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1

Draft Genome Sequence of Geobacillus sp. Strain FW23, Isolated from a Formation Water Sample  

PubMed Central

The thermophilic Geobacillus sp. strain FW23 was isolated from the Mehsana oil wells in Gujrat, India, during a screening for oil-degrading bacteria. Here, we report the draft genome sequence of Geobacillus sp. FW23, which may help reveal the genomic differences between this strain and the earlier reported species of the genus Geobacillus. PMID:24812215

Pore, Soham D.; Arora, Preeti

2014-01-01

2

Draft Genome Sequence of Geobacillus sp. Strain FW23, Isolated from a Formation Water Sample.  

PubMed

The thermophilic Geobacillus sp. strain FW23 was isolated from the Mehsana oil wells in Gujrat, India, during a screening for oil-degrading bacteria. Here, we report the draft genome sequence of Geobacillus sp. FW23, which may help reveal the genomic differences between this strain and the earlier reported species of the genus Geobacillus. PMID:24812215

Pore, Soham D; Arora, Preeti; Dhakephalkar, Prashant K

2014-01-01

3

Draft Genome Sequences of Geobacillus sp. Strains CAMR5420 and CAMR12739.  

PubMed

Thermophilic Geobacillus spp. can efficiently hydrolyze hemicellulose polymers and are therefore of interest in biotechnological applications. Here we report the genome sequences of two hemicellulolytic strains, Geobacillus sp. CAMR12739 and CAMR5420. PMID:24903881

De Maayer, Pieter; Williamson, Carolyn E; Vennard, Christopher T; Danson, Michael J; Cowan, Don A

2014-01-01

4

Draft Genome Sequences of Geobacillus sp. Strains CAMR5420 and CAMR12739  

PubMed Central

Thermophilic Geobacillus spp. can efficiently hydrolyze hemicellulose polymers and are therefore of interest in biotechnological applications. Here we report the genome sequences of two hemicellulolytic strains, Geobacillus sp. CAMR12739 and CAMR5420. PMID:24903881

De Maayer, Pieter; Williamson, Carolyn E.; Vennard, Christopher T.; Danson, Michael J.

2014-01-01

5

Characterization of two novel plasmids from Geobacillus sp. 610 and 1121 strains.  

PubMed

We describe two cryptic low molecular weight plasmids, pGTD7 (3279bp) and pGTG5 (1540bp), isolated from Geobacillus sp. 610 and 1121 strains, respectively. Homology analysis of the replication protein (Rep) sequences and detection of ssDNA indicate that both of them replicate via rolling circle mechanism. As revealed by sequence similarities of dso region and Rep protein, plasmid pGTD7 belongs to pC194/pUB110 plasmid family. The replicon of pGTD7 was proved to be functional in another Geobacillus host. For this purpose, a construct pUCK7, containing a replicon of the analyzed plasmid, was created and transferred to G. stearothermophilus NUB3621R strain by electroporation. Plasmid pGTG5, based on Rep protein sequence similarity, was found to be related mostly to some poorly characterized bacterial plasmids. Rep proteins encoded by these plasmids contain conservative motifs that are most similar to those of Microviridae phages. This feature suggests that pGTG5, together with other plasmids containing the same motifs, could constitute a new family of bacterial plasmids. To date, pGTG5 is the smallest plasmid identified in bacteria belonging to the genus Geobacillus. The two plasmids described in this study can be used for the construction of new vectors suitable for biotechnologically important bacteria of the genus Geobacillus. PMID:24177015

Kananavi?i?t?, R?ta; Butait?, Elena; Citavi?ius, Donaldas

2014-01-01

6

Gold nanoparticles synthesized by Geobacillus sp. strain ID17 a thermophilic bacterium isolated from Deception Island, Antarctica  

PubMed Central

Background The use of microorganisms in the synthesis of nanoparticles emerges as an eco-friendly and exciting approach, for production of nanoparticles due to its low energy requirement, environmental compatibility, reduced costs of manufacture, scalability, and nanoparticle stabilization compared with the chemical synthesis. Results The production of gold nanoparticles by the thermophilic bacterium Geobacillus sp. strain ID17 is reported in this study. Cells exposed to Au3+ turned from colourless into an intense purple colour. This change of colour indicates the accumulation of intracellular gold nanoparticles. Elemental analysis of particles composition was verified using TEM and EDX analysis. The intracellular localization and particles size were verified by TEM showing two different types of particles of predominant quasi-hexagonal shape with size ranging from 5–50 nm. The mayority of them were between 10?20 nm in size. FT-IR was utilized to characterize the chemical surface of gold nanoparticles. This assay supports the idea of a protein type of compound on the surface of biosynthesized gold nanoparticles. Reductase activity involved in the synthesis of gold nanoparticles has been previously reported to be present in others microorganisms. This reduction using NADH as substrate was tested in ID17. Crude extracts of the microorganism could catalyze the NADH-dependent Au3+ reduction. Conclusions Our results strongly suggest that the biosynthesis of gold nanoparticles by ID17 is mediated by enzymes and NADH as a cofactor for this biological transformation. PMID:23919572

2013-01-01

7

Characterization of thermostable lipase from thermophilic Geobacillus sp. TW1  

Microsoft Academic Search

A novel lipase-producing thermophilic strain TW1, assigned to Geobacillus sp. TW1 based on 16S rRNA sequence, was isolated from a hot spring in China. Based on this strain, a lipase gene encoding 417 amino acids was cloned. Subsequently, the lipase gene was expressed in Escherichia coli and purified as a fusion protein with glutathione S-transferase. The results showed that the

Hebin Li; Xiaobo Zhang

2005-01-01

8

Isolation and Characterization of Novel Denitrifying Bacterium Geobacillus sp. SG-01 Strain from Wood Chips Composted with Swine Manure  

PubMed Central

Nitrate contamination in ground and surface water is an increasingly serious environmental problem and only a few bacterial strains have been identified that have the ability to remove nitrogen pollutants from wastewater under thermophilic conditions. We therefore isolated thermophilic facultative bacterial strains from wood chips that had been composted with swine manure under aerated high temperature conditions so as to identify strains with denitrifying ability. Nine different colonies were screened and 3 long rod-shaped bacterial strains designated as SG-01, SG-02, and SG-03 were selected. The strain SG-01 could be differentiated from SG-02 and SG-03 on the basis of the method that it used for sugar utilization. The 16S rRNA genes of this strain also had high sequence similarity with Geobacillus thermodenitrificans 465T (99.6%). The optimal growth temperatures (55°C), pH values (pH 7.0), and NaCl concentrations (1%) required for the growth of strain SG-01 were established. This strain reduced 1.18 mM nitrate and 1.45 mM nitrite in LB broth after 48 h of incubation. These results suggest that the G. thermodenitrificans SG-01 strain may be useful in the removal of nitrates and nitrites from wastewater generated as a result of livestock farming. PMID:25049754

Yang, Seung-Hak; Cho, Jin-Kook; Lee, Soon-Youl; Abanto, Oliver D.; Kim, Soo-Ki; Ghosh, Chiranjit; Lim, Joung-Soo; Hwang, Seong-Gu

2013-01-01

9

Isolation and Characterization of Novel Denitrifying Bacterium Geobacillus sp. SG-01 Strain from Wood Chips Composted with Swine Manure.  

PubMed

Nitrate contamination in ground and surface water is an increasingly serious environmental problem and only a few bacterial strains have been identified that have the ability to remove nitrogen pollutants from wastewater under thermophilic conditions. We therefore isolated thermophilic facultative bacterial strains from wood chips that had been composted with swine manure under aerated high temperature conditions so as to identify strains with denitrifying ability. Nine different colonies were screened and 3 long rod-shaped bacterial strains designated as SG-01, SG-02, and SG-03 were selected. The strain SG-01 could be differentiated from SG-02 and SG-03 on the basis of the method that it used for sugar utilization. The 16S rRNA genes of this strain also had high sequence similarity with Geobacillus thermodenitrificans 465(T) (99.6%). The optimal growth temperatures (55°C), pH values (pH 7.0), and NaCl concentrations (1%) required for the growth of strain SG-01 were established. This strain reduced 1.18 mM nitrate and 1.45 mM nitrite in LB broth after 48 h of incubation. These results suggest that the G. thermodenitrificans SG-01 strain may be useful in the removal of nitrates and nitrites from wastewater generated as a result of livestock farming. PMID:25049754

Yang, Seung-Hak; Cho, Jin-Kook; Lee, Soon-Youl; Abanto, Oliver D; Kim, Soo-Ki; Ghosh, Chiranjit; Lim, Joung-Soo; Hwang, Seong-Gu

2013-11-01

10

Lipid composition of thermophilic Geobacillus sp. strain GWE1, isolated from sterilization oven.  

PubMed

GWE1 strain is an example of anthropogenic thermophilic bacterium, recently isolated from dark crusty material from sterilization ovens by Correa-Llantén et al. (Kor. J. Microb. Biotechnol. 2013. 41(3):278-283). Thermostability is likely to arise from the adaptation of macromolecules such as proteins, lipids and nucleic acids. Complex lipid arrangement and/or type in the cell membrane are known to affect thermostability of microorganisms and efforts were made to understand the chemical nature of the polar lipids of membrane. In this work, we extracted total lipids from GWE1 cell membrane, separated them by TLC into various fractions and characterize the lipid structures of certain fractions with analytical tools such as (1)H, (13)C, (31)P and 2D NMR spectroscopy, ATR-FTIR spectroscopy and MS(n) spectrometry. We were able to identify glycerophosphoethanolamine, glycerophosphate, glycerophosphocholine, glycerophosphoglycerol and cardiolipin lipid classes and an unknown glycerophospholipid class with novel MS/MS spectra pattern. We have also noticed the presence of saturated iso-branched fatty acids with NMR spectra in individual lipid classes. PMID:24613478

Shah, Siddharth P; Jansen, Susan A; Taylor, Leeandrew Jacques-Asa; Chong, Parkson Lee-Gau; Correa-Llantén, Daniela N; Blamey, Jenny M

2014-05-01

11

International Journal of Systematic and Evolutionary Microbiology (2002), 52, 22512255 DOI: 10.1099/ijs.0.02181-0 Geobacillus toebii sp. nov., a novel  

E-print Network

.1099/ijs.0.02181-0 NOTE Geobacillus toebii sp. nov., a novel thermophilic bacterium isolated from hay as those of the genus Geobacillus. Phylogenetic analysis based on 16S rDNA sequences showed that strain SK-1T is most closely related to Geobacillus thermoglucosidasius. However, the phenotypic properties

Bae, Jin-Woo

12

A thermoalkaliphilic lipase of Geobacillus sp. T1  

Microsoft Academic Search

A thermoalkaliphilic T1 lipase gene of Geobacillus sp. strain T1 was overexpressed in pGEX vector in the prokaryotic system. Removal of the signal peptide improved protein\\u000a solubility and promoted the binding of GST moiety to the glutathione-Sepharose column. High-yield purification of T1 lipase\\u000a was achieved through two-step affinity chromatography with a final specific activity and yield of 958.2 U\\/mg and 51.5%,

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

2007-01-01

13

Genome shuffling enhances lipase production of thermophilic Geobacillus sp.  

PubMed

Thermostable lipases are potential enzymes for biocatalytic application. In this study, the lipase production of Geobacillus sp. CF03 (WT) was improved by genome shuffling. After two rounds of genome shuffling, one fusant strain (FB1) achieved increase lipase activity from the populations generated by ultraviolet irradiation and ethyl methylsulfonate (EMS) mutagenesis. The growth rate and lipase production of FB1 increased highest by 150 and 238 %, respectively, in comparison to the wild type. The fusant enzyme had a significant change in substrate specificity but still prefers the long-chain length substrates. It had an optimum activity at 60 °C, pH at 7.0-8.0, with p-nitrophenyl palmitate (C16) as a substrate and retained about 50 % of their activity after 15 min at 70 °C, pH 8.0. Furthermore, the fusant lipase showed the preference of sesame oil, waste palm oil, and canola oil. Therefore, the genome shuffling strategy has been successful to strain improvement and selecting strain with multiple desirable characteristics. PMID:25119547

Chalopagorn, Pornchanok; Charoenpanich, Jittima; Choowongkomon, Kiattawee

2014-10-01

14

Thermostable hemicellulases of a bacterium, Geobacillus sp. DC3, isolated from the former Homestake Gold Mine in Lead, South Dakota  

Technology Transfer Automated Retrieval System (TEKTRAN)

A thermophilic strain, Geobacillus sp. DC3, capable of producing hemicellulolytic enzymes was isolated from the 1.5-km depth of the former Homestake gold mine in Lead, South Dakota. The DC3 strain expressed a high level of extracellular endoxylanase at 39.5 U/mg protein with additional hemicellulase...

15

Draft Genome Sequence of Geobacillus thermopakistaniensis Strain MAS1.  

PubMed

Geobacillus thermopakistaniensis strain MAS1 was isolated from a hot spring located in the Northern Areas of Pakistan. The draft genome sequence was 3.5 Mb and identified a number of genes of potential industrial importance, including genes encoding glycoside hydrolases, pullulanase, amylopullulanase, glycosidase, and alcohol dehydrogenases. PMID:24903880

Siddiqui, Masood Ahmed; Rashid, Naeem; Ayyampalayam, Saravanaraj; Whitman, William B

2014-01-01

16

?-Glucosidase from a strain of deep-sea Geobacillus : a potential enzyme for the biosynthesis of complex carbohydrates  

Microsoft Academic Search

An ?-glucosidase from Geobacillus sp. strain HTA-462, one of the deepest sea bacteria isolated from the sediment of the Mariana Trench, was purified to homogeneity\\u000a and estimated to be a 65-kDa protein by SDS-PAGE. At low ion strength, the enzyme exists in the homodimeric form (130 kDa).\\u000a It is a thermo- and alkaline-stable enzyme with a half-life of 13.4 h and a

Vo Si Hung; Yuji Hatada; Saori Goda; Jie Lu; Yuko Hidaka; Zhijun Li; Masatake Akita; Yukari Ohta; Kenji Watanabe; Hirokazu Matsui; Susumu Ito; Koki Horikoshi

2005-01-01

17

[Characterization of a thermophilic Geobacillus strain DM-2 degrading hydrocarbons].  

PubMed

A thermophilic Geobacillus strain DM-2 from a deep-subsurface oil reservoir was investigated on its capability of degrading crude oil under various conditions as well as its characters on degrading hydrocarbons in optimal conditions. The results showed that Geobacillus strain DM-2 was able to degrade crude oil under anoxic wide-range conditions with pH ranging from 4.0 to 10.0, high temperature in the range of 45-70 degrees C and saline concentration ranging from 0.2% to 3.0%. Furthermore, the optimal temperature and pH value for utilizing hydrocarbons by the strain were 60 degrees C and 7.0, respectively. Under such optimal conditions, the strain utilized liquid paraffine emulsified by itself as its carbon source for growth; further analysis by gas chromatography (GC) and infrared absorption spectroscopy demonstrated that it was able to degrade n-alkanes (C14-C30), branched-chain alkanes and aromatic hydrocarbons in crude oil and could also utilize long-chain n-alkanes from C16 to C36, among of which the degradation efficiency of C28 was the highest, up to 88.95%. One metabolite of the strain oxidizing alkanes is fatty acid.While utilizing C16 as carbon source for 5 d, only one fatty acid-acetic acid was detected by HPLC and MS as the product, with the amount of 0.312 g/L, which indicated that it degraded n-alkanes with pathway of inferior terminal oxidation,and then followed by a beta-oxidation pathway. Due to its characters of efficient emulsification, high-performance degradation of hydrocarbons and fatty-acid production under high temperature and anoxic condition, the strain DM-2 may be potentially applied to oil-waste treatment and microbial enhanced heavy oil recovery in extreme conditions. PMID:19256400

Liu, Qing-kun; Wang, Jun; Li, Guo-qiang; Ma, Ting; Liang, Feng-lai; Liu, Ru-lin

2008-12-01

18

Experimental fossilisation of the thermophilic Gram-positive bacterium Geobacillus SP7A: a long duration preservation study.  

E-print Network

Experimental fossilisation of the thermophilic Gram-positive bacterium Geobacillus SP7A: a long of fossilised microbes in recent and ancient rocks, we experimentally silicified a Gram-positive bacterium of Gram-positive bacteria was extremely rapid, thus allowing very good preservation of Geobacillus SP7A

Paris-Sud XI, Université de

19

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

Microsoft Academic Search

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

Raja Rahman; Thean Chor Leow; Abu Bakar Salleh; Mahiran Basri

2007-01-01

20

Permanent draft genome sequence of Geobacillus thermocatenulatus strain GS-1.  

