromate resistance in strain FB24 is primarily achieved by plasmid-mediated chromate efflux with the contribution of previously unrecognized accessory genes.

Henne, Kristene L.; Nakatsu, Cindy N.; Thompson, Dorothea K.; Konopka, Allan

2009-09-24

254

Genetic transformation of Geobacillus kaustophilus HTA426 by conjugative transfer of host-mimicking plasmids.  

PubMed

We established an efficient transformation method for thermophile Geobacillus kaustophilus HTA426 using conjugative transfer from Escherichia coli of host-mimicking plasmids that imitate DNA methylation of strain HTA426 to circumvent its DNA restriction barriers. Two conjugative plasmids, pSTE33T and pUCG18T, capable of shuttling between E. coli and Geobacillus spp., were constructed. The plasmids were first introduced into E. coli BR408, which expressed one inherent DNA methylase gene (dam) and two heterologous methylase genes from strain HTA426 (GK1380-GK1381 and GK0343-GK0344). The plasmids were then directly transferred from E. coli cells to strain HTA426 by conjugative transfer using pUB307 or pRK2013 as a helper plasmid. pUCG18T was introduced very efficiently (transfer efficiency, 10(-5)-10(-3) recipient(-1)). pSTE33T showed lower efficiency (10(-7)-10(-6) recipient(-1)) but had a high copy number and high segregational stability. Methylase genes in the donor substantially affected the transfer efficiency, demonstrating that the host-mimicking strategy contributes to efficient transformation. The transformation method, along with the two distinguishing plasmids, increases the potential of G. kaustophilus HTA426 as a thermophilic host to be used in various applications and as a model for biological studies of this genus. Our results also demonstrate that conjugative transfer is a promising approach for introducing exogenous DNA into thermophiles. PMID:22814504

Suzuki, Hirokazu; Yoshida, Ken-ichi

2012-09-01

255

Effect of Pesticides on Plant Growth Promoting Traits of Greengram-Symbiont, Bradyrhizobium sp. strain MRM6  

Microsoft Academic Search

The aim of this study was to investigate the toxicity of herbicides (metribuzin and glyphosate), insecticides (imidacloprid\\u000a and thiamethoxam) and fungicides (hexaconazole, metalaxyl and kitazin) at the recommended and the higher dose rates on plant\\u000a growth promoting activities of Bradyrhizobium sp. under in vitro conditions. The Bradyrhizobium sp. strain MRM6 was isolated from nodules of greengram plants. Pesticide-concentration dependent progressive-decline

Munees Ahemad; Mohammad Saghir Khan

2011-01-01

256

Thermophilic, Reversible ?-Resorcylate Decarboxylase from Rhizobium sp. Strain MTP-10005: Purification, Molecular Characterization, and Expression  

PubMed Central

We found the occurrence of thermophilic reversible ?-resorcylate decarboxylase (?-RDC) in the cell extract of a bacterium isolated from natural water, Rhizobium sp. strain MTP-10005, and purified the enzyme to homogeneity. The molecular mass of the enzyme was determined to be about 151 kDa by gel filtration, and that of the subunit was 37.5 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis; in other words, the enzyme was a homotetramer. The enzyme was induced specifically by the addition of ?-resorcylate to the medium. The enzyme required no coenzyme and did not act on 2,4-dihydroxybenzoate, 2,5-dihydroxybenzoate, 3,4-dihydroxybenzoate, 3,5-dihydroxybenzoate, 2-hydroxybenzoate, or 3-hydroxybenzoate. It was relatively thermostable to heat treatment, and its half-life at 50°C was estimated to be 122 min; furthermore, it catalyzed the reverse carboxylation of resorcinol. The values of kcat/Km (m??1?·?s?1) for ?-resorcylate and resorcinol at 30°C and pH 7 were 13.4 and 0.098, respectively. The enzyme contains 327 amino acid residues, and sequence identities were found with those of hypothetical protein AGR C 4595p from Agrobacterium tumefaciens strain C58 (96% identity), 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis (32%), and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylases from Bacillus cereus ATCC 10987 (26%), Rattus norvegicus (26%), and Homo sapiens (25%). The genes (graA [1,230 bp], graB [888 bp], and graC [1,056 bp]) that are homologous to those in the resorcinol pathway also exist upstream and downstream of the ?-RDC gene. Judging from these results, the resorcinol pathway also exists in Rhizobium sp. strain MTP-10005, and ?-RDC probably catalyzes a reaction just before the hydroxylase in it does.

Yoshida, Masahiro; Fukuhara, Nobuhiro; Oikawa, Tadao

2004-01-01

257

New metabolites in the degradation of fluorene by Arthrobacter sp. strain F101.  

PubMed

Identification of new metabolites and demonstration of key enzyme activities support and extend the pathways previously reported for fluorene metabolism by Arthrobacter sp. strain F101. Washed-cell suspensions of strain F101 with fluorene accumulated 9-fluorenone, 4-hydroxy-9-fluorenone, 3-hydroxy-1-indanone, 1-indanone, 2-indanone, 3-(2-hydroxyphenyl) propionate, and a compound tentatively identified as a formyl indanone. Incubations with 2-indanone produced 3-isochromanone. The growth yield with fluorene as a sole source of carbon and energy corresponded to an assimilation of about 34% of fluorene carbon. About 7.4% was transformed into 9-fluorenol, 9-fluorenone, and 4-hydroxy-9-fluorenone. Crude extracts from fluorene-induced cells showed 3,4-dihydrocoumarin hydrolase and catechol 2,3-dioxygenase activities. These results and biodegradation experiments with the identified metabolites indicate that metabolism of fluorene by Arthrobacter sp. strain F101 proceeds through three independent pathways. Two productive routes are initiated by dioxygenation at positions 1,2 and 3,4, respectively. meta cleavage followed by an aldolase reaction and loss of C-1 yield the detected indanones. Subsequent biological Baeyer-Villiger reactions produce the aromatic lactones 3,4-dihydrocoumarin and 3-isochromanone. Enzymatic hydrolysis of the former gives 3-(2-hydroxyphenyl) propionate, which could be a substrate for a beta oxidation cycle, to give salicylate. Further oxidation of the latter via catechol and 2-hydroxymuconic semialdehyde connects with the central metabolism, allowing the utilization of all fluorene carbons. Identification of 4-hydroxy-9-fluorenone is consistent with an alternative pathway initiated by monooxygenation at C-9 to give 9-fluorenol and then 9-fluorenone. Although dioxygenation at 3,4 positions of the ketone apparently occurs, this reaction fails to furnish a subsequent productive oxidation of this compound. PMID:9055403

Casellas, M; Grifoll, M; Bayona, J M; Solanas, A M

1997-03-01

258

New metabolites in the degradation of fluorene by Arthrobacter sp. strain F101.  

PubMed Central

Identification of new metabolites and demonstration of key enzyme activities support and extend the pathways previously reported for fluorene metabolism by Arthrobacter sp. strain F101. Washed-cell suspensions of strain F101 with fluorene accumulated 9-fluorenone, 4-hydroxy-9-fluorenone, 3-hydroxy-1-indanone, 1-indanone, 2-indanone, 3-(2-hydroxyphenyl) propionate, and a compound tentatively identified as a formyl indanone. Incubations with 2-indanone produced 3-isochromanone. The growth yield with fluorene as a sole source of carbon and energy corresponded to an assimilation of about 34% of fluorene carbon. About 7.4% was transformed into 9-fluorenol, 9-fluorenone, and 4-hydroxy-9-fluorenone. Crude extracts from fluorene-induced cells showed 3,4-dihydrocoumarin hydrolase and catechol 2,3-dioxygenase activities. These results and biodegradation experiments with the identified metabolites indicate that metabolism of fluorene by Arthrobacter sp. strain F101 proceeds through three independent pathways. Two productive routes are initiated by dioxygenation at positions 1,2 and 3,4, respectively. meta cleavage followed by an aldolase reaction and loss of C-1 yield the detected indanones. Subsequent biological Baeyer-Villiger reactions produce the aromatic lactones 3,4-dihydrocoumarin and 3-isochromanone. Enzymatic hydrolysis of the former gives 3-(2-hydroxyphenyl) propionate, which could be a substrate for a beta oxidation cycle, to give salicylate. Further oxidation of the latter via catechol and 2-hydroxymuconic semialdehyde connects with the central metabolism, allowing the utilization of all fluorene carbons. Identification of 4-hydroxy-9-fluorenone is consistent with an alternative pathway initiated by monooxygenation at C-9 to give 9-fluorenol and then 9-fluorenone. Although dioxygenation at 3,4 positions of the ketone apparently occurs, this reaction fails to furnish a subsequent productive oxidation of this compound.

Casellas, M; Grifoll, M; Bayona, J M; Solanas, A M

1997-01-01

259

Multiple Mechanisms of Uranium Immobilization by Cellulomonas sp. strain ES6  

SciTech Connect

Removal of hexavalent uranium (U(VI)) from aqueous solution was studied using a Gram-positive facultative anaerobe, Cellulomonas sp. strain ES6, under anaerobic, non growth conditions in bicarbonate and PIPES buffers. Inorganic phosphate was released by cells during the experiments providing ligands for formation of insoluble U(VI) phosphates. Phosphate release was most probably the result of anaerobic hydrolysis of intracellular polyphosphates accumulated by ES6 during aerobic growth. Microbial reduction of U(VI) to U(IV) was also observed. However, the relative magnitudes of U(VI) removal by abiotic (phosphate-based) precipitation and microbial reduction depended on the buffer chemistry. In bicarbonate buffer, X-ray absorption near edge structure (XANES) analysis showed U precipitates containing nearly equal fractions of U(IV) and U(VI), whereas in PIPES buffer, U precipitates consisted primarily of U(VI). Mass balance calculations for U and P corroborate these observations. High-resolution transmission electron microscopy (HR42TEM) and energy dispersive X-ray spectroscopy (EDS) showed both extracellular and intracellular accumulation of U solids. The U(VI)-phosphate precipitates, confirmed by EDS as containing U and P in equimolar concentrations, had nanometer sized lath structure. When anthraquinone-2,6-disulfonate (AQDS), a known electron shuttle, was added to the experimental reactors, U reduction became the dominant removal mechanism, in contrast to primarily phosphate-mediated precipitation observed in the absence of AQDS. Uranium immobilization by abiotic precipitation or microbial reduction has been extensively reported; however, present work suggests that strain ES6 can remove U(VI) from solution simultaneously through precipitation with phosphate ligands and microbial reduction, depending on the environmental conditions. Cellulomonadaceae are environmentally relevant subsurface bacteria and here, for the first time, t 52 he presence of multiple U immobilization mechanisms within one organism is reported using Cellulomonas sp. strain ES6.

Sivaswamy, Vaideeswaran; Brent Peyton; Viamajala, Sridhar; Robin Gerlach; William Apel; Rajesh Sani; Alice Dohnalkova; Thomas Borch

2011-02-01

260

Extracellular Signal Molecule(s) Involved in the Carbon Starvation Response of Marine Vibrio sp. Strain S14  

PubMed Central

The role of exogenous metabolites as putative signal molecules mediating and/or regulating the carbon starvation adaptation program in Vibrio sp. strain S14 was investigated. Addition of the stationary-phase supernatant extract (SSE) of Vibrio sp. strain S14 to logarithmic-phase cells resulted in a significant number of carbon starvation-induced proteins being up-regulated. Halogenated furanones, putative antagonists of acylated homoserine lactones (AHLs), inhibited the synthesis of proteins specifically induced upon carbon starvation. The effect of the furanone was the opposite of that caused by SSE with respect to the up- and down-regulation of protein expression, indicating that both the furanone and the putative signalling molecules were acting on the same regulatory pathway. Culturability was rapidly lost when Vibrio sp. strain S14 was starved in the presence of the furanone at a low concentration. The furanone also had a negative effect on the ability of carbon-starved cells to mount resistance against UV irradiation and hydrogen peroxide exposure. The SSE of Vibrio sp. strain S14 had the ability to provide cross-protection against the loss in viability caused by the furanone. We have further demonstrated that the SSE taken from low- as well as high-cell-density cultures of Vibrio sp. strain S14 induced luminescence in Vibrio harveyi. Taken together, the results in this report provide evidence that Vibrio sp. strain S14 produces extracellular signalling metabolites during carbon and energy starvation and that these molecules play an important role in the expression of proteins crucial to the development of starvation- and stress-resistant phenotypes.

Srinivasan, Sujatha; Ostling, Jorgen; Charlton, Timothy; de Nys, Rocky; Takayama, Kathy; Kjelleberg, Staffan

1998-01-01

261

Selectivity among organic sulfur compounds in one- and two-liquid-phase cultures of Rhodococcus sp. strain JVH1  

Microsoft Academic Search

The selectivity of Rhodococcus sp. strain JVH1 among selected sulfidic and thiophenic compounds was investigated in both single-liquid-phase (aqueous) cultures\\u000a and in two-liquid-phase cultures, where the sulfur compounds were dissolved in 2,2,4,4,6,8,8-heptamethylnonane as the immiscible\\u000a organic carrier phase. In the single-liquid-phase cultures, Rhodococcus sp. strain JVH1 showed a preference for benzyl sulfide over both 1,4-dithiane and benzothiophene. An increased lag

Kathlyn M. Kirkwood; Julia M. Foght; Murray R. Gray

2007-01-01

262

The degradation of alkylphenols by Sphingomonas sp. strain TTNP3 - a review on seven years of research.  

PubMed

Over the past seven years, we have been working with Sphingomonas sp. strain TTNP3, a bacterium capable of growing on numerous alkylphenolic compounds as a source of carbon and energy. We succeeded in elucidating an unusual pathway involving an attack at the quaternary alpha-carbon atom of the substrate, a position previously thought to be highly resistant to biodegradation. Combining analytical and bioanalytical methods, a good understanding of the reaction mechanisms, the enzymes catalysing them and the organization of the genes encoding them could be gained. First studies on the use of Sphingomonas sp. strain TTNP3 in wastewater treatment have been performed revealing promising results. PMID:22842087

Kolvenbach, B A; Corvini, P F-X

2012-07-27

263

Rhizosphere colonization and arsenic translocation in sunflower (Helianthus annuus L.) by arsenate reducing Alcaligenes sp. strain Dhal-L.  

PubMed

In the present study, six arsenic-resistant strains previously isolated were tested for their plant growth promoting characteristics and heavy metal resistance, in order to choose one model strain as an inoculum for sunflower plants in pot experiments. The aim was to investigate the effect of arsenic-resistant strain on sunflower growth and on arsenic uptake from arsenic contaminated soil. Based on plant growth promoting characteristics and heavy metal resistance, Alcaligenes sp. strain Dhal-L was chosen as an inoculum. Beside the ability to reduce arsenate to arsenite via an Ars operon, the strain exhibited 1-amino-cyclopropane-1-carboxylic acid deaminase activity and it was also able to produce siderophore and indole acetic acid. Pot experiments were conducted with an agricultural soil contaminated with arsenic (214 mg kg(-1)). A real time PCR method was set up based on the quantification of ACR3(2) type of arsenite efflux pump carried by Alcaligenes sp. strain Dhal-L, in order to monitor presence and colonisation of the strain in the bulk and rhizospheric soil. As a result of strain inoculation, arsenic uptake by plants was increased by 53 %, whereas ACR3(2) gene copy number in rhizospheric soil was 100 times higher in inoculated than in control pots, indicating the colonisation of strain. The results indicated that the presence of arsenate reducing strains in the rhizosphere of sunflower influences arsenic mobilization and promotes arsenic uptake by plant. PMID:23632906

Cavalca, Lucia; Corsini, Anna; Bachate, Sachin Prabhakar; Andreoni, Vincenza

2013-04-30

264

Hydrolytic potential of Trichoderma sp. strains evaluated by microplate-based screening followed by switchgrass saccharification.  

PubMed

Bioconversion of lignocellulosic biomass to fuel requires a hydrolysis step to obtain fermentable sugars, generally accomplished by fungal enzymes. Large-scale screening of different microbial strains would provide optimal enzyme cocktails for any target feedstock. The aim of this study was to screen a large collection of Trichoderma sp. strains for the hydrolytic potential towards switchgrass (Panicum virgatum L.). Strains were cultivated in a small-scale system and assayed in micro-plates for xylanase and cellulase activities. The population distributions of these traits are reported after growth on switchgrass in comparison with cellulose. The distribution profiles suggest that the growth on switchgrass strongly promotes xylanase production. The IK4 strain displayed the highest xylanase activity after growth on switchgrass (133U/mL). Enzymes (10FPU/g substrate) from IK4 were compared with those from 2 cellulolytic Trichoderma strains and a commercial enzyme in saccharification time-course experiments on untreated and pretreated switchgrass and on an artificial substrate. Samples were analysed by DNS assay and by an oxygraphic method for sugar equivalent or glucose concentration. On the untreated substrate, IK4 enzymes even outperformed a 5-fold load of commercial enzyme, suggesting that xylanase or accessory enzymes are a limiting factor on this type of recalcitrant substrate. On the other substrates, IK4 preparations showed intermediate behaviour if compared with the commercial enzyme at 10FPU/g substrate and at 5-fold load. IK4 also nearly halved the time to release 50% of the hydrolysable sugar equivalents (T(50%)), with respect to the other preparations at the same enzymatic load. DNS assay and oxygraphic method gave highly correlated results for the 3 saccharified substrates. The study suggests that accessory enzymes like xylanase play a key role in improving the performance of cellulase preparations on herbaceous lignocellulosic feedstocks like switchgrass. PMID:22500897

Cianchetta, Stefano; Galletti, Stefania; Burzi, Pier Luigi; Cerato, Claudio

2012-03-07

265

[Isolation of a methane-utilizing Klebsiella sp. strain and its application for detecting methane].  

PubMed

We have isolated a strain C611 that used methane as the sole carbon sources for growth from paddy soil in Taiyuan of Shanxi province. Based on the physiological characteristics and 16S rDNA sequence analysis, we identified the strain as Klebsiella sp.. We used statistic-based experimental design (RSM) to optimize the culture conditions for C611 strain. The optimum conditions were as follows: temperature of 24.4 degrees C, inoculum volume of 6.7% and methane content of 25%. We studied the response time and the relationship between consumption of dissolved oxygen and methane gas contents with PVA-H3BO3 immobilized cell of C611 using electrochemical method. The response time was no more than 100 s of this reaction system, and the linear range of detection of methane content was from 0 to 10%. The standard gas sample 3% methane was measured by this method with the mean content value of 3.09%, RSD of 3.48%, and the relative error of 3%. Hence, it has the potential in developing biosensor for methane. PMID:19670637

Zheng, Jun; Guo, Jun; Wang, Yujun; Yang, Yujing; Pang, Jinmei; Yang, Suping; Zhao, Gengui; Dong, Chuan

2009-05-01

266

Responses to arsenate stress by Comamonas sp. strain CNB-1 at genetic and proteomic levels.  

PubMed

Comamonas sp. strain CNB-1, a chloronitrobenzene-degrading bacterium, was demonstrated to possess higher arsenate tolerance as compared with the mutant strain CNB-2. pCNB1, a plasmid harboured by CNB-1 but not CNB-2, contained the genetic cluster ars(RPBC)Com, which putatively encodes arsenate-resistance regulator, family II arsenate reductase, arsenite efflux pump and family I arsenate reductase, respectively, in Comamonas strain CNB-1. The arsC-negative Escherichia coli could gain arsenate resistance by transformation with arsPCom or arsCCom, indicating that these two genes might express functional forms of arsenate reductases. Intriguingly, when CNB-1 cells were exposed to arsenate, the transcription of arsPCom and arsCCom was measurable by RT-PCR, but only ArsPCom was detectable at protein level. To explore the proteins responding to arsenate stress, CNB-1 cells were cultured with and without arsenate and differential proteomics was carried out by two-dimensional PAGE (2-DE) and MALDI-TOF MS. A total of 31 differential 2-DE spots were defined upon image analysis and 23 proteins were identified to be responsive specifically to arsenate. Of these spots, 18 were unique proteins. These proteins were identified to be phosphate transporters, heat-shock proteins involved in protein refolding, and enzymes participating in carbon and energy metabolism. PMID:17975079

Zhang, Yun; Ma, Ying-Fei; Qi, Su-Wei; Meng, Bo; Chaudhry, Muhammad Tausif; Liu, Si-Qi; Liu, Shuang-Jiang

2007-11-01

267

Biodegradation of buprofezin by Rhodococcus sp. strain YL-1 isolated from rice field soil.  

PubMed

A buprofezin-degrading bacterium, YL-1, was isolated from rice field soil. YL-1 was identified as Rhodococcus sp. on the basis of the comparative analysis of 16S rDNA sequences. The strain could use buprofezin as the sole source of carbon and nitrogen for growth and was able to degrade 92.4% of 50 mg L(-1) buprofezin within 48 h in liquid culture. During the degradation of buprofezin, four possible metabolites, 2-tert-butylimino-3-isopropyl-1,3,5-thiadiazinan-4-one, N-tert-butyl-thioformimidic acid formylaminomethyl ester, 2-isothiocyanato-2-methyl-propane, and 2-isothiocyanato-propane, were identified using gas chromatography-mass spectrometry (GC-MS) analysis. The catechol 2,3-dioxygenase activity was strongly induced during the degradation of buprofezin. A novel microbial biodegradation pathway for buprofezin was proposed on the basis of these metabolites. The inoculation of soils treated with buprofezin with strain YL-1 resulted in a higher degradation rate than that observed in noninoculated soils, indicating that strain YL-1 has the potential to be used in the bioremediation of buprofezin-contaminated environments. PMID:22335821

Li, Chao; Zhang, Ji; Wu, Zhi-Guo; Cao, Li; Yan, Xin; Li, Shun-Peng

2012-02-28

268

Purification and characterization of a novel thermo-active amidase from Geobacillus subterraneus RL-2a.  

PubMed

A thermostable amidase produced by Geobacillus subterraneus RL-2a was purified to homogeneity, with a yield of 9.54 % and a specific activity of 48.66 U mg(-1). The molecular weight of the native enzyme was estimated to be 111 kDa. The amidase of G. subterraneus RL-2a is constitutive in nature, active at a broad range of pH (4.5-11.5) and temperature (40-90 °C) and has a half-life of 5 h and 54 min at 70 °C. Inhibition of enzyme activity was observed in the presence of metal ions, such as Co(2+), Hg(2+), Cu(2+), Ni(2+), and thiol reagents. The presence of mid-chain aliphatic and amino acid amides enhances the enzymatic activity. The acyl transferase activity was detected with propionamide, butyramide and nicotinamide. The enzyme showed moderate stability toward toluene, carbon tetrachloride, benzene, ethylene glycol except acetone, ethanol, butanol, propanol and dimethyl sulfoxide. The K m and V max of the purified amidase with nicotinamide were 6.02 ± 0.56 mM and 132.6 ± 4.4 ?mol min(-1) mg(-1) protein by analyzing Michaelis-Menten kinetics. The results of MALDI-TOF analysis indicated that this amidase has homology with the amidase of Geobacillus sp. C56-T3 (gi|297530427). It is the first reported wide-spectrum thermostable amidase from a thermophilic G. subterraneus. PMID:23708550

Mehta, Praveen Kumar; Bhatia, Shashi Kant; Bhatia, Ravi Kant; Bhalla, Tek Chand

2013-05-26

269

Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134.  

PubMed

Proteorhodopsin phototrophy is expected to have considerable impact on the ecology and biogeochemical roles of marine bacteria. However, the genetic features contributing to the success of proteorhodopsin-containing bacteria remain largely unknown. We investigated the genome of Dokdonia sp. strain MED134 (Bacteroidetes) for features potentially explaining its ability to grow better in light than darkness. MED134 has a relatively high number of peptidases, suggesting that amino acids are the main carbon and nitrogen sources. In addition, MED134 shares with other environmental genomes a reduction in gene copies at the expense of important ones, like membrane transporters, which might be compensated by the presence of the proteorhodopsin gene. The genome analyses suggest Dokdonia sp. MED134 is able to respond to light at least partly due to the presence of a strong flavobacterial consensus promoter sequence for the proteorhodopsin gene. Moreover, Dokdonia sp. MED134 has a complete set of anaplerotic enzymes likely to play a role in the adaptation of the carbon anabolism to the different sources of energy it can use, including light or various organic matter compounds. In addition to promoting growth, proteorhodopsin phototrophy could provide energy for the degradation of complex or recalcitrant organic matter, survival during periods of low nutrients, or uptake of amino acids and peptides at low concentrations. Our analysis suggests that the ability to harness light potentially makes MED134 less dependent on the amount and quality of organic matter or other nutrients. The genomic features reported here may well be among the keys to a successful photoheterotrophic lifestyle. PMID:22003006

González, José M; Pinhassi, Jarone; Fernández-Gómez, Beatriz; Coll-Lladó, Montserrat; González-Velázquez, Mónica; Puigbò, Pere; Jaenicke, Sebastian; Gómez-Consarnau, Laura; Fernàndez-Guerra, Antoni; Goesmann, Alexander; Pedrós-Alió, Carlos

2011-10-14

270

Isolation of a novel microalgae strain Desmodesmus sp. and optimization of environmental factors for its biomass production.  

PubMed

A novel strain of unicellular green algae was isolated from fresh water samples collected from Yesanpo National Geopark, Laishui County of Hebei Province, China. The morphological and genomic identification of this strain was carried out using 18s rRNA analysis. This novel strain was identified as Desmodesmus sp. named as EJ15-2. Environmental factors for biomass production of Desmodesmus sp. EJ15-2 grown under autotrophic condition (BG11 medium) was optimized using response surface methodology (RSM). A high correlation coefficient (R(2)=0.923, p?0.01) indicated the adaptability of the second-order equation matched well with the growth condition of this strain. The optimal conditions for a relatively high biomass production (up to 0.758g/L) were at 30°C, 98?mol/m(2)/s and 14:10 (L:D), respectively. PMID:24055966

Ji, Fang; Hao, Rui; Liu, Ying; Li, Gang; Zhou, Yuguang; Dong, Renjie

2013-08-26

271

Biodegradation of p-cresol by immobilized cells of Bacillus sp. strain PHN 1.  

PubMed

The Bacillus sp. strain PHN 1 capable of degrading p-cresol was immobilized in various matrices namely, polyurethane foam (PUF), polyacrylamide, alginate and agar. The degradation rates of 20 and 40 mM p-cresol by the freely suspended cells and immobilized cells in batches and semi-continuous with shaken cultures were compared. The PUF-immobilized cells achieved higher degradation of 20 and 40 mM p-cresol than freely suspended cells and the cells immobilized in polyacrylamide, alginate and agar. The PUF- immobilized cells could be reused for more than 35 cycles, without losing any degradation capacity and showed more tolerance to pH and temperature changes than free cells. These results revealed that the immobilized cell systems are more efficient than freely suspended cells for degradation of p-cresol. PMID:18642119

Tallur, P N; Megadi, V B; Ninnekar, H Z

2008-07-20

272

Characterization of the Upper Pathway Genes for Fluorene Metabolism in Terrabacter sp. Strain DBF63  

PubMed Central

Genes involved in the degradation of fluorene to phthalate were characterized in the fluorene degrader Terrabacter sp. strain DBF63. The initial attack on both fluorene and 9-fluorenone was catalyzed by DbfA to yield 9-fluorenol and 1,1a-dihydroxy-1-hydro-9-fluorenone, respectively. The FlnB protein exhibited activities against both 9-fluorenol and 1,1a-dihydroxy-1-hydro-9-fluorenone to produce 9-fluorenone and 2?-carboxy-2,3-dihydroxybiphenyl, respectively. FlnD is a heteromeric protein encoded by flnD1 and ORF16, being a member of the class III two-subunit extradiol dioxygenase. FlnE was identified as a serine hydrolase for the meta-cleavage products that yield phthalate.