PubMed

Geobacillus thermocatenulatus strain GS-1 is a thermophilic bacillus having a growth optimum at 60°C, capable of degrading alkanes. It was isolated from the formation water of a high-temperature deep oil reservoir in Qinghai oilfield, China. Here, we report the draft genome sequence with an estimated assembly size of 3.5Mb. A total of 3371 protein-coding sequences, including monooxygenase, alcohol dehydrogenase, aldehyde dehydrogenase, fatty acid-CoA ligase, acyl-CoA dehydrogenase, enoyl-CoA hydrogenase, hydroxyacyl-CoA dehydrogenase and thiolase, were detected in the genome, which are involved in the alkane degradation pathway. Our results may provide insights into the genetic basis of the adaptation of this strain to high-temperature oilfield ecosystems. PMID:25280889

Zheng, Beiwen; Zhang, Fan; Chai, Lujun; Yu, Gaoming; Shu, Fuchang; Wang, Zhengliang; Su, Sanbao; Xiang, Tingsheng; Zhang, Zhongzhi; Hou, DuJie; She, Yuehui

2014-10-01

21

Thermostable hemicellulases of a bacterium, Geobacillus sp. DC3, isolated from the former Homestake gold mine in Lead, South Dakota.  

PubMed

A thermophilic strain, Geobacillus sp. DC3, capable of producing hemicellulolytic enzymes was isolated from the 1.5-km depth of the former Homestake gold mine in Lead, South Dakota. The DC3 strain expressed a high level of extracellular endoxylanase at 39.5 U/mg protein with additional hemicellulases including ?-xylosidase (0.209 U/mg) and arabinofuranosidase (0.230 U/mg), after the bacterium was grown in xylan for 24 h. Partially purified DC3 endoxylanase exhibited a molecular mass of approximately 43 kDa according to zymography with an optimal pH of 7 and optimal temperature of 70 °C. The kinetic constants, K m and V max, were 13.8 mg/mL and 77.5 ?mol xylose/min·mg xylan, respectively. The endoxylanase was highly stable and maintained 70 % of its original activity after 16 h incubation at 70 °C. The thermostable properties and presence of three different hemicellulases of Geobacillus sp. DC3 strain support its potential application for industrial hydrolysis of renewable biomass such as lignocelluloses. PMID:24549802

Bergdale, Terran E; Hughes, Stephen R; Bang, Sookie S

2014-04-01

22

Biosorption of Cd, Cu, Ni, Mn and Zn from aqueous solutions by thermophilic bacteria, Geobacillus toebii sub.sp. decanicus and Geobacillus thermoleovorans sub.sp. stromboliensis: Equilibrium, kinetic and thermodynamic studies  

Microsoft Academic Search

Biosorption of each of the ions Cd2+, Cu2+, Ni2+, Zn2+ and Mn2+ on Geobacillus toebii sub.sp. decanicus (G1) and Geobacillus thermoleovorans sub.sp. stromboliensis (G2) in a batch stirred system was investigated. The equilibrium adsorptive quantity was determined to be a function of the solution pH, contact time, biomass concentration, initial metal concentrations and temperature. The results obtained from biosorption experiments

Sadin Özdemir; Ersin Kilinc; Annarita Poli; Barbara Nicolaus; Kemal Güven

2009-01-01

23

Molecular cloning and characterization of a thermostable lipase from deep-sea thermophile Geobacillus sp. EPT9.  

PubMed

A gene (1,254 bp) encoding a lipase was identified from a deep-sea hydrothermal field thermophile Geobacillus sp. EPT9. The open reading frame of this gene encoded 417 amino acid residues. The gene was cloned, overexpressed in Escherichia coli, and the target protein was purified to homogeneity. The purified recombinant enzyme presented a molecular mass of 44.8 kDa. When p-nitrophenyl palmitate was used as a substrate, the recombinant lipase was optimally active at 55 °C and pH 8.5. The recombinant enzyme retained 44 % residual activity after incubation at 80 °C for 1 h, which indicated that Geobacillus sp. EPT9 lipase was thermostable. Homology modeling of strain EPT9 lipase was developed with the lipase from Bacillus sp. L2 as a template. The core structure exhibits an ?/?-hydrolase fold and the typical catalytic triad might consist of Ser142, Asp346, and His387. The enzymatic activity of EPT9 lipase was inhibited by addition of phenylmethylsulfonyl fluoride, indicating that it contains serine residue, which plays an important role in the catalytic mechanism. PMID:25388475

Zhu, Yanbing; Li, Hebin; Ni, Hui; Xiao, Anfeng; Li, Lijun; Cai, Huinong

2015-02-01

24

Purification and characterization of a thermostable protease from a newly isolated Geobacillus sp. YMTC 1049  

Microsoft Academic Search

A thermostable extracellular protease named protease RH-1 was purified from a thermophilic Geobacillus sp. YMTC 1049 isolated from a hotspring in Rehai, Tengchong, Yunnan Province, China. Protease RH-1 was a serine protease since it was inhibited by 10mM PMSF. It was a monomeric enzyme with molecular weight of 59.2kDa. The protease showed the highest activity at 85°C at pH 7.5

Wei Zhu; Dongmei Cha; Guyue Cheng; Qian Peng; Ping Shen

2007-01-01

25

Novel thermostable endo-xylanase cloned and expressed from bacterium Geobacillus sp. WSUCF1  

Technology Transfer Automated Retrieval System (TEKTRAN)

A gene encoding a GH10 endo-xylanase from Geobacillus sp. WSUCF1 was cloned and expressed in Escherichia coli. Recombinant endo-xylanase (37 kDa) exhibited high specific activity of 461.0 U/ mg of protein. Endo-xylanase was optimally active on birchwood xylan at 70°C and pH 6.5. Zn2+ and Ca2+ ions i...

26

Thermophilic fermentation of acetoin and 2,3-butanediol by a novel Geobacillus strain  

PubMed Central

Background Acetoin and 2,3-butanediol are two important biorefinery platform chemicals. They are currently fermented below 40°C using mesophilic strains, but the processes often suffer from bacterial contamination. Results This work reports the isolation and identification of a novel aerobic Geobacillus strain XT15 capable of producing both of these chemicals under elevated temperatures, thus reducing the risk of bacterial contamination. The optimum growth temperature was found to be between 45 and 55°C and the medium initial pH to be 8.0. In addition to glucose, galactose, mannitol, arabionose, and xylose were all acceptable substrates, enabling the potential use of cellulosic biomass as the feedstock. XT15 preferred organic nitrogen sources including corn steep liquor powder, a cheap by-product from corn wet-milling. At 55°C, 7.7?g/L of acetoin and 14.5?g/L of 2,3-butanediol could be obtained using corn steep liquor powder as a nitrogen source. Thirteen volatile products from the cultivation broth of XT15 were identified by gas chromatography–mass spectrometry. Acetoin, 2,3-butanediol, and their derivatives including a novel metabolite 2,3-dihydroxy-3-methylheptan-4-one, accounted for a total of about 96% of all the volatile products. In contrast, organic acids and other products were minor by-products. ?-Acetolactate decarboxylase and acetoin:2,6-dichlorophenolindophenol oxidoreductase in XT15, the two key enzymes in acetoin metabolic pathway, were found to be both moderately thermophilic with the identical optimum temperature of 45°C. Conclusions Geobacillus sp. XT15 is the first naturally occurring thermophile excreting acetoin and/or 2,3-butanediol. This work has demonstrated the attractive prospect of developing it as an industrial strain in the thermophilic fermentation of acetoin and 2,3-butanediol with improved anti-contamination performance. The novel metabolites and enzymes identified in XT15 also indicated its strong promise as a precious biological resource. Thermophilic fermentation also offers great prospect for improving its yields and efficiencies. This remains a core aim for future work. PMID:23217110

2012-01-01

27

Characterization of thermostable cellulases produced by Bacillus and Geobacillus strains  

Microsoft Academic Search

The composition of thermophilic (60°C) mixed cellulose-degrading enrichment culture initiated from compost samples was examined by constructing a 16S rRNA gene clone library and the presence of sequences related to Actinobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Firmicutes, and Proteobacteria were identified. Eight isolates capable of degrading cellulose, carboxymethyl cellulose (CMC), or ponderosa pine sawdust were identified as belonging to the genera Geobacillus,

Gurdeep Rastogi; Aditya Bhalla; Akash Adhikari; Kenneth M. Bischoff; Stephen R. Hughes; Lew P. Christopher; Rajesh K. Sani

2010-01-01

28

Protein Expression Analysis in Temparature-adaptated Mutant Strains of Moderately thermophile Geobacillus stearothermophilus  

Microsoft Academic Search

Optimum growth of moderately thermophile Geobacillus stearothermophilus (Bst) has been observed at 55ºC, and suppressed by the downshift to lower temperature. In order to understand the relationship between growth temperature and protein expression, we made Bst mutant strains which were adapted to lower temperature (30ºC) compared with wild type strain, and then we examined their protein expression under various growth

Hitomi Kyogoku; Yasuaki Yamaguchi; Momoyo Miyano-Ono; Ayano Yamaguchi; Takanori Satoh

29

Biosynthesis of a thermostable gellan lyase by newly isolated and characterized strain of Geobacillus stearothermophilus 98  

Microsoft Academic Search

The thermophilic strain able to degrade gellan was isolated from Bulgarian hot spring. According to its morphological and biochemical properties and by partial sequencing of its 16S rDNA, it was classified as Geobacillus stearothermophilus. It grew in a synthetic medium with gellan as the only carbon source with a specific growth rate of 0.69 h?1 and generation time of 60 min. The

Anna Derekova; Carsten Sjøholm; Rossica Mandeva; Lilia Michailova; Margarita Kambourova

2006-01-01

30

Cloning, overexpression, and characterization of a novel alkali-thermostable xylanase from Geobacillus sp. WBI.  

PubMed

An endo-?-1,4-xylanase gene xynA of a thermophilic Geobacillus sp. WBI from "hot" compost was isolated by PCR amplification. The gene encoding 407 residues were overexpressed in E. coli and purified by Ni-NTA chromatography. The purified enzyme (47?kDa) had a broad pH optimum of 6.0 to 9.0, and was active between 50 and 90?°C. The enzyme retained 100% of its activity when incubated at 65?°C for 1?h under alkaline condition (pH 10.0) and retained 75% activity at pH 11.0. The Km and Vmax of the enzyme were 0.9?mg?ml(-1) and 0.8?µmol?ml(-1) ?min(-1) , respectively. In molecular dynamics simulation at 338?K (65?°C), the enzyme was found to be stable. At an elevated temperature (450?K) specific ?-helix and ?-turns of the proteins were most denatured. The denaturation was less in WBI compared with its highest homolog G. stearothermophilus T-6 xylanase with difference of six residues. The results predict that these regions are responsible for the improved thermostability observed over related enzymes. The present work encourages further experimental demonstration to understand how these regions contribute thermostability to WBI xylanase. The study noted that WBI produces a xylanase with unique characteristics, specifically alkali-thermostability. PMID:25404211

Mitra, Suranjita; Mukhopadhyay, Bidhan Chandra; Mandal, Anisur Rahaman; Arukha, Ananta Prasad; Chakrabarty, Kuheli; Das, Gourab Kanti; Chakrabartty, Pran Krishna; Biswas, Swadesh Ranjan

2014-11-18

31

Thermostable lipase from Geobacillus sp. Iso5: bioseparation, characterization and native structural studies.  

PubMed

The extracellular thermoalkaline lipase from Geobacillus sp. Iso5 was purified to homogeneity by ultrafiltration, 6% cross-linked agarose and Phenyl spehrose HIC column chromatography. The final purified lipase resulted in 8.7-fold with 6.2% yield. The relative molecular weight of the enzyme was determined to be a monomer of 47?kDa by SDS-PAGE and MALDI-TOF MS/MS spectroscopy. The purified enzyme exhibit optimum activity at 70?°C and pH 8.0. The enzyme retained above 90% activity at temperatures of 70?°C and about 35% activity at 85?°C for 2?h. However, the stability of the enzyme decreased at the temperature over 90?°C. The enzyme activity was promoted in the presence of Ca(2+) and Mg(2+) and strongly inhibited by HgCl2 , PMSF, DTT, K(+) , Co(2+) , and Zn (2+) . EDTA did not affect the enzyme activity. The secondary structure of purified lipase contains 36% ?-helix and 64% ?-sheet which was determined by Circular dichromism, FTIR, and Raman Spectroscopy. PMID:23775834

Mahadevan, Gurumurthy D; Neelagund, Shivayogeeswar E

2014-05-01

32

Novel thermostable endo-xylanase cloned and expressed from bacterium Geobacillus sp. WSUCF1.  

PubMed

A gene encoding a GH10 endo-xylanase from Geobacillus sp. WSUCF1 was cloned and expressed in Escherichia coli. Recombinant endo-xylanase (37kDa) exhibited high specific activity of 461.0U/mg of protein. Endo-xylanase was optimally active on birchwood xylan at 70°C and pH 6.5. The endo-xylanase was found to be highly thermostable at 50 and 60°C, retaining 82% and 50% of its original activity, respectively, after 60h. High xylan conversions (92%) were obtained with oat-spelt xylan hydrolysis. Higher glucan and xylan conversions were obtained on AFEX-treated corn stover with an enzyme cocktail containing WSUCF1 endo-xylanase (71% and 47%) as compared to enzyme cocktail containing commercial fungal endo-xylanase (64% and 41%). High specific activity, active at high pH's, wide substrate specificity, and higher hydrolytic activity on recalcitrant lignocellulose, make this endo-xylanase a suitable candidate for biofuel and bioprocess industries. PMID:24725385

Bhalla, Aditya; Bischoff, Kenneth M; Uppugundla, Nirmal; Balan, Venkatesh; Sani, Rajesh K

2014-08-01

33

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

PubMed

Due to potential use for variety of biotechnological applications, genes encoding thermoalkalophilic esterase from three different Geobacillus strains isolated from thermal environmental samples in Balçova (Agamemnon) geothermal site were cloned and respective proteins were expressed in Escherichia coli (E.coli) and characterized in detail. Three esterases (Est1, Est2, Est3) were cloned directly by PCR amplification using consensus degenerate primers from genomic DNA of the strains Est1, Est2 and Est3 which were from mud, reinjection water and uncontrolled thermal leak, respectively. The genes contained an open reading frame (ORF) consisting of 741 bp for Est1 and Est2, which encoded 246 amino acids and ORF of Est3 was 729 bp encoded 242 amino acids. The esterase genes were expressed in E. coli and purified using His-Select HF nickel affinity gel. The molecular mass of the recombinant enzyme for each esterase was approximately 27.5 kDa. The three esterases showed high specific activity toward short chain p-NP esters. Recombinant Est1, Est2, Est3 have exhibited similar activity and the highest esterase activity of 1,100 U/mg with p-nitrophenyl acetate (pNPC(2)) as substrate was observed with Est1. All three esterase were most active around 65°C and pH 9.5-10.0. The effect of organic solvents, several metal ions, inhibitors and detergents on enzyme activity for purified Est1, Est2, Est3 were determined separately and compared. PMID:21181486

Tekedar, Hasan Cihad; Sanl?-Mohamed, Gül?ah

2011-03-01

34

Optimization of thermostable lipase production from a thermophilic Geobacillus sp. using Box-Behnken experimental design  

Microsoft Academic Search

Thermostable lipase production by Geobacillus thermoleovorans was optimized in shake-flask cultures using Box-Behnken experimental design. An empirical model was developed through response surface methodology to describe the relationship between tested variables (Tween 80, olive oil, temperature and pH) and enzyme activity. Maximum enzyme activity (495 U l-1) was attained with Tween 80 at 5 g l-1; olive oil at 60

Yasser Refaat Abdel-Fattah

2002-01-01

35

Freezing/thawing pretreatment coupled with biological process of thermophilic Geobacillus sp. G1: Acceleration on waste activated sludge hydrolysis and acidification.  

PubMed

A novel pretreatment method combining freezing/thawing with Geobacillus sp. G1 was employed to pretreat waste activated sludge (WAS) for enhancing the WAS hydrolysis and subsequent short-chain fatty acids (SCFAs) production. Results showed that freezing/thawing combined with Geobacillus sp. G1 pretreatment achieved the maximal concentrations of soluble protein from 40±6mg COD/L (non-pretreated) to 1226±24mg COD/L (pretreated), and accumulated SCFAs concentration increased from 248±81mg COD/L to 3032±53mg COD/L. Excitation emission matrix (EEM) fluorescence spectroscopy revealed the highest fluorescence intensity (FI) of protein-like substances, which was the dominant fluorescent organic matters, indicating the synergistic effect of freezing/thawing and Geobacillus sp. G1 pretreatment on organics hydrolysis. High-throughput pyrosequencing analysis investigated that the abundance of bacteria responsible for WAS hydrolysis (such as Clostridium and Caloramator) and SCFAs production (such as Parabacteroides and Bacterodies) was greatly enhanced due to the novel pretreatment method used. PMID:25459862

Yang, Chunxue; Liu, Wenzong; He, Zhangwei; Thangavel, Sangeetha; Wang, Ling; Zhou, Aijuan; Wang, Aijie

2014-11-01

36

Novel bacteriocins produced by Geobacillus stearothermophilus  

Microsoft Academic Search

Four novel heat-stable bacteriocin-like substances were found to be produced by Geobacillus stearothermophilus strains isolated from oil-wells in Lithuania. Geobacillus stearothermophilus 32A, 17, 30 and 31 strains were identified as producers of bacteriocins with bactericidal activity against closely related\\u000a Geobacillus species and several pathogenic strains: Bacillus cereus DSM 12001 and Staphylococcus haemolyticus P903. The secretion of the analysed bacteriocins started

Karina Pokusaeva; Nomeda Kuisiene; Dziuginta Jasinskyte; Kazimiera Rutiene; Jordana Saleikiene; Donaldas Chitavichius

2009-01-01

37

Draft Genome Sequences of Geobacillus stearothermophilus Strains 22 and 53, Isolated from the Garga Hot Spring in the Barguzin River Valley of the Russian Federation  

PubMed Central

Geobacillus stearothermophilus strains 22 and 53 were isolated from sediment samples isolated from the Garga hot spring (72°C) located in the valley of the river Barguzin (the Baikal region, Russian Federation) (54°19?3.72?N, 110°59?38.4?E). PMID:25414504

Logacheva, Maria D.; Peltek, Sergey E.

2014-01-01

38

Draft Genome Sequences of Geobacillus stearothermophilus Strains 22 and 53, Isolated from the Garga Hot Spring in the Barguzin River Valley of the Russian Federation.  

PubMed

Geobacillus stearothermophilus strains 22 and 53 were isolated from sediment samples isolated from the Garga hot spring (72°C) located in the valley of the river Barguzin (the Baikal region, Russian Federation) (54°19'3.72?N, 110°59'38.4?E). PMID:25414504

Rozanov, Aleksey S; Logacheva, Maria D; Peltek, Sergey E

2014-01-01

39

Thermoactive extracellular proteases of Geobacillus caldoproteolyticus , sp. nov., from sewage sludge  

Microsoft Academic Search

A proteolytic thermophilic bacterial strain, designated as strain SF03, was isolated from sewage sludge in Singapore. Strain SF03 is a strictly aerobic, Gram stain-positive, catalase-positive, oxidase-positive, and endospore-forming rod. It grows at temperatures ranging from 35 to 65°C, pH ranging from 6.0 to 9.0, and salinities ranging from 0 to 2.5%. Phylogenetic analyses revealed that strain SF03 was most similar

Xiao-Ge Chen; Olena Stabnikova; Joo-Hwa Tay; Jing-Yuan Wang; Stephen Tiong-Lee Tay

2004-01-01

40

Isolation and characterization of a thermotolerant ene reductase from Geobacillus sp. 30 and its heterologous expression in Rhodococcus opacus.  

PubMed

Rhodococcus opacus B-4 cells are adhesive to and even dispersible in water-immiscible hydrocarbons owing to their highly lipophilic nature. In this study, we focused on the high operational stability of thermophilic enzymes and applied them to a biocatalytic conversion in an organic reaction medium using R. opacus B-4 as a lipophilic capsule of enzymes to deliver them into the organic medium. A novel thermo- and organic-solvent-tolerant ene reductase, which can catalyze the enantioselective reduction of ketoisophorone to (6R)-levodione, was isolated from Geobacillus sp. 30, and the gene encoding the enzyme was heterologously expressed in R. opacus B-4. Another thermophilic enzyme which catalyzes NAD(+)-dependent dehydrogenation of cyclohexanol was identified from the gene-expression library of Thermus thermophilus and the gene was coexpressed in R. opacus B-4 for cofactor regeneration. While the recombinant cells were not viable in the mixture due to high reaction temperature, 634 mM of (6R)-levodione could be produced with an enantiopurity of 89.2 % ee by directly mixing the wet cells of the recombinant R. opacus with a mixture of ketoisophorone and cyclohexanol at 50 °C. The conversion rate observed with the heat-killed recombinant cells was considerably higher than that obtained with a cell-free enzyme solution, demonstrating that the accessibility between the substrates and enzymes could be improved by employing R. opacus cells as a lipophilic enzyme capsule. These results imply that a combination of thermophilic enzymes and lipophilic cells can be a promising approach for the biocatalytic production of water-insoluble chemicals. PMID:24927695

Tsuji, Naoto; Honda, Kohsuke; Wada, Mayumi; Okano, Kenji; Ohtake, Hisao

2014-07-01

41

Draft Genome Sequence of Geobacillus icigianus Strain G1w1T Isolated from Hot Springs in the Valley of Geysers, Kamchatka (Russian Federation)  

PubMed Central

The Geobacillus icigianus G1w1T strain was isolated from sludge samples of unnamed vaporing hydrothermal (97°?) outlets situated in a geyser in the Troinoy region (Valley of Geysers, Kronotsky Nature Reserve, Kamchatka, Russian Federation; 54°25?51.40?N, 160°7?41.40?E). The sequenced and annotated genome is 3,457,810 bp and encodes 3,342 genes. PMID:25342695

Bryanskaya, Alla V.; Logacheva, Maria D.; Kotenko, Anastasia V.; Peltek, Sergey E.

2014-01-01

42

Draft Genome Sequence of Geobacillus icigianus Strain G1w1T Isolated from Hot Springs in the Valley of Geysers, Kamchatka (Russian Federation).  

PubMed

The Geobacillus icigianus G1w1(T) strain was isolated from sludge samples of unnamed vaporing hydrothermal (97°?) outlets situated in a geyser in the Troinoy region (Valley of Geysers, Kronotsky Nature Reserve, Kamchatka, Russian Federation; 54°25'51.40?N, 160°7'41.40?E). The sequenced and annotated genome is 3,457,810 bp and encodes 3,342 genes. PMID:25342695

Bryanskaya, Alla V; Rozanov, Aleksey S; Logacheva, Maria D; Kotenko, Anastasia V; Peltek, Sergey E

2014-01-01

43

Transformable facultative thermophile Geobacillus stearothermophilus NUB3621 as a host strain for metabolic engineering.  

PubMed

Metabolic engineers develop inexpensive enantioselective syntheses of high-value compounds, but their designs are sometimes confounded by the misfolding of heterologously expressed proteins. Geobacillus stearothermophilus NUB3621 is a readily transformable facultative thermophile. It could be used to express and properly fold proteins derived from its many mesophilic or thermophilic Bacillaceae relatives or to direct the evolution of thermophilic variants of mesophilic proteins. Moreover, its capacity for high-temperature growth should accelerate chemical transformation rates in accordance with the Arrhenius equation and reduce the risks of microbial contamination. Its tendency to sporulate in response to nutrient depletion lowers the costs of storage and transportation. Here, we present a draft genome sequence of G. stearothermophilus NUB3621 and describe inducible and constitutive expression plasmids that function in this organism. These tools will help us and others to exploit the natural advantages of this system for metabolic engineering applications. PMID:24788326

Blanchard, Kristen; Robic, Srebrenka; Matsumura, Ichiro

2014-08-01

44

Preconditioning with cations increases the attachment of Anoxybacillus flavithermus and Geobacillus species to stainless steel.  

PubMed

Preconditioning of Anoxybacillus flavithermus E16 and Geobacillus sp. strain F75 with cations prior to attachment often significantly increased (P ? 0.05) the number of viable cells that attached to stainless steel (by up to 1.5 log CFU/cm(2)) compared with unconditioned bacteria. It is proposed that the transition of A. flavithermus and Geobacillus spp. from milk formulations to stainless steel product contact surfaces in milk powder manufacturing plants is mediated predominantly by bacterial physiological factors (e.g., surface-exposed adhesins) rather than the concentrations of cations in milk formulations surrounding bacteria. PMID:23645192

Somerton, Ben; Flint, Steve; Palmer, Jon; Brooks, John; Lindsay, Denise

2013-07-01

45

Preconditioning with Cations Increases the Attachment of Anoxybacillus flavithermus and Geobacillus Species to Stainless Steel  

PubMed Central

Preconditioning of Anoxybacillus flavithermus E16 and Geobacillus sp. strain F75 with cations prior to attachment often significantly increased (P ? 0.05) the number of viable cells that attached to stainless steel (by up to 1.5 log CFU/cm2) compared with unconditioned bacteria. It is proposed that the transition of A. flavithermus and Geobacillus spp. from milk formulations to stainless steel product contact surfaces in milk powder manufacturing plants is mediated predominantly by bacterial physiological factors (e.g., surface-exposed adhesins) rather than the concentrations of cations in milk formulations surrounding bacteria. PMID:23645192

Flint, Steve; Palmer, Jon; Brooks, John; Lindsay, Denise

2013-01-01

46

Geobacillus jurassicus sp. nov., a new thermophilic bacterium isolated from a high-temperature petroleum reservoir, and the validation of the Geobacillus species  

Microsoft Academic Search

Four thermophilic, spore-forming bacterial strains, DS1T, DS2, 46 and 49, were isolated from the high-temperature Dagang oilfield, located in China. The strains were identified by using the polyphasic taxonomy approach. These were aerobic, gram-positive, rod-shaped, moderately thermophilic (with an optimum growth temperature of 60–65°C), chemoorganotrophic bacteria capable of growing on various sugars, carboxylic acids and crude oil. Two strains, DS1T

Tamara N. Nazina; Diana Sh. Sokolova; Alexander A. Grigoryan; Nataliya M. Shestakova; Ekaterina M. Mikhailova; Andrei B. Poltaraus; Tatiyana P. Tourova; Anatolii M. Lysenko; George A. Osipov; Sergey S. Belyaev

2005-01-01

47

Isolation and characterization of a cellulolytic Geobacillus thermoleovorans T4 strain from sugar refinery wastewater  

Microsoft Academic Search

A novel, cellulolytic, bacterial thermophilic strain, T4, was isolated from sugar refinery wastewater in southern Taiwan. This isolate, a Gram-negative, motile, aerobically growing sporulating rod, can secrete thermostable endocellulase (endo-1,4-?-D-glucanase, EC 3.2.1.4) and hydrolyze carboxymethylcellulose (CMC), phosphoric acid-swollen cellulose, Avicel, filter paper, and salicin. When strain T4 was grown in CMC medium, the cellulolytic enzyme activity in culture supernatants was

Shang-Kai Tai; Hsiu-Ping Pearl Lin; Jimmy Kuo; Jong-Kang Liu

2004-01-01

48

Purification and characterization of an l-arabinose isomerase from an isolated strain of Geobacillus thermodenitrificans producing d-tagatose  

Microsoft Academic Search

The araA gene, encoding l-arabinose isomerase (AI), from the thermophilic bacterium Geobacillus thermodenitrificans was cloned and expressed in Escherichia coli. Recombinant AI was isolated with a final purity of about 97% and a final specific activity of 2.10U\\/mg. The molecular mass of the purified AI was estimated to be about 230kDa to be a tetramer composed of identical subunits. The

Hye-Jung Kim; Deok-Kun Oh

2005-01-01

49

Calcium Carbonate Formation by Synechococcus sp. Strain PCC 8806 and Synechococcus sp. Strain PCC 8807  

SciTech Connect

Precipitation of CaCO3 catalyzed by the growth and physiology of cyanobacteria in the Genus Synechococcus represents a potential mechanism for sequestration of CO2 produced during the burning of coal for power generation. Microcosm experiments were performed in which Synechococcus sp. strain PCC 8806 and Synechococcus sp. strain PCC 8807 were tested for their ability to calcify when exposed to a fixed calcium concentration of 3.4 mM and bicarbonate concentrations of 0.5, 1.25 and 2.5 mM. Disappearance of soluble calcium was used as an indicator of CaCO3 formation; results from metabolically active microcosms were compared to controls with no cells or no carbonate added. Synechococcus sp. strain PCC 8806 removed calcium continuously over the duration of the experiment with approximately 18.6 mg of calcium in the solid phase. Calcium removal occurred over a two-day time period when Synechococcus sp. strain PCC 8807 was tested and only 8.9 mg of calcium was removed in the solid phase. The ability of the cyanobacteria to create an alkaline growth environment appeared to be the primary factor responsible for CaCO3 precipitation in these experiments. Removal of inorganic carbon by fixation into biomass was insignificant compared to the mass of inorganic carbon removed by incorporation into the growing CaCO3 solid.

Lee, Brady D.; William A. Apel; Michelle R. Walton

2006-12-01

50

Calcium carbonate formation by Synechococcus sp. strain PCC 8806 and Synechococcus sp. strain PCC 8807.  

PubMed

Precipitation of CaCO3 catalyzed by the growth and physiology of cyanobacteria in the genus Synechococcus represents a potential mechanism for sequestration of atmospheric CO2 produced during the burning of coal for power generation. Synechococcus sp. strain PCC 8806 and Synechococcus sp. strain PCC 8807 were tested in microcosm experiments for their ability to calcify when exposed to a fixed calcium concentration of 3.4 mM and dissolved inorganic carbon concentrations of 0.5, 1.25 and 2.5 mM. Synechococcus sp. strain PCC 8806 removed calcium continuously over the duration of the experiment producing approximately 18.6 mg of solid phase calcium. Calcium removal occurred over a two-day time period when Synechococcus sp. strain PCC 8807 was tested and only 8.9 mg of solid phase calcium was produced. Creation of an alkaline growth environment catalyzed by the physiology of the cyanobacteria appeared to be the primary factor responsible for CaCO3 precipitation in these experiments. PMID:16289626

Lee, Brady D; Apel, William A; Walton, Michelle R

2006-12-01

51

Nitrogen Control of Atrazine Utilization in Pseudomonas sp. Strain ADP  

Microsoft Academic Search

Pseudomonas sp. strain ADP uses the herbicide atrazine as the sole nitrogen source. We have devised a simple atrazine degradation assay to determine the effect of other nitrogen sources on the atrazine degradation pathway. The atrazine degradation rate was greatly decreased in cells grown on nitrogen sources that support rapid growth of Pseudomonas sp. strain ADP compared to cells cultivated

V. Garcia-Gonzalez; Fernando Govantes; Liz J. Shaw; Richard G. Burns; Eduardo Santero

2003-01-01

52

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. PMID:23045508

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

2012-01-01

53

[Xylanase activity of phytopathogenic and endophytic strains of Ceratocystis sp].  