Habe, Hiroshi; Chung, Jin-Sung; Kato, Hiroyuki; Ayabe, Yuko; Kasuga, Kano; Yoshida, Takako; Nojiri, Hideaki; Yamane, Hisakazu; Omori, Toshio

2004-01-01

273

Growth yield coefficients of Sphingomonas sp. strain P5 on various chlorophenols in chemostat culture  

Microsoft Academic Search

A polychlorophenol-degrading bacterium, Sphingomonas sp. strain P5, was grown in 2,6-dichlo-rophenol(26-DCP)-limited, 2,3,6-trichlorophenol(236-TCP)-limited, 2,4,6-trichlorophenol(246-TCP)-limited,\\u000a 2,3,4,6-tetrachlorophenol(2346-TeCP)-limited, and pentachlorophenol(PCP)-limited chemostat cultures at a dilution rate of\\u000a 0.02?±?0.002?h?1. The cultures were analyzed for the yield coefficient for growth on chlorophenol during steady-state conditions. The average\\u000a growth yields coefficients (as carbon conversion efficiencies) were 0.252, 0.230, 0.219, 0.157, and 0.121?mol C mol C?1 for 26-DCP,

M. Rutgers; A. M. Breure; J. G. van Andel; W. A. Duetz

1997-01-01

274

Unique modification of adenine in genomic DNA of the marine cyanobacterium Trichodesmium sp. strain NIBB 1067.  

PubMed Central

The genomic DNA of the marine nonheterocystous nitrogen-fixing cyanobacterium Trichodesmium sp. strain NIBB 1067 was found to be highly resistant to DNA restriction endonucleases. The DNA was digested extensively by the restriction enzyme DpnI, which requires adenine methylation for activity. The DNA composition, determined by high-performance liquid chromatography (HPLC), was found to be 69% AT. Surprisingly, it was found that a modified adenine which was not methylated at the usual N6 position was present and made up 4.7 mol% of the nucleosides in Trichodesmium DNA (15 mol% of deoxyadenosine). In order for adenine residues to be modified at this many positions, there must be many modifying enzymes or at least one of the modifying enzymes must have a degenerate recognition site. The reason(s) for this extensive methylation has not yet been determined but may have implications for the ecological success of this microorganism in nature. Images FIG. 1 FIG. 2

Zehr, J P; Ohki, K; Fujita, Y; Landry, D

1991-01-01

275

[Site-directed mutagenesis of the dichloromethane dehalogenase gene from Methylophilus sp. strain DM11].  

PubMed

In order to investigate the role of different residues of Methylophilus sp. strain DM11 dichloromethane dehalogenase for substrate binding, glutathione affinity, and catalytic activity, site-directed mutagenesis studies of the gene encoding the enzyme were carried out. The conserved tryptophane residue at 103 region was respectively substituted by phenylalanine, valine or asparagine. The conserved arginine residue at 109 region was substituted by leucine. The conserved tryptophane residue at 117 region was respectively substituted by tyrosine or phenylalanine. Six mutant enzymes were produced. Among them three possess lower activities, other three do not possess activity. The properties of the mutant enzyme W117Y are very different from wild-type enzyme. PMID:12549326

Cai, B; Vuilleumier, S; Wackett, L P

1998-06-01

276

Purification and properties of haloalkane dehalogenase from Corynebacterium sp. strain m15-3.  

PubMed Central

A haloalkane dehalogenase was purified to electrophoretic homogeneity from cell extracts of a 1-chlorobutane-utilizing strain, m15-3, which was identified as a Corynebacterium sp. The enzyme hydrolyzed C2 to C12 mono- and dihalogenated alkanes, some haloalcohols, and haloacids. The Km value of the enzyme for 1-chlorobutane was 0.18 mM. Its molecular weight was estimated to be 36,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and 33,000 by gel filtration. The isoelectric point was pH 4.5. The optimum pH for enzyme activity was found to be 9.4, and the optimum temperature was 30 to 35 degrees C. The enzyme was stable for 1 h at temperatures ranging from 4 to 30 degrees C but was progressively less stable at 40 and 50 degrees C. Images

Yokota, T; Omori, T; Kodama, T

1987-01-01

277

A new polyketide from Diaporthe sp. SXZ-19, an endophytic fungal strain of Camptotheca acuminate.  

PubMed

A new polyketide named (1R,2E,4S,5R)-1-[(2R)-5-oxotetrahydrofuran-2-yl]-4,5-dihydroxy-hex-2-en-1-yl(2E)-2-methylbut-2-enoate (1), along with eight known polyketide including one monoterpene (2), three linear furanopolyketides (3-5) and four lovastatin analogues (6-9), was isolated from the endophytic fungal strain Diaporthe sp. SXZ-19 of Camptotheca acuminate. The chemical structures of compounds 1-9 were elucidated on the basis of extensive spectroscopic analyses, including FT-ICR-MS, IR and 1D and 2D NMR experiments. The in vitro cytotoxicity of 1 against the human colon cancer cell line HCT 116 was evaluated but showed no evident activity. PMID:23701441

Liu, Yuanzhen; Hu, Zhiyu; Lin, Xiang; Lu, Chunhua; Shen, Yuemao

2013-05-24

278

An unexpected gene cluster for downstream degradation of alkylphenols in Sphingomonas sp. strain TTNP3.  

PubMed

In silico analysis of nucleotide sequences flanking the recently found hydroquinone dioxygenase in Sphingomonas sp. strain TTNP3 revealed a gene cluster that encodes a hydroquinone catabolic pathway. In addition to the two open-reading frames encoding the recently characterized hydroquinone dioxygenase, the cluster consisted of six open-reading frames. We were able to express the three open-reading frames, hqdC, hqdD, and hqdE, and demonstrated that the three gene products, HqdC, HqdD, and HqdE had 4-hydroxymuconic semialdehyde dehydrogenase, maleylacetate reductase, and intradiol dioxygenase activity, respectively. Surprisingly, the gene cluster showed similarities to functionally related clusters found in members of the ?- and ?-proteobacteria rather than to those found in other members of the genus Sphingomonas sensu latu. PMID:21755281

Kolvenbach, Boris A; Dobrowinski, Hyazinth; Fousek, Jan; Vlcek, Cestmir; Schäffer, Andreas; Gabriel, Frederic L P; Kohler, Hans-Peter E; Corvini, Philippe F X

2011-07-14

279

Xanthan Lyase of Bacillus sp. Strain GL1 Liberates Pyruvylated Mannose from Xanthan Side Chains  

PubMed Central

When the bacterium Bacillus sp. strain GL1 was grown in a medium containing xanthan as the carbon source, the viscosity of the medium decreased in association with growth, showing that the bacterium had xanthan-depolymerizing enzymes. One of the xanthan-depolymerizing enzymes (xanthan lyase) was present in the medium and was found to be induced by xanthan. The xanthan lyase purified from the culture fluid was a monomer with a molecular mass of 75 kDa, and was most active at pH 5.5 and 50°C. The enzyme was highly specific for xanthan and produced pyruvylated mannose. The result indicates that the enzyme cleaved the linkage between the terminal pyruvylated mannosyl and glucuronyl residues in the side chain of xanthan.

Hashimoto, Wataru; Miki, Hikaru; Tsuchiya, Noriaki; Nankai, Hirokazu; Murata, Kousaku

1998-01-01

280

Organic solvent tolerance of halophilic alpha-amylase from a Haloarchaeon, Haloarcula sp. strain S-1.  

PubMed

A halophilic archaeon, Haloarcula sp. strain S-1, produced extracellular organic solvent-tolerant alpha-amylase. Molecular mass of the enzyme was estimated to be 70 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This amylase exhibited maximal activity at 50 degrees C in buffer containing 4.3 M NaCl, pH 7.0. Moreover, the enzyme was active and stable in various organic solvents (benzene, toluene, and chloroform, etc.). Activity was not detected at low ionic strengths, but it was detected in the presence of chloroform at low salt concentrations. On the other hand, no activity was detected in the presence of ethyl alcohol and acetone. PMID:15378403

Fukushima, Tadamasa; Mizuki, Toru; Echigo, Akinobu; Inoue, Akira; Usami, Ron

2004-09-17

281

Genome-wide responses of the model archaeon Halobacterium sp. strain NRC-1 to oxygen limitation.  

PubMed

As part of a comprehensive postgenomic investigation of the model archaeon Halobacterium sp. strain NRC-1, we used whole-genome DNA microarrays to compare transcriptional profiles of cells grown under anaerobic or aerobic conditions. When anaerobic growth supported by arginine fermentation was compared to aerobic growth, genes for arginine fermentation (arc) and anaerobic respiration (dms), using trimethylamine N-oxide (TMAO) as the terminal electron acceptor, were highly upregulated, as was the bop gene, required for phototrophic growth. When arginine fermentation was compared to anaerobic respiration with TMAO, the arc and dms genes were both induced with arginine, while TMAO induced the bop gene and major gas vesicle protein (gvpAC) genes specifying buoyant gas vesicles. Anaerobic conditions with either TMAO or arginine also upregulated the cba genes, encoding one of three cytochrome oxidases. In-frame deletion of two COG3413 family regulatory genes, bat and dmsR, showed downregulation of the bop gene cluster and loss of purple membrane synthesis and downregulation of the dms operon and loss of anaerobic respiration capability, respectively. Bioinformatic analysis identified additional regulatory and sensor genes that are likely involved in the full range of cellular responses to oxygen limitation. Our results show that the Halobacterium sp. has evolved a carefully orchestrated set of responses to oxygen limitation. As conditions become more reducing, cells progressively increase buoyancy, as well as capabilities for phototrophy, scavenging of molecular oxygen, anaerobic respiration, and fermentation. PMID:22865851

DasSarma, Priya; Zamora, Regie C; Müller, Jochen A; DasSarma, Shiladitya

2012-08-03

282

Isolation and Characterization of Frankia sp. Strain FaC1 Genes Involved in Nitrogen Fixation.  

PubMed

Genomic DNA was isolated from Frankia sp. strain FaC1, an Alnus root nodule endophyte, and used to construct a genomic library in the cosmid vector pHC79. The genomic library was screened by in situ colony hybridization to identify clones of Frankia nitrogenase (nif) genes based on DNA sequence homology to structural nitrogenase genes from Klebsiella pneumoniae. Several Frankia nif clones were isolated, and hybridization with individual structural nitrogenase gene fragments (nifH, nifD, and nifK) from K. pneumoniae revealed that they all contain the nifD and nifK genes, but lack the nifH gene. Restriction endonuclease mapping of the nifD and nifK hybridizing region from one clone revealed that the nifD and nifK genes in Frankia sp. are contiguous, while the nifH gene is absent from a large region of DNA on either side of the nifDK gene cluster. Additional hybridizations with gene fragments derived from K. pneumoniae as probes and containing other genes involved in nitrogen fixation demonstrated that the Frankia nifE and nifN genes, which play a role in the biosynthesis of the iron-molybdenum cofactor, are located adjacent to the nifDK gene cluster. PMID:16347453

Ligon, J M; Nakas, J P

1987-10-01

283

Isolation and Characterization of Frankia sp. Strain FaC1 Genes Involved in Nitrogen Fixation  

PubMed Central

Genomic DNA was isolated from Frankia sp. strain FaC1, an Alnus root nodule endophyte, and used to construct a genomic library in the cosmid vector pHC79. The genomic library was screened by in situ colony hybridization to identify clones of Frankia nitrogenase (nif) genes based on DNA sequence homology to structural nitrogenase genes from Klebsiella pneumoniae. Several Frankia nif clones were isolated, and hybridization with individual structural nitrogenase gene fragments (nifH, nifD, and nifK) from K. pneumoniae revealed that they all contain the nifD and nifK genes, but lack the nifH gene. Restriction endonuclease mapping of the nifD and nifK hybridizing region from one clone revealed that the nifD and nifK genes in Frankia sp. are contiguous, while the nifH gene is absent from a large region of DNA on either side of the nifDK gene cluster. Additional hybridizations with gene fragments derived from K. pneumoniae as probes and containing other genes involved in nitrogen fixation demonstrated that the Frankia nifE and nifN genes, which play a role in the biosynthesis of the iron-molybdenum cofactor, are located adjacent to the nifDK gene cluster. Images

Ligon, James M.; Nakas, James P.

1987-01-01

284

Synechococcus sp. Strain PCC 7002 Transcriptome: Acclimation to Temperature, Salinity, Oxidative Stress, and Mixotrophic Growth Conditions  

PubMed Central

Synechococcus sp. strain PCC 7002 is a unicellular, euryhaline cyanobacterium. It is a model organism for studies of cyanobacterial metabolism and has great potential for biotechnological applications. It exhibits an exceptional tolerance of high-light irradiation and shows very rapid growth. The habitats from which this and closely related strains were isolated are subject to changes in several environmental factors, including light, nutrient supply, temperature, and salinity. In this study global transcriptome profiling via RNAseq has been used to perform a comparative and integrated study of global changes in cells grown at different temperatures, at different salinities, and under mixotrophic conditions, when a metabolizable organic carbon source was present. Furthermore, the transcriptomes were investigated for cells that were subjected to a heat shock and that were exposed to oxidative stress. Lower growth temperatures caused relatively minor changes of the transcriptome; the most prominent changes affected fatty acid desaturases. A heat shock caused severe changes of the transcriptome pattern; transcripts for genes associated with major metabolic pathways declined and those for different chaperones increased dramatically. Oxidative stress, however, left the transcript pattern almost unaffected. When grown at high salinity, Synechococcus sp. PCC 7002 had increased expression of genes involved in compatible solute biosynthesis and showed increased mRNA levels for several genes involved in electron transport. Transcripts of two adjacent genes dramatically increased upon growth at high salinity; the respective proteins are putatively involved in coping with oxidative stress and in triggering ion channels. Only minor changes were observed when cells were grown at low salinity or when the growth medium was supplemented with glycerol. However, the transcriptome data suggest that cells must acclimate to excess reducing equivalents when a reduced C-source is present.

Ludwig, Marcus; Bryant, Donald A.

2012-01-01

285

Distinct Actions by Paenibacillus sp. Strain E18 ?-l-Arabinofuranosidases and Xylanase in Xylan Degradation  

PubMed Central

We cloned a Paenibacillus sp. strain E18 5.3-kb xylanolytic gene cluster that contains three open reading frames encoding two family 43 ?-l-arabinofuranosidases (Abf43A and Abf43B) and one family 10 xylanase (XynBE18). The deduced amino acid sequences of Abf43A and Abf43B were at most 68% and 63% identical to those of two putative family 43 proteins from Clostridium sp. strain DL-VIII (EHI98634.1 and EHI98635.1), respectively, but were only 11% identical to each other. Recombinant Abf43A and Abf43B had similar activities at 45°C and pH 6.0 but varied in thermostabilities and substrate specificities. Abf43B was active against only 4-nitrophenyl ?-l-arabinofuranoside, whereas Abf43A acted on 4-nitrophenyl ?-l-arabinofuranoside, wheat arabinoxylan, 4-nitrophenyl ?-d-xylopyranoside, and sugar beet arabinan. The sequential and combined effects on xylan degradation by XynBE18, Abf43A, and Abf43B were characterized. For beechwood, birchwood, and oat spelt xylans as the substrates, synergistic effects were found when XynBE18 and Abf43A or Abf43B were incubated together and when the substrates were first incubated with Abf43A or Abf43B and then with XynBE18. Further high-performance liquid chromatography (HPLC) analysis showed that the amounts of xylobiose and xylose increased sharply in the aforementioned reactions. For water-soluble wheat arabinoxylan as the substrate, Abf43A not only released arabinose but also had a synergistic effect with XynBE18. Synergy may arise as the result of removal of arabinose residues from xylans by ?-l-arabinofuranosidases, which eliminates steric hindrance caused by the arabinose side chains and which allows xylanases to then degrade the xylan backbone, producing short xylooligosaccharides.

Shi, Pengjun; Chen, Xiaoyan; Meng, Kun; Huang, Huoqing; Bai, Yingguo; Luo, Huiying; Yang, Peilong

2013-01-01

286

DL-7-azatryptophan and citrulline metabolism in the cyanobacterium Anabaena sp. strain 1F  

SciTech Connect

An alternative route for the primary assimilation of ammonia proceeds via glutamine synthetase-carbamyl phosphate synthetase and its inherent glutaminase activity in Anabaena sp. strain 1F, a marine filamentous, heterocystous cyanobacterium. Evidence for the presence of this possible alternative route to glutamate was provided by the use of amino acid analogs as specific enzyme inhibitors, enzymological studies, and radioistopic labeling experiments. The amino acid pool patterns of continuous cultures of Anabaena sp. strain 1F were markedly influenced by the nitrogen source. A relatively high concentration of glutamate was maintained in the amino acid pools of all cultures irrespective of the nitrogen source, reflecting the central role of glutamate in nitrogen metabolism. The addition of 1.0 microM azaserine increased the intracellular pools of glutamate and glutamine. All attempts to detect any enzymatic activity for glutamate synthase by measuring the formation of L-(/sup 14/C)glutamate from 2-keto-(1-/sup 14/C)glutarate and glutamine failed. The addition of 10 microM DL-7-azatryptophan caused a transient accumulation of intracellular citrulline and alanine which was not affected by the presence of chloramphenicol. The in vitro activity of carbamyl phosphate synthetase and glutaminase increased severalfold in the presence of azatryptophan. Results from radioisotopic labeling experiments with (/sup 14/C)bicarbonate and L-(1-/sup 14/C)ornithine also indicated that citrulline was formed via carbamyl phosphate synthetase and ornithine transcarbamylase. In addition to its effects on nitrogen metabolism, azatryptophan also affected carbon metabolism by inhibiting photosynthetic carbon assimilation and photosynthetic oxygen evolution.

Chen, C.H.; Van Baalen, C.; Tabita, F.R.

1987-03-01

287

Responses to multiple-nutrient starvation in marine Vibrio sp. strain CCUG 15956.  

PubMed Central

The response of marine Vibrio sp. strain S14 (CCUG 15956) to long-term (48-h) multiple-nutrient starvation (i.e., starvation for glucose, amino acids, ammonium, and phosphate simultaneously) can be described as a three-phase process. The first phase, defined as the stringent control phase, encompasses an accumulation of guanosine 5'-diphosphate 3'-diphosphate (ppGpp) and decreases in RNA and protein synthesis during the first 40 min. In the second phase, there is a temporary increase in the rates of RNA and protein synthesis between 1 and 3 h paralleling a decrease in the ppGpp pool. The third phase includes gradual decline in macromolecular synthesis after 3 h. Using two-dimensional gel electrophoresis of pulse-labeled proteins, a total of 66 proteins were identified as starvation inducible (Sti), temporally expressed throughout the three phases of starvation. The inhibition of protein synthesis during the first phase of starvation partly disrupted the subsequent temporally ordered synthesis of starvation proteins and prevented the expression of some late starvation proteins. It was also found that the early temporal class of starvation proteins, which included the majority of the Sti proteins, was the most essential for long-term survival. Vibrio sp. strain S14 cultures prestarved (1 h) for glucose, amino acids, ammonium, or phosphate as well as cultures exposed (1 h) to CdCl2 exhibited enhanced survival during the subsequent multiple-nutrient starvation in the presence of chloramphenicol or rifampin, while heat or the addition of cyclic AMP or nalidixic acid prior to starvation had no effect. It was demonstrated that amino acid starvation and CdCl2 exposure, which induced the stringent response, were the most effective in conferring enhanced survival. A few Sti proteins were common to all starvation conditions. In addition, the total number of proteins induced by multiple-nutrient starvation significantly exceeded the sum of those induced by starvation for each of the individual nutrients. Images

Nystrom, T; Flardh, K; Kjelleberg, S

1990-01-01

288

Penicillium sp. strain that efficiently adsorbs lignosulfonate in the presence of sulfate ion.  

PubMed

Lignin is one of the major water insoluble substances that support the physical properties of plants and can be solubilized by sulfite or alkaline treatment in accordance with pulpification. The lignin derivatives produced by both the sulfite and the kraft processes are called lignosulfonate (LS) and kraft lignin (KL), respectively, and both derivatives show a broad spectrum of optical absorbance from ultraviolet to visible light. When the spore suspension of an isolated Penicillium sp., Penicillium sp. A, was inoculated to a medium containing 0.1% commercial LS, absorbance at 480 nm (A480) almost completely disappeared after 5 days of cultivation. Maximum decolorization of the culture broth was observed when the microbe was cultured in the 0.8% LS medium reaching 88%, and the amount of LS removed was calculated to be 7 g/L. In a similar assay with the dark-liquid containing KL, 80% of the A480 of a 20% (v/v) dark-liquid medium disappeared after 5 days of culturing and the amount of KL removed was calculated to be 2.9 g/L. These values significantly exceeded the previously reported amounts with respect to substrate concentration and decolorization. Furthermore, since similar results were obtained in the cases of both LS and KL, it is expected that the present strain is able to non-specifically adsorb a wide range of lignin derivatives, because most of the colored substances were recovered in the culture sediments. Thus, the strain can be used to clean up waste fluids containing water soluble lignin derivatives, adsorb lignin derivatives in waste fluids before dehydration. PMID:23085419

Aoyama, Akihisa; Kurane, Ryuichiro; Nagai, Kazuo

2012-10-22

289

Characterization and Implications of the Cell Surface Reactivity of Calothrix sp. Strain KC97  

PubMed Central

The cell surface reactivity of the cyanobacterium Calothrix sp. strain KC97, an isolate from the Krisuvik hot spring, Iceland, was investigated in terms of its proton binding behavior and charge characteristics by using acid-base titrations, electrophoretic mobility analysis, and transmission electron microscopy. Analysis of titration data with the linear programming optimization method showed that intact filaments were dominated by surface proton binding sites inferred to be carboxyl groups (acid dissociation constants [pKa] between 5.0 and 6.2) and amine groups (mean pKa of 8.9). Sheath material isolated by using lysozyme and sodium dodecyl sulfate generated pKa spectra similarly dominated by carboxyls (pKa of 4.6 to 6.1) and amines (pKa of 8.1 to 9.2). In both intact filaments and isolated sheath material, the lower ligand concentrations at mid-pKa values were ascribed to phosphoryl groups. Whole filaments and isolated sheath material displayed total reactive-site densities of 80.3 × 10?5 and 12.3 × 10?5 mol/g (dry mass) of cyanobacteria, respectively, implying that much of the surface reactivity of this microorganism is located on the cell wall and not the sheath. This is corroborated by electrophoretic mobility measurements that showed that the sheath has a net neutral charge at mid-pHs. In contrast, unsheathed cells exhibited a stronger negative-charge characteristic. Additionally, transmission electron microscopy analysis of ultrathin sections stained with heavy metals further demonstrated that most of the reactive binding sites are located upon the cell wall. Thus, the cell surface reactivity of Calothrix sp. strain KC97 can be described as a dual layer composed of a highly reactive cell wall enclosed within a poorly reactive sheath.

Phoenix, V. R.; Martinez, R. E.; Konhauser, K. O.; Ferris, F. G.

2002-01-01

290

Paenibacillus sp. Strain JDR-2 and XynA1: a Novel System for Methylglucuronoxylan Utilization  

PubMed Central

Environmental and economic factors predicate the need for efficient processing of renewable sources of fuels and chemicals. To fulfill this need, microbial biocatalysts must be developed to efficiently process the hemicellulose fraction of lignocellulosic biomass for fermentation of pentoses. The predominance of methylglucuronoxylan (MeGAXn), a ?-1,4 xylan in which 10% to 20% of the xylose residues are substituted with ?-1,2-4-O-methylglucuronate residues, in hemicellulose fractions of hardwood and crop residues has made this a target for processing and fermentation. A Paenibacillus sp. (strain JDR-2) has been isolated and characterized for its ability to efficiently utilize MeGAXn. A modular xylanase (XynA1) of glycosyl hydrolase family 10 (GH 10) was identified through DNA sequence analysis that consists of a triplicate family 22 carbohydrate binding module followed by a GH 10 catalytic domain followed by a single family 9 carbohydrate binding module and concluding with C-terminal triplicate surface layer homology (SLH) domains. Immunodetection of the catalytic domain of XynA1 (XynA1 CD) indicates that the enzyme is associated with the cell wall fraction, supporting an anchoring role for the SLH modules. With MeGAXn as substrate, XynA1 CD generated xylobiose and aldotetrauronate (MeGAX3) as predominant products. The inability to detect depolymerization products in medium during exponential growth of Paenibacillus sp. strain JDR-2 on MeGAXn, as well as decreased growth rate and yield with XynA1 CD-generated xylooligosaccharides and aldouronates as substrates, indicates that XynA1 catalyzes a depolymerization process coupled to product assimilation. This depolymerization/assimilation system may be utilized for development of biocatalysts to efficiently convert MeGAXn to alternative fuels and biobased products.

StJohn, Franz J.; Rice, John D.; Preston, James F.

2006-01-01

291

[14C]methylammonium transport by Frankia sp. strain CpI1.  

PubMed

We describe an NH4+-specific transport system in the N2-fixing symbiotic actinomycete Frankia sp. strain CpI1. [14C]methylammonium was used as an NH4+ analog. No specific transport process was detected when cells were grown on high concentrations of NH4+. A transport system with a high affinity for CH3NH3+ was synthesized after 3 to 4 h of nitrogen starvation. Methylammonium transport was not significantly inhibited by a variety of amino acids, primary amines, and polyamines. Ammonium completely eliminated CH3NH3+ transport. The Km for CH3NH3+ transport was around 2 +/- 1.8 microM with a Vmax of 4 to 5 nmol/min per mg of protein. The electron transport inhibitors cyanide and azide eliminated uptake, as did the uncoupler carbonyl cyanide-m-chlorophenylhydrazone. The sulfydryl reagent p-chloromercuribenzoic acid and the heavy metal thallium also inhibited uptake, suggesting the presence of an NH4+-specific permease. Concentration of CH3NH3+ across the membrane was demonstrated by conducting uptakes at low temperature to slow the metabolism of CH3NH3+ by glutamine synthetase. At 7 degrees C most of the label was concentrated inside the cells in a form that could be chased from the cells by adding excess NH4+ to the medium. At 30 degrees C most of the label was present as an impermeant metabolite. Thin-layer chromatography of cell extracts confirmed that the radioactivity inside the cells was mainly in the form of CH3NH3+ at 7 degrees C but was present as an unidentified metabolite at 30 degrees C. These studies demonstrate that Frankia sp. strain CpI1 has a high-affinity NH4+ transport system that is synthesized in response to NH4+ starvation. PMID:6501218

Mazzucco, C E; Benson, D R

1984-11-01

292

[14C]methylammonium transport by Frankia sp. strain CpI1.  

PubMed Central

We describe an NH4+-specific transport system in the N2-fixing symbiotic actinomycete Frankia sp. strain CpI1. [14C]methylammonium was used as an NH4+ analog. No specific transport process was detected when cells were grown on high concentrations of NH4+. A transport system with a high affinity for CH3NH3+ was synthesized after 3 to 4 h of nitrogen starvation. Methylammonium transport was not significantly inhibited by a variety of amino acids, primary amines, and polyamines. Ammonium completely eliminated CH3NH3+ transport. The Km for CH3NH3+ transport was around 2 +/- 1.8 microM with a Vmax of 4 to 5 nmol/min per mg of protein. The electron transport inhibitors cyanide and azide eliminated uptake, as did the uncoupler carbonyl cyanide-m-chlorophenylhydrazone. The sulfydryl reagent p-chloromercuribenzoic acid and the heavy metal thallium also inhibited uptake, suggesting the presence of an NH4+-specific permease. Concentration of CH3NH3+ across the membrane was demonstrated by conducting uptakes at low temperature to slow the metabolism of CH3NH3+ by glutamine synthetase. At 7 degrees C most of the label was concentrated inside the cells in a form that could be chased from the cells by adding excess NH4+ to the medium. At 30 degrees C most of the label was present as an impermeant metabolite. Thin-layer chromatography of cell extracts confirmed that the radioactivity inside the cells was mainly in the form of CH3NH3+ at 7 degrees C but was present as an unidentified metabolite at 30 degrees C. These studies demonstrate that Frankia sp. strain CpI1 has a high-affinity NH4+ transport system that is synthesized in response to NH4+ starvation.

Mazzucco, C E; Benson, D R

1984-01-01

293

An Evolutionary Hot Spot: the pNGR234b Replicon of Rhizobium sp. Strain NGR234  

Microsoft Academic Search

Rhizobium sp. strain NGR234 has an exceptionally broad host range and is able to nodulate more than 112 genera of legumes. Since the overall organization of the NGR234 genome is strikingly similar to that of the narrow-host-range symbiont Rhizobium meliloti strain 1021 (also known as Sinorhizobium meliloti), the obvious question is why are the spectra of hosts so different? Study

W. R. Streit; R. A. Schmitz; X. Perret; C. Staehelin; W. J. Deakin; C. Raasch; H. Liesegang; W. J. Broughton

2004-01-01

294

Isolation of an alkane-degrading Alcanivorax sp. strain 2B5 and cloning of the alkB gene  

Microsoft Academic Search

A Gram-negative coccus, strain 2B5, was isolated from the sea mud of the crude oil-polluted Donghai area in China and identified as Alcanivorax sp. based on its physiological characteristics and analysis of its 16S rRNA gene sequence. Strain 2B5 was able to degrade C13–C30n-alkanes and branched alkanes (pristane and phytane) from crude oil as the sole carbon source. The optimal

Yi-Chen Liu; Ling-Zhi Li; Ying Wu; Wei Tian; Li-Ping Zhang; Lian Xu; Qi-Rong Shen; Biao Shen

2010-01-01

295

Alkaliphilic Bacillus sp. strain KSM-LD1 contains a record number of subtilisin-like serine proteases genes  

Microsoft Academic Search

The presence of 11 genes encoding subtilisin-like serine proteases was demonstrated by cloning from the genome of alkaliphilic\\u000a Bacillus sp. strain KSM-LD1. This strain exoproduces the oxidatively stable alkaline protease LD-1 (Saeki et al. Curr Microbiol, 47:337–340,\\u000a 2003). Among the 11 genes, six genes encoding alkaline proteases (SA, SB, SC, SD, SE, and LD-1) were expressed in Bacillus hosts. However,

Yasushi Takimura; Kazuhiro Saito; Mitsuyoshi Okuda; Yasushi Kageyama; Katsuhisa Saeki; Katsuya Ozaki; Susumu Ito; Tohru Kobayashi

2007-01-01

296

Permeable Reactive Biobarriers for In Situ Cr(VI) Reduction: Bench Scale Tests Using Cellulomonas sp. Strain ES6  

Microsoft Academic Search

Chromate (Cr(VI)) reduction studies were performed in bench scale flow columns using the fermentative subsurface isolate Cellulomonas sp. strain ES6. In these tests, columns packed with either quartz sand or hydrous ferric oxide (HFO)-coated quartz sand, were inoculated with strain ES6 and fed nutrients to stimulate growth before nutrient-free Cr(VI) solutions were injected. Results show that in columns containing quartz

Sridhar Viamajala; Brent M. Peyton; Robin Gerlach; Vaideeswaran; William A. Apel; James N. Petersen

2008-01-01

297

Metal Reduction and Iron Biomineralization by a Psychrotolerant Fe(III)Reducing Bacterium, Shewanella sp. Strain PV4  

Microsoft Academic Search

A marine psychrotolerant, dissimilatory Fe(III)-reducing bacterium, Shewanella sp. strain PV-4, from the microbial mat at a hydrothermal vent of Loihi Seamount in the Pacific Ocean has been further characterized, with emphases on metal reduction and iron biomineralization. The strain is able to reduce metals such as Fe(III), Co(III), Cr(VI), Mn(IV), and U(VI) as electron acceptors while using lactate, formate, pyruvate,

Yul Roh; Haichun Gao; Hojatollah Vali; David W. Kennedy; Zamin K. Yang; Weimin Gao; Alice C. Dohnalkova; Raymond D. Stapleton; Ji-Won Moon; Tommy J. Phelps; James K. Fredrickson; Jizhong Zhou

2006-01-01

298

Mutation breeding of chitosanase-producing strain Bacillus sp. S65 by low-energy ion implantation  

Microsoft Academic Search

In order to obtain an industrial strain with higher chitosanase yield, the wild strain Bacillus sp. S65 cells were mutated by a novel mutagen, nitrogen ion beam, with energy of 15 keV and dose ranging from 2.6 × 1014 to 5.2 × 1015 ions\\/cm2. One mutant, s65F5 with high yield of chitosanase was isolated. Results showed that the production of chitosanase of s65F5 was dramatically increased

Caixin Su; Wei Zhou; Yonghong Fan; Li Wang; Shiguang Zhao; Zengliang Yu

2006-01-01

299

Genome Sequence of Bacillus sp. Strain HYC-10, Isolated from Intestinal Tract Contents from a Marine Fish (Mugil cephalus)  

PubMed Central

Bacillus sp. strain HYC-10 was isolated with intestinal tract content of a fish, Mugil cephalus, captured from the sea close to Xiamen Island, China. Here, we present the draft genome of strain HYC-10, which contains 3,611,918 bp with a G+C content of 41.30% and contains 3,687 protein-coding genes and 33 tRNA genes.

Lai, Qiliang; Liu, Yang

2012-01-01

300

Relationship between surface physicochemical properties and its demulsifying ability of an alkaliphilic strain of Alcaligenes sp. S-XJ-1  

Microsoft Academic Search

To investigate the relationship between physicochemical properties and demulsifying ability, the influence of culture pH on physicochemical properties of a demulsifying strain of Alcaligenes sp. S-XJ-1 was studied. The demulsifying strain grew slowly in acidic conditions but grew well under alkaline conditions, indicating that S-XJ-1 was an alkaliphile. The optimal culture pH was observed at 10 for cultivation of Alcaligenes

Jia Liu; Li-jun Lu; Xiang-feng Huang; Jia-jia Shang; Ming-xia Li; Jing-cheng Xu; Hui-ping Deng

2011-01-01

301

Biodegradation of malachite green by Pseudomonas sp. strain DY1 under aerobic condition: characteristics, degradation products, enzyme analysis and phytotoxicity  

Microsoft Academic Search

Malachite green (MG), a widely-used and recalcitrant dye, has been confirmed to be carcinogenic and mutagenic against many\\u000a organisms. The main objective of this study is to investigate the capability of Pseudomonas sp. strain DY1 to decolorize MG, and to explore the possible mechanism. The results showed that this strain demonstrated\\u000a high decolorizing capability (90.3–97.2%) at high concentrations of MG

Lin-Na Du; Sheng Wang; Gang Li; Bing Wang; Xiao-Ming Jia; Yu-Hua Zhao; Yun-Long Chen

2011-01-01

302

Ecotoxicological assessment of pesticides towards the plant growth promoting activities of Lentil ( Lens esculentus )-specific Rhizobium sp. strain MRL3  

Microsoft Academic Search

This study was designed to evaluate the effect of the selected pesticides [herbicides (metribuzin and glyphosate), insecticides\\u000a (imidacloprid and thiamethoxam) and fungicides (hexaconazole, metalaxyl and kitazin)] at the recommended and the higher dose\\u000a rates on plant growth promoting traits of Rhizobium sp. strain MRL3 isolated from lentil-nodules. Strain MRL3 was explicitly selected owing to its high pesticide-tolerance ability\\u000a and substantial

Munees Ahemad; Mohammad Saghir Khan

2011-01-01

303

Regio- and stereospecific oxidation of fluorene, dibenzofuran, and dibenzothiophene by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4  

SciTech Connect

Fluorene, dibenzofuran, dibenzothiophene, and carbazole are structural analogs differing only in the type of atom bridging the two aromatic rings. These compounds are constituents of fossil fuels. The authors have examined the oxidation of fluorene, dibenzofuran, and dibenzothiophene by mutant and recombinant strains which express NDO from Pseudomonas sp. strain NCIB 9816-4 and reports the yields, region chemistry, absolute stereochemistry, and enantiomeric purity of the isolated initial metabolites. 71 refs., 3 figs., 2 tabs.

Resnick, S.M.; Gibson, D.T. [Univ. of Iowa, Iowa City, IA (United States)

1996-11-01

304

Metabolism of hydroxydibenzofurans, methoxydibenzofurans, acetoxydibenzofurans, and nitrodibenzofurans by Sphingomonas sp. strain HH69  

SciTech Connect

The metabolism of 11 substituted dibenzofurans by the dibenzofuran-degrading Sphingomonas sp. strain HH69 was investigated. Strain HH69 utilizes 2-, 3-, and 4-acetoxydibenzofuran as well as 2-, 3-, and 4-hydroxydibenzofuran as sole sources of carbon and energy. The degradation of acetoxydibenzofurans is initiated by hydrolysis of the ester bonds, yielding the corresponding hydroxydibenzofurans and acetate. Strain HH69 grew on 2-methoxydibenzofuran only after it was adapted to the utilization of 5-methoxysalicylic acid, whereas 3- and 4-methoxydibenzofuran as well as 2- and 3-nitrodibenzofuran were only cooxidized. During the breakdown of all eight hydroxy-, methoxy-, and nitrodibenzofurans studied here, the corresponding substituted salicylic acids accumulated in the culture broth. In the cases of 2- and 3-hydroxydibenzofuran as well as 2- and 3-nitrodibenzofuran, salicylic acid was also formed. Those four dibenzofurans which did not serve as carbon sources for strain HH69 were converted to a nonutilizable salicylic acid derivative. From turnover experiments with the mutant HH69/II, which is deficient in meta-cleavage, 2,2{prime}, 3,4{prime}-tetrahydroxybiphenyl, 2,2{prime},3-trihydroxy-5{prime}-methoxybiphenyl, 2,2{prime},3-trihydroxy-5{prime}-nitrobiphenyl, and 2,2{prime},3-trihydroxy-4{prime}-nitrobiphenyl were isolated as the main products formed from 3-hydroxydibenzofuran, 2-methoxydibenzofuran, and 2- and 3-nitrodibenzo-furan, respectively. These results indicate significant regioselectivity for the dioxygenolytic cleavage of the ether bond of these monosubstituted dibenzofurans, with a preference for the nonsubstituted aromatic nucleus. Substituted trihydroxybiphenyls are converted further by meta-cleavage followed by the removal of the side chain of the resulting product. A stepwise degradation of this side chain was found to be involved in the metabolism of 2-hydroxydibenzofuran. 34 refs., 5 figs., 2 tabs.

Harms, H. [Swiss Federal Institute for Environmental Science and Technology, Duebendorf (Switzerland)]|[Universitaet of Hamburg (Germany); Wittich, R.M.; Fortnagel, P. [Universitaet of Hamburg (Germany)

1995-07-01

305

Genome Sequence of Halomonas sp. Strain A3H3, Isolated from Arsenic-Rich Marine Sediments.  

PubMed

We report the genome sequence of Halomonas sp. strain A3H3, a bacterium with a high tolerance to arsenite, isolated from multicontaminated sediments of the l'Estaque harbor in Marseille, France. The genome is composed of a 5,489,893-bp chromosome and a 157,085-bp plasmid. PMID:24115546

Koechler, Sandrine; Plewniak, Frédéric; Barbe, Valérie; Battaglia-Brunet, Fabienne; Jost, Bernard; Joulian, Catherine; Philipps, Muriel; Vicaire, Serge; Vincent, Stéphanie; Ye, Tao; Bertin, Philippe N

2013-10-10

306

Complete Genome Sequence of Rahnella sp Strain Y9602, a Gammaproteobacterium Isolate from Metal- and Radionuclide-Contaminated Soil  

SciTech Connect

Rahnella sp. strain Y9602 is a gammaproteobacterium isolated from contaminated subsurface soils that is capable of promoting uranium phosphate mineralization as a result of constitutive phosphatase activity. Here we report the first complete genome sequence of an isolate belonging to the genus Rahnella.

Martinez, Robert J [University of Alabama, Tuscaloosa; Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Held, Brittany [Los Alamos National Laboratory (LANL); Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Sobeckya, Patricia A. [University of Alabama, Tuscaloosa

2012-01-01

307

Draft Genome Sequence of Treponema sp. Strain JC4, a Novel Spirochete Isolated from the Bovine Rumen  

PubMed Central

Morphologically and biochemically diverse members of the Treponema genus are present in the gastrointestinal tract of ruminants, yet very little is understood about their functional importance to this microbiome. Here we describe the annotated draft genome sequence of Treponema sp. strain JC4, a novel spirochete isolated from a bovine rumen sample.

Rosewarne, Carly P.; Cheung, Jane L.; Smith, Wendy J. M.; Evans, Paul N.; Tomkins, Nigel W.; Denman, Stuart E.; O Cuiv, Paraic

2012-01-01

308

Draft Genome Sequence of the Polyextremophilic Exiguobacterium sp. Strain S17, Isolated from Hyperarsenic Lakes in the Argentinian Puna.  

PubMed

Exiguobacterium sp. strain S17 is a moderately halotolerant, arsenic-resistant bacterium that was isolated from Laguna Socompa stromatolites in the Argentinian Puna. The draft genome sequence suggests potent enzyme candidates that are essential for survival under multiple environmental extreme conditions, such as high levels of UV radiation, elevated salinity, and the presence of critical arsenic concentrations. PMID:23887911

Ordoñez, Omar F; Lanzarotti, Esteban; Kurth, Daniel; Gorriti, Marta F; Revale, Santiago; Cortez, Néstor; Vazquez, Martin P; Farías, María E; Turjanski, Adrian G

2013-07-25

309

Complete Genome Sequence of the Denitrifying and N2O-Reducing Bacterium Azoarcus sp. Strain KH32C  

PubMed Central

We report the finished and annotated genome sequence of a denitrifying and N2O-reducing betaproteobacterium, Azoarcus sp. strain KH32C. The genome is composed of one chromosome and one megaplasmid and contains genes for plant-microbe interactions and the gene clusters for aromatic-compound degradations.

Tago, Kanako; Oshima, Kenshiro; Hattori, Masahira; Ishii, Satoshi; Otsuka, Shigeto; Senoo, Keishi

2012-01-01

310

Complete genome sequence of the denitrifying and N2O-reducing bacterium Azoarcus sp. strain KH32C.  

PubMed

We report the finished and annotated genome sequence of a denitrifying and N(2)O-reducing betaproteobacterium, Azoarcus sp. strain KH32C. The genome is composed of one chromosome and one megaplasmid and contains genes for plant-microbe interactions and the gene clusters for aromatic-compound degradations. PMID:22328754

Nishizawa, Tomoyasu; Tago, Kanako; Oshima, Kenshiro; Hattori, Masahira; Ishii, Satoshi; Otsuka, Shigeto; Senoo, Keishi

2012-03-01

311

Tetracycline resistance-encoding plasmid from Bacillus sp. strain #24, isolated from the marine sponge Haliclona simulans.  

PubMed

Knowledge of the nature of resistance determinants in natural habitats is fundamental to increasing our understanding of the development of antibiotic resistance in clinical settings. Here we provide the first report of a tetracycline resistance-encoding plasmid, pBHS24, from a marine sponge-associated bacterium, Bacillus sp. strain #24, isolated from Haliclona simulans. PMID:21057017

Phelan, Robert W; Clarke, Charles; Morrissey, John P; Dobson, Alan D W; O'Gara, Fergal; Barbosa, Teresa M

2010-11-05

312

Molecular cloning of the gene which encodes beta-N-acetylglucosaminidase from a marine bacterium, Alteromonas sp. strain O-7.  

PubMed Central

The gene encoding the periplasmic beta-N-acetylglucosaminidase (GlcNAcase B) from a marine Alteromonas sp. strain, O-7, was cloned and sequenced. The protein sequence of GlcNAcase B revealed a highly significant homology with Vibrio GlcNAcase and alpha- and beta-chains of human beta-hexosaminidase.

Tsujibo, H; Fujimoto, K; Tanno, H; Miyamoto, K; Kimura, Y; Imada, C; Okami, Y; Inamori, Y

1995-01-01

313

Genome sequence of the leaf-colonizing Bacterium Bacillus sp. strain 5B6, isolated from a cherry tree.  

PubMed

Plant growth-promoting bacteria colonize various habitats, including the phyllosphere. Here, we present the high-quality draft genome sequence of Bacillus sp. strain 5B6, which was isolated from the leaf of a cherry tree. The 3.9-Mb genome uncovers its potential for understanding the nature of leaf colonization as well as antibiosis against plant pathogens. PMID:22740678

Kim, Byung Kwon; Chung, Joon-hui; Kim, Seon-Young; Jeong, Haeyoung; Kang, Sung Gyun; Kwon, Soon-Kyeong; Lee, Choong Hoon; Song, Ju Yeon; Yu, Dong Su; Ryu, Choong-Min; Kim, Jihyun F

2012-07-01

314

Genome Sequence of the Leaf-Colonizing Bacterium Bacillus sp. Strain 5B6, Isolated from a Cherry Tree  

PubMed Central

Plant growth-promoting bacteria colonize various habitats, including the phyllosphere. Here, we present the high-quality draft genome sequence of Bacillus sp. strain 5B6, which was isolated from the leaf of a cherry tree. The 3.9-Mb genome uncovers its potential for understanding the nature of leaf colonization as well as antibiosis against plant pathogens.

Kim, Byung Kwon; Chung, Joon-hui; Kim, Seon-Young; Jeong, Haeyoung; Kang, Sung Gyun; Kwon, Soon-Kyeong; Lee, Choong Hoon; Song, Ju Yeon; Yu, Dong Su

2012-01-01

315

Cloning, characterization and expression of a gene encoding dihydroxyacetone synthase in Mycobacterium sp. strain JC1 DSM 3803.  

PubMed

Dihydroxyacetone synthase (DHAS) is a key enzyme involved in the assimilation of methanol in Mycobacterium sp. strain JC1 DSM 3803. The structural gene encoding DHAS in Mycobacterium sp. strain JC1 was cloned using random-primed probes synthesized after PCR with synthetic primers based on the amino acid sequences conserved in two yeast DHASs and several transketolases. The cloned gene, dasS, had an ORF of 2193 nt, encoding a protein with a calculated molecular mass of 78,197 Da. The deduced amino acid sequence of dasS contained an internal sequence of Mycobacterium sp. strain JC1 DHAS and exhibited 29.2 and 27.3 % identity with those of Candida boidinii and Hansenula polymorpha enzymes, respectively. Escherichia coli transformed with the cloned gene produced a novel protein with a molecular mass of approximately 78 kDa, which cross-reacted with anti-DHAS antiserum and exhibited DHAS activity. Primer-extension analysis revealed that the transcriptional start site of the gene was the nucleotide A located 31 bp upstream from the dasS start codon. RT-PCR showed that dasS was transcribed as a monocistronic message. Northern hybridization and beta-galactosidase assay with the putative promoter region of dasS revealed that the gene was transcribed only in cells growing on methanol. The expression of dasS in Mycobacterium sp. strain JC1 was free from catabolite repression. PMID:18048931

Seo, Jae-Gu; Park, Sae W; Park, Hyuk; Kim, Seo Y; Ro, Young T; Kim, Eungbin; Cho, Jin W; Kim, Young M

2007-12-01

316

Biodegradation of n-Alkylcycloalkanes and n-Alkylbenzenes via New Pathways in Alcanivorax sp. Strain MBIC 4326  

PubMed Central

The degradation of long-chain n-alkylbenzenes and n-alkylcyclohexanes by Alcanivorax sp. strain MBIC 4326 was investigated. The alkyl side chain of these compounds was mainly processed by ?-oxidation. In the degradation of n-alkylcyclohexanes, cyclohexanecarboxylic acid was formed as an intermediate. This compound was further transformed to benzoic acid via 1-cyclohexene-1-carboxylic acid.

Dutta, Tapan K.; Harayama, Shigeaki

2001-01-01

317

Identification of the Major Glycolipid from Mycoplasma SP., Strain J as 3,4,6-Triacyl-beta-D-Glucopyranose.  

National Technical Information Service (NTIS)

Mycoplasma sp., strain J, contains two glycolipids, cholesteryl beta-D-glucoside and 3,4,6-triacyl-beta-D-glucopyranose. The structure of the latter was proven by standard chemical procedures. Glycolipids comprise about 20% of the total lipids of the orga...

P. F. Smith W. R. Mayberry

1968-01-01

318

A MANNANASE, MANA, OF THE POLYCENTRIC ANAEROBIC FUNGUS ORPINOMYCES SP. STRAIN PC-2 HAS CARBOHYDRATE BINDING AND DOCKING MODULES  

Technology Transfer Automated Retrieval System (TEKTRAN)

The anaerobic fungus Orpinomyces sp. strain PC-2 produces a broad spectrum of glycoside hydrolases, most of which are components of a high molecular mass cellusomal complex. Here we report about a cDNA (manA) having 1,924 bp isolated from the fungus and found to encode a polypeptide of 579 amino ac...

319

Draft Genome Sequence of the Polyextremophilic Exiguobacterium sp. Strain S17, Isolated from Hyperarsenic Lakes in the Argentinian Puna  

PubMed Central

Exiguobacterium sp. strain S17 is a moderately halotolerant, arsenic-resistant bacterium that was isolated from Laguna Socompa stromatolites in the Argentinian Puna. The draft genome sequence suggests potent enzyme candidates that are essential for survival under multiple environmental extreme conditions, such as high levels of UV radiation, elevated salinity, and the presence of critical arsenic concentrations.

Ordonez, Omar F.; Lanzarotti, Esteban; Kurth, Daniel; Gorriti, Marta F.; Revale, Santiago; Cortez, Nestor; Vazquez, Martin P.; Farias, Maria E.

2013-01-01

320

Dynamic analysis of a genomic island in Magnetospirillum sp. strain AMB-1 reveals how magnetosome synthesis developed  

Microsoft Academic Search

The entire structure of a 98kb genomic region that abounds in genes related to magnetosome synthesis was first described in the Magnetospirillum sp. strain AMB-1. The deletion of this 98kb genomic region and the circular form after excision from the chromosome was detected by PCR amplification. This strongly suggests that the region has undergone a lateral gene transfer. The region

Yorikane Fukuda; Yoshiko Okamura; Haruko Takeyama; Tadashi Matsunaga

2006-01-01

321

Variation in composition and yield of exopolysaccharides produced by Klebsiella sp. strain K32 and Acinetobacter calcoaceticus BD4.  

PubMed Central

The exopolysaccharides produced by Klebsiella sp. strain K32 and Acinetobacter calcoaceticus BD4 under different growth conditions have been analyzed for sugar composition. The first use of ion chromatography for the quantitative determination of microbial exopolysaccharide composition is reported. Klebsiella sp. strain K32 produced a polymer composed of rhamnose, galactose, and mannose early in its fermentation. The composition of the polymer varied markedly depending on the growth stage of the organism. Klebsiella sp. strain K32 grown in a fermentor produced a polymer which was rich in mannose during early exponential growth in a complex medium, but in the late stationary phase it did not contain detectable levels of mannose. The rhamnose present in the polymer increased from 12 to 55% over the course of growth, whereas galactose decreased from 63 to 45%. A. calcoaceticus BD4 produced a polymer containing rhamnose, glucose, mannose throughout its growth and stationary phase. Klebsiella sp. strain K32 and A. calcoaceticus BD4 were grown on various carbon sources in shake flasks. The polymer yield and composition from both organisms were found to vary with the carbon source. The exopolysaccharide with the highest mannose composition was obtained by using rhamnose as a carbon source for both organisms. These and other data suggest that regulatory changes caused by growth on different substrates result in either the production of a different distribution of polymers or a change in exopolysaccharide structure.

Bryan, B A; Linhardt, R J; Daniels, L

1986-01-01

322

Draft Genome Sequence of Marine-Derived Streptomyces sp. Strain AA0539, Isolated from the Yellow Sea, China  

PubMed Central

Here, we report the draft genome sequence of Streptomyces sp. strain AA0539, isolated from marine sediment of the Yellow Sea, China. Its small genome (?5.8 Mb) contains large, unique genes and gene clusters for diverse secondary metabolites, suggesting great potential as a source for the discovery of novel natural products.

Xiong, Zhi-Qiang

2012-01-01

323

Genome Sequence of a Novel Polymer-Grade L-Lactate-Producing Alkaliphile, Exiguobacterium sp. Strain 8-11-1.  

PubMed

Exiguobacterium sp. strain 8-11-1 is a newly isolated alkaliphile, which was reported to efficiently produce l-lactate using NaOH as the neutralizing agent. Here, we present the first 2.9-Mb assembly of its genome sequence, which may provide useful information related to its efficient lactate production and sodium ion tolerance capacities. PMID:23950124

Jiang, Xu; Xue, Yanfen; Wang, Limin; Yu, Bo; Ma, Yanhe

2013-08-15

324

Genome Sequence of Halomonas sp. Strain A3H3, Isolated from Arsenic-Rich Marine Sediments  

PubMed Central

We report the genome sequence of Halomonas sp. strain A3H3, a bacterium with a high tolerance to arsenite, isolated from multicontaminated sediments of the l’Estaque harbor in Marseille, France. The genome is composed of a 5,489,893-bp chromosome and a 157,085-bp plasmid.