PubMed

A comparative analysis of xylanase activity of 36 phytopathogenic and endophytic Ceratocystis sp. strains was conducted. The rate of their linear growth on the medium with xylan was studied. The rate of linear growth of phytopathogenic strains was 0.003-0.004 mm/h that was almost 70 times less than in endophytic ones. There were no correlation between levels of xylanase activity of studied strains and rates of their linear growth. Xylanase activity ofendophytic Ceratocystis sp. strains varied from complete absence to high level. Phytopathogenic strains possessed only high xylanase activity; maximum values of their xylanase activity zones were three times more than in endophytic strains. The differences in xylanase activity were observed on the strain level. The xylanase activity of 24% endophytic and 64% phytopathogenic strains became higher with increasing of cultivation period. The clear dependence of xylanase activity on the species and organs of host plants was not demonstrated. It was shown that the xylanase activity level of phytopathogenic Ceratocystis sp. strains was too much higher than in such phytopathogens as Fusarium poae, F. oxysporum and Alternaria alternata strains. The conclusion was made that the studied endophytic Ceratocystis sp. strains can be related to latent pathogens, which are able to cause the diseases of host plants in conditions favorable for them. PMID:21117291

Kurchenko, I M; Sokolova, O V; Iur'ieva, O M

2010-01-01

54

Characterization of a recombinant thermostable xylanase from deep-sea thermophilic Geobacillus sp. MT1 in East Pacific  

Microsoft Academic Search

A novel xylanase-producing thermophilic strain MT-1 was isolated from a deep-sea hydrothermal field in east Pacific. A xylanase gene encoding 331 amino-acid peptide from this isolate was cloned and expressed in Escherichia\\u000a coli. The recombinant xylanase exhibited maximum activity at 70°C and had an optimum pH of 7.0. It was active up to 90°C and showed activity over a wide

Suijie Wu; Bin Liu; Xiaobo Zhang

2006-01-01

55

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. PMID:16751511

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

2006-01-01

56

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

57

Influence of Cations on Growth of Thermophilic Geobacillus spp. and Anoxybacillus flavithermus in Planktonic Culture  

PubMed Central

Free ions of Na+, K+, Ca2+, and Mg2+ influenced the optical density of planktonic cultures of thermophilic bacilli. Anoxybacillus flavithermus E16 and Geobacillus sp. strain F75 (milk powder manufacturing plant isolates) and A. flavithermus DSM 2641 and G. thermoleovorans DSM 5366 were studied. Ca2+ and Mg2+ were associated with increases in optical density more so than Na+ and K+. Overall, it appeared that Ca2+ and/or Mg2+ was required for the production of protein in thermophilic bacilli, as shown by results obtained with A. flavithermus E16, which was selected for further study. PMID:22287005

Palmer, Jon; Brooks, John; Smolinski, Edward; Lindsay, Denise; Flint, Steve

2012-01-01

58

Influence of cations on growth of thermophilic Geobacillus spp. and Anoxybacillus flavithermus in planktonic culture.  

PubMed

Free ions of Na(+), K(+), Ca(2+), and Mg(2+) influenced the optical density of planktonic cultures of thermophilic bacilli. Anoxybacillus flavithermus E16 and Geobacillus sp. strain F75 (milk powder manufacturing plant isolates) and A. flavithermus DSM 2641 and G. thermoleovorans DSM 5366 were studied. Ca(2+) and Mg(2+) were associated with increases in optical density more so than Na(+) and K(+). Overall, it appeared that Ca(2+) and/or Mg(2+) was required for the production of protein in thermophilic bacilli, as shown by results obtained with A. flavithermus E16, which was selected for further study. PMID:22287005

Somerton, Ben; Palmer, Jon; Brooks, John; Smolinski, Edward; Lindsay, Denise; Flint, Steve

2012-04-01

59

Complete Genome Assembly of Corynebacterium sp. Strain ATCC 6931  

PubMed Central

The genus Corynebacterium is best known for the pathogen C. diphtheriae; however, it contains mostly commensal and nonpathogenic, as well as several opportunistic, pathogens. Here, we present the 2.47-Mb scaffolded assembly of the type strain, Corynebacterium sp. ATCC 6931 (NCTC 1914), as deposited into GenBank under accession number CP008913. PMID:25342684

Daligault, H. E.; Davenport, K. W.; Minogue, T. D.; Bishop-Lilly, K. A.; Bruce, D. C.; Chain, P. S.; Coyne, S. R.; Frey, K. G.; Jaissle, J.; Koroleva, G. I.; Ladner, J. T.; Li, P-E.; Meincke, L.; Munk, A. C.; Palacios, G. F.; Redden, C. L.

2014-01-01

60

Identification of a gene cluster encoding an arginine ATP-binding-cassette transporter in the genome of the thermophilic Gram-positive bacterium Geobacillus stearothermophilus strain DSMZ 13240  

Microsoft Academic Search

A single gene cluster encoding components of a putative ATP-binding cassette (ABC) transporter for basic amino acids was identified in the incomplete genome sequence of the thermophilic Gram-positive bacterium Geobacillus stearothermophilus by BLAST searches. The cluster comprises three genes, and these were amplified from chromosomal DNA of G. stearothermophilus, ligated into plasmid vectors and expressed in Escherichia coli. The purified

Rebecca Fleischer; Antje Wengner; Frank Scheffel; Heidi Landmesser; Erwin Schneider

2005-01-01

61

Isolation and characterization of a Geobacillus thermoleovorans strain from an ultra-deep South African gold mine.  

PubMed

A thermophilic facultative bacterial isolate was recovered from 3.2km depth in a gold mine in South Africa. This isolate, designated GE-7, was cultivated from pH 8.0, 50 degrees C water from a dripping fracture near the top of an exploration tunnel. GE-7 grows optimally at 65 degrees C and pH 6.5 on a wide range of carbon substrates including cellobiose, hydrocarbons and lactate. In addition to O(2), GE-7 also utilizes nitrate as an electron acceptor. GE-7 is a long rod-shaped bacterium (4-6microm longx0.5microm wide) with terminal endospores and flagella. Phylogenetic analysis of GE-7 16S rDNA sequence revealed high sequence similarity with G. thermoleovorans DSM 5366(T) (99.6%), however, certain phenotypic characteristics of GE-7 were distinct from this and other previously described strains of G. thermoleovorans. PMID:16709445

Deflaun, M F; Fredrickson, J K; Dong, H; Pfiffner, S M; Onstott, T C; Balkwill, D L; Streger, S H; Stackebrandt, E; Knoessen, S; van Heerden, E

2007-03-01

62

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

63

Integrative Gene Cloning and Expression System for Streptomyces sp. US 24 and Streptomyces sp. TN 58 Bioactive Molecule Producing Strains  

PubMed Central

Streptomyces sp. US 24 and Streptomyces sp. TN 58, two strains producing interesting bioactive molecules, were successfully transformed using E. coli ET12567 (pUZ8002), as a conjugal donor, carrying the integrative plasmid pSET152. For the Streptomyces sp. US 24 strain, two copies of this plasmid were tandemly integrated in the chromosome, whereas for Streptomyces sp. TN 58, the integration was in single copy at the attB site. Plasmid pSET152 was inherited every time for all analysed Streptomyces sp. US 24 and Streptomyces sp. TN 58 exconjugants under nonselective conditions. The growth, morphological differentiation, and active molecules production of all studied pSET152 integrated exconjugants were identical to those of wild type strains. Consequently, conjugal transfer using pSET152 integration system is a suitable means of genes transfer and expression for both studied strains. To validate the above gene transfer system, the glucose isomerase gene (xylA) from Streptomyces sp. SK was expressed in strain Streptomyces sp. TN 58. Obtained results indicated that heterologous glucose isomerase could be expressed and folded effectively. Glucose isomerase activity of the constructed TN 58 recombinant strain is of about eighteenfold higher than that of the Streptomyces sp. SK strain. Such results are certainly of importance due to the potential use of improved strains in biotechnological process for the production of high-fructose syrup from starch. PMID:19547659

Sioud, Samiha; Aigle, Bertrand; Karray-Rebai, Ines; Smaoui, Slim; Bejar, Samir; Mellouli, Lotfi

2009-01-01

64

Natural transformation of Thermotoga sp. strain RQ7  

PubMed Central

Background Thermotoga species are organisms of enormous interest from a biotechnological as well as evolutionary point of view. Genetic modifications of Thermotoga spp. are often desired in order to fully release their multifarious potentials. Effective transformation of recombinant DNA into these bacteria constitutes a critical step of such efforts. This study aims to establish natural competency in Thermotoga spp. and to provide a convenient method to transform these organisms. Results Foreign DNA was found to be relatively stable in the supernatant of a Thermotoga culture for up to 6 hours. Adding donor DNA to T. sp. strain RQ7 at its early exponential growth phase (OD600 0.18?~?0.20) resulted in direct acquisition of the DNA by the cells. Both T. neapolitana chromosomal DNA and Thermotoga-E. coli shuttle vectors effectively transformed T. sp. strain RQ7, rendering the cells resistance to kanamycin. The kan gene carried by the shuttle vector pDH10 was detected by PCR from the plasmid extract of the transformants, and the amplicons were verified by restriction digestions. A procedure for natural transformation of Thermotoga spp. was established and optimized. With the optimized method, T. sp. strain RQ7 sustained a transformation frequency in the order of 10-7 with both genomic and plasmid DNA. Conclusions T. sp. strain RQ7 cells are naturally transformable during their early exponential phase. They acquire DNA from both closely and distantly related species. Both chromosomal DNA and plasmid DNA serve as suitable substrates for transformation. Our findings lend a convenient technical tool for the genetic engineering of Thermotoga spp. PMID:24884561

2014-01-01

65

Desulfurization of dibenzothiophene by Corynebacterium sp. strain SY1.  

PubMed Central

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, CS2, FeS2, 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. PMID:1575493

Omori, T; Monna, L; Saiki, Y; Kodama, T

1992-01-01

66

J. Microbiol. Biotechnol. (2003), 13(6), 10131017 Symbiobacterium toebii sp. nov., Commensal Thermophile Isolated from  

E-print Network

. The strain exhibited a commensal interaction with Geobacillus toebii SK-1T and was isolated using cell strain SC-1T is a commensal bacterium, cell-free crude extracts of Geobacillus toebii SK-1T were on cell-to-cell communication with Geobacillus toebii strain SK-1T [12, 13], the strain SC-1T was isolated

Bae, Jin-Woo

67

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

68

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. PMID:22675593

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

69

Pseudomonas sp. Strain 273, an Aerobic ?,?-DichloroalkaneDegrading Bacterium  

PubMed Central

A gram-negative, aerobic bacterium was isolated from soil; this bacterium grew in 50% (vol/vol) suspensions of 1,10-dichlorodecane (1,10-DCD) as the sole source of carbon and energy. Phenotypic and small-subunit ribosomal RNA characterizations identified the organism, designated strain 273, as a member of the genus Pseudomonas. After induction with 1,10-DCD, Pseudomonas sp. strain 273 released stoichiometric amounts of chloride from C5 to C12 ?,?-dichloroalkanes in the presence of oxygen. No dehalogenation occurred under anaerobic conditions. The best substrates for dehalogenation and growth were C9 to C12 chloroalkanes. The isolate also grew with nonhalogenated aliphatic compounds, and decane-grown cells dechlorinated 1,10-DCD without a lag phase. In addition, cells grown on decane dechlorinated 1,10-DCD in the presence of chloramphenicol, indicating that the 1,10-DCD-dechlorinating enzyme system was also induced by decane. Other known alkane-degrading Pseudomonas species did not grow with 1,10-DCD as a carbon source. Dechlorination of 1,10-DCD was demonstrated in cell extracts of Pseudomonas sp. strain 273. Cell-free activity was strictly oxygen dependent, and NADH stimulated dechlorination, whereas EDTA had an inhibitory effect. PMID:9726906

Wischnak, Catrin; Löffler, Frank E.; Li, Jieran; Urbance, John W.; Müller, Rudolf

1998-01-01

70

Nitrogen Control of Atrazine Utilization in Pseudomonas sp. Strain ADP  

PubMed Central

Pseudomonas sp. strain ADP uses the herbicide atrazine as the sole nitrogen source. We have devised a simple atrazine degradation assay to determine the effect of other nitrogen sources on the atrazine degradation pathway. The atrazine degradation rate was greatly decreased in cells grown on nitrogen sources that support rapid growth of Pseudomonas sp. strain ADP compared to cells cultivated on growth-limiting nitrogen sources. The presence of atrazine in addition to the nitrogen sources did not stimulate degradation. High degradation rates obtained in the presence of ammonium plus the glutamine synthetase inhibitor MSX and also with an Nas? mutant derivative grown on nitrate suggest that nitrogen regulation operates by sensing intracellular levels of some key nitrogen-containing metabolite. Nitrate amendment in soil microcosms resulted in decreased atrazine mineralization by the wild-type strain but not by the Nas? mutant. This suggests that, although nitrogen repression of the atrazine catabolic pathway may have a strong impact on atrazine biodegradation in nitrogen-fertilized soils, the use of selected mutant variants may contribute to overcoming this limitation. PMID:14660340

García-González, Vicente; Govantes, Fernando; Shaw, Liz J.; Burns, Richard G.; Santero, Eduardo

2003-01-01

71

Expression of the Nitroarene Dioxygenase Genes in Comamonas sp. Strain JS765 and Acidovorax sp. Strain JS42 Is Induced by Multiple Aromatic Compounds  

Microsoft Academic Search

This work reports a genetic analysis of the expression of nitrobenzene dioxygenase (NBDO) in Comamonas sp. strain JS765 and 2-nitrotoluene dioxygenase (2NTDO) in Acidovorax sp. strain JS42. Strains JS765 and JS42 possess identical LysR-type regulatory proteins, NbzR and NtdR, respectively. NbzR\\/NtdR is homologous to NahR, the positive salicylate-responsive transcriptional activator of the naphthalene degradation genes in Pseudomonas putida G7. The

Daniel J. Lessner; Rebecca E. Parales; Shakti Narayan; David T. Gibson

2003-01-01

72

Genome Sequence of Ralstonia sp. Strain PBA, a Bacterium Involved in the Biodegradation of 4-Aminobenzenesulfonate  

PubMed Central

Ralstonia sp. strain PBA was isolated from textile wastewater in a coculture with Hydrogenophaga sp. strain PBC. Here we present the assembly and annotation of its genome, which may provide further insights into the mechanism of its interaction with strain PBC during 4-aminobenzenesulfonate degradation. PMID:22933765

Chew, Teong Han; Tay, Yea-Ling; Lye, Siew Fen; Yahya, Adibah

2012-01-01

73

Metabolic engineering of Geobacillus thermoglucosidasius for high yield ethanol production  

Microsoft Academic Search

We describe the metabolic engineering of two strains of Geobacillus thermoglucosidasius to divert their fermentative carbon flux from a mixed acid pathway, to one in which ethanol becomes the major product. This involved elimination of the lactate dehydrogenase and pyruvate formate lyase pathways by disruption of the ldh and pflB genes, respectively, together with upregulation of expression of pyruvate dehydrogenase.

R. E. Cripps; K. Eley; D. J. Leak; B. Rudd; M. Taylor; M. Todd; S. Boakes; S. Martin; T. Atkinson

2009-01-01

74

Genome Sequence of a Thermophilic Bacillus, Geobacillus thermodenitrificans DSM465  

PubMed Central

Geobacillus thermodenitrificans NG80-2 encodes a LadA-mediated alkane degradation pathway, while G. thermodenitrificans DSM465 cannot utilize alkanes. Here, we report the draft genome sequence of G. thermodenitrificans DSM465, which may help reveal the genomic differences between these two strains in regards to the biodegradation of alkanes. PMID:24336381

Yao, Nana; Ren, Yi

2013-01-01

75

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

2012-03-01

76

Toxicity of chlorobenzene on Pseudomonas sp. strain RHO1, a chlorobenzene-degrading strain  

Microsoft Academic Search

Pseudomonas sp. strain RHO1 able to use chloro- and 1,4-dichlorobenzene as growth substrates was tested towards sensitivity against chlorobenzene. Concentrations of chlorobenzene higher than 3.5 mM were found to be toxic to cells independent of pregrowth with chlorobenzene or nutrient broth. Below this concentration, sensitivity towards chlorobenzene depended on the precultivation of the cells, i.e. type of growth substrate (chlorobenzene

Heidi Fritz; Walter Reineke; Eberhard Schmidt

1991-01-01

77

Draft Genome Sequence of the Antarctic Polyextremophile Nesterenkonia sp. Strain AN1.  

PubMed

Nesterenkonia sp. strain AN1 was isolated from Antarctic soil and is a polyextremophile, being tolerant of low temperatures, high salt concentrations, and high alkalinity. Here we report the draft genome sequence of this strain. PMID:24675854

Aliyu, Habibu; De Maayer, Pieter; Rees, Jasper; Tuffin, Marla; Cowan, Don A

2014-01-01

78

Draft Genome Sequence of the Antarctic Polyextremophile Nesterenkonia sp. Strain AN1  

PubMed Central

Nesterenkonia sp. strain AN1 was isolated from Antarctic soil and is a polyextremophile, being tolerant of low temperatures, high salt concentrations, and high alkalinity. Here we report the draft genome sequence of this strain. PMID:24675854

Aliyu, Habibu; De Maayer, Pieter; Rees, Jasper; Tuffin, Marla

2014-01-01

79

Draft Genome Sequence of the Brazilian Cyanobium sp. Strain CACIAM 14  

PubMed Central

Given the scarcity of data pertaining to whole-genome sequences of cyanobacterial strains isolated in Brazil, we hereby present the draft genome sequence of the Cyanobium sp. strain CACIAM 14, isolated in southeastern Amazonia. PMID:25013140

Siqueira, Andrei Santos; dos Santos, Bruno Garcia Simões; da Silva, Fábio Daniel Florêncio; Lima, Clayton Pereira; Cardoso, Jedson Ferreira; Vianez Júnior, João Lídio da Silva Gonçalves; Dall'Agnol, Leonardo Teixeira; McCulloch, John Anthony; Nunes, Márcio Roberto Teixeira; Gonçalves, Evonnildo Costa

2014-01-01

80

Draft Genome Sequences of Devosia sp. Strain 17-2-E-8 and Devosia riboflavina Strain IFO13584  

PubMed Central

Here we report the draft genome of Devosia sp. strain 17-2-E-8, isolated from Ontario agricultural soil (Canada) with promising deoxynivalenol biotransformation capabilities. In addition, we report the draft genome of Devosia riboflavina strain IFO13584, used as a control strain in our studies aimed at highlighting unique gene clusters involved in deoxynivalenol epimerization. PMID:25278537

Hassan, Yousef I.; Lepp, Dion; He, Jianwei

2014-01-01

81

Draft Genome Sequences of Devosia sp. Strain 17-2-E-8 and Devosia riboflavina Strain IFO13584.  