Plewniak, Frederic; Barbe, Valerie; Battaglia-Brunet, Fabienne; Jost, Bernard; Joulian, Catherine; Philipps, Muriel; Vicaire, Serge; Vincent, Stephanie; Ye, Tao; Bertin, Philippe N.

2013-01-01

325

Application of waste frying oils in the biosynthesis of biodemulsifier by a demulsifying strain Alcaligenes sp. S-XJ-1  

Microsoft Academic Search

Exploration of biodemulsifiers has become a new research aspect. Using waste frying oils (WFOs) as carbon source to synthesize biodemulsifiers has a potential prospect to decrease production cost and to improve the application of biodemulsifiers in the oilfield. In this study, a demulsifying strain, Alcaligenes sp. S-XJ-1, was investigated to synthesize a biodemulsifier using waste frying oils as carbon source.

Jia Liu; Kaiming Peng; Xiangfeng Huang; Lijun Lu; Hang Cheng; Dianhai Yang; Qi Zhou; Huiping Deng

2011-01-01

326

Biosynthesis of ursolic acid derivatives by microbial metabolism of ursolic acid with Nocardia sp. strains—Proposal of new biosynthetic pathways  

Microsoft Academic Search

Our studies of the microbial-metabolism of triterpenoid ursolic acid by various Nocardia sp. strains, have led to the proposal of two novel pathways to produce triterpenoid derivatives. Nocardia sp. NRRL 5646, Nocardia sp. 44822 and Nocardia sp. 44000 generated the following ursolic acid derivatives: ursolic acid methyl ester, ursonic acid, ursonic acid methyl ester, 3-oxoursa-1,12-dien-28-oic acid and 3-oxoursa-1,12-dien-28-oic acid methyl

Doris Leipold; Gesine Wünsch; Melanie Schmidt; Hans-Jörg Bart; Thomas Bley; H. Ekkehard Neuhaus; Hannah Bergmann; Elke Richling; Kai Muffler; Roland Ulber

2010-01-01

327

Soluble and particulate methane monooxygenase gene clusters in the marine methanotroph Methylomicrobium sp. strain NI.  

PubMed

Soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO) gene clusters in the marine methanotroph Methylomicrobium sp. strain NI were completely sequenced and analysed. Degenerated primers were newly designed and used to amplify the gene fragments containing intergenic mmoX-Y and mmoD-C regions and a partial pmoC region. Phylogenetic analysis of amino acid sequences deduced from mmoX and pmoA, as well as of 16S rRNA gene sequences, indicated that this strain was most closely related to the halotolerant methanotroph Methylomicrobium buryatense. There were putative sigma(54)- and sigma(70)-dependent promoter sequences upstream of the sMMO and pMMO genes, respectively, and mmoG, which is known to be related to the expression and assembly of sMMO, existed downstream of the sMMO genes. These findings suggest that the major components and regulation of MMOs in this marine methanotroph are quite similar to those in freshwater methane oxidizers, despite the difference in their habitats. PMID:18031335

Nakamura, Takamichi; Hoaki, Toshihiro; Hanada, Satoshi; Maruyama, Akihiko; Kamagata, Yoichi; Fuse, Hiroyuki

2007-12-01

328

Studies on hydrogenase activity and chlorobenzene respiration in Dehalococcoides sp. strain CBDB1.  

PubMed

Hydrogen oxidation and electron transport were studied in the chlorobenzene-utilizing anaerobe Dehalococcoides sp. strain CBDB1. While Cu(2+) and Hg(2+) ions irreversibly inhibited hydrogenase activity in intact cells, Ni(2+) ions inhibited reversibly. About 80% of the initial hydrogenase activity was inactivated within 30 s when the cells were exposed to air. In contrast, hydrogenase was active at a redox potential of +10 mV when this redox potential was established anoxically with a redox indicator. Viologen dyes served both as electron acceptor for hydrogenase and electron donor for the dehalogenase. A menaquinone analogue, 2,3-dimethyl 1,4-naphthoquinone, served neither as electron acceptor for the hydrogenase nor as electron donor for the dehalogenase. In addition, the menaquinone antagonist 2-n-heptyl-4-hydroxyquinoline-N-oxide had no effect on dechlorination catalyzed by cell suspensions or isolated membranes with hydrogen as electron donor, lending further support to the notion that menaquinone is not involved in electron transport. The ionophores tetrachlorosalicylanilide and carbonylcyanide m-chlorophenylhydrazone did not inhibit dechlorination by cell suspensions, indicating that strain CBDB1 does not require reverse electron transport. The ATP-synthase inhibitor N,N'-dicyclohexylcarbodiimide inhibited the dechlorination reaction with cell suspensions; however, the latter effect was partially relieved by the addition of tetrachlorosalicylanilide. 1,2,3,4-tetrachlorobenzene strongly inhibited dechlorination of other chlorobenzenes by cell suspensions with hydrogen as electron donor, but it did not interfere with either hydrogenase or dehalogenase activity. PMID:15490122

Jayachandran, Gopalakrishnan; Görisch, Helmut; Adrian, Lorenz

2004-10-15

329

2,4-Dinitrotoluene dioxygenase from Burkholderia sp. strain DNT: similarity to naphthalene dioxygenase.  

PubMed Central

2,4-Dinitrotoluene (DNT) dioxygenase from Burkholderia sp. strain DNT catalyzes the initial oxidation of DNT to form 4-methyl-5-nitrocatechol (MNC) and nitrite. The displacement of the aromatic nitro group by dioxygenases has only recently been described, and nothing is known about the evolutionary origin of the enzyme systems that catalyze these reactions. We have shown previously that the gene encoding DNT dioxygenase is localized on a degradative plasmid within a 6.8-kb NsiI DNA fragment (W.-C. Suen and J. C. Spain, J. Bacteriol. 175:1831-1837, 1993). We describe here the sequence analysis and the substrate range of the enzyme system encoded by this fragment. Five open reading frames were identified, four of which have a high degree of similarity (59 to 78% identity) to the components of naphthalene dioxygenase (NDO) from Pseudomonas strains. The conserved amino acid residues within NDO that are involved in cofactor binding were also identified in the gene encoding DNT dioxygenase. An Escherichia coli clone that expressed DNT dioxygenase converted DNT to MNC and also converted naphthalene to (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. In contrast, the E. coli clone that expressed NDO did not oxidize DNT. Furthermore, the enzyme systems exhibit similar broad substrate specificities and can oxidize such compounds as indole, indan, indene, phenetole, and acenaphthene. These results suggest that DNT dioxygenase and the NDO enzyme system share a common ancestor.

Suen, W C; Haigler, B E; Spain, J C

1996-01-01

330

Purification and Characterization of an ?-Glucosidase from Rhizobium sp. (Robinia pseudoacacia L.) Strain USDA 4280  

PubMed Central

A novel ?-glucosidase with an apparent subunit mass of 59 ± 0.5 kDa was purified from protein extracts of Rhizobium sp. strain USDA 4280, a nodulating strain of black locust (Robinia pseudoacacia L), and characterized. After purification to homogeneity (475-fold; yield, 18%) by ammonium sulfate precipitation, cation-exchange chromatography, hydrophobic chromatography, dye chromatography, and gel filtration, this enzyme had a pI of 4.75 ± 0.05. The enzyme activity was optimal at pH 6.0 to 6.5 and 35°C. The activity increased in the presence of NH4+ and K+ ions but was inhibited by Cu2+, Ag+, Hg+, and Fe2+ ions and by various phenyl, phenol, and flavonoid derivatives. Native enzyme activity was revealed by native gel electrophoresis and isoelectrofocusing-polyacrylamide gel electrophoresis with fluorescence detection in which 4-methylumbelliferyl ?-glucoside was the fluorogenic substrate. The enzyme was more active with ?-glucosides substituted with aromatic aglycones than with oligosaccharides. This ?-glucosidase exhibited Michaelis-Menten kinetics with 4-methylumbelliferyl ?-d-glucopyranoside (Km, 0.141 ?M; Vmax, 6.79 ?mol min?1 mg?1) and with p-nitrophenyl ?-d-glucopyranoside (Km, 0.037 ?M; Vmax, 2.92 ?mol min?1 mg?1). Maltose, trehalose, and sucrose were also hydrolyzed by this enzyme.

Berthelot, Karine; Delmotte, Francis M.

1999-01-01

331

Enhancement of the potential to utilize octopine in the nonfluorescent Pseudomonas sp. strain 92  

SciTech Connect

The nonfluorescent Pseudomonas sp. strain 92 requires the presence of a supplementary carbon source for growth on octopine, whereas the spontaneous mutant RB100 has acquired the capacity to utilize this opine as the sole carbon and nitrogen source. Insertional mutagenesis of RB100 with transposon Tn5 generated mutants which were unable to grow on octopine and others which grew slowly on this substrate. Both types of mutants yielded revertants that had regained the ability to utilize octopine. Some of the revertants had lost the transposon, whereas in others the transposon was retained but with rearrangements of the insertion site. Genes of octopine catabolism from strain 92 were cloned on a cosmid vector to generate pK3. The clone pK3 conferred the ability to utilize octopine as the sole carbon and nitrogen source on the host Pseudomonas putida KT2440. Although they conferred an equivalent growth phenotype, the mutant genes carried by RB100 and the cloned genes on pK3 differed in their regulation. Utilization of ({sup 14}C)octopine was inducible by octopine in RB100 and was constitutive in KT2440(pK3).

Gill, S.S.; Boivin, R.; Dion, P. (Univ. Laval, Quebec City, Quebec (Canada))

1991-08-01

332

Anilofos tolerance and its mineralization by the cyanobacterium Synechocystis sp. strain PUPCCC 64.  

PubMed

This study deals with anilofos tolerance and its mineralization by the common rice field cyanobacterium Synechocystis sp. strain PUPCCC 64. The organism tolerated anilofos up to 25 mg L(-1). The herbicide caused inhibitory effects on photosynthetic pigments of the test organism in a dose-dependent manner. The organism exhibited 60, 89, 96, 85 and 79% decrease in chlorophyll a, carotenoids, phycocyanin, allophycocyanin and phycoerythrin, respectively, in 20 mg L(-1) anilofos on day six. Activities of superoxide dismutase, catalase and peroxidase increased by 1.04 to 1.80 times over control cultures in presence of 20 mg L(-1) anilofos. Glutathione content decreased by 26% while proline content was unaffected by 20 mg L(-1) anilofos. The test organism showed intracellular uptake and metabolized the herbicide. Uptake of herbicide by test organism was fast during initial six hours followed by slow uptake until 120 hours. The organism exhibited maximum anilofos removal at 100 mg protein L(-1), pH 8.0 and 30°C. Its growth in phosphate deficient basal medium in the presence of anilofos (2.5 mg L(-1)) indicated that herbicide was used by the strain PUPCCC 64 as a source of phosphate. PMID:23382844

Singh, D P; Khattar, J I S; Kaur, Mandeep; Kaur, Gurdeep; Gupta, Meenu; Singh, Yadvinder

2013-01-31

333

Biodegradation of chlorinated alkanes and their commercial mixtures by Pseudomonas sp. strain 273.  

PubMed

The biodegradation of chlorinated alkanes was studied under oxic conditions with the objective of identifying favorable and unfavorable intramolecular chlorination sequences with respect to the enzymes studied. Several dehalogenating bacterial strains were screened for their ability to degrade middle-chain polychlorinated alkanes as well as a commercial mixture. Of the organisms tested, the most promising was Pseudomonas sp. strain 273, which possesses an oxygenolytic dehalogenase. The effects of carbon chain length (C(6)-C(16)), halogen position, and overall chlorine content (14-61% w/w) were examined using both commercially available compounds and molecules synthesized in our laboratory. The effects of co-substrates, solvents, and inducing agents were also studied. The results with pure chlorinated alkanes showed that the relative positions of the chlorine atoms strongly influenced the total amount of dehalogenation achieved. The greatest dehalogenation yields were associated with terminally chlorinated alkanes. The alpha- and alpha,omega-chlorinated compounds yielded similar results. Vicinal chlorination had the most dramatic impact on degradation. When present on both ends or at the center of the molecule, no dehalogenation was detected. Although partial dehalogenation of 1,2-dichlorodecane was observed, it was likely due to a combination of beta-oxidation and an abiotic mechanism. Cereclor S52 was appreciably dehalogenated in shake flasks only when 1,10-dichlorodecane was present as a co-substrate and after increasing the oil surface area through mechanical emulsification, demonstrating the importance of abiotic factors in degrading commercial polychlorinated alkane mixtures. PMID:16491365

Heath, Ester; Brown, Wayne A; Jensen, Soren R; Bratty, Michael P

2004-11-30

334

Natural Electrotransformation of Lightning-Competent Pseudomonas sp. Strain N3 in Artificial Soil Microcosms  

PubMed Central

The lightning-competent Pseudomonas sp. strain N3, recently isolated from soil, has been used to study the extent of natural electrotransformation (NET) or lightning transformation as a horizontal gene transfer mechanism in soil. The variation of electrical fields applied to the soil with a laboratory-scale lightning system provides an estimate of the volume of soil affected by NET. Based on the range of the electric field that induces NET of Pseudomonas strain N3, the volume of soil, where NET could occur, ranges from 2 to 950 m3 per lightning strike. The influence of DNA parameters (amount, size, and purity) and DNA soil residence time were also investigated. NET frequencies (electrotransformants/recipient cells) ranged from 10?8 for cell lysate after 1 day of residence in soil to 4 × 10?7 with a purified plasmid added immediately before the lightning. The electrical field gradient (in kilovolts per cm) also played a role as NET frequencies ranging from 1 × 10?5 at 2.3 kV/cm to 1.7 × 10?4 at 6.5 kV/cm.

Ceremonie, Helene; Buret, Francois; Simonet, Pascal; Vogel, Timothy M.

2006-01-01

335

Multiple mechanisms of uranium immobilization by Cellulomonas sp. strain ES6.  

PubMed

Removal of hexavalent uranium (U(VI)) from aqueous solution was studied using a Gram-positive facultative anaerobe, Cellulomonas sp. strain ES6, under anaerobic, non-growth conditions in bicarbonate and PIPES buffers. Inorganic phosphate was released by cells during the experiments providing ligands for formation of insoluble U(VI) phosphates. Phosphate release was most probably the result of anaerobic hydrolysis of intracellular polyphosphates accumulated by ES6 during aerobic growth. Microbial reduction of U(VI) to U(IV) was also observed. However, the relative magnitudes of U(VI) removal by abiotic (phosphate-based) precipitation and microbial reduction depended on the buffer chemistry. In bicarbonate buffer, X-ray absorption fine structure (XAFS) spectroscopy showed that U in the solid phase was present primarily as a non-uraninite U(IV) phase, whereas in PIPES buffer, U precipitates consisted primarily of U(VI)-phosphate. In both bicarbonate and PIPES buffer, net release of cellular phosphate was measured to be lower than that observed in U-free controls suggesting simultaneous precipitation of U and PO?³?. In PIPES, U(VI) phosphates formed a significant portion of U precipitates and mass balance estimates of U and P along with XAFS data corroborate this hypothesis. High-resolution transmission electron microscopy (HR-TEM) and energy dispersive X-ray spectroscopy (EDS) of samples from PIPES treatments indeed showed both extracellular and intracellular accumulation of U solids with nanometer sized lath structures that contained U and P. In bicarbonate, however, more phosphate was removed than required to stoichiometrically balance the U(VI)/U(IV) fraction determined by XAFS, suggesting that U(IV) precipitated together with phosphate in this system. When anthraquinone-2,6-disulfonate (AQDS), a known electron shuttle, was added to the experimental reactors, the dominant removal mechanism in both buffers was reduction to a non-uraninite U(IV) phase. Uranium immobilization by abiotic precipitation or microbial reduction has been extensively reported; however, the present work suggests that strain ES6 can remove U(VI) from solution simultaneously through precipitation with phosphate ligands and microbial reduction, depending on the environmental conditions. Cellulomonadaceae are environmentally relevant subsurface bacteria and here, for the first time, the presence of multiple U immobilization mechanisms within one organism is reported using Cellulomonas sp. strain ES6. PMID:20872821

Sivaswamy, Vaideeswaran; Boyanov, Maxim I; Peyton, Brent M; Viamajala, Sridhar; Gerlach, Robin; Apel, William A; Sani, Rajesh K; Dohnalkova, Alice; Kemner, Kenneth M; Borch, Thomas

2011-02-01

336

Novel pathway of salicylate degradation by Streptomyces sp. strain WA46.  

PubMed

A novel salicylate-degrading Streptomyces sp., strain WA46, was identified by UV fluorescence on solid minimal medium containing salicylate; trace amounts of gentisate were detected by high-pressure liquid chromatography when strain WA46 was grown with salicylate. PCR amplification of WA46 DNA with degenerate primers for gentisate 1,2-dioxygenase (GDO) genes produced an amplicon of the expected size. Sequential PCR with nested GDO primers was then used to identify a salicylate degradation gene cluster in a plasmid library of WA46 chromosomal DNA. The nucleotide sequence of a 13.5-kb insert in recombinant plasmid pWD1 (which was sufficient for the complete degradation of salicylate) showed that nine putative open reading frames (ORFs) (sdgABCDEFGHR) were involved. Plasmid pWD1 derivatives disrupted in each putative gene were transformed into Streptomyces lividans TK64. Disruption of either sdgA or sdgC blocked salicylate degradation; constructs lacking sdgD accumulated gentisate. Cell extracts from Escherichia coli DH5 alpha transformants harboring pUC19 that expressed each of the sdg ORFs showed that conversions of salicylate to salicylyl-coenzyme A (CoA) and salicylyl-CoA to gentisyl-CoA required SdgA and SdgC, respectively. SdgA required CoA and ATP as cofactors, while NADH was required for SdgC activity; SdgC was identified as salicylyl-CoA 5-hydroxylase. Gentisyl-CoA underwent spontaneous cleavage to gentisate and CoA. SdgA behaved as a salicylyl-CoA ligase despite showing amino acid sequence similarity to an AMP-ligase. SdgD was identified as a GDO. These results suggest that Streptomyces sp. strain WA46 degrades salicylate by a novel pathway via a CoA derivative. Two-dimensional polyacrylamide gel electrophoresis and reverse transcriptase-PCR studies indicated that salicylate induced expression of the sdg cluster. PMID:15006746

Ishiyama, Daisuke; Vujaklija, Dusica; Davies, Julian

2004-03-01

337

Characterization and purification of bile salt hydrolase from Lactobacillus sp. strain 100-100  

SciTech Connect

The authors have characterized and purified the bile salt hydrolase from Lactobacillus sp. strain 100-100. Bile salt hydrolase from cells of the strain was purified with column and high-performance liquid chromatography. The activity was assayed in whole cells and cell-free extracts with either a radiochemical assay involving ({sup 14}C)taurocholic acid or a nonradioactive assay involving trinitrobenzene sulfonate. The activity was detectable only in stationary-phase cells. Within 20 min after conjugated bile acids were added to stationary-phase cultures of strain 100-100, the activity in whole cells increased to levels three- to fivefold higher than in cells from cultures grown in medium free of bile salts. In cell-free extracts, however, the activity was about equal whether or not the cells have been grown with bile salts present. When supernatant solutions from cultures grown in medium containing taurocholic acid were used to suspend cells grown in medium free of the bile salt, the bile salt hydrolase activity detected in whole cells increased two- to threefold. Two forms of the hydrolase were purified from the cells and designated hydrolases A and B. They eluted from anion-exchange high-performance liquid chromatography in two sets of fractions, A at 0.15 M NaCl and B at 0.18 M NaCl. Their apparent molecular weights in nondenaturing polyacrylamide gel electrophoresis were 115,000 and 105,000, respectively. However, discrepancies existed in the apparent molecular weights and number of peptides detected in sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the two forms. Whether the enzyme exists in two forms in the cells remains to be determined.

Lundeen, S.G.; Savage, D.C. (Univ. of Tennessee, Knoxville (USA))

1990-08-01

338

Properties of two different Na+/H+ antiport systems in alkaliphilic Bacillus sp. strain C-125.  

PubMed Central

Na+/H+ antiport was studied in alkaliphilic Bacillus sp. strain C-125, its alkali-sensitive mutant 38154, and a transformant (pALK2) with recovered alkaliphily. The transformed was able to maintain an intracellular pH (pHin) that was lower than that of external milieu and contained an electrogenic Na+/H+ antiporter driven only by delta psi (membrane potential, interior negative). The activity of this delta psi-dependent Na+/H+ antiporter was highly dependent on pHin, increasing with increasing pHin, and was found only in cells grown at alkaline pH. On the other hand, the alkali-sensitive mutant, which had lost the ability to grow above pH 9.5, lacked the delta psi-dependent Na+/H+ antiporter and showed defective regulation of pHin at the alkaline pH range. However, this mutant, like the parent strain, still required sodium ions for growth and for an amino acid transport system. Moreover, another Na+/H+ antiporter, driven by the imposed delta pH (pHin > extracellular pHout), was active in this mutant strain, showing that the previously reported delta pH-dependent antiport activity is probably separate from delta psi-dependent antiporter activity. The delta pH-dependent Na+/H+ antiporter was found in cells grown at either pH 7 or pH 9. This latter antiporter was reconstituted into liposomes by using a dilution method. When a transmembrane pH gradient was applied, downhill sodium efflux was accelerated, showing that the antiporter can be reconstituted into liposomes and still retain its activity.

Kitada, M; Hashimoto, M; Kudo, T; Horikoshi, K

1994-01-01

339

Defluorination of organofluorine sulfur compounds by Pseudomonas sp. strain D2  

SciTech Connect

Little is known of the potential for biodegradation of fluorinated sulfonates. Because of the apparent stability of fluorinated organics, their bioactivity, and their potential for accumulation in the environment, it is important to understand their environmental fate and the mechanisms by which they might be degraded. To evaluate this potential, the following model compounds were selected: difluoromethane sulfonate (DFMS), trifluoromethane sulfonate (TFMS), 2,2,2-trifluoroethane sulfonate (TES), perfluorooctane sulfonate (PFOS), and 1H,1H,2H,2H-perfluorooctane sulfonate (H-PFOS). A laboratory isolate designated Pseudomonas sp. strain D2 completely defluorinated DFMS under aerobic sulfur-limiting conditions in a defined mineral medium. Strain D2 utilized DFMS as the sole source of sulfur, but not as a source of carbon or energy. DFMS utilization was inhibited by other forms of sulfur, and noncompetitive inhibition kinetics were observed, with K{sub i}-values of 3--4 {micro}M for sulfate, sulfite, methane sulfonate, and cystine. Strain D2 was subsequently used to evaluate degradation of other fluorinated sulfonates. Growth and defluorination were only observed for those compounds containing hydrogen (TES and H-PFOS). TFMS and PFOS were not degraded. TES was completely defluorinated, and H-PFOS was partially defluorinated. No volatile transformation products were detected for TES or DFMS, but six volatile products were detected for H-PFOS. All of the volatile products contained oxygen and fluorine, but not sulfur. This is the first report of defluorination of fluorinated sulfonates, a linkage between sulfur assimilation and defluorination, and generation of volatile fluorinated biotransformation products.

Key, B.D.; Criddle, C.S. [Michigan State Univ., East Lansing, MI (United States); Howell, R.D. [3M Environmental Technology and Safety Services, St. Paul, MN (United States)

1998-08-01

340

Cyclodextrin glycosyltransferase production by new Bacillus sp. strains isolated from brazilian soil  

PubMed Central

Three strains of Bacillus sp. (BACRP, BACNC-1 and BACAR) were isolated from soil adhered to cassava husk. CGTase specific activity for the three isolated strains was higher when cultivated at 40°C. Potato starch, cassava starch, maltodextrin and glucose were used as carbon source and growth temperatures varied from 25 to 55°C. The three isolates presented higher CGTase specific activity when cultivated with potato starch at 40°C. Isolated BACRP and BACAR presented specific activity of 4.0×10–3 and 2.2×10–3 U/mg prot at pH 7.0, respectively, when cultivated in mediums added with NaCl 2%; at pH 10,0 their activities were of 3.4×10–3 and 3.0×10–3 U/mg prot, respectively, in the same concentration of NaCl. On the other hand, the isolated BACNC-1 presented activity specific of 2.4×10–3 U/mg prot when cultivated at pH 7.0 added of NaCl 1%, and at pH 10.0 the specific activity was of 3.4×10–3 U/mg prot without NaCl addition. This work also showed the presence of cyclodextrins formed during fermentation process and that precipitation with acetone or lyophilization followed by dialysis was efficient at removing CDs (cyclodextrins), thus, eliminating interference in the activity assays. The enzyme produced by the BACAR strain was partially purified and ?-CD was liberated as a reaction product.

Menocci, Vivian; Goulart, Antonio Jose; Adalberto, Paulo Roberto; Tavano, Olga Luisa; Marques, Daniela Parreira; Contiero, Jonas; Monti, Rubens

2008-01-01

341

Genes for phycocyanin subunits in Synechocystis sp. strain PCC 6701 and assembly mutant UV16.  

PubMed Central

The cyanobacterial phycobilisome is a large protein complex located on the photosynthetic membrane. It harvests light energy and transfers it to chlorophyll for use in photosynthesis. Phycobilisome assembly mutants in the unicellular cyanobacterium Synechocystis sp. strain 6701 have been characterized. One such mutant, UV16, contains a defect in the assembly of the biliprotein phycocyanin. We report the cloning and sequencing of the phycocyanin genes from wild-type Synechocystis strain 6701 and demonstrate an alteration in the gene for the phycocyanin alpha subunit in UV16. Possible consequences of the lesion on phycobilisome assembly were assessed from its position in the phycocyanin tertiary and quaternary structures. The UV16 phenotype is complex and includes a reduced level of phycocyanin relative to that in the wild type. To determine whether the lower phycocyanin content results from lower transcript levels, a fragment of cpcBA was used as a probe for quantitating phycocyanin mRNA. Both the wild type and UV16 contained two phycocyanin transcripts of approximately 1.4 and 1.5 kilobases that were equal in abundance and that did not vary with light quality during cell growth. Equal levels of these transcripts in the wild type and UV16 suggest that the lower phycocyanin content in the mutant may be due to posttranscriptional events. The 5' ends of the two phycocyanin mRNAs were mapped at 100 and 223 base pairs upstream of the cpcB initiation codon. Homologous regions upstream of the putative transcription initiation sites may be important for maintaining high levels of transcription from the Synechocystis strain 6701 phycocyanin gene set. Images FIG. 3 FIG. 6 FIG. 7

Anderson, L K; Grossman, A R

1990-01-01

342

Soluble methane monooxygenase gene clusters from trichloroethylene-degrading Methylomonas sp. strains and detection of methanotrophs during in situ bioremediation  

SciTech Connect

The soluble MMO (sMMO) gene clusters from group 1 methanotrophs were characterized. An 9.1-kb KpmI fragment from Methylomonas sp. strain KSWIII and a 7.5-kb SalI fragment from methylomonas sp. strain KSPIII which contained the sMMO gene clusters were cloned and sequenced. The sequences of these two fragments were almost identical. The sMMO gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described sMMO gene clusters of the group 2 and group 10 methanotrophs. The phylogenetic analysis of the predicted amino acid sequences of sMMO demonstrated that the sMMOs from these strains were closer to that from M. capsulatus Bath in the group X methanotrophs than to those from Methylosinus trichosporium OB3b and Methylocystis sp. strain M in the group 2 methanotrophs. Based on the sequence data of sMMO genes of the strains and other methanotrophs, the authors designed a new PCR primer to amplify sMMO gene fragments of all the known methanotrophs harboring the mmoX gene. The primer set was successfully used for detecting methanotrophs in the ground-water of trichloroethylene-contaminated sites during in situ-biostimulation treatments.

Shigematsu, Toru; Hanada, Satoshi; Eguchi, Masahiro; Kamagata, Yoichi; Kanagawa, Takahiro; Kurane; Ryuichiro

1999-12-01

343

Bioenergetic Properties of the Thermoalkaliphilic Bacillus sp. Strain TA2.A1  

PubMed Central

The thermoalkaliphilic Bacillus sp. strain TA2.A1 was able to grow in pH-controlled batch culture containing a nonfermentable growth substrate from pH 7.5 to 10.0 with no significant change in its specific growth rate, demonstrating that this bacterium is a facultative alkaliphile. Growth at pH 10.0 was sensitive to the protonophore carbonyl cyanide m-chlorophenylhydrazone, suggesting that a proton motive force (?p) generated via aerobic respiration was an obligate requirement for growth of strain TA2.A1. Strain TA2.A1 exhibited intracellular pH homeostasis as the external pH increased from 7.5 to 10.0; however, the maximum ?pH generated over this pH range was only 1.1 units at an external pH of 9.5. The membrane potential (??) was maintained between ?114 mV and ?150 mV, and little significant change was observed over the pH range for growth. In contrast, the ?p declined from ?164 mV at pH 7.5 to approximately ?78 mV at pH 10.0. An inwardly directed sodium motive force (?pNa+) of ?100 mV at pH 10.0 indicated that cellular processes (i.e., solute transport) dependent on a sodium gradient would not be affected by the adverse ?p. The phosphorylation potential of strain TA2.A1 was maintained between ?300 mV and ?418 mV, and the calculated H+/ATP stoichiometry of the ATP synthase increased from 2.0 at pH 7.5 to 5.7 at pH 10.0. Based on these data, vigorous growth of strain TA2.A1 correlated well with the ?pNa+, phosphorylation potential, and the ATP/ADP ratio, but not with ?p. This communication represents the first report on the bioenergetics of an extremely thermoalkaliphilic aerobic bacterium.

Olsson, Karen; Keis, Stefanie; Morgan, Hugh W.; Dimroth, Peter; Cook, Gregory M.

2003-01-01

344

Isolation and characterization of a new Achromobacter sp. strain CAR1389 as a carbazole-degrading bacterium.  

PubMed

In this work, a bacterial strain with suitable capability to metabolize carbazole (CAR) as a main nitrogen containing compound of petroleum was isolated and characterized. 16S rDNA gene analysis and morphological characteristics of the strain showed that the isolate belonged to the genus Achromobacter and was tentatively named as Achromobacter sp. strain CAR1389. The growth monitoring and biodegradation rate measurements of carbazole in minimal medium supplemented by 6 mM CAR revealed that the strain CAR1389 is able to remove more than 90 % of this compound at 25, 30, and 37 °C during 7 days. The effect of higher concentrations of the carbazole on growth rate and metabolizing activity of the strain exhibited the Achromobacter sp. strain CAR1389 can tolerate increasing levels of CAR concentration up to 21 mM in culture media and degrade 43 % of this toxic material. According to these results and high tolerance of this bacterium in regards to higher concentrations of CAR, we suggest the strain CAR1389 as a suitable isolate to do biorefining of crude oil and also bioremediation processes in highly contaminated area of carbazole. PMID:22806735

Farajzadeh, Zahra; Karbalaei-Heidari, Hamid Reza

2012-06-20

345

Two Angular Dioxygenases Contribute to the Metabolic Versatility of Dibenzofuran-Degrading Rhodococcus sp. Strain HA01?  

PubMed Central

Rhodococcus sp. strain HA01, isolated through its ability to utilize dibenzofuran (DBF) as the sole carbon and energy source, was also capable, albeit with low activity, of transforming dibenzo-p-dioxin (DD). This strain could also transform 3-chlorodibenzofuran (3CDBF), mainly by angular oxygenation at the ether bond-carrying carbon (the angular position) and an adjacent carbon atom, to 4-chlorosalicylate as the end product. Similarly, 2-chlorodibenzofuran (2CDBF) was transformed to 5-chlorosalicylate. However, lateral oxygenation at the 3,4-positions was also observed and yielded the novel product 2-chloro-3,4-dihydro-3,4-dihydroxydibenzofuran. Two gene clusters encoding enzymes for angular oxygenation (dfdA1A2A3A4 and dbfA1A2) were isolated, and expression of both was observed during growth on DBF. Heterologous expression revealed that both oxygenase systems catalyze angular oxygenation of DBF and DD but exhibited complementary substrate specificity with respect to CDBF transformation. While DfdA1A2A3A4 oxygenase, with high similarity to DfdA1A2A3A4 oxygenase from Terrabacter sp. strain YK3, transforms 3CDBF by angular dioxygenation at a rate of 29% ± 4% that of DBF, 2CDBF was not transformed. In contrast, DbfA1A2 oxygenase, with high similarity to the DbfA1A2 oxygenase from Terrabacter sp. strain DBF63, exhibited complementary activity with angular oxygenase activity against 2CDBF but negligible activity against 3CDBF. Thus, Rhodococcus sp. strain HA01 constitutes the first described example of a bacterial strain where coexpression of two angular dioxygenases was observed. Such complementary activity allows for the efficient transformation of chlorinated DBFs.

Aly, Hamdy A. H.; Huu, Nguyen B.; Wray, Victor; Junca, Howard; Pieper, Dietmar H.

2008-01-01

346

A novel thermostable carboxylesterase from Geobacillus thermodenitrificans: evidence for a new carboxylesterase family.  

PubMed

A novel gene encoding an esterase from Geobacillus thermodenitrificans strain CMB-A2 was cloned, sequenced and functionally expressed in Escherichia coli M15. Sequence analysis revealed an open reading frame of 747 bp corresponding to a polypeptide of 249 amino acid residues (named EstGtA2). After purification, a specific activity of 2.58 U mg(-1) was detected using p-NP caprylate (C8) at 50 degrees C and pH 8.0 (optimal conditions). The enzyme catalyses the hydrolysis of triglycerides (tributyrin) and a variety of p-nitrophenyl esters with different fatty acyl chain length (C4-C16). The enzyme has potential for various industrial applications since it is characterized by its activity under a wide range of pH, from 25 to 65 degrees C. Using Geobacillus stearothermophilus Est30 esterase structure as template, a model of EstGtA2 was built using ESyPred3D. Analysis of this structural model allowed identifying putative sequence features that control EstGtA2 enzymatic properties. Based on sequence properties, multiple sequence comparisons and phylogenetic analyses, this enzyme appears to belong to a new family of carboxylesterases. PMID:20587647

Charbonneau, David M; Meddeb-Mouelhi, Fatma; Beauregard, Marc

2010-06-29

347

Enhanced degradation of naphthalene by immobilization of Pseudomonas sp. strain NGK1 in polyurethane foam.  

PubMed

A Pseudomonas sp. strain NGKI (NCIM 5120) capable of degrading naphthalene was immobilized in polyurethane foam. The naphthalene-degrading activity of the freely suspended cells was compared with that of immobilized cells in batches in shaken culture and in a continuous culture system in a packed-bed reactor. Increasing concentrations of naphthalene were better tolerated and more quickly degraded by immobilized cell cultures than by free cells. An initial naphthalene concentration of 25 mM was completely degraded by freely suspended cells (4 x 10(10) cfu ml(-1)) and polyurethane-foam-immobilized cells (0.8-1 x 10(12) cfu g(-1) foam cubes) after 4 days and 2 days of incubation, respectively. Free cells degraded a maximum of 30 mM naphthalene after 4 days of incubation with 50 mM naphthalene, and no further degradation was observed even after 15 days of incubation, whereas foam-immobilized cells brought about the complete degradation of 50 mM initial naphthalene after 6 days of incubation. Furthermore, with 25 mM naphthalene, the polyurethane-foam-immobilized cells were re-used 45 times over a period of 90 days without losing naphthalene-degrading activity. By contrast, with the same amount of naphthalene, alginate-, agar-, and polyacrylamide-entrapped cells could be reused for 18, 12, and 23 times over a period of 44, 28, and 50 days, respectively. During continuous degradation in a packed-bed reactor, foam-immobilized cells degraded 80 mM naphthalene at a rate of 150 ml(-1) h(-1). With the same flow rate and 40 mM naphthalene, this system operated efficiently and continuously for about 120 days, whereas the packed-bed reactor with alginate-, agar-, and polyacrylamide-entrapped cells could be operated only for 45, 40, and 60 days respectively. Thus, more efficient degradation of naphthalene could be achieved by immobilizing cells of Pseudomonas sp. strain NGK1 in polyurethane foam, rather than in the other matrices tested. PMID:11341312

Manohar, S; Kim, C K; Karegoudar, T B

2001-04-01

348

Novel alkaline- and heat-stable serine proteases from alkalophilic Bacillus sp. strain GX6638.  

PubMed Central

An alkalophilic Bacillus sp., strain GX6638 (ATCC 53278), was isolated from soil and shown to produce a minimum of three alkaline proteases. The proteases were purified by ion-exchange chromatography and were distinguishable by their isoelectric point, molecular weight, and electrophoretic mobility. Two of the proteases, AS and HS, which exhibited the greatest alkaline and thermal stability, were characterized further. Protease HS had an apparent molecular weight of 36,000 and an isoelectric point of approximately 4.2, whereas protease AS had a molecular weight of 27,500 and an isoelectric point of 5.2. Both enzymes had optimal proteolytic activities over a broad pH range (pH 8 to 12) and exhibited temperature optima of 65 degrees C. Proteases HS and AS were further distinguished by their proteolytic activities, esterolytic activities, sensitivity to inhibitors, and their alkaline and thermal stability properties. Protease AS was extremely alkali stable, retaining 88% of initial activity at pH 12 over a 24-h incubation period at 25 degrees C; protease HS exhibited similar alkaline stability properties to pH 11. In addition, protease HS had exceptional thermal stability properties. At pH 9.5 (0.1 M CAPS buffer, 5 mM EDTA), the enzyme had a half-life of more than 200 min at 50 degrees C and 25 min at 60 degrees C. At pH above 9.5, protease HS readily lost enzymatic activity even in the presence of exogenously supplied Ca2+. In contrast, protease AS was more stable at pH above 9.5, and Ca2+ addition extended the half-life of the enzyme 10-fold at 60 degrees C. In contrast, protease AS was more stable at pH above 9.5, and Ca2+ addition extended the half-life of the enzyme 10-fold at 60 degrees C. The data presented here clearly indicate that these two alkaline proteases from Bacillus sp. strain GX6638 represent novel proteases that differ fundamentally from the proteases previously described for members of the genus Bacillus. Images

Durham, D R; Stewart, D B; Stellwag, E J

1987-01-01

349

Purification and sequence analysis of 4-methyl-5-nitrocatechol oxygenase from Burkholderia sp. strain DNT.  

PubMed Central

4-Methyl-5-nitrocatechol (MNC) is an intermediate in the degradation of 2,4-dinitrotoluene by Burkholderia sp. strain DNT. In the presence of NADPH and oxygen, MNC monooxygenase catalyzes the removal of the nitro group from MNC to form 2-hydroxy-5-methylquinone. The gene (dntB) encoding MNC monooxygenase has been previously cloned and characterized. In order to examine the properties of MNC monooxygenase and to compare it with other enzymes, we sequenced the gene encoding the MNC monooxygenase and purified the enzyme from strain DNT. dntB was localized within a 2.2-kb ApaI DNA fragment. Sequence analysis of this fragment revealed an open reading frame of 1,644 bp with an N-terminal amino acid sequence identical to that of purified MNC monooxygenase from strain DNT. Comparison of the derived amino acid sequences with those of other genes showed that DntB contains the highly conserved ADP and flavin adenine dinucleotide (FAD) binding motifs characteristic of flavoprotein hydroxylases. MNC monooxygenase was purified to homogeneity from strain DNT by anion exchange and gel filtration chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a single protein with a molecular weight of 60,200, which is consistent with the size determined from the gene sequence. The native molecular weight determined by gel filtration was 65,000, which indicates that the native enzyme is a monomer. It used either NADH or NADPH as electron donors, and NADPH was the preferred cofactor. The purified enzyme contained 1 mol of FAD per mol of protein, which is also consistent with the detection of an FAD binding motif in the amino acid sequence of DntB. MNC monooxygenase has a narrow substrate specificity. MNC and 4-nitrocatechol are good substrates whereas 3-methyl-4-nitrophenol, 3-methyl-4-nitrocatechol, 4-nitrophenol, 3-nitrophenol, and 4-chlorocatechol were not. These studies suggest that MNC monooxygenase is a flavoprotein that shares some properties with previously studied nitrophenol oxygenases.

Haigler, B E; Suen, W C; Spain, J C

1996-01-01

350

NolL of Rhizobium sp. Strain NGR234 Is Required for O-Acetyltransferase Activity  

PubMed Central

Following (iso)flavonoid induction, nodulation genes of the symbiotic nitrogen-fixing bacterium Rhizobium sp. strain NGR234 elaborate a large family of lipooligosaccharidic Nod factors (NodNGR factors). When secreted into the rhizosphere of compatible legumes, these signal molecules initiate root hair deformation and nodule development. The nonreducing glucosamine residue of NodNGR factors are N acylated, N methylated, and mono- or biscarbamoylated, while position C-6 of the reducing extremity is fucosylated. This fucose residue is normally 2-O methylated and either sulfated or acetylated. Here we present an analysis of all acetylated NodNGR factors, which clearly shows that the acetate group may occupy position C-3 or C-4 of the fucose moiety. Disruption of the flavonoid-inducible nolL gene, which is preceded by a nod box, results in the synthesis of NodNGR factors that lack the 3-O- or 4-O-acetate groups. Interestingly, the nodulation capacity of the mutant NGR?nolL is not impaired, whereas introduction of the nod box::nolL construct into the related strain Rhizobium fredii USDA257 extends the host range of this bacterium to Calopogonium caeruleum, Leucaena leucocephala, and Lotus halophilus. Nod factors produced by a USDA257(pnolL) transconjugant were also acetylated. The nod box::nolL construct was also introduced into ANU265 (NGR234 cured of its symbiotic plasmid), along with extra copies of the nodD1 gene. When permeabilized, these cells possessed acetyltransferase activity, although crude extracts did not.

Berck, S.; Perret, X.; Quesada-Vincens, D.; Prome, J.-C.; Broughton, W. J.; Jabbouri, S.

1999-01-01

351

Pathways for degrading TNT by Thu-Z: a Pantoea sp. strain.  

PubMed

2,4,6-Trinitrotoluene (TNT), an extensively used and versatile explosive, is harmful in soil and water. In the present study, four bacterial strains capable of degrading TNT have been isolated from contaminated sites and named as Thu-A, Thu-B, Thu-C, and Thu-Z. Thu-Z, which gave the highest degradation efficiency compared to the others, was assigned to the genus Pantoea according to its 16S rRNA gene. Similarities in both biochemical properties and morphology suggested that Thu-Z was a Pantoea sp. strain. Thu-Z was proved to be capable of using TNT as a sole nitrogen source by cleaving NO(2) from the nitroaromatic ring by direct aromatic ring reduction. Under nitrogen-limited conditions, 96.6 %?N of TNT was consumed by Thu-Z for growth, which was determined in terms of NaNO(2). Trace nitro reduction metabolites such as 2,4-diamino-6-nitrotoluene (24Dam) and 2,6-diamino-4-nitrotoluene (26Dam) were identified in the presence of (NH(4))(2)SO(4). On the other hand, 4,4',6,6'-tetranitro-2,2'-azoxytoluene (22Azo) and 2,2',6,6'-tetranitro-4,4'-azoxytoluene (44Azo) were detected in the absence of (NH(4))(2)SO(4). These indicated the existence of a dual pathway for Thu-Z, while the direct aromatic ring reduction was predominant. Addition of a nitrogen source ((NH(4))(2)SO(4)) after inoculation stimulated the growth of Thu-Z and accelerated TNT degradation. PMID:23076565

Zou, Liangdong; Lu, Diannan; Liu, Zheng

2012-10-18

352

Starvation-specific formation of a peripheral exopolysaccharide by a marine Pseudomonas sp., strain S9.  

PubMed Central

The marine bacterium Pseudomonas sp. strain S9 produces exopolysaccharides (EPS) during both growth and total energy source and nutrient starvation. Transmission electron microscopy of immunogold-labeled cells demonstrated that the EPS is closely associated with the cell surface during growth (integral EPS), while both the integral form and a loosely associated extracellular (peripheral) form were observed during starvation. Formation and release of the latter rendered the starvation medium viscous. In addition, after 3 h of starvation in static conditions, less than 5% of the cells were motile, compared with 100% at the onset of starvation and approximately 80% subsequent to release of the peripheral EPS at 27 h of starvation. Inhibition of protein synthesis with chloramphenicol added before 3 h of starvation caused no increase in viscosity. However, addition of chloramphenicol at 3 h did not prevent the subsequent increase in viscosity displayed by S9 cells. The amount of integral EPS increased for both nontreated and chloramphenicol-treated S9 cells during the first hour of starvation, with a subsequent equal decrease. The chloramphenicol-treated cells, as well as cells of a transposon-generated mutant strain deficient in peripheral EPS formation, remained adhesive to a hydrophobic inanimate surface during the initial 5 h of starvation, whereas nontreated wild-type cells had progressively decreased adhesion capacity. During the initial 5 h of starvation, most of the nontreated cells but only a small fraction of the chloramphenicol-treated and mutant cells detached from the hydrophobic substratum.(ABSTRACT TRUNCATED AT 250 WORDS) Images

Wrangstadh, M; Szewzyk, U; Ostling, J; Kjelleberg, S

1990-01-01

353

Cloning of a novel arylamidase gene from Paracoccus sp. strain FLN-7 that hydrolyzes amide pesticides.  

PubMed

The bacterial isolate Paracoccus sp. strain FLN-7 hydrolyzes amide pesticides such as diflubenzuron, propanil, chlorpropham, and dimethoate through amide bond cleavage. A gene, ampA, encoding a novel arylamidase that catalyzes the amide bond cleavage in the amide pesticides was cloned from the strain. ampA contains a 1,395-bp open reading frame that encodes a 465-amino-acid protein. AmpA was expressed in Escherichia coli BL21 and homogenously purified using Ni-nitrilotriacetic acid affinity chromatography. AmpA is a homodimer with an isoelectric point of 5.4. AmpA displays maximum enzymatic activity at 40°C and a pH of between 7.5 and 8.0, and it is very stable at pHs ranging from 5.5 to 10.0 and at temperatures up to 50°C. AmpA efficiently hydrolyzes a variety of secondary amine compounds such as propanil, 4-acetaminophenol, propham, chlorpropham, dimethoate, and omethoate. The most suitable substrate is propanil, with K(m) and k(cat) values of 29.5 ?M and 49.2 s(-1), respectively. The benzoylurea insecticides (diflubenzuron and hexaflumuron) are also hydrolyzed but at low efficiencies. No cofactor is needed for the hydrolysis activity. AmpA shares low identities with reported arylamidases (less than 23%), forms a distinct lineage from closely related arylamidases in the phylogenetic tree, and has different biochemical characteristics and catalytic kinetics with related arylamidases. The results in the present study suggest that AmpA is a good candidate for the study of the mechanism for amide pesticide hydrolysis, genetic engineering of amide herbicide-resistant crops, and bioremediation of amide pesticide-contaminated environments. PMID:22544249

Zhang, Jun; Yin, Jin-Gang; Hang, Bao-Jian; Cai, Shu; He, Jian; Zhou, Shun-Gui; Li, Shun-Peng

2012-04-27

354

Metabolism of cyclohexaneacetic acid and cyclohexanebutyric acid by Arthrobacter sp. strain CA1.  

PubMed Central

A strain of Arthrobacter was isolated by enrichment culture with cyclohexaneacetate as the sole source of carbon and grew with a doubling time of 4.2 h. In addition to growing with cyclohexaneacetate, the organism also grew with cyclohexanebutyrate at concentrations not above 0.05%, and with a variety of alicyclic ketones and alcohols. Oxidation of cyclohexaneacetate proceeded through formation of the coenzyme A (CoA) ester followed by initiation of a beta-oxidation cycle. beta-Oxidation was blocked before the second dehydrogenation step due to the formation of a tertiary alcohol, and the side chain was eliminated as acetyl-CoA by the action of (1-hydroxycyclohexan-1-yl)acetyl-CoA lyase. The cyclohexanone thus formed was degraded by a well-described route that involves ring-oxygen insertion by a biological Baeyer-Villiger oxygenase. All enzymes of the proposed metabolic sequence were demonstrated in cell-free extracts. Arthrobacter sp. strain CA1 synthesized constitutive beta-oxidative enzymes, but further induction of enzymes active toward cyclohexaneacetate and its metabolites could occur during growth with the alicyclic acid. Other enzymes of the sequence, (1-hydroxycyclohexan-1-yl)acetyl-CoA lyase and enzymes of cyclohexanone oxidation, were present at negligible levels in succinate-grown cells but induced by growth with cyclohexaneacetate. The oxidation of cyclohexanebutyrate was integrated into the pathway for cyclohexaneacetate oxidation by a single beta-oxidation cycle. Oxidation of the compound could be divided into two phases. Initial oxidation to (1-hydroxycyclohexan-1-yl)acetate could be catalyzed by constitutive enzymes, whereas the further degradation of (1-hydroxycyclohexan-1-yl)acetate was dependent on induced enzyme synthesis which could be inhibited by chloramphenicol with the consequent accumulation of cyclohexaneacetate and (1-hydroxycyclohexan-1-yl)acetate.

Ougham, H J; Trudgill, P W

1982-01-01

355

Functional Characterization of a Catabolic Plasmid from Polychlorinated- Biphenyl-Degrading Rhodococcus sp. Strain RHA1† ‡  

PubMed Central

Rhodococcus sp. strain RHA1, a potent polychlorinated-biphenyl (PCB)-degrading strain, contains three linear plasmids ranging in size from 330 to 1,100 kb. As part of a genome sequencing project, we report here the complete sequence and characterization of the smallest and least-well-characterized of the RHA1 plasmids, pRHL3. The plasmid is an actinomycete invertron, containing large terminal inverted repeats with a tightly associated protein and a predicted open reading frame (ORF) that is similar to that of a mycobacterial rep gene. The pRHL3 plasmid has 300 putative genes, almost 21% of which are predicted to have a catabolic function. Most of these are organized into three clusters. One of the catabolic clusters was predicted to include limonene degradation genes. Consistent with this prediction, RHA1 grew on limonene, carveol, or carvone as the sole carbon source. The plasmid carries three cytochrome P450-encoding (CYP) genes, a finding consistent with the high number of CYP genes found in other actinomycetes. Two of the CYP genes appear to belong to novel families; the third belongs to CYP family 116 but appears to belong to a novel class based on the predicted domain structure of its reductase. Analyses indicate that pRHL3 also contains four putative “genomic islands” (likely to have been acquired by horizontal transfer), insertion sequence elements, 19 transposase genes, and a duplication that spans two ORFs. One of the genomic islands appears to encode resistance to heavy metals. The plasmid does not appear to contain any housekeeping genes. However, each of the three catabolic clusters contains related genes that appear to be involved in glucose metabolism.

Warren, Rene; Hsiao, William W. L.; Kudo, Hisashi; Myhre, Matt; Dosanjh, Manisha; Petrescu, Anca; Kobayashi, Hiroyuki; Shimizu, Satoru; Miyauchi, Keisuke; Masai, Eiji; Yang, George; Stott, Jeff M.; Schein, Jacquie E.; Shin, Heesun; Khattra, Jaswinder; Smailus, Duane; Butterfield, Yaron S.; Siddiqui, Asim; Holt, Robert; Marra, Marco A.; Jones, Steven J. M.; Mohn, William W.; Brinkman, Fiona S. L.; Fukuda, Masao; Davies, Julian; Eltis, Lindsay D.

2004-01-01

356

Heterotrophic sulfur reduction by Thermotoga sp. strain FjSS3.B1.  

PubMed

Thermotoga sp. strain FjSS3.B1 was able to reduce sulfur to sulfide when grown on a mineral medium with glucose as the sole carbon and energy source. There was no increase in specific growth yield coupled to sulfur reduction, but the specific growth rate, final growth yield, and tolerance of H2 were all increased in the presence of sulfur. At dissolved H2 concentrations, of 550 to 600 mumol/l (at 77 degrees C) growth was not possible unless sulfur was added. Glucose was fermented via the Embden-Meyerhof-Parnas pathway to lactate, acetate, H2 and CO2 (and other unidentified minor products). The thermodynamic problems associated with the relatively high redox potential electrons from the 1,3-bisphosphoglycerate/glyceraldehyde 3-phosphate couple (E'0 = -350 mV) are overcome by reducing sulfur to sulfide (E'0 = -270 mV) rather than the energetically unfavourable production of H2 (E'0 = -414 mV). Under high hydrogen partial pressures there was increased production of lactate as an alternative electron sink. The results indicate that sulfur reduction operates primarily as an electron sink rather than as a detoxification reaction or energy-generating mechanism. PMID:1398039

Janssen, P H; Morgan, H W

1992-09-15

357

Purification and properties of glutathione reductase from the cyanobacterium Anabaena sp. strain 7119.  