PubMed

Here we report the draft genome of Devosia sp. strain 17-2-E-8, isolated from Ontario agricultural soil (Canada) with promising deoxynivalenol biotransformation capabilities. In addition, we report the draft genome of Devosia riboflavina strain IFO13584, used as a control strain in our studies aimed at highlighting unique gene clusters involved in deoxynivalenol epimerization. PMID:25278537

Hassan, Yousef I; Lepp, Dion; He, Jianwei; Zhou, Ting

2014-01-01

82

Complete genome sequence of Arthrobacter sp. strain FB24  

SciTech Connect

Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in the family Micrococcaceae and class Actinobacteria. A number of Arthrobacter genome sequences have been completed because of their important role in soil, especially bioremediation. This isolate is of special interest because it is tolerant to multiple metals and it is extremely resistant to elevated concentrations of chromate. The genome consists of a 4,698,945 bp circular chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of 5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function. This genome was sequenced as part of the DOE Joint Genome Institute Program.

Nakatsu, C. H.; Barabote, Ravi; Thompson, Sue; Bruce, David; Detter, Chris; Brettin, T.; Han, Cliff F.; Beasley, Federico; Chen, Weimin; Konopka, Allan; Xie, Gary

2013-09-30

83

Draft Genome Sequence of Rhodovulum sp. Strain NI22, a Naphthalene-Degrading Marine Bacterium.  

PubMed

Rhodovulum sp. strain NI22 is a hydrocarbon-degrading member of the genus Rhodovulum. The draft genome of Rhodovulum sp. NI22 is 3.8 Mb in size, with 3,756 coding sequences and 64.4% G+C content. The catechol and gentisate pathways for naphthalene degradation are predicted to be present in Rhodovulum sp. NI22. PMID:25614575

Brown, Lisa M; Gunasekera, Thusitha S; Bowen, Loryn L; Ruiz, Oscar N

2015-01-01

84

Draft Genome Sequence of the Alga-Aggregating Bacterium Bacillus sp. Strain RP1137  

PubMed Central

Bacillus sp. strain RP1137 is a bacterium that is able to rapidly and efficiently aggregate biofuel-producing microalgae. By 16S rRNA gene sequencing, it was found to be related to the industrially important Bacillus megaterium. Here, we report the draft genome sequence of Bacillus sp. strain RP1137. PMID:24385572

Powell, Ryan J.; Bachvaroff, Tsvetan R.

2014-01-01

85

Draft Genome Sequences of Vibrio sp. Strains Isolated from Tetrodotoxin-Bearing Scavenging Gastropod  

PubMed Central

Vibrio sp. strains JCM 18905 and JCM 19053 were isolated from a tetrodotoxin (TTX)-bearing scavenging gastropod, and Vibrio sp. strain JCM 18904 was isolated from a sea cucumber. All these are closely related to Vibrio alginolyticus. Their comparative genome information is useful for studies of TTX production in bacteria. PMID:24948773

Kawauchi, Ayumi; Nakahara, Tomomi; Zhang, Xiaochi; Taniyama, Shigeto; Takatani, Tomohiro; Arakawa, Osamu; Oshima, Kenshiro; Suda, Wataru; Kitamura, Keiko; Iida, Toshiya; Iino, Takao; Inoue, Tetsushi; Hongoh, Yuichi; Hattori, Masahira

2014-01-01

86

Potassium uptake in the unicellular cyanobacterium Synechocystis sp. strain PCC 6803 mainly depends on  

E-print Network

Potassium uptake in the unicellular cyanobacterium Synechocystis sp. strain PCC 6803 mainly depends First published online 3 July 2003 Edited by Stuart Ferguson Abstract The molecular basis of potassium potassium transporters can be identi¢ed in the genome of Synechocystis sp. strain PCC 6803. Mutants

Roegner, Matthias

87

Mechanism of Algal Aggregation by Bacillus sp. Strain RP1137  

PubMed Central

Alga-derived biofuels are one of the best alternatives for economically replacing liquid fossil fuels with a fungible renewable energy source. Production of fuel from algae is technically feasible but not yet economically viable. Harvest of dilute algal biomass from the surrounding water remains one of the largest barriers to economic production of algal biofuel. We identified Bacillus sp. strain RP1137 in a previous study and showed that this strain can rapidly aggregate several biofuel-producing algae in a pH- and divalent-cation-dependent manner. In this study, we further characterized the mechanism of algal aggregation by RP1137. We show that aggregation of both algae and bacteria is optimal in the exponential phase of growth and that the density of ionizable residues on the RP1137 cell surface changes with growth stage. Aggregation likely occurs via charge neutralization with calcium ions at the cell surface of both algae and bacteria. We show that charge neutralization occurs at least in part through binding of calcium to negatively charged teichoic acid residues. The addition of calcium also renders both algae and bacteria more able to bind to hydrophobic beads, suggesting that aggregation may occur through hydrophobic interactions. Knowledge of the aggregation mechanism may enable engineering of RP1137 to obtain more efficient algal harvesting. PMID:24771029

Powell, Ryan J.

2014-01-01

88

Mechanism of algal aggregation by Bacillus sp. strain RP1137.  

PubMed

Alga-derived biofuels are one of the best alternatives for economically replacing liquid fossil fuels with a fungible renewable energy source. Production of fuel from algae is technically feasible but not yet economically viable. Harvest of dilute algal biomass from the surrounding water remains one of the largest barriers to economic production of algal biofuel. We identified Bacillus sp. strain RP1137 in a previous study and showed that this strain can rapidly aggregate several biofuel-producing algae in a pH- and divalent-cation-dependent manner. In this study, we further characterized the mechanism of algal aggregation by RP1137. We show that aggregation of both algae and bacteria is optimal in the exponential phase of growth and that the density of ionizable residues on the RP1137 cell surface changes with growth stage. Aggregation likely occurs via charge neutralization with calcium ions at the cell surface of both algae and bacteria. We show that charge neutralization occurs at least in part through binding of calcium to negatively charged teichoic acid residues. The addition of calcium also renders both algae and bacteria more able to bind to hydrophobic beads, suggesting that aggregation may occur through hydrophobic interactions. Knowledge of the aggregation mechanism may enable engineering of RP1137 to obtain more efficient algal harvesting. PMID:24771029

Powell, Ryan J; Hill, Russell T

2014-07-01

89

Genome sequence of Rheinheimera sp. strain A13L, isolated from Pangong Lake, India.  

PubMed

Rheinheimera sp. strain A13L, which has antimicrobial activity, was isolated from alkaline brackish water of the high-altitude Pangong Lake of Ladakh, India. Here we report the draft genome sequence of Rhienheimera sp. strain A13L (4,523,491 bp with a G+C content of 46.23%). The genome is predicted to contain genes for marinocine and colicin V production, which may be responsible for the antimicrobial activity of the strain. PMID:21742876

Gupta, Hemant Kumar; Gupta, Rinkoo Devi; Singh, Ajit; Chauhan, Nar Singh; Sharma, Rakesh

2011-10-01

90

Dynamics of Genome Architecture in Rhizobium sp. Strain NGR234†  

PubMed Central

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

91

Draft Genome Sequence of Ristocetin-Producing Strain Amycolatopsis sp. Strain MJM2582 Isolated in South Korea  

PubMed Central

The draft genome sequence of a ristocetin-producing Amycolatopsis strain (sp. MJM2582) isolated in South Korea is reported here. This strain has a genome of approximately 8.9 Mb containing 7,933 predicted genes, including the ristocetin cluster and 32 additional predicted secondary metabolite biosynthesis clusters. PMID:25359910

Kwun, Min Jung; Cheng, Jinhua; Yang, Seung Hwan; Lee, Dong-Ryung; Suh, Joo-Won

2014-01-01

92

Draft Genome Sequence of Serratia sp. Strain DD3, Isolated from the Guts of Daphnia magna.  

PubMed

We report the draft genome sequence of Serratia sp. strain DD3, a gammaproteobacterium from the family Enterobacteriaceae. It was isolated from homogenized guts of Daphnia magna. The genome size is 5,274 Mb. PMID:25212623

Poehlein, Anja; Freese, Heike M; Daniel, Rolf; Simeonova, Diliana D

2014-01-01

93

Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1  

PubMed Central

The draft genome sequence of a soil bacterium, Aquabacterium sp. strain NJ1, capable of utilizing both liquid and solid alkanes, was deciphered. This is the first report of an Aquabacterium genome sequence. PMID:25477416

Shiwa, Yuh; Yoshikawa, Hirofumi; Zylstra, Gerben J.

2014-01-01

94

Draft Genome Sequence of Serratia sp. Strain DD3, Isolated from the Guts of Daphnia magna  

PubMed Central

We report the draft genome sequence of Serratia sp. strain DD3, a gammaproteobacterium from the family Enterobacteriaceae. It was isolated from homogenized guts of Daphnia magna. The genome size is 5,274 Mb. PMID:25212623

Poehlein, Anja; Freese, Heike M.; Daniel, Rolf

2014-01-01

95

Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1.  

PubMed

The draft genome sequence of a soil bacterium, Aquabacterium sp. strain NJ1, capable of utilizing both liquid and solid alkanes, was deciphered. This is the first report of an Aquabacterium genome sequence. PMID:25477416

Masuda, Hisako; Shiwa, Yuh; Yoshikawa, Hirofumi; Zylstra, Gerben J

2014-01-01

96

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 PMID:7085564

Lapidus, I R; Berg, H C

1982-01-01

97

alk B homologs in thermophilic bacteria of the genus Geobacillus  

Microsoft Academic Search

Screening for alkane hydroxylase genes (alkB) was performed in thermophilic aerobic bacteria of the genus Geobacillus. Total DNAs were isolated from the biomass of 11 strains grown on a mixture of saturated C10–C20 hydrocarbons. Fragments of alkB genes were amplified by PCR with degenerate oligonucleotide primers, and the PCR products were cloned and sequenced. For\\u000a the first time, a set

T. P. Tourova; T. N. Nazina; E. M. Mikhailova; T. A. Rodionova; A. N. Ekimov; A. V. Mashukova; A. B. Poltaraus

2008-01-01

98

Draft Genome of Pseudomonas sp. Strain 11/12A, Isolated from Lake Washington Sediment  

PubMed Central

We announce here the genome sequencing of Pseudomonas sp. strain 11/12A from Lake Washington sediment. From the genome content, a versatile lifestyle is predicted but not one of bona fide methylotrophy. With the availability of its genomic sequence, Pseudomonas sp. 11/12A presents a prospective model for studying microbial communities in lake sediments.

McTaggart, Tami L.; Shapiro, Nicole; Woyke, Tanja

2015-01-01

99

Draft Genome Sequence of Spirochaeta sp. Strain JC202, an Endosymbiont of the Termite (Isoptera) Gut.  

PubMed

We announce here the draft genome sequence of Spirochaeta sp. strain JC202 isolated from gut of a termite (Isoptera). The genome suggests that Spirochaeta sp. JC202 has the capability for natural conjugation with the help of fimbriae and pili. Experimental evidence and the genome sequence suggest that strain JC202 is capable of producing colicin V and a bacteriocin group of peptides in a specific interaction. PMID:25614577

Tushar, L; Sravanthi, T; Sasikala, C; Ramana, C V

2015-01-01

100

Identification of two clusters of genes involved in salt tolerance in Sinorhizobium sp. strain BL3  

Microsoft Academic Search

Sinorhizobium sp. strain BL3 was isolated from the nodules of Phaseolus lathyroides plants that were found growing under saline conditions in the northeastern region of Thailand. It can tolerate up to 600 mM NaCl and is effective in N2 fixation. A genomic DNA clone library of BL3 was constructed and transferred to the salt-sensitive Rhizobium sp. strain TAL1145 by conjugation

Waraporn Payakapong; Panlada Tittabutr; Neung Teaumroong; Nantakorn Boonkerd; Paul W. Singleton; Dulal Borthakur

101

Molecular Mechanism of Nicotine Degradation by a Newly Isolated Strain, Ochrobactrum sp. Strain SJY1.  

PubMed

A newly isolated strain, SJY1, identified as Ochrobactrum sp., utilizes nicotine as a sole source of carbon, nitrogen, and energy. Strain SJY1 could efficiently degrade nicotine via a variant of the pyridine and pyrrolidine pathways (the VPP pathway), which highlights bacterial metabolic diversity in relation to nicotine degradation. A 97-kbp DNA fragment containing six nicotine degradation-related genes was obtained by gap closing from the genome sequence of strain SJY1. Three genes, designated vppB, vppD, and vppE, in the VPP pathway were cloned and heterologously expressed, and the related proteins were characterized. The vppB gene encodes a flavin-containing amine oxidase converting 6-hydroxynicotine to 6-hydroxy-N-methylmyosmine. Although VppB specifically catalyzes the dehydrogenation of 6-hydroxynicotine rather than nicotine, it shares higher amino acid sequence identity with nicotine oxidase (38%) from the pyrrolidine pathway than with its isoenzyme (6-hydroxy-l-nicotine oxidase, 24%) from the pyridine pathway. The vppD gene encodes an NADH-dependent flavin-containing monooxygenase, which catalyzes the hydroxylation of 6-hydroxy-3-succinoylpyridine to 2,5-dihydroxypyridine. VppD shows 62% amino acid sequence identity with the hydroxylase (HspB) from Pseudomonas putida strain S16, whereas the specific activity of VppD is ?10-fold higher than that of HspB. VppE is responsible for the transformation of 2,5-dihydroxypyridine. Sequence alignment and phylogenetic analysis suggested that the VPP pathway, which evolved independently from nicotinic acid degradation, might have a closer relationship with the pyrrolidine pathway. The proteins and functional pathway identified here provide a sound basis for future studies aimed at a better understanding of molecular principles of nicotine degradation. PMID:25344232

Yu, Hao; Tang, Hongzhi; Zhu, Xiongyu; Li, Yangyang; Xu, Ping

2015-01-01

102

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

2013-11-01

103

Complete genome sequence of Kosakonia sacchari type strain SP1T  

PubMed Central

Kosakonia sacchari sp. nov. is a new species within the new genus Kosakonia, which was included in the genus Enterobacter. K sacchari is a nitrogen-fixing bacterium named for its association with sugarcane (Saccharum officinarum L.). K sacchari bacteria are Gram-negative, aerobic, non-spore-forming, motile rods. Strain SP1T (=CGMCC1.12102T=LMG 26783T) is the type strain of the K sacchari sp. nov and is able to colonize and fix N2 in association with sugarcane plants, thus promoting plant growth. Here we summarize the features of strain SP1T and describe its complete genome sequence. The genome contains a single chromosome and no plasmids, 4,902,024 nucleotides with 53.7% GC content, 4,460 protein-coding genes and 105 RNA genes including 22 rRNA genes, 82 tRNA genes, and 1 ncRNA gene. PMID:25197499

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

2014-01-01

104

Draft Genome Sequences of Type Strain Sediminibacterium salmoneum NJ-44 and Sediminibacterium sp. Strain C3, a Novel Strain Isolated from Activated Sludge  

PubMed Central

The genus Sediminibacterium comprises species present in diverse natural and engineered environments. Here, we report for the first time the genome sequences of the type strain Sediminibacterium salmoneum NJ-44 (NBRC 103935) and Sediminibacterium sp. strain C3 (BNM541), isolated from activated sludge, a valuable model for the study of substrate-dependent autoaggregation. PMID:24435857

Ayarza, Joaquín M.; Figuerola, Eva L. M.