PubMed Central

An NADPH-glutathione reductase (EC 1.6.4.2) has been purified 6,000-fold to electrophoretic homogeneity from the filamentous cyanobacterium Anabaena sp. strain 7119. The purified enzyme exhibits a specific activity of 249 U/mg and is characterized by being a dimeric flavin adenine dinucleotide-containing protein with a ratio of absorbance at 280 nm to absorbance at 462 nm of 5.8, a native molecular weight of 104,000, a Stokes radius of 4.13 nm, and a pI of 4.02. The enzyme activity is inhibited by sulfhydryl reagents and heavy-metal ions, especially in the presence of NADPH, with oxidized glutathione behaving as a protective agent. As is the case with the same enzyme from other sources, the kinetic data are consistent with a branched mechanism. Nevertheless, the cyanobacterial enzyme presents three distinctive features with respect to that isolated from non-photosynthetic organisms: (i) absolute specificity for NADPH, (ii) an alkaline optimum pH value of ca. 9.0, and (iii) strong acidic character of the protein, as estimated by column chromatofocusing. The kinetic parameters are very similar to those found for the chloroplast enzyme, but the molecular weight is lower, being comparable to that of non-photosynthetic microorganisms. A protective function, analogous to that assigned to the chloroplast enzyme, is suggested. Images

Serrano, A; Rivas, J; Losada, M

1984-01-01

358

Rhizobium sp. Strain NGR234 Possesses a Remarkable Number of Secretion Systems? †  

PubMed Central

Rhizobium sp. strain NGR234 is a unique alphaproteobacterium (order Rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other microsymbiont. We report here that the 3.93-Mbp chromosome (cNGR234) encodes most functions required for cellular growth. Few essential functions are encoded on the 2.43-Mbp megaplasmid (pNGR234b), and none are present on the second 0.54-Mbp symbiotic plasmid (pNGR234a). Among many striking features, the 6.9-Mbp genome encodes more different secretion systems than any other known rhizobia and probably most known bacteria. Altogether, 132 genes and proteins are linked to secretory processes. Secretion systems identified include general and export pathways, a twin arginine translocase secretion system, six type I transporter genes, one functional and one putative type III system, three type IV attachment systems, and two putative type IV conjugation pili. Type V and VI transporters were not identified, however. NGR234 also carries genes and regulatory networks linked to the metabolism of a wide range of aromatic and nonaromatic compounds. In this way, NGR234 can quickly adapt to changing environmental stimuli in soils, rhizospheres, and plants. Finally, NGR234 carries at least six loci linked to the quenching of quorum-sensing signals, as well as one gene (ngrI) that possibly encodes a novel type of autoinducer I molecule.

Schmeisser, Christel; Liesegang, Heiko; Krysciak, Dagmar; Bakkou, Nadia; Le Quere, Antoine; Wollherr, Antje; Heinemeyer, Isabelle; Morgenstern, Burkhard; Pommerening-Roser, Andreas; Flores, Margarita; Palacios, Rafael; Brenner, Sydney; Gottschalk, Gerhard; Schmitz, Ruth A.; Broughton, William J.; Perret, Xavier; Strittmatter, Axel W.; Streit, Wolfgang R.

2009-01-01

359

Inhibitor studies of dissimilative Fe(III) reduction by Pseudomonas sp. strain 200 (Pseudomonas ferrireductans)  

SciTech Connect

Aerobic respiration and dissimilative iron reduction were studied in pure, batch cultures of Pseudomonas sp. strain 200 (Pseudomonas ferrireductans). Specific respiratory inhibitors were used to identify elements of electron transport chains involved in the reduction of molecular oxygen and Fe(III). When cells were grown at a high oxygen concentration, dissimilative iron reduction occurred via an abbreviated electron transport chain. The induction of alternative respiratory pathways resulted from growth at low oxygen tension (<0.01 atm (1 atm = 101.29 kPa)). Induced cells were capable of O/sub 2/ utilization at moderately increased rates; dissimilative iron reduction was accelerated by a factor of 6 to 8. In cells grown at low oxygen tension, dissimilative iron reduction appeared to be uncoupled from oxidative phosphorylation. Models of induced and uninduced electron transport chains, including a mathematical treatment of chemical inhibition within the uninduced, aerobic electron transport system, are presented. In uninduced cells respiring anaerobically, electron transport was limited by ferrireductase activity. This limitation may disappear among induced cells.

Arnold, R.G.; DiChristina, T.J.; Hoffman, M.R.

1986-08-01

360

Inhibitor studies of dissimilative Fe(III) reduction by Pseudomonas sp. strain 200 ("Pseudomonas ferrireductans")  

PubMed Central

Aerobic respiration and dissimilative iron reduction were studied in pure, batch cultures of Pseudomonas sp. strain 200 ("Pseudomonas ferrireductans"). Specific respiratory inhibitors were used to identify elements of electron transport chains involved in the reduction of molecular oxygen and Fe(III). When cells were grown at a high oxygen concentration, dissimilative iron reduction occurred via an abbreviated electron transport chain. The induction of alternative respiratory pathways resulted from growth at low oxygen tension (less than 0.01 atm [1 atm = 101.29 kPa]). Induced cells were capable of O2 utilization at moderately increased rates; dissimilative iron reduction was accelerated by a factor of 6 to 8. In cells grown at low oxygen tension, dissimilative iron reduction appeared to be uncoupled from oxidative phosphorylation. Models of induced and uninduced electron transport chains, including a mathematical treatment of chemical inhibition within the uninduced, aerobic electron transport system, are presented. In uninduced cells respiring anaerobically, electron transport was limited by ferrireductase activity. This limitation may disappear among induced cells.

Arnold, R G; DiChristina, T J; Hoffmann, M R

1986-01-01

361

Purification and Characterization of Benzonitrilases from Arthrobacter sp. Strain J-1  

PubMed Central

We found two kinds of benzonitrilases, designated benzonitrilases A and B, in a cell extract of Arthrobacter sp. strain J-1 grown on benzonitrile as a sole carbon and nitrogen source. Benzonitrilases A and B were purified approximately 409-fold and 38-fold, respectively. Purified benzonitrilase A appeared to be homogeneous according to the criteria of polyacrylamide gel electrophoresis. Both the enzymes hydrolyzed benzonitrile to benzoic acid and ammonia without forming benzamide as an intermediate. The molecular weights of benzonitrilases A and B were found to be 30,000 and 23,000, respectively. The subunit molecular weight of benzonitrilase A was the same as its molecular weight. The isoelectric points of benzonitrilases A and B were 4.95 and 4.80, respectively. The optimum temperature and pH, respectively, for benzonitrilase A were 40°C and 8.5, and those for benzonitrilase B were 30°C and 7.5. The Km values for benzonitrilases A and B were 6.7 mM and 4.5 mM, respectively. Both the enzymes degraded p-tolunitrile, 4-cyanopyridine, and p-chlorobenzonitrile, but they did not attack aliphatic nitriles or amides. Both the enzymes were inhibited by thiol reagents.

Bandyopadhyay, Amal Kumar; Nagasawa, Toru; Asano, Yasuhisa; Fujishiro, Kinya; Tani, Yoshiki; Yamada, Hideaki

1986-01-01

362

Enhanced phenol degradation by immobilized Acinetobacter sp. strain AQ5NOL 1.  

PubMed

A locally isolated Acinetobacter sp. Strain AQ5NOL 1 was encapsulated in gellan gum and its ability to degrade phenol was compared with the free cells. Optimal phenol degradation was achieved at gellan gum concentration of 0.75% (w/v), bead size of 3 mm diameter (estimated surface area of 28.26 mm(2)) and bead number of 300 per 100 ml medium. At phenol concentration of 100 mg l(-1), both free and immobilized bacteria exhibited similar rates of phenol degradation but at higher phenol concentrations, the immobilized bacteria exhibited a higher rate of degradation of phenol. The immobilized cells completely degrade phenol within 108, 216 and 240 h at 1,100, 1,500 and 1,900 mg l(-1) phenol, respectively, whereas free cells took 240 h to completely degrade phenol at 1,100 mg l(-1). However, the free cells were unable to completely degrade phenol at higher concentrations. Overall, the rates of phenol degradation by both immobilized and free bacteria decreased gradually as the phenol concentration was increased. The immobilized cells showed no loss in phenol degrading activity after being used repeatedly for 45 cycles of 18 h cycle. However, phenol degrading activity of the immobilized bacteria experienced 10 and 38% losses after the 46 and 47th cycles, respectively. The study has shown an increased efficiency of phenol degradation when the cells are encapsulated in gellan gum. PMID:22806810

Ahmad, Siti Aqlima; Shamaan, Nor Aripin; Arif, Noorliza Mat; Koon, Gan Bee; Shukor, Mohd Yunus Abdul; Syed, Mohd Arif

2011-06-28

363

Utilization of Ganglioside-Degrading Paenibacillus sp. Strain TS12 for Production of Glucosylceramide  

PubMed Central

Gangliosides, sialic acid-containing glycosphingolipids, are membrane constituents of vertebrates and are known to have important roles in cellular differentiation, adhesion, and recognition. We report here the isolation of a bacterium capable of degrading gangliotetraose-series gangliosides and a new method for the production of glucosylceramide with this bacterium. GM1a ganglioside was found to be sequentially degraded by Paenibacillus sp. strain TS12, which was isolated from soil, as follows: GM1a ? asialo GM1 ? asialo GM2 ? lactosylceramide ? glucosylceramide. TS12 was found to produce a series of ganglioside-degrading enzymes, such as sialidases, ?-galactosidases, and ?-hexosaminidases. TS12 also produced ?-glucosidases, but glucosylceramide was somewhat resistant to the bacterial enzyme under the conditions used. Taking advantage of the specificity, we developed a new method for the production of glucosylceramide using TS12 as a biocatalyst. The method involves the conversion of crude bovine brain gangliosides to glucosylceramide by coculture with TS12 and purification of the product by chromatography with Wakogel C-300 HG.

Sumida, Tomomi; Sueyoshi, Noriyuki; Ito, Makoto

2002-01-01

364

Isolation of a Paenibacillus sp. Strain and Structural Elucidation of Its Broad-Spectrum Lipopeptide Antibiotic  

PubMed Central

This research was initiated to search for novel antimicrobial compounds produced by food or environmental microorganisms. A new bacterial strain, designated OSY-SE, which produces a unique and potent antimicrobial agent was isolated from soil. The isolate was identified as a Paenibacillus sp. through cultural, biochemical, and genetic analyses. An antimicrobial compound was extracted from Paenibacillus OSY-SE with acetonitrile and purified using liquid chromatography. After analyses by mass spectrometry (MS) and nuclear magnetic resonance (NMR), the antimicrobial compound was determined to be a cyclic lipopeptide consisting of a C15 fatty acyl (FA) chain and 13 amino acids. The deduced sequence is FA-Orn-Val-Thr-Orn-Ser-Val-Lys-Ser-Ile-Pro-Val-Lys-Ile. The carboxyl-terminal Ile is connected to Thr by ester linkage. The new compound, designated paenibacterin, showed antagonistic activities against most Gram-positive and Gram-negative bacteria tested, including Listeria monocytogenes, methicillin-resistant Staphylococcus aureus, Escherichia coli O157:H7, and Salmonella enterica serovar Typhimurium. Paenibacterin is resistant to trypsin, lipase, ?-glucosidase, and lysozyme. Its antimicrobial activity was lost after digestion by pronase and polymyxin acylase. Paenibacterin is readily soluble in water and fairly stable to exposure to heat and a wide range of pH values. The new isolate and its antimicrobial agent are being investigated for usefulness in food and medical applications.

Guo, Yaoqi; Huang, En; Yuan, Chunhua; Zhang, Liwen

2012-01-01

365

Impact of iron-based nanoparticles on microbial denitrification by Paracoccus sp. strain YF1.  

PubMed

This study investigates the effects of Fe and Fe/Ni nanoparticles on biological denitrification when using Paracoccus sp. strain YF1. Results show that adding Fe and Fe/Ni nanoparticles to the cells decreased their growth and denitrification rate. Compared to that of free cells (control 89.47%), a decrease (64.33%) in the presence of 1000mg/L Fe/Ni nanoparticles was observed, while a small decline in the denitrification rate (76.36%) was obtained when the concentration of Fe nanoparticles was 1000mg/L. These were further confirmed by adding Fe(2+), Fe(3+), Fe3O4, Fe(2+)/Ni(2+) and Fe(3+)/Ni(2+) individually to the free cell system. Furthermore, Fe and Fe/Ni nanoparticles influenced the nitrate removal and bacterial growth under different pH and temperature conditions. SEM, XRD and EDS demonstrated that iron oxides formed as a result of nanoparticles corrosion in biological medium. Finally the presence of nanoparticles around some bacteria was observed. PMID:24090609

Jiang, Chenghong; Liu, Yan; Chen, Zuliang; Megharaj, Mallavarapu; Naidu, Ravendra

2013-09-16

366

Regulation of the aromatic pathway in the cyanobacterium Synechococcus sp. strain Pcc6301 (Anacystis nidulans).  

PubMed Central

A pattern of allosteric control for aromatic biosynthesis in cyanobacteria relies upon early-pathway regulation as the major control point for the entire branched pathway. In Synechococcus sp. strain PCC6301 (Anacystis nidulans), two enzymes which form precursors for L-phenylalanine biosynthesis are subject to control by feedback inhibition. 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase (first pathway enzyme) is feedback inhibited by L-tyrosine, whereas prephenate dehydratase (enzyme step 9) is feedback inhibited by L-phenylalanine and allosterically activated by L-tyrosine. Mutants lacking feedback inhibition of prephenate dehydratase excreted relatively modest quantities of L-phenylalanine. In contrast, mutants deregulated in allosteric control of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase excreted large quantities of L-phenylalanine (in addition to even greater quantities of L-tyrosine). Clearly, in the latter mutants, the elevated levels of prephenate must overwhelm the inhibition of prephenate dehydratase by L-phenylalanine, an effect assisted by increased intracellular L-tyrosine, an allosteric activator. The results show that early-pathway flow regulated in vivo by 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase is the dominating influence upon metabolite flow-through to L-phenylalanine. L-Tyrosine biosynthesis exemplifies such early-pathway control even more simply, since 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase is the sole regulatory enzyme subject to end-product control by L-tyrosine.

Hall, G C; Flick, M B; Jensen, R A

1983-01-01

367

Regulation of an Osmoticum-Responsive Gene in Anabaena sp. Strain PCC 7120  

PubMed Central

Salt-induced genes in the cyanobacterium Anabaena sp. strain PCC 7120 were identified by use of a Tn5-based transposon bearing luxAB as a reporter. The genomic sequence adjacent to one site of insertion of the transposon was identical in part to the sequence of the lti2 gene, which was previously identified in a differential screen for cold-induced transcripts in Anabaena variabilis. The lti2-like gene was induced by sucrose and other osmotica and by low temperature, in addition to salt. Regulatory components necessary for the induction of this gene by osmotica were sought by a further round of transposon mutagenesis. One mutant that displayed reduced transcriptional activity of the lti2-like gene in response to exposure to osmotica had an insertion in an open reading frame, which was denoted orrA, whose predicted product showed sequence similarity to response regulators from two-component regulatory systems. The corresponding mutation was reconstructed and was shown, like the second-site transposon mutation, to result in reduced response to osmotic stress. Induction of the lux reporter gene by osmotica was restored by complementation with a genomic fragment containing the entire open reading frame for the presumptive response regulator, whereas a fragment containing a truncated copy of the open reading frame for the response regulator did not complement the mutation.

Schwartz, Steven H.; Black, Todd A.; Jager, Karin; Panoff, Jean-Michel; Wolk, C. Peter

1998-01-01

368

Response surface optimization for efficient dye removal by isolated strain Pseudomonas sp.  

NASA Astrophysics Data System (ADS)

Response surface methodology (RSM) involving the central composite design (CCD) was employed to optimize three important process variables for the decolourization of synthetic dye solutions containing Remazol Turquoise Blue (RTB) and Reactive Black 5 (RB5) with isolated bacterial strain Pseudomonas sp. The interaction between three variables i.e. Initial concentration of dye, carbon source and nitrogen source were studied and modeled. According to the Analysis of variance (ANOVA) results the predicted results were found to be in good agreement with experimental results ( R 2: 0.9726; Adj R 2: 0.9480 for RTB and R 2: 0.9789; Adj R 2: 0.9750 for RB5) which indicated excellent evaluation of experimental data from the second order polynomial regression model. Mathematical models were developed by the proposed system, for each process variable showed the effect of each factor and their interactions on biodecolourization process. The optimum concentrations of Dye, Carbon source, and Nitrogen source were found to be 20 mgL-1, 1.5 g/L and 1.5 g/L, respectively for RTB and RB5 to obtain maximum dye removing capacity. Predicted values were validated with experimental results, which indicated appropriateness of the employed model and the success of RSM.

Senthilkumar, Shanmugam; Perumalsamy, Muthiah; Prabhuy, Harinarayan Janardhana; AhmedBasha, Chiya; Anantharaman, Narayan

2012-09-01

369

Characterization of a Novel Phenol Hydroxylase in Indoles Biotranformation from a Strain Arthrobacter sp. W1  

PubMed Central

Background Indigoids, as popular dyes, can be produced by microbial strains or enzymes catalysis. However, the new valuable products with their transformation mechanisms, especially inter-conversion among the intermediates and products have not been clearly identified yet. Therefore, it is necessary to investigate novel microbial catalytic processes for indigoids production systematically. Findings A phenol hydroxylase gene cluster (4,606 bp) from Arthrobacter sp. W1 (PHw1) was obtained. This cluster contains six components in the order of KLMNOP, which exhibit relatively low sequence identities (37–72%) with known genes. It was suggested that indole and all the tested indole derivatives except for 3-methylindole were transformed to various substituted indigoid pigments, and the predominant color products derived from indoles were identified by spectrum analysis. One new purple product from indole, 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one, should be proposed as the dimerization of isatin and 7-hydroxylindole at the C-2 and C-6 positions. Tunnel entrance and docking studies were used to predict the important amino acids for indoles biotransformation, which were further proved by site-directed mutagenesis. Conclusions/Significance We showed that the phenol hydroxylase from genus Arthrobacter could transform indoles to indigoids with new chemical compounds being produced. Our work should show high insights into understanding the mechanism of indigoids bio-production.

Li, Xinliang; Zhang, Xuwang; Zhou, Jiti

2012-01-01

370

Phenylacetate Catabolism in Rhodococcus sp. Strain RHA1: a Central Pathway for Degradation of Aromatic Compounds  

PubMed Central

In gram-negative bacteria, a pathway for aerobic degradation of phenylacetic acid (PAA) that proceeds via phenylacetyl-coenzyme A (CoA) and hydrolytic ring fission plays a central role in the degradation of a range of aromatic compounds. In contrast, the PAA pathway and its role are not well characterized in gram-positive bacteria. A cluster including 13 paa genes encoding enzymes orthologous to those of gram-negative bacteria was identified on the chromosome of Rhodococcus sp. strain RHA1. These genes were transcribed during growth on PAA, with 11 of the genes apparently in an operon yielding a single transcript. Quantitative proteomic analyses revealed that at least 146 proteins were more than twice as abundant in PAA-grown cells of RHA1 than in pyruvate-grown cells. Of these proteins, 29 were identified, including 8 encoded by the paa genes. Knockout mutagenesis indicated that paaN, encoding a putative ring-opening enzyme, was essential for growth on PAA. However, paaF, encoding phenylacetyl-CoA ligase, and paaR, encoding a putative regulator, were not essential. paaN was also essential for growth of RHA1 on phenylacetaldehyde, phenylpyruvate, 4-phenylbutyrate, 2-phenylethanol, 2-phenylethylamine, and l-phenylalanine. In contrast, growth on 3-hydroxyphenylacetate, ethylbenzene, and styrene was unaffected. These results suggest that the range of substrates degraded via the PAA pathway in RHA1 is somewhat limited relative to the range in previously characterized gram-negative bacteria.

Navarro-Llorens, Juana Maria; Patrauchan, Marianna A.; Stewart, Gordon R.; Davies, Julian E.; Eltis, Lindsay D.; Mohn, William W.

2005-01-01

371

A novel regulatory role of the Rnf complex of Azoarcus sp. strain BH72.  

PubMed

The superfamily of P(II) proteins contains the most widely distributed signalling proteins in nature. Remarkable is the variety of targets whose activity is affected by protein-protein interactions. Here we identified as novel partner for interaction with GlnK an Rnf complex, known to couple the energy of ion transport to reduce ferredoxins. The endophytic diazotrophic betaproteobacterium Azoarcus sp. strain BH72 harbours two rnf-like clusters in the genome, of which only the rnf1 cluster was induced under conditions of N(2) fixation under control of the transcriptional activator NifA. Rapid inactivation ('DraT-independent switch off') of nitrogenase activity upon ammonium upshift was dependent on the Rnf1 complex. Membrane sequestration of GlnK in steady-state N-surplus conditions occurred in its unmodified form, signalling N-surplus, and was dependent on presence of the Rnf1 complex, suggesting physical interaction. In vitro binding studies by Far-Western analysis indicated interactions of RnfC1 with specifically GlnK but not with GlnB. As ammonium upshift led to decreased activity of the Rnf1 complex in membranes, it might be inactivated by GlnK binding, leading to an interruption of electron flow to nitrogenase and thus a rapid, DraT-independent nitrogenase switch off. Our data imply a hitherto unknown interaction partner for a P(II)-like protein and an additional process under its control. PMID:22188282

Sarkar, Abhijit; Köhler, Jörg; Hurek, Thomas; Reinhold-Hurek, Barbara

2011-12-21

372

A further insight into the mechanism of Ag + biosorption by Lactobacillus sp. strain A09  

NASA Astrophysics Data System (ADS)

The mechanism of Ag + biosorption by resting cell of Lactobacillus sp. strain A09 has been further investigated at the molecular level using spectroscopic techniques. The values of estimated equilibrium constants, rate constants, half-life periods and apparent enthalpies of the binding reaction were calculated via the determination of Ag + adsorbed by the biomass using atomic absorption spectrophotometry (AAS). The reductive ratio of the Ag + to Ag 0 by the A09 biomass was examined by X-ray photoelectron spectroscopy (XPS). Analysis for sulfur and nitrogen atomic contents in dry powder of the biomass with EA-1110 elemental analysis (EA) showed that amino acid residues retaining the reductive property of Ag + to Ag 0 are very small quantity, whereas glucose content in the hydrolysates of the biomass analyzed by ultraviolet-visible spectrophotometry (UV-vis) indicated that the amount of reducing sugars in the biomass is much larger than 2.71%. The fourier transform infrared (FTIR) spectrophotometry on blank and silver-loaded biomass demonstrated that the chemical functional group such as the free aldehyde group of the hemiacetalic hydroxyl group from reducing sugars, i.e. the hydrolysates of the polysaccharides from the cell wall plays a leading role in serving as the electron donor for reducing the Ag + to Ag 0. This result was further supported by characterizations on the interaction of the Ag + with glucose using X-ray powder diffractometry (XRD) and FTIR spectroscopy.

Lin, Zhongyu; Zhou, Chaohui; Wu, Jianming; Zhou, Jianzhang; Wang, Lin

2005-04-01

373

Identification, cloning, and characterization of a novel ketoreductase from the cyanobacterium Synechococcus sp. strain PCC 7942.  

PubMed

A new ketoreductase useful for asymmetric synthesis of chiral alcohols was identified in the cyanobacterium Synechococcus sp. strain PCC 7942. Mass spectrometry of trypsin-digested peptides identified the protein as 3-ketoacyl-[acyl-carrier-protein] reductase (KR) (EC 1.1.1.100). The gene, referred to as fabG, was cloned, functionally expressed in Escherichia coli, and subsequently purified to homogeneity. The enzyme displayed a temperature optimum at 44 degrees C and a broad pH optimum between pH 7 and pH 9. The NADPH-dependent KR was able to asymmetrically reduce a variety of prochiral ketones with good to excellent enantioselectivities (>99.8%). The KR showed particular high specific activity for asymmetric reduction of ethyl 4-chloroacetoacetate (38.29 +/- 2.15 U mg(-1)) and 2',3',4',5',6'-pentafluoroacetophenone (8.57 +/- 0.49 U mg(-1)) to the corresponding (S)-alcohols. In comparison with an established industrial enzyme like the alcohol dehydrogenase from Lactobacillus brevis, the KR showed seven-times-higher activity toward 2',3',4',5',6'-pentafluoroacetophenone, with a remarkably higher enantiomeric excess (>99.8% [S] versus 43.3% [S]). PMID:18791006

Hölsch, Kathrin; Havel, Jan; Haslbeck, Martin; Weuster-Botz, Dirk

2008-09-12

374

Polysaccharide covalently linked to the peptidoglycan of the cyanobacterium Synechocystis sp. strain PCC6714.  

PubMed Central

A polysaccharide was found to be covalently linked to the peptidoglycan of the unicellular cyanobacterium Synechocystis sp. strain PCC6714 via phosphodiester bonds. It could be cleaved from the peptidoglycan-polysaccharide (PG-PS) complex by hydrofluoric acid (HF) treatment in the cold (48% HF, 0 degrees C, 48 h) yielding a pure, HF-insoluble peptidoglycan fraction and an HF-soluble polysaccharide fraction. The PG-PS complex was isolated from the Triton X-100-insoluble cell wall fraction by hot sodium dodecyl sulfate treatment and digestion with proteases. Digestion of the complex with N-acetylmuramidase released the glycopeptide-linked polysaccharide, which was further purified by dialysis and gel filtration on Sephadex G-50 and G-200. The polysaccharide consisted of glucosamine, mannosamine, galactosamine, mannose, and glucose and had a molecular weight of 25,000 to 30,000. Muramic acid-6-phosphate was identified as the binding site of the covalently linked, nonphosphorylated polysaccharide as revealed by chemical analysis of linkage fragments of the PG-PS complex. Images

Jurgens, U J; Weckesser, J

1986-01-01

375

Purification and characterization of haloalcohol dehalogenase from Arthrobacter sp. strain AD2.  

PubMed Central

An enzyme capable of dehalogenating vicinal haloalcohols to their corresponding epoxides was purified from the 3-chloro-1,2-propanediol-utilizing bacterium Arthrobacter sp. strain AD2. The inducible haloalcohol dehalogenase converted 1,3-dichloro-2-propanol, 3-chloro-1,2-propanediol, 1-chloro-2-propanol, and their brominated analogs, 2-bromoethanol, as well as chloroacetone and 1,3-dichloroacetone. The enzyme possessed no activity for epichlorohydrin (3-chloro-1,2-epoxypropane) or 2,3-dichloro-1-propanol. The dehalogenase had a broad pH optimum at about 8.5 and a temperature optimum of 50 degrees C. The enzyme followed Michaelis-Menten kinetics, and the Km values for 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol were 8.5 and 48 mM, respectively. Chloroacetic acid was a competitive inhibitor, with a Ki of 0.50 mM. A subunit molecular mass of 29 kDa was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. With gel filtration, a molecular mass of 69 kDa was found, indicating that the native protein is a dimer. The amino acid composition and N-terminal amino acid sequence are given. Images

van den Wijngaard, A J; Reuvekamp, P T; Janssen, D B

1991-01-01

376

Identification, Cloning, and Characterization of a Novel Ketoreductase from the Cyanobacterium Synechococcus sp. Strain PCC 7942?  

PubMed Central

A new ketoreductase useful for asymmetric synthesis of chiral alcohols was identified in the cyanobacterium Synechococcus sp. strain PCC 7942. Mass spectrometry of trypsin-digested peptides identified the protein as 3-ketoacyl-[acyl-carrier-protein] reductase (KR) (EC 1.1.1.100). The gene, referred to as fabG, was cloned, functionally expressed in Escherichia coli, and subsequently purified to homogeneity. The enzyme displayed a temperature optimum at 44°C and a broad pH optimum between pH 7 and pH 9. The NADPH-dependent KR was able to asymmetrically reduce a variety of prochiral ketones with good to excellent enantioselectivities (>99.8%). The KR showed particular high specific activity for asymmetric reduction of ethyl 4-chloroacetoacetate (38.29 ± 2.15 U mg?1) and 2?,3?,4?,5?,6?-pentafluoroacetophenone (8.57 ± 0.49 U mg?1) to the corresponding (S)-alcohols. In comparison with an established industrial enzyme like the alcohol dehydrogenase from Lactobacillus brevis, the KR showed seven-times-higher activity toward 2?,3?,4?,5?,6?-pentafluoroacetophenone, with a remarkably higher enantiomeric excess (>99.8% [S] versus 43.3% [S]).