2014-01-01

105

Proposal of Chlamydia pecorum sp. nov. for Chlamydia Strains Derived from Ruminants  

Microsoft Academic Search

Chlamydia pecorum sp. nov. is proposed as the fourth species of the genus ChZamydia on the basis of the results of a genetic analysis of Chlamydia strains that were isolated from cattle and sheep which had various diseases, including sporadic encephalitis, infectious polyarthritis, pneumonia, and diarrhea. The levels of DNA-DNA homology between C. pecorum and strains of C. psittaci, Chlamydia

HIDETO FUKUSHI; KATSUYA HIRAI

106

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

Technology Transfer Automated Retrieval System (TEKTRAN)

A Pseudomonas sp. that may be useful in bioremediation projects was isolated from soil. The strain is of potential value because it reduces selenite to elemental red selenium and is unusual in that it was resistant to high concentrations of both selenate and selenite. Cell of the strain removed 1....

107

Draft Genome Sequence of Enterobacter sp. Strain UCD-UG_FMILLET (Phylum Proteobacteria).  

PubMed

Here, we present the draft genome of Enterobacter sp. strain UCD-UG_FMILLET. This strain is an endophyte isolated from the roots of finger millet, an Afro-Indian cereal crop. The genome contains 4,801,411 bp in 53 scaffolds. PMID:25614569

Ettinger, Cassandra L; Mousa, Walaa M; Raizada, Manish N; Eisen, Jonathan A

2015-01-01

108

Draft Genome Sequence of Sphingopyxis sp. Strain MWB1, a Crude-Oil-Degrading Marine Bacterium  

PubMed Central

Sphingopyxis sp. strain MWB1, which is capable of degrading crude oil, diesel, and kerosene, was isolated from crude oil–contaminated seashore in Tae-an, South Korea. Here, we report the draft genome sequence of this strain, which comprises 3,118,428 bp with a G+C content of 62.85 mol%. PMID:25477411

Kim, Jonghyun; Kim, Soo Jung; Kim, Seon Hee; Kim, Seung Il; Moon, Yoon-Jung; Park, Sung-Joon

2014-01-01

109

Complete Genome Sequence of Exiguobacterium sp. Strain MH3, Isolated from Rhizosphere of Lemna minor.  

PubMed

We report the complete genome sequence of Exiguobacterium sp. strain MH3, isolated from the rhizosphere of duckweed. The genome assembly is 3.16 Mb, with a G+C content of 47.24%, and it may provide useful information about plant-microbe interactions and the genetic basis for the tolerance of the strain to various environmental stresses. PMID:24356831

Tang, Jie; Zhang, Ying; Meng, Hao; Xue, Zhiquan; Ma, Jiong

2013-01-01

110

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...

111

Draft Genome Sequence of Sphingopyxis sp. Strain MWB1, a Crude-Oil-Degrading Marine Bacterium.  

PubMed

Sphingopyxis sp. strain MWB1, which is capable of degrading crude oil, diesel, and kerosene, was isolated from crude oil-contaminated seashore in Tae-an, South Korea. Here, we report the draft genome sequence of this strain, which comprises 3,118,428 bp with a G+C content of 62.85 mol%. PMID:25477411

Kim, Jonghyun; Kim, Soo Jung; Kim, Seon Hee; Kim, Seung Il; Moon, Yoon-Jung; Park, Sung-Joon; Kahng, Hyung-Yeel; Chung, Young-Ho

2014-01-01

112

Draft genome sequence of Shewanella sp. strain HN-41, which produces arsenic-sulfide nanotubes.  

PubMed

The dissimilatory metal reducing bacterium Shewanella sp. strain HN-41 was first reported to produce novel photoactive As-S nanotubes via reduction of As(V) and S(2)O(3)(2-) under anaerobic conditions. Here we report the draft genome sequence and annotation of strain HN-41. PMID:21868804

Kim, Dong-Hun; Jiang, Shenghua; Lee, Ji-Hoon; Cho, Yong-Joon; Chun, Jongsik; Choi, Sang-Haeng; Park, Hong-Seog; Hur, Hor-Gil

2011-09-01

113

3-Nitrotoluene dioxygenase from Diaphorobacter sp. strains: cloning, sequencing and evolutionary studies.  

PubMed

The first step in the degradation of 3-nitrotoluene by Diaphorobacter sp. strain DS2 is the dihydroxylation of the benzene ring with the concomitant removal of nitro group. This is catalyzed by a dioxygenase enzyme system. We report here the cloning and sequencing of the complete dioxygenase gene with its putative regulatory sequence from the genomic DNA of Diaphorobacter sp. strains DS1, DS2 and DS3. Analysis of the 5 kb DNA stretch that was cloned, revealed five complete open reading frames (ORFs) encoding for a reductase, a ferredoxin and two dioxygenase subunits with predicted molecular weights (MW) of 35, 12, 50 and 23 kDa respectively. A regulatory protein was also divergently transcribed from the reductase subunit and has a predicated MW of 34 kDa. Presence of parts of two functional ORFs in between the reductase and the ferredoxin subunits reveals an evolutionary route from a naphthalene dioxygenase like system of Ralstonia sp. strain U2. Further a 100 % identity of its ferredoxin subunit reveals its evolution via dinitrotoluene dioxygenase like system present in Burkholderia cepacia strain R34. A modeled structure of oxygenase3NT from strain DS2 was generated using nitrobenzene dioxygenase as a template. The modeled structure only showed minor changes at its active site. Comparison of growth patterns of strains DS1, DS2 and DS3 revealed that Diaphorobacter sp. strain DS1 has been evolved to degrade 4-nitrotoluene better by an oxidative route amongst all three strains. PMID:24217981

Singh, Deepak; Kumari, Archana; Ramanathan, Gurunath

2014-07-01

114

Butyric acid from anaerobic fermentation of lignocellulosic biomass hydrolysates by Clostridium sp. strain RPT-4213  

Technology Transfer Automated Retrieval System (TEKTRAN)

A novel Clostridium sp. strain RPT-4213 was found producing butyrate under strict anaerobic conditions. This strain produced 9.47 g L-1 butyric acid from MRS media (0.48 g/g glucose). RPT-4213 was also used to ferment dilute acid pretreated hydrolysates including wheat straw (WSH), corn fiber (CFH...

115

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. PMID:21097599

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

2011-01-01

116

Thiols in Nitric Oxide Synthase-Containing Nocardia sp. Strain NRRL 5646?  

PubMed Central

Mycothiol (MSH) [1-d-myo-inosityl-2-(N-acetyl-l-cysteinyl)amido-2-deoxy-?-d-glucopyranoside], isolated as the bimane derivative, was established to be the major thiol in Nocardia sp. strain NRRL 5646, a species most closely related to Nocardia brasiliensis strain DSM 43758T. Thiol formation and detection of MSH-dependent formaldehyde dehydrogenase activity in cell extracts are relevant to the possible modulation of nitric oxide toxicity generated by strain NRRL 5646. PMID:17337559

Lee, Sungwon; Bergeron, Hélène; Lau, Peter C. K.; Rosazza, John P. N.

2007-01-01

117

RESEARCH ARTICLE Transcriptomes of Frankia sp. strain CcI3 in growth transitions  

E-print Network

Background: Frankia sp. strains are actinobacteria that form N2-fixing root nodules on angiosperms. Several reference genome sequences are available enabling transcriptome studies in Frankia sp. Genomes from Frankia sp. strains differ markedly in size, a consequence proposed to be associated with a high number of indigenous transposases, more than 200 of which are found in Frankia sp. strain CcI3 used in this study. Because Frankia exhibits a high degree of cell heterogeneity as a consequence of its mycelial growth pattern, its transcriptome is likely to be quite sensitive to culture age. This study focuses on the behavior of the Frankia sp. strain CcI3 transcriptome as a function of nitrogen source and culture age. Results: To study global transcription in Frankia sp. CcI3 grown under different conditions, complete transcriptomes were determined using high throughput RNA deep sequencing. Samples varied by time (five days vs. three days) and by culture conditions (NH4 + added vs. N2 fixing). Assembly of millions of reads revealed more diversity of gene expression between five-day and three-day old cultures than between three day old cultures differing in nitrogen sources. Heat map analysis organized genes into groups that were expressed or repressed under the various conditions compared to median expression values. Twenty-one SNPs common to all three transcriptome samples were detected indicating culture heterogeneity in this slow-growing organism. Significantly

Derek M Bickhart; David R Benson

118

A Desulfitobacterium sp. strain PR reductively dechlorinates both 1,1,1-trichloroethane and chloroform.  

PubMed

1,1,1-Trichloroethane (TCA) and chloroform are two notorious groundwater pollutants. Here we report the isolation and characterization of Desulfitobacterium sp. strain PR that rapidly dechlorinates both compounds. In pyruvate-amended medium, strain PR reductively dechlorinates ??1.0?mM TCA completely to monochloroethane within 15 days. Under the same conditions, strain PR dechlorinates ??1.2?mM chloroform to predominantly dichloromethane (??1.14?mM) and trace amount of monochloromethane (??0.06?mM) within 10 days. Strain PR shares 96.7% 16S rRNA gene sequence similarity with its closest relative - Desulfitobacterium metallireducens strain 853-15; however, it distinguishes itself from known Desulfitobacterium strains by its inability of utilizing several of their commonly shared substrates such as lactate, thiosulfate and sulfite. A reductive dehalogenase gene (ctrA) in strain PR was identified to be responsible for dechlorination of both TCA and chloroform, showing a maximum expression level of 5.95???6.25 copies of transcripts cell(-1) . CtrA shares 94% amino acid sequence identity with CfrA in Dehalobacter sp. strain CF50 and DcrA in Dehalobacter sp. strain DCA. Interestingly, strain PR could tolerate high aqueous concentrations (up to 0.45?mM) of trichloroethene, another groundwater pollutant that often coexists with TCA/chloroform. As the first chloroform-respiring and the second TCA-respiring isolate that has been identified, Desulfitobacterium sp. strain PR may prove useful in remediation of halogenated alkanes with trihalomethyl (-CX?) groups. PMID:24428759

Ding, Chang; Zhao, Siyan; He, Jianzhong

2014-11-01

119

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. PMID:17873075

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

2007-01-01

120

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

PubMed Central

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 N2-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.

2007-01-01

121

Biodegradation of mixtures of substituted benzenes by Pseudomonas sp. strain JS150.  

PubMed Central

Pseudomonas sp. strain JS150 was isolated as a nonencapsulated variant of Pseudomonas sp. strain JS1 that contains the genes for the degradative pathways of a wide range of substituted aromatic compounds. Pseudomonas sp. strain JS150 grew on phenol, ethylbenzene, toluene, benzene, naphthalene, benzoate, p-hydroxybenzoate, salicylate, chlorobenzene, and several 1,4-dihalogenated benzenes. We designed experiments to determine the conditions required for induction of the individual pathways and to determine whether multiple substrates could be biodegraded simultaneously. Oxygen consumption studies with whole cells and enzyme assays with cell extracts showed that the enzymes of the meta, ortho, and modified ortho cleavage pathways can be induced in strain JS150. Strain JS150 contains a nonspecific toluene dioxygenase with a substrate range similar to that found in strains of Pseudomonas putida. The presence of the dioxygenase along with multiple pathways for metabolism of substituted catechols allows facile extension of the growth range by spontaneous mutation and degradation of mixtures of substituted benzenes and phenols. Chlorobenzene-grown cells of strain JS150 degraded mixtures of chlorobenzene, benzene, toluene, naphthalene, trichloroethylene, and 1,2- and 1,4-dichlorobenzenes in continuous culture. Under similar conditions, phenol-grown cells degraded a mixture of phenol, 2-chloro-, 3-chloro, and 2,5-dichlorophenol and 2-methyl- and 3-methylphenol. These results indicate that induction of appropriate biodegradative pathways in strain JS150 permits the biodegradation of complex mixtures of aromatic compounds. PMID:1637161

Haigler, B E; Pettigrew, C A; Spain, J C

1992-01-01

122

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. PMID:23204415

Ding, Chang; Chow, Wai Ling

2013-01-01

123

Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park  

SciTech Connect

Paenibacillus speciesY412MC10 was one of a number of organisms initially isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA. The isolate Y412MC10 was initially classified as a Geobacillus sp. based on its isolation conditions and similarity to other organisms isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered with Paenibacillus species and not Geobacillus; the 16S rRNA analysis indicated the organism was a strain of Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute. The genome of Paenibacillus lautus strain Y412MC10 consists of one circular chromosome of 7,121,665 bp with an average G+C content of 51.2%. The Paenibacillus sp.Y412MC10 genome sequence was deposited at the NCBI in October 2009 (NC{_}013406). Comparison to other Paenibacillus species shows the organism lacks nitrogen fixation, antibiotic production and social interaction genes reported in other Paenibacilli. Over 25% of the proteins predicted by the Y412MC10 genome share no identity with the closest sequenced Paenibacillus species; most of these are predicted hypothetical proteins and their specific function in the environment is unknown.

Mead, David [University of Wisconsin, Madison; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Zhang, Xiaojing [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Brumm, Catherine [United States Department of Energy Joint Genome Institute; Hochstein, Rebecca [Lucigen Corporation, Middleton, Wisconsin; Schoenfeld, Thomas [Lucigen Corporation, Middleton, Wisconsin; Brumm, Phillip [University of Wisconsin, Madison

2012-01-01

124

Characterization of a Novel Angular Dioxygenase from Fluorene-Degrading Sphingomonas sp. Strain LB126?  

PubMed Central

In this study, the genes involved in the initial attack on fluorene by Sphingomonas sp. strain LB126 were investigated. The ? and ? subunits of a dioxygenase complex (FlnA1-FlnA2), showing 63 and 51% sequence identity, respectively, to the subunits of an angular dioxygenase from the gram-positive dibenzofuran degrader Terrabacter sp. strain DBF63, were identified. When overexpressed in Escherichia coli, FlnA1-FlnA2 was responsible for the angular oxidation of fluorene, 9-hydroxyfluorene, 9-fluorenone, dibenzofuran, and dibenzo-p-dioxin. Moreover, FlnA1-FlnA2 was able to oxidize polycyclic aromatic hydrocarbons and heteroaromatics, some of which were not oxidized by the dioxygenase from Terrabacter sp. strain DBF63. The quantification of resulting oxidation products showed that fluorene and phenanthrene were the preferred substrates of FlnA1-FlnA2. PMID:18156320

Schuler, Luc; Ní Chadhain, Sinéad M.; Jouanneau, Yves; Meyer, Christine; Zylstra, Gerben J.; Hols, Pascal; Agathos, Spiros N.

2008-01-01

125

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

2012-01-01

126

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. PMID:21057013

Chaurasia, Akhilesh Kumar; Apte, Shree Kumar

2011-01-01

127

Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417  

PubMed Central

Bradyrhizobium sp. strain WSM1417 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N2) fixing root nodule of Lupinus sp. collected in Papudo, Chile, in 1995. However, this microsymbiont is a poorly effective N2 fixer with the legume host Lupinus angustifolius L.; a lupin species of considerable economic importance in both Chile and Australia. The symbiosis formed with L. angustifolius produces less than half of the dry matter achieved by the symbioses with commercial inoculant strains such as Bradyrhizobium sp. strain WSM471. Therefore, WSM1417 is an important candidate strain with which to investigate the genetics of effective N2 fixation in the lupin-bradyrhizobia symbioses. Here we describe the features of Bradyrhizobium sp. strain WSM1417, together with genome sequence information and annotation. The 8,048,963 bp high-quality-draft genome is arranged in a single scaffold of 2 contigs, contains 7,695 protein-coding genes and 77 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. PMID:24976884

Reeve, Wayne; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Tian, Rui; De Meyer, Sofie; Tiwari, Ravi; Yates, Ronald; O’Hara, Graham; Howieson, John; Ninawi, Mohamed; Teshima, Hazuki; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavrommatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Peters, Lin; Woyke, Tanja; Kyrpides, Nikos

2013-01-01

128

Molecular characterization of a thermophilic and salt and alkaline-tolerant xylanase from Planococcus sp. SL4, a strain isolated from the sediment of a soda lake.  