Holsch, Kathrin; Havel, Jan; Haslbeck, Martin; Weuster-Botz, Dirk

2008-01-01

377

Mechanism of biosynthesis of unsaturated fatty acids in Pseudomonas sp. strain E-3, a psychrotrophic bacterium  

SciTech Connect

Biosynthesis of palmitic, palmitoleic, and cis-vaccenic acids in Pseudomonas sp. strain E-3 was investigated with in vitro and in vivo systems. (1-{sup 14}C)palmitic acid was aerobically converted to palmitoleate and cis-vaccenate, and the radioactivities on their carboxyl carbons were 100 and 43%, respectively, of the total radioactivity in the fatty acids. Palmitoyl coenzyme A desaturase activity was found in the membrane fraction. (1-{sup 14}C)stearic acid was converted to octadecenoate and C16 fatty acids. The octadecenoate contained oleate and cis-vaccenate, but only oleate was produced in the presence of cerulenin. (1-{sup 14}C)lauric acid was aerobically converted to palmitate, palmitoleate, and cis-vaccenate. Under anaerobic conditions, palmitate (62%), palmitoleate (4%), and cis-vaccenate (34%) were produced from (1-{sup 14}C)acetic acid, while they amounted to 48, 39, and 14%, respectively, under aerobic conditions. In these incorporation experiments, 3 to 19% of the added radioactivity was detected in released {sup 14}CO{sub 2}, indicating that part of the added fatty acids were oxidatively decomposed. Partially purified fatty acid synthetase produced saturated and unsaturated fatty acids with chain lengths of C10 to C18. These results indicated that both aerobic and anaerobic mechanisms for the synthesis of unsaturated fatty acid are operating in this bacterium.

Wada, M.; Fukunaga, N.; Sasaki, S. (Hokkaido Univ., Sapporo (Japan))

1989-08-01

378

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

PubMed Central

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

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

2013-01-01

379

Isolation and Molecular Characterization of Five Marine Cyanophages Propagated on Synechococcus sp. Strain WH7803.  

PubMed

Five marine cyanophages propagated on Synechococcus sp. strain WH7803 were isolated from three different oceanographic provinces during the months of August and September 1992: coastal water from the Sargasso Sea, Bermuda; Woods Hole harbor, Woods Hole, Mass.; and coastal water from the English Channel, off Plymouth Sound, United Kingdom. The five cyanophage isolates were found to belong to two families, Myoviridae and Styloviridae, on the basis of their morphology observed in the transmission electron microscope. DNA purified from each of the cyanophage isolates was restricted with a selection of restriction endonucleases, and three distinguishably different patterns were observed. DNA isolated from Myoviridae isolates from Bermuda and the English Channel had highly related restriction patterns, as did DNA isolated from Styloviridae isolates from Bermuda and the English Channel. DNA isolated from the Myoviridae isolate from Woods Hole had a unique restriction pattern. The genome size for each of the Myoviridae isolates was ca. 80 to 85 kb, and it was ca. 90 to 100 kb for each of the Styloviridae isolates. Southern blotting analysis revealed that there was a limited degree of homology among all cyanophage DNAs probed, but clear differences were observed between cyanophage DNA from the Myoviridae and that from the Styloviridae isolates. Polypeptide analysis revealed a clear difference between Myoviridae and Styloviridae polypeptide profiles, although the major, presumably structural, protein in each case was ca. 53 to 54 kDa. PMID:16349088

Wilson, W H; Joint, I R; Carr, N G; Mann, N H

1993-11-01

380

A thermostable humic acid peroxidase from Streptomyces sp. strain AH4: purification and biochemical characterization.  

PubMed

An extracellular thermostable humic acid peroxidase (HaP3) was isolated from a Streptomyces sp. strain AH4. MALDI-TOF MS analysis showed that the purified enzyme was a monomer with a molecular mass of 60,215.18Da. The 26N-terminal residues of HaP3 displayed high homology with Streptomyces peroxidases. Optimal peroxidase activity was obtained at pH 5 and 80°C. HaP3 was stable at pH and temperature ranges of 4-8 and 60-90°C for 72 and 4h, respectively. HaP3 catalyzed the oxidation of 2,4-dichlorophenol, commercial humic acid, guiacol, and 2,6-dichlorophenol (50mM); L-3,4-dihydroxyphenylalanine (40 mM); 4-chlorophenol, 2,4,5-trichlorophenol, and 2,4,6-trichlorophenol (30 mM) in the presence of hydrogen peroxide. Sodium azide and potassium cyanide inhibited HaP3, which indicated the presence of heme components. These properties make HaP3 a potential strong candidate for future application in the elimination of natural humic acids in drinking water. PMID:22342039

Fodil, Djamila; Jaouadi, Bassem; Badis, Abdelmalek; Nadia, Zaraî Jaouadi; Ferradji, Fatma Zohra; Bejar, Samir; Boutoumi, Houcine

2012-02-06

381

Purification and some properties of an alkaline xylanase from alkaliphilic Bacillus sp. strain 41M-1.  

PubMed Central

An alkaliphilic Bacillus sp. strain, 41M-1, isolated from soil produced multiple xylanases extracellularly. One of these xylanases was purified to homogeneity by ammonium sulfate fractionation and anion-exchange chromatography. The moleculr mass of this enzyme (xylanase J) was 36 kDa, and the isoelectric point was pH 5.3. Xylanase J was most active at pH 9.0. The optimum temperature for the activity at pH 9.0 was around 50 degrees C. The enzyme was stable up to 55 degrees C at pH 9.0 for 30 min. Xylanase J was completely inhibited by the Hg2+ion and N-bromosuccinimide. The predominant products of xylan hydrolysate were xylobiose, xylotriose, and higher oligosaccharides, indicating that the enzyme was an endoxylanase. The apparent Km and Vmax values on xylan were 3.3 mg/ml and 1,100 micromol-1 mg-1, respectively. Xylanase J showed high sequence homology with the xylanases from Bacillus pumilus and Clostridium acetobutylicum in the N-terminal region. Xylanase J acted on neither crystalline cellulose nor carboxymethyl cellulose, indicating a possible application of the enzyme in biobleaching processes. Images

Nakamura, S; Wakabayashi, K; Nakai, R; Aono, R; Horikoshi, K

1993-01-01

382

Anti-Parasitic Compounds from Streptomyces sp. Strains Isolated from Mediterranean Sponges  

PubMed Central

Actinomycetes are prolific producers of pharmacologically important compounds accounting for about 70% of the naturally derived antibiotics that are currently in clinical use. In this study, we report on the isolation of Streptomyces sp. strains from Mediterranean sponges, on their secondary metabolite production and on their screening for anti-infective activities. Bioassay-guided isolation and purification yielded three previously known compounds namely, cyclic depsipeptide valinomycin, indolocarbazole alkaloid staurosporine and butenolide. This is the first report of the isolation of valinomycin from a marine source. These compounds exhibited novel anti-parasitic activities specifically against Leishmania major (valinomycin IC50 < 0.11 ?M; staurosporine IC50 5.30 ?M) and Trypanosoma brucei brucei (valinomycin IC50 0.0032 ?M; staurosporine IC50 0.022 ?M; butenolide IC50 31.77 ?M). These results underscore the potential of marine actinomycetes to produce bioactive compounds as well as the re-evaluation of previously known compounds for novel anti-infective activities.

Pimentel-Elardo, Sheila Marie; Kozytska, Svitlana; Bugni, Tim S.; Ireland, Chris M.; Moll, Heidrun; Hentschel, Ute

2010-01-01

383

Emulsification potential of a newly isolated biosurfactant-producing bacterium, Rhodococcus sp. strain TA6.  

PubMed

An indigenous biosurfactant producing bacterium, Rhodococcus sp. strain TA6 was isolated from Iranian oil contaminated soil using an efficient enrichment and screening method. During growth on sucrose and several hydrocarbon substrates as sole carbon source, the bacterium could produce biosurfactants. As a result of biosurfactant synthesis, the surface tension of the growth medium was reduced from 68mNm(-1) to values below 30mNm(-1). The biosurfactant was capable of forming stable emulsions with various hydrocarbons ranging from pentane to light motor oil. Preliminary chemical characterization revealed that the TA6 biosurfactant consisted of extracellular lipids and glycolipids. The biosurfactant was stable during exposure to high salinity (10% NaCl), elevated temperatures (120°C for 15min) and within a wide pH range (4.0-10.0). The culture broth was effective in recovering up to 70% of the residual oil from oil-saturated sand packs which indicates the potential value of the biosurfactant in enhanced oil recovery. PMID:21030223

Shavandi, Mahmoud; Mohebali, Ghasemali; Haddadi, Azam; Shakarami, Heidar; Nuhi, Ashrafossadat

2010-10-28

384

Transcriptomic Analysis Reveals a Bifurcated Terephthalate Degradation Pathway in Rhodococcus sp. Strain RHA1?  

PubMed Central

Phthalate isomers and their esters are important pollutants whose biodegradation is not well understood. Rhodococcus sp. strain RHA1 is notable for its ability to degrade a wide range of aromatic compounds. RHA1 was previously shown to degrade phthalate (PTH) and to have genes putatively encoding terephthalate (TPA) degradation. Transcriptomic analysis of 8,213 genes indicated that 150 were up-regulated during growth on PTH and that 521 were up-regulated during growth on TPA. Distinct ring cleavage dioxygenase systems were differentially expressed during growth on PTH and TPA. Genes encoding the protocatechuate (PCA) pathway were induced on both substrates, while genes encoding the catechol branch of the PCA pathway were additionally induced only on TPA. Accordingly, protocatechuate-3,4-dioxygenase activity was induced in cells grown on both substrates, while catechol-1,2-dioxygenase activity was induced only in cells grown on TPA. Knockout analysis indicated that pcaL, encoding 3-oxoadipate enol-lactone hydrolase and 4-carboxymuconolactone decarboxylase, was required for growth on both substrates but that pcaB, encoding ?-carboxy-cis,cis-muconate lactonizing enzyme, was required for growth on PTH only. These results indicate that PTH is degraded solely via the PCA pathway, whereas TPA is degraded via a bifurcated pathway that additionally includes the catechol branch of the PCA pathway.

Hara, Hirofumi; Eltis, Lindsay D.; Davies, Julian E.; Mohn, William W.

2007-01-01

385

Characterization of the Protocatechuic Acid Catabolic Gene Cluster from Streptomyces sp. Strain 2065  

PubMed Central

Protocatechuate 3,4-dioxygenase (EC 1.13.11.3) catalyzes the ring cleavage step in the catabolism of aromatic compounds through the protocatechuate branch of the ?-ketoadipate pathway. A protocatechuate 3,4-dioxygenase was purified from Streptomyces sp. strain 2065 grown in p-hydroxybenzoate, and the N-terminal sequences of the ?- and ?-subunits were obtained. PCR amplification was used for the cloning of the corresponding genes, and DNA sequencing of the flanking regions showed that the pcaGH genes belonged to a 6.5-kb protocatechuate catabolic gene cluster; at least seven genes in the order pcaIJFHGBL appear to be transcribed unidirectionally. Analysis of the cluster revealed the presence of a pcaL homologue which encodes a fused ?-carboxymuconolactone decarboxylase/?-ketoadipate enol-lactone hydrolase previously identified in the pca gene cluster from Rhodococcus opacus 1CP. The pcaIJ genes encoded proteins with a striking similarity to succinyl-coenzyme A (CoA):3-oxoacid CoA transferases of eukaryotes and contained an indel which is strikingly similar between high-G+C gram-positive bacteria and eukaryotes.

Iwagami, Sakura G.; Yang, Keqian; Davies, Julian

2000-01-01

386

Strain selection and scale-up fermentation for FR901379 acylase production by Streptomyces sp. no. 6907.  

PubMed

Micafungin (FK463) is a widely used treatment for life-threatening, deep-seated fungal infections. It is an echinocandin-like lipopeptide derived from the chemical modification of deacylated FR901379, a type of lipopeptide antibiotic produced by Coleophoma empetri F-11899. The palmitoyl moiety of FR901379 is deacylated by FR901379 acylase produced by Streptomyces sp. no. 6907. In this study, our goal was to generate an improved strain of Streptomyces sp. no. 6907 capable of hyperproducing the FR901379-acylase enzyme. To accomplish this goal, modified strains of Streptomyces sp. no. 6907 were generated using UV-irradiation mutagenesis, and strain selection was performed using an agar-plate screening method to efficiently select an acylase-hyperproducing strain. Three marker indices were shown to correlate with elevated acylase production: decreased candidacidal activity of FR901379, decreased proteolytic activity on skim milk, and phenotypic characteristics. Cloning and subsequent sequencing of the acylase gene from the hyperproducing mutant revealed no mutations in either the acylase structural gene or the 5'-flanking region required for gene expression. The growth medium was also modified to maximize acylase production. We successfully increased acylase activity approximately 65-fold, compared with the original growth conditions (wild strain cultured in the original unmodified medium). To minimize formation of excess foam during the fermentation process, we optimized the parameters of agitation speed, as calculated from the discharge flow rate. Using our improved strain and the optimized medium and growth conditions, we have developed an improved and highly reproducible method for stable large-scale production of FR901379-acylase. PMID:21752710

Ueda, Satoshi; Kinoshita, Masayoshi; Tanaka, Fumihiro; Tsuboi, Masaru; Shimizu, Shiho; Oohata, Nobutaka; Hino, Motohiro; Yamada, Masato; Isogai, Yasuhiro; Hashimoto, Seiji

2011-07-12

387

Identification and cloning of a regulatory gene for nitrogen assimilation in the cyanobacterium Synechococcus sp. strain PCC 7942.  

PubMed Central

Twenty-seven mutants that were unable to assimilate nitrate were isolated from Synechococcus sp. strain PCC 7942. In addition to mutants that lacked nitrate reductase or nitrite reductase, seven pleiotropic mutants impaired in both reductases, glutamine synthetase, and methylammonium transport were also isolated. One of the pleiotropic mutants was complemented by transformation with a cosmid gene bank from wild-type strain PCC 7942. Three complementing cosmids were isolated, and a 3.1-kilobase-pair DNA fragment that was still able to complement the mutant was identified. The regulatory gene that was cloned (ntcA) appeared to be required for full expression of proteins subject to ammonium repression in Synechococcus sp.

Vega-Palas, M A; Madueno, F; Herrero, A; Flores, E

1990-01-01

388

The Biosynthetic Pathway for Synechoxanthin, an Aromatic Carotenoid Synthesized by the Euryhaline, Unicellular Cyanobacterium Synechococcus sp. Strain PCC 7002? †  

PubMed Central

The euryhaline, unicellular cyanobacterium Synechococcus sp. strain PCC 7002 produces the dicyclic aromatic carotenoid synechoxanthin (?,?-caroten-18,18?-dioic acid) as a major pigment (>15% of total carotenoid) and when grown to stationary phase also accumulates small amounts of renierapurpurin (?,?-carotene) (J. E. Graham, J. T. J. Lecomte, and D. A. Bryant, J. Nat. Prod. 71:1647-1650, 2008). Two genes that were predicted to encode enzymes involved in the biosynthesis of synechoxanthin were identified by comparative genomics, and these genes were insertionally inactivated in Synechococcus sp. strain PCC 7002 to verify their function. The cruE gene (SYNPCC7002_A1248) encodes ?-carotene desaturase/methyltransferase, which converts ?-carotene to renierapurpurin. The cruH gene (SYNPCC7002_A2246) encodes an enzyme that is minimally responsible for the hydroxylation/oxidation of the C-18 and C-18? methyl groups of renierapurpurin. Based on observed and biochemically characterized intermediates, a complete pathway for synechoxanthin biosynthesis is proposed.

Graham, Joel E.; Bryant, Donald A.

2008-01-01

389

Genome Sequence of Nitrosomonas sp. Strain AL212, an Ammonia-Oxidizing Bacterium Sensitive to High Levels of Ammonia  

PubMed Central

Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to Nitrosomonas cluster 6A, which is characterized by sensitivity to high ammonia concentrations, higher substrate affinity (lower Km), and lower maximum growth rates than strains in Nitrosomonas cluster 7, which includes Nitrosomonas europaea and Nitrosomonas eutropha. Genome-informed studies of this ammonia-sensitive cohort of AOB are needed, as these bacteria are found in freshwater environments, drinking water supplies, wastewater treatment systems, and soils worldwide.

Yuichi, Suwa; Norton, Jeanette M.; Bollmann, Annette; Klotz, Martin G.; Stein, Lisa Y.; Laanbroek, Hendrikus J.; Arp, Daniel J.; Goodwin, Lynne A.; Chertkov, Olga; Held, Brittany; Bruce, David; Detter, J. Chris; Detter, Janine C.; Tapia, Roxanne; Han, Cliff S.

2011-01-01

390

Slr2013 Is a Novel Protein Regulating Functional Assembly of Photosystem II in Synechocystis sp. Strain PCC 6803  

Microsoft Academic Search

The Synechocystis sp. strain PCC 6803, which has a T192H mutation in the D2 protein of photosystem II, is an obligate photoheterotroph due to the lack of assembled photosystem II complexes. A secondary mutant, Rg2, has been selected that retains the T192H mutation but is able to grow photoautotrophically. Restoration of photoautotrophic growth in this mutant was caused by early

Galyna I. Kufryk; Wim F. J. Vermaas

2003-01-01

391

Structural studies of the O-specific polysaccharide(s) from the lipopolysaccharide of Azospirillum brasilense type strain Sp7.  

PubMed

Lipopolysaccharide was obtained by phenol-water extraction from dried bacterial cells of Azospirillum brasilense type strain Sp7. Mild acid hydrolysis of the lipopolysaccharide followed by GPC on Sephadex G-50 resulted in a polysaccharide mixture, which was studied by composition and methylation analyses, Smith degradation and (1)H and (13)C NMR spectroscopy. The following polysaccharide structures were established, where italics indicate a non-stoichiometric (?40%) 2-O-methylation of l-rhamnose. PMID:23978662

Sigida, Elena N; Fedonenko, Yuliya P; Shashkov, Alexander S; Zdorovenko, Evelina L; Konnova, Svetlana A; Ignatov, Vladimir V; Knirel, Yuriy A

2013-08-02

392

Genetic Analysis of Dioxin Dioxygenase of Sphingomonas sp. Strain RW1: Catabolic Genes Dispersed on the Genome  

Microsoft Academic Search

The dioxin dioxygenase of Sphingomonas sp. strain RW1 activates dibenzo-p-dioxin and dibenzofuran for further metabolism by introducing two atoms of oxygen at a pair of vicinal carbon atoms, one of which is involved in one of the bridges between the two aromatic rings, i.e., an angular dioxygenation. The dxnA1 and dxnA2 cistrons encoding this dioxygenase have been cloned and shown

JEAN ARMENGAUD; BIRGITTA HAPPE; KENNETH N. TIMMIS

393

A TRAP Transporter for Pyruvate and Other Monocarboxylate 2-Oxoacids in the Cyanobacterium Anabaena sp. Strain PCC 7120?  

PubMed Central

In the cyanobacterium Anabaena sp. strain PCC 7120, open reading frames (ORFs) alr3026, alr3027, and all3028 encode a tripartite ATP-independent periplasmic transporter (TRAP-T). Wild-type filaments showed significant uptake of [14C]pyruvate, which was impaired in the alr3027 and all3028 mutants and was inhibited by several monocarboxylate 2-oxoacids, identifying this TRAP-T system as a pyruvate/monocarboxylate 2-oxoacid transporter.

Pernil, Rafael; Herrero, Antonia; Flores, Enrique

2010-01-01

394

A TRAP transporter for pyruvate and other monocarboxylate 2-oxoacids in the cyanobacterium Anabaena sp. strain PCC 7120.  

PubMed

In the cyanobacterium Anabaena sp. strain PCC 7120, open reading frames (ORFs) alr3026, alr3027, and all3028 encode a tripartite ATP-independent periplasmic transporter (TRAP-T). Wild-type filaments showed significant uptake of [(14)C]pyruvate, which was impaired in the alr3027 and all3028 mutants and was inhibited by several monocarboxylate 2-oxoacids, identifying this TRAP-T system as a pyruvate/monocarboxylate 2-oxoacid transporter. PMID:20851902

Pernil, Rafael; Herrero, Antonia; Flores, Enrique

2010-09-17

395

Identification of Novel Genes Involved in Long-Chain n-Alkane Degradation by Acinetobacter sp. Strain DSM 17874  

Microsoft Academic Search

Acinetobacter sp. strain DSM 17874 is capable of utilizing n-alkanes with chain lengths ranging from that of decane (C10H22) to that of tetracontane (C40H82) as a sole carbon source. Two genes encoding AlkB-type alkane hydroxylase homologues, designated alkMa and alkMb, have been shown to be involved in the degradation of n-alkanes with chain lengths of from 10 to 20 C

Mimmi Throne-Holst; Alexander Wentzel; Trond E. Ellingsen; Hans-Kristian Kotlar; Sergey B. Zotchev

2007-01-01

396

Cloning, expression, and characterization of a chitinase gene from the Antarctic psychrotolerant bacterium Vibrio sp. strain Fi:7  

Microsoft Academic Search

A marine psychrotolerant bacterium from the Antarctic Ocean showing high chitinolytic activity on chitin agar at 5°C was isolated. The sequencing of the 16S rRNA indicates taxonomic affiliation of the isolate Fi:7 to the genus Vibrio. By chitinase activity screening of a genomic DNA library of Vibrio sp. strain Fi:7 in Escherichia coli, three chitinolytic clones could be isolated. Sequencing

Anne Bendt; Heike Hüller; Ulrike Kammel; Elisabeth Helmke; Thomas Schweder

2001-01-01

397

Complete Genome Sequence of Clostridium sp. Strain DL-VIII, a Novel Solventogenic Clostridium Species Isolated from Anaerobic Sludge.  

PubMed

We report the genome sequence of Clostridium sp. strain DL-VIII, a novel Gram-positive, endospore-forming, solventogenic bacterium isolated from activated anaerobic sludge of a wastewater treatment plant. Aside from a complete sol operon, the 6,477,357-bp genome of DL-VIII reveals genes for several unique enzymes with applications in lignocellulose degradation, including two phenolic acid decarboxylases. PMID:23929491

Taghavi, Safiyh; Izquierdo, Javier A; van der Lelie, Daniel

2013-08-08

398

Phenyl methyl ethers: novel electron donors for respiratory growth of Desulfitobacterium hafniense and Desulfitobacterium sp. strain PCE-S  

Microsoft Academic Search

Desulfitobacterium hafniense and Desulfitobacterium sp. strain PCE-S grew under anoxic conditions with a variety of phenyl methyl ethers as electron donors in combination with fumarate as electron acceptor. The phenyl methyl ethers were O-demethylated to the corresponding phenol compounds. O-demethylation was strictly dependent on the presence of fumarate; no O-demethylation occurred with CO 2 as electron acceptor. One mol phenyl

Anke Neumann; Tina Engelmann; Roland Schmitz; Yvonne Greiser; Adelheid Orthaus; Gabriele Diekert

2004-01-01

399

Influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons by Sphingomonas sp. strain PheB4  

Microsoft Academic Search

The influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons (PAHs) was investigated when\\u000a Sphingomonas sp. strain PheB4 isolated from surface mangrove sediments was grown in either phenanthrene-containing mineral salts medium\\u000a (PMSM) or nutrient broth (NB). The NB-grown culture exhibited a more rapid cometabolic degradation of single and mixed non-growth\\u000a substrate PAHs compared to the PMSM-grown culture. The

Yin Zhong; Tiangang Luan; Xiaowei Wang; Chongyu Lan; Nora F. Y. Tam

2007-01-01

400

arsRBOCT Arsenic Resistance System Encoded by Linear Plasmid pHZ227 in Streptomyces sp. Strain FR008  

Microsoft Academic Search

In the arsenic resistance gene cluster from the large linear plasmid pHZ227, two novel genes, arsO (for a putative flavin-binding monooxygenase) and arsT (for a putative thioredoxin reductase), were coactivated and cotranscribed with arsR1-arsB and arsC, respectively. Deletion of the ars gene cluster on pHZ227 in Streptomyces sp. strain FR-008 resulted in sensitivity to arsenic, and heterologous expression of the

Lianrong Wang; Shi Chen; Xiang Xiao; Xi Huang; Delin You; Xiufen Zhou; Zixin Deng

2006-01-01

401

Isolation and Partial Characterization of Antagonistic Peptides Produced by Paenibacillus sp. Strain B2 Isolated from the Sorghum Mycorrhizosphere  

Microsoft Academic Search

Paenibacillus sp. strain B2, isolated from the mycorrhizosphere of sorghum colonized by Glomus mosseae, produces an antagonistic factor. This factor has a broad spectrum of activity against gram-positive and gram-negative bacteria and also against fungi. The antagonistic factor was isolated from the bacterial culture medium and purified by cation-exchange, reverse-phase, and size exclusion chromatography. The purified factor could be separated

S. Selim; J. Negrel; C. Govaerts; S. Gianinazzi; D. van Tuinen

2005-01-01

402

Effects of insecticides on plant-growth-promoting activities of phosphate solubilizing rhizobacterium Klebsiella sp. strain PS19  

Microsoft Academic Search

In this study, four technical grade insecticides, fipronil, pyriproxyfen, imidacloprid and thiamethoxam were applied at the recommended and the higher doses to investigate their effects on plant growth-promoting activities of phosphate-solubilizing Klebsiella sp. strain PS19, isolated from mustard rhizosphere. All tested insecticides displayed a concentration-dependent inhibition in plant growth promoting traits, like, inorganic phosphate solubilization, biosynthesis of phytohormones and siderophores,

Munees Ahemad; Mohammad Saghir Khan

2011-01-01

403

Effects of ultraviolet radiation on productivity and nitrogen fixation in the Cyanobacterium, Anabaena sp. (Newton’s strain)  

Microsoft Academic Search

The biological effects of ultraviolet radiation (UVR; 290–400 nm), especially the UV-B (320–400 nm) component of the spectrum,\\u000a include both direct and indirect effects on many cellular processes. In cyanobacteria both photosynthesis and nitrogen fixation\\u000a can be affected directly by UVR, and indirectly by UVR through the production of reactive oxygen species (ROS). For the heterocystous\\u000a cyanobacterium, Anabaena sp. (Newton’s strain), exposure

Michael P. Lesser

2008-01-01

404

Isolation of a gene (pbsC) required for siderophore biosynthesis in fluorescent Pseudomonas sp. strain M114  

Microsoft Academic Search

An iron-regulated gene, pbsC, required for siderophore production in fluorescent Pseudomonas sp. strain M114 has been identified. A kanamycin-resistance cassette was inserted at specific restriction sites within a 7 kb genomic fragment of M114 DNA and by marker exchange two siderophore-negative mutants, designated M1 and M2, were isolated. The nucleotide sequence of approximately 4 kb of the region flanking the

Claire Adams; David N. Dowling; Dan J. O'Sullivan; Fergal O'Gara

1994-01-01

405

Y4lO of Rhizobium sp. Strain NGR234 Is a Symbiotic Determinant Required for Symbiosome Differentiation  

Microsoft Academic Search

Type 3 (T3) effector proteins, secreted by nitrogen-fixing rhizobia with a bacterial T3 secretion system, affect the nodulation of certain host legumes. The open reading frame y4lO of Rhizobium sp. strain NGR234 encodes a protein with sequence similarities to T3 effectors from pathogenic bacteria (the YopJ effector family). Transcription studies showed that the promoter activity of y4lO depended on the

Feng-Juan Yang; Li-Li Cheng; Ling Zhang; Wei-Jun Dai; Zhe Liu; Nan Yao; Zhi-Ping Xie; Christian Staehelin

2009-01-01

406

Bioremediation of BTEX Hydrocarbons: Effect of Soil Inoculation with the Toluene-Growing Fungus Cladophialophora Sp. Strain T1  

Microsoft Academic Search

The biodegradation of a mixture of benzene, toluene, ethylbenzene, xylene, (BTEX) and methyl-tert-butyl ether (MTBE) was studied in soil microcosms. Soil inoculation with the toluene-metabolising fungusCladophialophora sp. strain T1 was evaluated in sterile and non-sterile soil. Induction of biodegradation capacity following BTEX addition was faster in the soil native microflora than in axenic soil cultures of the fungus. Toluene, ethylbenzenes,

F. X. Prenafeta-Boldú; H. Ballerstedt; J. Gerritse; J. T. C. Grotenhuis

2004-01-01

407

Degradation of a nonylphenol single isomer by Sphingomonas sp. strain TTNP3 leads to a hydroxylation-induced migration product.  