PubMed

To enrich the genetic resource of microbial xylanases with high activity and stability under alkaline conditions, a xylanase gene (xynSL4) was cloned from Planococcus sp. SL4, an alkaline xylanase producing strain isolated from the sediment of soda lake Dabusu. Deduced XynSL4 consists of a putative signal peptide of 29 residues and a catalytic domain (30?380 residues) of glycosyl hydrolase (GH) family 10, and shares the highest identity of 77% to a hypothetical protein from Planomicrobium glaciei CHR43. Phylogenetic analysis indicated that deduced XynSL4 is closely related with thermophilic and alkaline xylanases from Geobacillus and Bacillus species. The gene xynSL4 was expressed heterologously in Escherichia coli and the recombinant enzyme showed some superior properties. Purified recombinant XynSL4 (rXynSL4) was highly active and stable over the neutral and alkaline pH range from 6 to 11, with maximum activity at pH 7 and more than 60% activity at pH 11. It had an apparent temperature optimum of 70°C and retained stable at this temperature in the presence of substrate. rXynSL4 was highly halotolerant, retaining more than 55% activity with 0.25-3.0 M NaCl and was stable at the concentration of NaCl up to 4 M. The enzyme activity was significantly enhanced by ?-mercaptoethanol and Ca(2+) but strongly inhibited by heavy metal ions and SDS. This thermophilic and alkaline and salt-tolerant enzyme has great potentials for basic research and industrial applications. PMID:25381738

Huang, Xiaoyun; Lin, Juan; Ye, Xiuyun; Wang, Guozeng

2014-11-10

129

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

130

Genome Sequence of the Petroleum Hydrocarbon-Degrading Bacterium Alcanivorax sp. Strain 97CO-5.  

PubMed

Alcanivorax sp. strain 97CO-5 was isolated from a crude-oil-degrading consortium, enriched from Yellow Sea sediment of China. Here, we present the draft genome of strain 97CO-5, which comprises 3,251,558 bp with a G+C content of 54.54% and contains 2,962 protein-coding genes and 42 tRNAs. PMID:25502673

Luan, Xiao; Cui, Zhisong; Gao, Wei; Li, Qian; Yin, Xiaofei; Zheng, Li

2014-01-01

131

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72  

Microsoft Academic Search

Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is of agrobiotechnological interest because it supplies biologically fixed nitrogen to its host and colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding sequences. Genome comparison with the Azoarcus-related soil bacterium strain EbN1 revealed a

Andrea Krause; Adarsh Ramakumar; Daniela Bartels; Federico Battistoni; Thomas Bekel; Jens Boch; Melanie Böhm; Frauke Friedrich; Thomas Hurek; Lutz Krause; Burkhard Linke; Alice C McHardy; Abhijit Sarkar; Susanne Schneiker; Arshad Ali Syed; Rudolf Thauer; Frank-Jörg Vorhölter; Stefan Weidner; Alfred Pühler; Olaf Kaiser; Alexander Goesmann; Barbara Reinhold-Hurek

2006-01-01

132

Genome Sequence of the Petroleum Hydrocarbon-Degrading Bacterium Alcanivorax sp. Strain 97CO-5  

PubMed Central

Alcanivorax sp. strain 97CO-5 was isolated from a crude-oil-degrading consortium, enriched from Yellow Sea sediment of China. Here, we present the draft genome of strain 97CO-5, which comprises 3,251,558 bp with a G+C content of 54.54% and contains 2,962 protein-coding genes and 42 tRNAs. PMID:25502673

Luan, Xiao; Gao, Wei; Li, Qian; Yin, Xiaofei; Zheng, Li

2014-01-01

133

Genome sequence of the acid-tolerant strain Rhizobium sp. LPU83.  

PubMed

Rhizobia are important members of the soil microbiome since they enter into nitrogen-fixing symbiosis with different legume host plants. Rhizobium sp. LPU83 is an acid-tolerant Rhizobium strain featuring a broad-host-range. However, it is ineffective in nitrogen fixation. Here, the improved draft genome sequence of this strain is reported. Genome sequence information provides the basis for analysis of its acid tolerance, symbiotic properties and taxonomic classification. PMID:24556327

Wibberg, Daniel; Tejerizo, Gonzalo Torres; Del Papa, María Florencia; Martini, Carla; Pühler, Alfred; Lagares, Antonio; Schlüter, Andreas; Pistorio, Mariano

2014-04-20

134

Isolation of Rhodococcus sp. Strain ECU0066, a New Sulfide Monooxygenase-Producing Strain for Asymmetric Sulfoxidation? †  

PubMed Central

A new and efficient sulfide monooxygenase-producing strain, ECU0066, was isolated and identified as a Rhodococcus sp. that could transform phenylmethyl sulfide (PMS) to (S)-sulfoxide with 99% enantiomeric excess via two steps of enantioselective oxidations. Its enzyme activity could be effectively induced by adding PMS or phenylmethyl sulfoxide (PMSO) directly to a rich medium at the early log phase (6 h) of fermentation, resulting in over 10-times-higher production of the enzyme. This bacterial strain also displayed fairly good activity and enantioselectivity toward seven other sulfides, indicating a good potential for practical application in asymmetric synthesis of chiral sulfoxides. PMID:18836022

Li, Ai-Tao; Zhang, Jian-Dong; Xu, Jian-He; Lu, Wen-Ya; Lin, Guo-Qiang

2009-01-01

135

Complete Genome Sequence of Pseudoalteromonas sp. Strain OCN003, Isolated from K?ne'ohe Bay, O'ahu, Hawaii.  

PubMed

Pseudoalteromonas sp. strain OCN003 is a marine gammaproteobacterium that was isolated from a diseased colony of the common Hawaiian reef coral, Montipora capitata, found on a reef surrounding Moku o Lo'e in K?ne'ohe Bay, Hawaii. Here, we report the complete genome of Pseudoalteromonas sp. strain OCN003. PMID:25593253

Beurmann, Silvia; Videau, Patrick; Ushijima, Blake; Smith, Ashley M; Aeby, Greta S; Callahan, Sean M; Belcaid, Mahdi

2015-01-01

136

Complete Genome Sequence of Pseudoalteromonas sp. Strain OCN003, Isolated from K?ne’ohe Bay, O’ahu, Hawaii  

PubMed Central

Pseudoalteromonas sp. strain OCN003 is a marine gammaproteobacterium that was isolated from a diseased colony of the common Hawaiian reef coral, Montipora capitata, found on a reef surrounding Moku o Lo’e in K?ne’ohe Bay, Hawaii. Here, we report the complete genome of Pseudoalteromonas sp. strain OCN003. PMID:25593253

Beurmann, Silvia; Videau, Patrick; Ushijima, Blake; Smith, Ashley M.; Aeby, Greta S.; Callahan, Sean M.

2015-01-01

137

Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil  

PubMed Central

Burkholderia species are common soil Betaproteobacteria capable of degrading recalcitrant aromatic compounds and xenobiotics. Burkholderia sp. strain LIG30 was isolated from wet tropical forest soil and is capable of utilizing lignin as a sole carbon source. Here we report the draft genome sequence of Burkholderia sp. strain LIG30. PMID:24948777

Woo, Hannah L.; Utturkar, Sagar; Klingeman, Dawn; Simmons, Blake A.; DeAngelis, Kristen M.; Brown, Steven D.

2014-01-01

138

Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil.  

PubMed

Burkholderia species are common soil Betaproteobacteria capable of degrading recalcitrant aromatic compounds and xenobiotics. Burkholderia sp. strain LIG30 was isolated from wet tropical forest soil and is capable of utilizing lignin as a sole carbon source. Here we report the draft genome sequence of Burkholderia sp. strain LIG30. PMID:24948777

Woo, Hannah L; Utturkar, Sagar; Klingeman, Dawn; Simmons, Blake A; DeAngelis, Kristen M; Brown, Steven D; Hazen, Terry C

2014-01-01

139

Classification of 'Anaerocellum thermophilum' strain DSM 6725 as Caldicellulosiruptor bescii sp. nov.  

PubMed

The thermophilic, cellulolytic, anaerobic bacterium 'Anaerocellum thermophilum' strain Z-1320 was isolated from a hot spring almost two decades ago and deposited in the German Collection of Microorganisms and Cell Cultures (DSMZ) as DSM 6725. The organism was classified as representing a new genus, 'Anaerocellum', primarily on its growth physiology, cell-wall type and morphology. The results of recent physiological studies and of phylogenetic and genome sequence analyses of strain DSM 6725 of 'A. thermophilum' obtained from the DSMZ showed that its properties differed from those originally described for strain Z-1320. In particular, when compared with strain Z-1320, strain DSM 6725 grew at higher temperatures and had an expanded range of growth substrates. Moreover, the 16S rRNA gene sequence of strain DSM 6725 fell within the Caldicellulosiruptor clade. It is therefore suggested that 'Anaerocellum thermophilum' should be classified as a member of the genus Caldicellulosiruptor, for which the name Caldicellulosiruptor bescii sp. nov. is proposed (type strain DSM 6725(T)=ATCC BAA-1888(T)). C. bescii sp. nov. DSM 6725(T) is the most thermophilic cellulose-degrading organism known. The strain was able to grow up to 90 degrees C (pH 7.2) and degraded crystalline cellulose and xylan as well as untreated plant biomass, including potential bioenergy plants such as poplar and switchgrass. PMID:19801388

Yang, Sung-Jae; Kataeva, Irina; Wiegel, Juergen; Yin, Yanbin; Dam, Phuongan; Xu, Ying; Westpheling, Janet; Adams, Michael W W

2010-09-01

140

Draft Genome Sequence of Alkaliphilic Exiguobacterium sp. Strain HUD, Isolated from a Polymicrobial Consortia.  

PubMed

An alkaliphilic microorganism from the genus Exiguobacterium, Exiguobacterium sp. strain HUD was isolated from a fermentative, methanogenic polymicrobial microcosm operating at pH 10. The draft genome shows the presence of genes encoding for the metabolism of a range of carbohydrates under both aerobic and anaerobic conditions. PMID:25614564

Rout, Simon P; Rai, Anup; Humphreys, Paul N

2015-01-01

141

Draft Genome Sequence of the Naphthalene Degrader Herbaspirillum sp. Strain RV1423  

PubMed Central

Herbaspirillum sp. strain RV1423 was isolated from a site contaminated with alkanes and aromatic compounds and harbors the complete pathway for naphthalene degradation. The new features found in RV1423 increase considerably the versatility and the catabolic potential of a genus of bacteria previously considered mainly to be diazotrophic endophytes to plants. PMID:24652979

Jauregui, Ruy; Rodelas, Belén; Geffers, Robert; Boon, Nico; Pieper, Dietmar H.

2014-01-01

142

Complete Genome Sequence of Winogradskyella sp. Strain PG-2, a Proteorhodopsin-Containing Marine Flavobacterium  

PubMed Central

Winogradskyella sp. strain PG-2 is a marine flavobacterium isolated from surface seawater. This organism contains proteorhodopsin, which can convert light energy into available forms of biochemical energy. Here, we present its complete genome sequence and annotation, which provide further insights into the life strategy of proteorhodopsin-mediated phototrophy in the ocean. PMID:24874677

Kumagai, Yohei; Oshima, Kenshiro; Hattori, Masahira; Iwasaki, Wataru; Kogure, Kazuhiro

2014-01-01

143

Study of Biochemical Pathways and Enzymes Involved in Pyrene Degradation by Mycobacterium sp. Strain KMS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Pyrene degradation is known in bacteria. In this study, Mycobacterium sp. Strain KMS was used to study the metabolites produced during, and enzymes involved in, pyrene degradation. Several key metabolites, including pyrene-4,5-dione, cis-4,5-pyrene-dihydrodiol, phenanthrene-4,5-dicarboxylic acid, ...

144

Draft Genome Sequence of Pseudoalteromonas sp. Strain PLSV, an Ulvan-Degrading Bacterium.  

PubMed

We present the draft genome sequence of Pseudoalteromonas sp. strain PLSV, isolated from the feces of an Aplysia sea slug. The addition of the PLSV genome to the existing genomes of three other ulvan-degrading bacterial species will enhance our understanding of ulvan utilization. PMID:25502665

Kopel, Moran; Helbert, William; Henrissat, Bernard; Doniger, Tirza; Banin, Ehud

2014-01-01

145

Draft Genome Sequence of the Oyster Larval Probiotic Bacterium Vibrio sp. Strain OY15  

PubMed Central

We report the draft genome sequence of Vibrio sp. strain OY15, a Gram-negative marine bacterium isolated from an oyster (Crassostrea virginica) digestive tract and shown to possess probiotic activity. The availability of this genome sequence will facilitate the study of the mechanisms of probiotic activity as well as virulence capacity. PMID:25278542

Schott, Eric J.

2014-01-01

146

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

147

Draft Genome Sequence of Hoeflea sp. Strain BAL378, a Potential Producer of Bioactive Compounds  

PubMed Central

Some phytoplankton-associated marine bacteria produce bioactive compounds. Members of the genus Hoeflea may be examples of such bacteria; however, data describing their metabolisms are scarce. Here, we report the draft genome sequence of Hoeflea sp. strain BAL378, a putative producer of bacteriocins, polyketides, and auxins, as demonstrated by genome mining. PMID:25414510

Riemann, Lasse; Gram, Lone

2014-01-01

148

Study of Biochemical Pathways and Enzymes Involved in Pyrene Degradation by Mycobacterium sp. Strain KMS?  

PubMed Central

Pyrene degradation is known in bacteria. In this study, Mycobacterium sp. strain KMS was used to study the metabolites produced during, and enzymes involved in, pyrene degradation. Several key metabolites, including pyrene-4,5-dione, cis-4,5-pyrene-dihydrodiol, phenanthrene-4,5-dicarboxylic acid, and 4-phenanthroic acid, were identified during pyrene degradation. Pyrene-4,5-dione, which accumulates as an end product in some gram-negative bacterial cultures, was further utilized and degraded by Mycobacterium sp. strain KMS. Enzymes involved in pyrene degradation by Mycobacterium sp. strain KMS were studied, using 2-D gel electrophoresis. The first protein in the catabolic pathway, aromatic-ring-hydroxylating dioxygenase, which oxidizes pyrene to cis-4,5-pyrene-dihydrodiol, was induced with the addition of pyrene and pyrene-4,5-dione to the cultures. The subcomponents of dioxygenase, including the alpha and beta subunits, 4Fe-4S ferredoxin, and the Rieske (2Fe-2S) region, were all induced. Other proteins responsible for further pyrene degradation, such as dihydrodiol dehydrogenase, oxidoreductase, and epoxide hydrolase, were also found to be significantly induced by the presence of pyrene and pyrene-4,5-dione. Several nonpathway-related proteins, including sterol-binding protein and cytochrome P450, were induced. A pyrene degradation pathway for Mycobacterium sp. strain KMS was proposed and confirmed by proteomic study by identifying almost all the enzymes required during the initial steps of pyrene degradation. PMID:17041157

Liang, Yanna; Gardner, Dale R.; Miller, Charles D.; Chen, Dong; Anderson, Anne J.; Weimer, Bart C.; Sims, Ronald C.

2006-01-01

149

Genome sequence of the plant growth-promoting rhizobacterium Bacillus sp. strain JS.  

PubMed

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. PMID:22740679

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; Kwon, Suk Yoon; Kim, Jihyun F

2012-07-01

150

Draft Genome Sequence of Pseudoalteromonas sp. Strain PLSV, an Ulvan-Degrading Bacterium  

PubMed Central

We present the draft genome sequence of Pseudoalteromonas sp. strain PLSV, isolated from the feces of an Aplysia sea slug. The addition of the PLSV genome to the existing genomes of three other ulvan-degrading bacterial species will enhance our understanding of ulvan utilization. PMID:25502665

Kopel, Moran; Helbert, William; Henrissat, Bernard; Doniger, Tirza

2014-01-01

151

Draft Genome Sequence of Sphingobium sp. Strain HDIPO4, an Avid Degrader of Hexachlorocyclohexane  

PubMed Central

Sphingobium sp. strain HDIPO4 was isolated from a hexachlorocyclohexane (HCH) dumpsite and degraded HCH isomers rapidly. The draft genome sequence of HDIPO4 (~4.7 Mbp) contains 143 contigs and 4,646 coding sequences with a G+C content of 65%. PMID:24051321

Mukherjee, Udita; Kumar, Roshan; Mahato, Nitish Kumar; Khurana, J. P.

2013-01-01

152

Draft Genome Sequence of Streptomyces sp. Strain CT34, Isolated from a Ghanaian Soil Sample.  