PubMed

Sphingomonas sp. strain TTNP3 degrades 4(3',5'-dimethyl-3'-heptyl)-phenol and unidentified metabolites that were described previously. The chromatographic analyses of the synthesized reference compound and the metabolites led to their identification as 2(3',5'-dimethyl-3'-heptyl)-1,4-benzenediol. This finding indicates that the nonylphenol metabolism of this bacterium involves unconventional degradation pathways where an NIH shift mechanism occurs. PMID:15528560

Corvini, P F X; Meesters, R J W; Schäffer, A; Schröder, H F; Vinken, R; Hollender, J

2004-11-01

408

Degradation of a Nonylphenol Single Isomer by Sphingomonas sp. Strain TTNP3 Leads to a Hydroxylation-Induced Migration Product  

PubMed Central

Sphingomonas sp. strain TTNP3 degrades 4(3?,5?-dimethyl-3?-heptyl)-phenol and unidentified metabolites that were described previously. The chromatographic analyses of the synthesized reference compound and the metabolites led to their identification as 2(3?,5?-dimethyl-3?-heptyl)-1,4-benzenediol. This finding indicates that the nonylphenol metabolism of this bacterium involves unconventional degradation pathways where an NIH shift mechanism occurs.

Corvini, P. F. X.; Meesters, R. J. W.; Schaffer, A.; Schroder, H. F.; Vinken, R.; Hollender, J.

2004-01-01

409

Continuous hydrogen production by Clostridium sp. strain no. 2 from cellulose hydrolysate in an aqueous two-phase system  

Microsoft Academic Search

Continuous hydrogen production by fermentation of Avicel hydrolysate in an aqueous two-phase system, using Clostridium sp. strain no. 2, was investigated. Continuous hydrolysis of Avicel with a commercial cellulase preparation was performed in an aqueous two-phase system consisting of 10% polyethylene glycol and 5% dextran. The hydrolysate was continuously pumped at a dilution rate of 0.17 h?1 into a 300-ml

Fumiaki Taguchi; Kiharu Yamada; Katsushige Hasegawa; Tatsuo Taki-Saito; Kazuya Hara

1996-01-01

410

Structure and Evolution of NGRRS-1, a Complex, Repeated Element in the Genome of Rhizobium sp. Strain NGR234  

Microsoft Academic Search

Much of the remarkable ability of Rhizobium sp. strain NGR234 to nodulate at least 110 genera of legumes, as well as the nonlegume Parasponia andersonii, stems from the more than 80 different Nod factors it secretes. Except for nodE, nodG, and nodPQ, which are on the chromosome, most Nod factor biosynthesis genes are dispersed over the 536,165-bp symbiotic plasmid, pNGR234a.

X. PERRET; V. VIPREY; C. FREIBERG; W. J. BROUGHTON

1997-01-01

411

Circadian Clocks of Synechocystis sp. Strain PCC 6803, Thermosynechococcus elongatus, Prochlorococcus spp., Trichodesmium spp. and Other Species  

Microsoft Academic Search

The cyanobacterium Synechococcus elongatus PCC 7942 has been established as the model system for studying the molecular\\u000a mechanisms of the cir-cadian clock in cyanobacteria. This chapter mainly focuses on other cyanobacteria, such as SynechocystisL sp. strain PCC 6803, Thermosynechococcus elongatus and the genera Trichodesmium and Prochlorococcus. Here, we describe the research background, current status, possible problems and perspectives for studying

Setsuyuki Aoki; Kiyoshi Onai

412

Stimulation of aryl metabolite production in the basidiomycete Bjerkandera sp. strain BOS55 with biosynthetic precursors and lignin degradation products  

Microsoft Academic Search

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

TUNDE MESTER; HENK J. SWARTS; I. Romero; S. Sole; Bont de J. A. M; J. A. Field

1997-01-01

413

Influence of carbon sources and electron shuttles on ferric iron reduction by Cellulomonas sp. strain ES6.  

PubMed

Microbially reduced iron minerals can reductively transform a variety of contaminants including heavy metals, radionuclides, chlorinated aliphatics, and nitroaromatics. A number of Cellulomonas spp. strains, including strain ES6, isolated from aquifer samples obtained at the U.S. Department of Energy's Hanford site in Washington, have been shown to be capable of reducing Cr(VI), TNT, natural organic matter, and soluble ferric iron [Fe(III)]. This research investigated the ability of Cellulomonas sp. strain ES6 to reduce solid phase and dissolved Fe(III) utilizing different carbon sources and various electron shuttling compounds. Results suggest that Fe(III) reduction by and growth of strain ES6 was dependent upon the type of electron donor, the form of iron present, and the presence of synthetic or natural organic matter, such as anthraquinone-2,6-disulfonate (AQDS) or humic substances. This research suggests that Cellulomonas sp. strain ES6 could play a significant role in metal reduction in the Hanford subsurface and that the choice of carbon source and organic matter addition can allow for independent control of growth and iron reduction activity. PMID:21318474

Gerlach, Robin; Field, Erin K; Viamajala, Sridhar; Peyton, Brent M; Apel, William A; Cunningham, Al B

2011-02-13

414

Influence of Carbon Sources and Electron Shuttles on Ferric Iron Reduction by Cellulomonas sp. Strain ES6  

SciTech Connect

Microbially reduced iron minerals can reductively transform a variety of contaminants including heavy metals, radionuclides, chlorinated aliphatics, and nitroaromatics. A number of Cellulomonas spp. strains, including strain ES6, isolated from aquifer samples obtained at the U.S. Department of Energy's Hanford site in Washington, have been shown to be capable of reducing Cr(VI), TNT, natural organic matter, and soluble ferric iron [Fe(III)]. This research investigated the ability of Cellulomonas sp. strain ES6 to reduce solid phase and dissolved Fe(III) utilizing different carbon sources and various electron shuttling compounds. Results suggest that Fe(III) reduction by and growth of strain ES6 was dependent upon the type of electron donor, the form of iron present, and the presence of synthetic or natural organic matter, such as anthraquinone-2,6-disulfonate (AQDS) or humic substances. This research suggests that Cellulomonas sp. strain ES6 could play a significant role in metal reduction in the Hanford subsurface and that the choice of carbon source and organic matter addition can allow for independent control of growth and iron reduction activity.

Dr Robin Gerlach; Erin K. Field; Sridhar Viamajala; Brent M. Peyton; William A. Apel; Al B. Cunningham

2011-09-01

415

Isolation and characterization of a phenol-degrading Rhodococcus sp. strain AQ5NOL 2 KCTC 11961BP.  

PubMed

In this work, we report on the isolation of a phenol-degrading Rhodococcus sp. with a high tolerance towards phenol. The isolate was identified as Rhodococcus sp. strain AQ5NOL 2, based on 16S rDNA analysis. The strain degraded phenol using the meta pathway, a trait shared by many phenol-degraders. In addition to phenol biodegradation, the strain was also capable of degrading diesel. Strain AQ5NOL 2 exhibited a broad optimum temperature for growth on phenol at between 20?°C and 35?°C. The best nitrogen sources were ammonium sulphate, glycine or phenylalanine, followed by proline, nitrate, leucine, and alanine (in decreasing efficiency). Strain AQ5NOL 2 showed a high tolerance and degradation capacity of phenol, for it was able to register growth in the presence of 2000?mg l(-1) phenol. The growth of this strain on phenol as sole carbon and energy source were modeled using Haldane kinetics with a maximal specific growth rate (?(max)) of 0.1102 hr(-1), a half-saturation constant (K(s) ) of 99.03?mg l(-1) or 1.05?mmol l(-1), and a substrate inhibition constant (K(i)) of 354?mg l(-1) or 3.76?mmol l(-1). Aside from phenol, the strain could utilize diesel, 2,4-dinitrophenol and ?-cresol as carbon sources for growth. Strain AQ5NOL 2 exhibited inhibition of phenol degradation by Zn(2+), Cu(2+), Cr(6+), Ag(+) and Hg(2+) at 1?mg l(-1). PMID:22581645

Arif, N M; Ahmad, S A; Syed, M A; Shukor, M Y

2012-05-14

416

?-Tocopherol Is Essential for Acquired Chill-Light Tolerance in the Cyanobacterium Synechocystis sp. Strain PCC 6803? †  

PubMed Central

Unlike Escherichia coli, the cyanobacterium Synechocystis sp. strain PCC 6803 is insensitive to chill (5°C) in the dark but rapidly losses viability when exposed to chill in the light (100 ?mol photons m?2 s?1). Preconditioning at a low temperature (15°C) greatly enhances the chill-light tolerance of Synechocystis sp. strain PCC 6803. This phenomenon is called acquired chill-light tolerance (ACLT). Preconditioned wild-type cells maintained a substantially higher level of ?-tocopherol after exposure to chill-light stress. Mutants unable to synthesize ?-tocopherol, such as slr1736, slr1737, slr0089, and slr0090 mutants, almost completely lost ACLT. When exposed to chill without light, these mutants showed no or a slight difference from the wild type. When complemented, the slr0089 mutant regained its ACLT. Copper-regulated expression of slr0090 from PpetE controlled the level of ?-tocopherol and ACLT. We conclude that ?-tocopherol is essential for ACLT of Synechocystis sp. strain PCC 6803. The role of ?-tocopherol in ACLT may be based largely on a nonantioxidant activity that is not possessed by other tocopherols or pathway intermediates.

Yang, Yang; Yin, Chuntao; Li, Weizhi; Xu, Xudong

2008-01-01

417

Characterization of Thermostable Cellulases Produced by Bacillus and Geobacillus Strains  

Technology Transfer Automated Retrieval System (TEKTRAN)

Bacterial community composition of thermophilic (60 deg C) mixed cellulose-enrichment cultures was examined by constructing a 16S rDNA clone library which demonstrated major lineages affiliated to Actinobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Firmicutes, and Proteobacteria. A tot...

418

Photosynthetic Bradyrhizobium Sp. strain ORS285 synthesizes 2-O-methylfucosylated lipochitooligosaccharides for nod gene-dependent interaction with Aeschynomene plants.  

PubMed

Bradyrhizobium sp. strain ORS285 is a photosynthetic bacterium that forms nitrogen-fixing nodules on the roots and stems of tropical aquatic legumes of the Aeschynomene genus. The symbiotic interaction of Bradyrhizobium sp. strain ORS285 with certain Aeschynomene spp. depends on the presence of nodulation (nod) genes whereas the interaction with other species is nod gene independent. To study the nod gene-dependent molecular dialogue between Bradyrhizobium sp. strain ORS285 and Aeschynomene spp., we used a nodB-lacZ reporter strain to monitor the nod gene expression with various flavonoids. The flavanones liquiritigenin and naringenin were found to be the strongest inducers of nod gene expression. Chemical analysis of the culture supernatant of cells grown in the presence of naringenin showed that the major Nod factor produced by Bradyrhizobium sp. strain ORS285 is a modified chitin pentasaccharide molecule with a terminal N-C(18:1)-glucosamine and with a 2-O-methyl fucose linked to C-6 of the reducing glucosamine. In this respect, the Bradyrhizobium sp. strain ORS285 Nod factor is the same as the major Nod factor produced by the nonphotosynthetic Bradyrhizobium japonicum USDA110 that nodulates the roots of soybean. This suggests a classic nod gene-dependent molecular dialogue between Bradyrhizobium sp. strain ORS285 and certain Aeschynomene spp. This is supported by the fact that B. japonicum USDA110 is able to form N(2)-fixing nodules on both the roots and stems of Aeschynomene afraspera. PMID:21864045

Renier, Adeline; Maillet, Fabienne; Fardoux, Joel; Poinsot, Verena; Giraud, Eric; Nouwen, Nico

2011-12-01

419

Lack of Control of Nitrite Assimilation by Ammonium in an Oceanic Picocyanobacterium, Synechococcus sp. Strain WH 8103?  

PubMed Central

In cyanobacteria, the transcriptional activator NtcA is involved in global nitrogen control and, in the absence of ammonium, regulates the expression of genes involved in the assimilation of alternative nitrogen sources. The oceanic picocyanobacterium Synechococcus sp. strain WH 8103 harbors a copy of ntcA, but in the present study, we show that unlike other marine cyanobacteria that have been investigated, this strain is capable of coassimilating nitrite when grown in the presence of ammonium. Transcript levels for the genes encoding the nitrate/nitrite-bispecific permease NrtP and nitrate reductase (NarB) were substantially down-regulated by ammonium, whereas the abundances of nitrite reductase (NirA) transcripts were similar in nitrite- and ammonium-grown cells. The growth of Synechococcus sp. strain WH 8103 in medium containing both ammonium and nitrite resulted in only minor changes in the expression profile in comparison to that of nitrite-grown cells with the exception that the gene encoding the high-affinity ammonium transporter Amt1 was down-regulated to the levels seen in ammonium-grown cells. Whereas the expression of nrtP, narB, and amt1 appears to be NtcA dependent in this marine cyanobacterium, the transcription and expression of nirA appear not to be. The ability to coassimilate nitrite and reduced-nitrogen sources like ammonium may be an adaptive trait that enables oceanic strains like Synechococcus sp. strain WH 8103 to exploit the low nitrite concentrations found in oceanic surface waters that are not available to their principal and more numerous competitor, Prochlorococcus.

Wyman, Michael; Bird, Clare

2007-01-01

420

Isolation and complementation analysis of 10 methanol oxidation mutant classes and identification of the methanol dehydrogenase structural gene of Methylobacterium sp. strain AM1  

SciTech Connect

A method has been developed for the direct selection of methanol oxidation mutants of the facultative methylotroph Methylobacterium sp. strain AM1 (formerly Pseudomonas sp. strain AM1). Using this direct selection technique, we have isolated mutants of Methylobacterium sp. strain AM1 that are no longer capable of growth on methanol but retain the ability to grow on methylamine. These methanol oxidation (Mox) mutants were complemented with a genomic clone bank of this organism constructed in the broad-host-range cosmid pVK100, and subcloning and Tn5 mutagenesis experiments have assigned the Mox mutants to 10 distinct complementation groups. Using an open reading frame beta-galactosidase fusion vector and antibodies specific for Methylobacterium sp. strain AM1 methanol dehydrogenase, we have identified the methanol dehydrogenase structural gene and determined the direction of transcription. The results suggest that the synthesis and utilization of an active methanol dehydrogenase in this organism requires at least 10 different gene functions.

Nunn, D.N.; Lidstrom, M.E.

1986-05-01

421

Draft Genome Sequence of Marine Streptomyces sp. Strain W007, Which Produces Angucyclinone Antibiotics with a Benz[a]anthracene Skeleton  

PubMed Central

A series of angucyclinone antibiotics have been isolated from marine Streptomyces sp. strain W007 and identified. Here, a draft genome sequence of Streptomyces sp. W007 is presented. The genome contains an intact biosynthetic gene cluster for angucyclinone antibiotics, which provides insight into the combinatorial biosynthesis of angucyclinone antibiotics produced by marine streptomycetes.

Zhang, Hongyu; Zhu, Benwei; Zheng, Huajun

2012-01-01

422

Localization and Characterization of the Carbon Tetrachloride Transformation Activity of Pseudomonas sp. Strain KC  

PubMed Central

Previous research has established that Pseudomonas sp. strain KC rapidly transforms carbon tetrachloride (CT) to carbon dioxide (45 to 55%), a nonvolatile fraction (45 to 55%), and a cell-associated fraction ((equiv)5%) under denitrifying, iron-limited conditions. The present study provides additional characterization of the nonvolatile fraction, demonstrates that electron transfer plays a role in the transformation, and establishes the importance of both extracellular and intracellular factors. Experiments with (sup14)C-labeled CT indicate that more than one nonvolatile product is produced during CT transformation by strain KC. One of these products, accounting for about 20% of the [(sup14)C]CT transformed, was identified as formate on the basis of its elution time from an ion-exchange column, its boiling point, and its conversion to (sup14)CO(inf2) when incubated with formate dehydrogenase. Production of formate requires transfer of two electrons to the CT molecule. The role of electron transfer was also supported by experiments demonstrating that stationary-phase cells that do not transform CT can be stimulated to transform CT when supplemented with acetate (electron donor), nitrate (electron acceptor), or a protonophore (carbonyl cyanide m-chlorophenylhydrazone). The location of transformation activity was also evaluated. By themselves, washed cells did not transform CT to a significant degree. Occasionally, CT transformation was observed by cell-free culture supernatant, but this activity was not reliable. Rapid and reliable CT transformation was only obtained when washed whole cells were reconstituted with culture supernatant, indicating that both extracellular and intracellular factors are normally required for CT transformation. Fractionation of culture supernatant by ultrafiltration established that the extracellular factor or factors are small, with an apparent molecular mass of less than 500 Da. The extracellular factor or factors were stable after lyophilization to powder and were extractable with acetone. Addition of micromolar levels of iron inhibited CT transformation in whole cultures, but the level of iron needed to inhibit CT transformation was over 100-fold higher for washed cells reconstituted with a 10,000-Da supernatant filtrate. Thus, the inhibitory effects of iron are exacerbated by a supernatant factor or factors with a molecular mass greater than 10,000 Da.

Dybas, M. J.; Tatara, G. M.; Criddle, C. S.

1995-01-01

423

Exo-Oligosaccharides of Rhizobium sp. Strain NGR234 Are Required for Symbiosis with Various Legumes  

PubMed Central

Rhizobia are nitrogen-fixing bacteria that establish endosymbiotic associations with legumes. Nodule formation depends on various bacterial carbohydrates, including lipopolysaccharides, K-antigens, and exopolysaccharides (EPS). An acidic EPS from Rhizobium sp. strain NGR234 consists of glucosyl (Glc), galactosyl (Gal), glucuronosyl (GlcA), and 4,6-pyruvylated galactosyl (PvGal) residues with ?-1,3, ?-1,4, ?-1,6, ?-1,3, and ?-1,4 glycoside linkages. Here we examined the role of NGR234 genes in the synthesis of EPS. Deletions within the exoF, exoL, exoP, exoQ, and exoY genes suppressed accumulation of EPS in bacterial supernatants, a finding that was confirmed by chemical analyses. The data suggest that the repeating subunits of EPS are assembled by an ExoQ/ExoP/ExoF-dependent mechanism, which is related to the Wzy polymerization system of group 1 capsular polysaccharides in Escherichia coli. Mutation of exoK (NGR?exoK), which encodes a putative glycanase, resulted in the absence of low-molecular-weight forms of EPS. Analysis of the extracellular carbohydrates revealed that NGR?exoK is unable to accumulate exo-oligosaccharides (EOSs), which are O-acetylated nonasaccharide subunits of EPS having the formula Gal(Glc)5(GlcA)2PvGal. When used as inoculants, both the exo-deficient mutants and NGR?exoK were unable to form nitrogen-fixing nodules on some hosts (e.g., Albizia lebbeck and Leucaena leucocephala), but they were able to form nitrogen-fixing nodules on other hosts (e.g., Vigna unguiculata). EOSs of the parent strain were biologically active at very low levels (yield in culture supernatants, ?50 ?g per liter). Thus, NGR234 produces symbiotically active EOSs by enzymatic degradation of EPS, using the extracellular endo-?-1,4-glycanase encoded by exoK (glycoside hydrolase family 16). We propose that the derived EOSs (and not EPS) are bacterial components that play a crucial role in nodule formation in various legumes.

Staehelin, Christian; Forsberg, Lennart S.; D'Haeze, Wim; Gao, Mu-Yun; Carlson, Russell W.; Xie, Zhi-Ping; Pellock, Brett J.; Jones, Kathryn M.; Walker, Graham C.; Streit, Wolfgang R.; Broughton, William J.

2006-01-01

424

Rhizobium sp. strain NGR234 NodZ protein is a fucosyltransferase.  

PubMed Central

Rhizobium sp. strain NGR234 produces a large family of lipochitooligosaccharide Nod factors carrying specific substituents. Among them are 3-O- (or 4-O-) and 6-O-carbamoyl groups, an N-methyl group, and a 2-O-methylfucose residue which may bear either 3-O-sulfate or 4-O-acetyl substitutions. Investigations on the genetic control of host specificity revealed a number of loci which directly affect Nod factor structure. Here we show that insertion and frameshift mutations in the nodZ gene abolish fucosylation of Nod factors. In vitro assays using GDP-L-fucose as the fucose donor show that fucosyltransferase activity is associated with the nodZ gene product (NodZ). NodZ is located in the soluble protein fraction of NGR234 cells. Together with extra copies of the nodD1 gene, the nodZ gene and its associated nod box were introduced into ANU265, which is NGR234 cured of the symbiotic plasmid. Crude extracts of this transconjugant possess fucosyltransferase activity. Fusion of a His6 tag to the NodZ protein expressed in Escherichia coli yielded a protein able to fucosylate both nonfucosylated NodNGR factors and oligomers of chitin. NodZ is inactive on monomeric N-acetyl-D-glucosamine and on desulfated Rhizobium meliloti Nod factors. Kinetic analyses showed that the NodZ protein is more active on oligomers of chitin than on nonfucosylated NodNGR factors. Pentameric chitin is the preferred substrate. These data suggest that fucosylation occurs before acylation of the Nod factors.

Quesada-Vincens, D; Fellay, R; Nasim, T; Viprey, V; Burger, U; Prome, J C; Broughton, W J; Jabbouri, S

1997-01-01

425

Characterization of the response to zinc deficiency in the cyanobacterium Anabaena sp. strain PCC 7120.  

PubMed

Zur regulators control zinc homeostasis by repressing target genes under zinc-sufficient conditions in a wide variety of bacteria. This paper describes how part of a survey of duplicated genes led to the identification of the open reading frame all2473 as the gene encoding the Zur regulator of the cyanobacterium Anabaena sp. strain PCC 7120. All2473 binds to DNA in a zinc-dependent manner, and its DNA-binding sequence was characterized, which allowed us to determine the relative contribution of particular nucleotides to Zur binding. A zur mutant was found to be impaired in the regulation of zinc homeostasis, showing sensitivity to elevated concentrations of zinc but not other metals. In an effort to characterize the Zur regulon in Anabaena, 23 genes containing upstream putative Zur-binding sequences were identified and found to be regulated by Zur. These genes are organized in six single transcriptional units and six operons, some of them containing multiple Zur-regulated promoters. The identities of genes of the Zur regulon indicate that Anabaena adapts to conditions of zinc deficiency by replacing zinc metalloproteins with paralogues that fulfill the same function but presumably with a lower zinc demand, and with inducing putative metallochaperones and membrane transport systems likely being involved in the scavenging of extracellular zinc, including plasma membrane ABC transport systems and outer membrane TonB-dependent receptors. Among the Zur-regulated genes, the ones showing the highest induction level encode proteins of the outer membrane, suggesting a primary role for components of this cell compartment in the capture of zinc cations from the extracellular medium. PMID:22389488

Napolitano, Mauro; Rubio, Miguel Ángel; Santamaría-Gómez, Javier; Olmedo-Verd, Elvira; Robinson, Nigel J; Luque, Ignacio

2012-03-02

426

Purification, characterization, and properties of an aryl aldehyde oxidoreductase from Nocardia sp. strain NRRL 5646.  

PubMed Central

An aryl aldehyde oxidoreductase from Nocardia sp. strain NRRL 5646 was purified 196-fold by a combination of Mono-Q, Reactive Green 19 agarose affinity, and hydroxyapatite chromatographies. The purified enzyme runs as a single band of 140 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The molecular mass was estimated to be 163 +/- 3.8 kDa by gel filtration, indicating that this enzyme is a monomeric protein. The binding of the enzyme to Reactive Green 19 agarose was Mg2+ dependent. The binding capacity was estimated to be about 0.2 mg of Reactive Green agarose per ml in the presence of 10 mM MgCl2. This enzyme can catalyze the reduction of a wide range of aryl carboxylic acids, including substituted benzoic acids, phenyl-substituted aliphatic acids, heterocyclic carboxylic acids, and polyaromatic ring carboxylic acids, to produce the corresponding aldehydes. The Km values for benzoate, ATP, and NADPH were determined to be 645 +/- 75, 29.3 +/- 3.1, and 57.3 +/- 12.5 microM, respectively. The Vmax was determined to be 0.902 +/- 0.04 micromol/min/mg of protein. Km values for (S)-(+)-alpha-methyl-4-(2-methylpropyl)-benzeneacetic acid (ibuprofen) and its (R)-(-) isomer were determined to be 155 +/- 18 and 34.5 +/- 2.5 microM, respectively. The Vmax for the (S)-(+) and (R)-(-) isomers were 1.33 and 0.15 micromol/min/mg of protein, respectively. Anthranilic acid is a competitive inhibitor with benzoic acid as a substrate, with a Ki of 261 +/- 30 microM. The N-terminal and internal amino acid sequences of a 76-kDa peptide from limited alpha-chymotrypsin digestion were determined.

Li, T; Rosazza, J P

1997-01-01

427