PubMed

Presented here is a draft genome sequence of Streptomyces sp. strain CT34, which produces a novel ribosomally synthesized and posttranslationally modified peptide (RiPP). Analysis of the deduced open reading frame set identified the putative RiPP biosynthesis gene cluster, as well as other secondary metabolite gene clusters. PMID:25657278

Zhai, Yin; Cheng, Bin; Hu, Juan; Kyeremeh, Kwaku; Wang, Xiaoling; Jaspars, Marcel; Deng, Hai; Deng, Zi-Xin; Hong, Kui

2015-01-01

153

Modular Synthase-Encoding Gene Involved in ?-Olefin Biosynthesis in Synechococcus sp. Strain PCC 7002 ? †  

PubMed Central

A gene involved in the production of medium-chain ?-olefins was identified in the cyanobacterium Synechococcus sp. strain PCC 7002. The gene encodes a large multidomain protein with homology to type I polyketide synthases, suggesting a route for hydrocarbon biosynthesis from fatty acids via an elongation decarboxylation mechanism. PMID:21531827

Mendez-Perez, Daniel; Begemann, Matthew B.; Pfleger, Brian F.

2011-01-01

154

Transport of mevalonate by Pseudomonas sp. strain M.  

PubMed Central

Pseudomonas sp. M, isolated from soil by elective culture on R,S-mevalonate as the sole source of carbon, possessed an inducible transport system for mevalonate. This high-affinity system had a pH optimum of 7.0, a temperature optimum of 30 degrees C, a Km for R,S-mevalonate of 88 microM, and a V max of 26 nmol of mevalonate transported per min/mg of cells (dry weight). Transport was energy dependent since azide, cyanide, or m-chlorophenylhydrazone caused complete cessation of transport activity. Transport of mevalonate was highly substrate specific. Of the 16 structural analogs of mevalonate tested, only acetoacetate, mevinolin, and mevaldehyde significantly inhibited transport. Growth of cells on mevalonate induced transport activity by 40- to 65-fold over that observed in cells grown on alternate carbon sources. A biphasic pattern for cell growth, as well as for induction of mevalonate transport activity, was observed when mevalonate was added to a culture actively growing on glucose. The induction of transport activity under these conditions began within 30 min after the addition of mevalonate and reached 60% of maximal activity during phase I. A further increase in mevalonate transport activity occurred during phase II of growth. Glucose was the preferred carbon source for growth during phase I, whereas mevalonate was preferred during phase II. Only one isomer of the R,S-mevalonate mixture appeared to be utilized, since growth ceased after 45 to 50% of the total mevalonate was depleted from the medium. However, nearly 30% of the preferred mevalonate isomer was depleted from the medium during phase I without significant metabolism to CO2. These results suggest that mevalonate or a mevalonate catabolite may accumulate in cells of Pseudomonas sp. M during phase I and that glucose metabolism may inhibit or repress the expression of enzymes further along the mevalonate catabolic pathway. PMID:6434521

Gill, J F; Beach, M J; Rodwell, V W

1984-01-01

155

Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471  

PubMed Central

Bradyrhizobium sp. strain WSM471 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen- (N2) fixing root nodule formed on the annual legume Ornithopus pinnatus (Miller) Druce growing at Oyster Harbour, Albany district, Western Australia in 1982. This strain is in commercial production as an inoculant for Lupinus and Ornithopus. Here we describe the features of Bradyrhizobium sp. strain WSM471, together with genome sequence information and annotation. The 7,784,016 bp high-quality-draft genome is arranged in 1 scaffold of 2 contigs, contains 7,372 protein-coding genes and 58 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. PMID:24976882

Reeve, Wayne; De Meyer, Sofie; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Tian, Rui; Tiwari, Ravi; Howieson, John; Yates, Ronald; O’Hara, Graham; Ninawi, Mohamed; Lu, Megan; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Woyke, Tanja; Kyrpides, Nikos

2013-01-01

156

Transcriptomes of Frankia sp. strain CcI3 in growth transitions  

PubMed Central

Background Frankia sp. strains are actinobacteria that form N2-fixing root nodules on angiosperms. Several reference genome sequences are available enabling transcriptome studies in Frankia sp. Genomes from Frankia sp. strains differ markedly in size, a consequence proposed to be associated with a high number of indigenous transposases, more than 200 of which are found in Frankia sp. strain CcI3 used in this study. Because Frankia exhibits a high degree of cell heterogeneity as a consequence of its mycelial growth pattern, its transcriptome is likely to be quite sensitive to culture age. This study focuses on the behavior of the Frankia sp. strain CcI3 transcriptome as a function of nitrogen source and culture age. Results To study global transcription in Frankia sp. CcI3 grown under different conditions, complete transcriptomes were determined using high throughput RNA deep sequencing. Samples varied by time (five days vs. three days) and by culture conditions (NH4+ added vs. N2 fixing). Assembly of millions of reads revealed more diversity of gene expression between five-day and three-day old cultures than between three day old cultures differing in nitrogen sources. Heat map analysis organized genes into groups that were expressed or repressed under the various conditions compared to median expression values. Twenty-one SNPs common to all three transcriptome samples were detected indicating culture heterogeneity in this slow-growing organism. Significantly higher expression of transposase ORFs was found in the five-day and N2-fixing cultures, suggesting that N starvation and culture aging provide conditions for on-going genome modification. Transposases have previously been proposed to participate in the creating the large number of gene duplication or deletion in host strains. Subsequent RT-qPCR experiments confirmed predicted elevated transposase expression levels indicated by the mRNA-seq data. Conclusions The overall pattern of gene expression in aging cultures of CcI3 suggests significant cell heterogeneity even during normal growth on ammonia. The detection of abundant transcription of nif (nitrogen fixation) genes likely reflects the presence of anaerobic, N-depleted microsites in the growing mycelium of the culture, and the presence of significantly elevated transposase transcription during starvation indicates the continuing evolution of the Frankia sp. strain CcI3 genome, even in culture, especially under stressed conditions. These studies also sound a cautionary note when comparing the transcriptomes of Frankia grown in root nodules, where cell heterogeneity would be expected to be quite high. PMID:21867524

2011-01-01

157

Expression of the Nitroarene Dioxygenase Genes in Comamonas sp. Strain JS765 and Acidovorax sp. Strain JS42 Is Induced by Multiple Aromatic Compounds  

PubMed Central

This work reports a genetic analysis of the expression of nitrobenzene dioxygenase (NBDO) in Comamonas sp. strain JS765 and 2-nitrotoluene dioxygenase (2NTDO) in Acidovorax sp. strain JS42. Strains JS765 and JS42 possess identical LysR-type regulatory proteins, NbzR and NtdR, respectively. NbzR/NtdR is homologous to NahR, the positive salicylate-responsive transcriptional activator of the naphthalene degradation genes in Pseudomonas putida G7. The genes encoding NBDO and 2NTDO in each strain are cotranscribed, and transcription starts at the same site within identical promoter regions for each operon. Results from a lacZ reporter gene fusion demonstrated that expression of NBDO and 2NTDO is induced by multiple aromatic compounds, including an array of nitroaromatic compounds (nitrobenzene, 2-, 3-, and 4-nitrotoluene, 2,4- and 2,6-dinitrotoluene, and aminodinitrotoluenes), as well as salicylate and anthranilate. The nitroaromatic compounds appear to be the actual effector molecules. Analysis of ?-galactosidase and 2NTDO activities with strain JS42 demonstrated that NtdR was required for induction by all of the inducing compounds, high basal-level expression of 2NTDO, and complementation of a JS42 ntdR null mutant. Complementation with the closely related regulators NagR (from Ralstonia sp. strain U2) and NahR restored only induction by the archetype inducers, salicylate or salicylate and anthranilate, respectively, and did not restore the high basal level of expression of 2NTDO. The mechanism of 2NTDO gene regulation in JS42, and presumably that of NBDO gene regulation in JS765, appear similar to that of NahR-regulated genes in Pseudomonas putida G7. However, NbzR and NtdR appear to have evolved a broader specificity in JS42 and JS765, allowing for recognition of nitroaromatic compounds while retaining the ability to respond to salicylate and anthranilate. NtdR is also the first example of a nitroarene-responsive LysR-type transcriptional activator. PMID:12813084

Lessner, Daniel J.; Parales, Rebecca E.; Narayan, Shakti; Gibson, David T.

2003-01-01

158

Migratory Response of Soil Bacteria to Lyophyllum sp. Strain Karsten in Soil Microcosms?  

PubMed Central

In this study, the selection of bacteria on the basis of their migration via fungal hyphae in soil was investigated in microcosm experiments containing Lyophyllum sp. strain Karsten (DSM2979). One week following inoculation with a bacterial community obtained from soil, selection of a few specific bacterial types was noticed at 30 mm in the growth direction of Lyophyllum sp. strain Karsten in sterile soil. Cultivation-based analyses showed that the migration-proficient types encompassed 10 bacterial groups, as evidenced by (GTG)5 genomic fingerprinting as well as 16S rRNA gene sequencing. These were (>97% similarity) Burkholderia terrae BS001, Burkholderia sordidicola BS026, Burkholderia sediminicola BS010, and Burkholderia phenazinium BS028; Dyella japonica BS013, BS018, and BS021; “Sphingoterrabacterium pocheensis” BS024; Sphingobacterium daejeonense BS025; and Ralstonia basilensis BS017. Migration as single species was subsequently found for B. terrae BS001, D. japonica BS018 and BS021, and R. basilensis BS017. Typically, migration occurred only when these organisms were introduced at the fungal growth front and only in the direction of hyphal growth. Migration proficiency showed a one-sided correlation with the presence of the hrcR gene, used as a marker for the type III secretion system (TTSS), as all single-strain migrators were equipped with this system and most non-single-strain migrators were not. The presence of the TTSS stood in contrast to the low prevalence of TTSSs within the bacterial community used as an inoculum (<3%). Microscopic examination of B. terrae BS001 in contact with Lyophyllum sp. strain Karsten hyphae revealed the development of a biofilm surrounding the hyphae. Migration-proficient bacteria interacting with Lyophyllum sp. strain Karsten may show complex behavior (biofilm formation) at the fungal tip, leading to their translocation and growth in novel microhabitats in soil. PMID:19286795

Warmink, J. A.; van Elsas, J. D.

2009-01-01

159

Engineering the Genotype of Acinetobacter sp. Strain ADP1 To Enhance Biosynthesis of Cyanophycin  

PubMed Central

To study the importance of arginine provision and phosphate limitation for synthesis and accumulation of cyanophycin (CGP) in Acinetobacter sp. strain ADP1, genes encoding the putative arginine regulatory protein (argR) and the arginine succinyltransferase (astA) were inactivated, and the effects of these mutations on CGP synthesis were analyzed. The inactivation of these genes resulted in a 3.5- or 7-fold increase in CGP content, respectively, when the cells were grown on glutamate. Knockout mutations in both genes led to a better understanding of the effect of the addition of other substrates to arginine on CGP synthesis during growth of the cells of Acinetobacter sp. strain ADP1. Overexpression of ArgF (ornithine carbamoyltransferase), CarA-CarB (small and large subunits of carbamoylphosphate synthetase), and PepC (phosphoenolpyruvate carboxylase) triggered synthesis of CGP if amino acids were used as a carbon source whereas it was not triggered by gluconate or other sugars. Cells of Acinetobacter sp. strain ADP1, which is largely lacking genes for carbohydrate metabolism, showed a significant increase in CGP contents when grown on mineral medium supplemented with glutamate, aspartate, or arginine. The Acinetobacter sp. ?astA(pYargF) strain is unable to utilize arginine but synthesizes more arginine, resulting in CGP contents as high as 30% and 25% of cell dry matter when grown on protamylasse or Luria-Bertani medium, respectively. This recombinant strain overcame the bottleneck of the costly arginine provision where it produces about 75% of the CGP obtained from the parent cells grown on mineral medium containing pure arginine as the sole source of carbon. Phosphate starvation is the only known trigger for CGP synthesis in this bacterium, which possesses the PhoB/PhoR phosphate regulon system. Overexpression of phoB caused an 8.6-fold increase in CGP content in comparison to the parent strain at a nonlimiting phosphate concentration. PMID:16461694

Elbahloul, Yasser; Steinbüchel, Alexander

2006-01-01

160

Migratory response of soil bacteria to Lyophyllum sp. strain Karsten in soil microcosms.  

PubMed

In this study, the selection of bacteria on the basis of their migration via fungal hyphae in soil was investigated in microcosm experiments containing Lyophyllum sp. strain Karsten (DSM2979). One week following inoculation with a bacterial community obtained from soil, selection of a few specific bacterial types was noticed at 30 mm in the growth direction of Lyophyllum sp. strain Karsten in sterile soil. Cultivation-based analyses showed that the migration-proficient types encompassed 10 bacterial groups, as evidenced by (GTG)(5) genomic fingerprinting as well as 16S rRNA gene sequencing. These were (>97% similarity) Burkholderia terrae BS001, Burkholderia sordidicola BS026, Burkholderia sediminicola BS010, and Burkholderia phenazinium BS028; Dyella japonica BS013, BS018, and BS021; "Sphingoterrabacterium pocheensis" BS024; Sphingobacterium daejeonense BS025; and Ralstonia basilensis BS017. Migration as single species was subsequently found for B. terrae BS001, D. japonica BS018 and BS021, and R. basilensis BS017. Typically, migration occurred only when these organisms were introduced at the fungal growth front and only in the direction of hyphal growth. Migration proficiency showed a one-sided correlation with the presence of the hrcR gene, used as a marker for the type III secretion system (TTSS), as all single-strain migrators were equipped with this system and most non-single-strain migrators were not. The presence of the TTSS stood in contrast to the low prevalence of TTSSs within the bacterial community used as an inoculum (<3%). Microscopic examination of B. terrae BS001 in contact with Lyophyllum sp. strain Karsten hyphae revealed the development of a biofilm surrounding the hyphae. Migration-proficient bacteria interacting with Lyophyllum sp. strain Karsten may show complex behavior (biofilm formation) at the fungal tip, leading to their translocation and growth in novel microhabitats in soil. PMID:19286795

Warmink, J A; van Elsas, J D

2009-05-01

161

Draft Genome Sequence of the Organophosphorus-Degrading Bacterium Pseudomonas sp. Strain 1-7, Isolated from Organophosphorus-Polluted Sludge  

PubMed Central

Pseudomonas sp. strain 1-7, isolated from organophosphorus-polluted sludge, is able to degrade many organophosphorus compounds. Here, we report the draft genome sequence of Pseudomonas sp. strain 1-7. PMID:25278536

Tian, Jian; Xu, Li; Zhang, Shuangyu; Sun, Wen; Chu, Xiaoyu

2014-01-01

162

Transmission Dynamics of Bartonella sp. Strain OE 1-1 in Sundevall's Jirds (Meriones crassus)  

PubMed Central

A high prevalence of Bartonella infection is found in many natural systems; however, the transmission dynamics leading to observations of these infections is not fully understood. The capability of Xenopsylla ramesis fleas to serve as competent vectors of Bartonella sp. OE 1-1 (a strain closely related to the zoonotic Bartonella elizabethae) to Meriones crassus jirds was investigated. Naïve X. ramesis fleas were placed for 72 h on naïve jirds or jirds that were either experimentally or naturally infected with Bartonella sp. strain OE 1-1, after which they were placed on naïve jirds. Postfeeding, 69 to 100% of the fleas collected from each Bartonella-positive jird contained Bartonella DNA, and all naïve jirds became positive for Bartonella sp. OE 1-1 after infestation with the infected fleas. In addition, maternal transmission of Bartonella sp. OE 1-1 in jirds was tested by mating 5 Bartonella-positive and 5 naïve female jirds with 10 naïve male jirds in the absence of fleas. Fifteen offspring were delivered by each group. Cultures of blood drawn from all offspring on days 35 and 47 postdelivery were found to be negative for Bartonella. A single spleen sample from the offspring of a Bartonella-positive mother was found molecularly positive for Bartonella sp. OE 1-1. This study demonstrates that X. ramesis fleas are competent vectors of Bartonella sp. OE 1-1 to M. crassus jirds and indicates that maternal transmission is probably not the major transmission route from female jirds to their offspring. We suggest that the dynamics of Bartonella sp. OE 1-1 in the M. crassus jird population in nature is mostly dependent on its vectors. PMID:23241972

Morick, Danny; Krasnov, Boris R.; Khokhlova, Irina S.; Gottlieb, Yuval

2013-01-01

163

Production of Proteasome Inhibitor Syringolin A by the Endophyte Rhizobium sp. Strain AP16  

PubMed Central

Syringolin A, the product of a mixed nonribosomal peptide synthetase/polyketide synthase encoded by the syl gene cluster, is a virulence factor secreted by certain Pseudomonas syringae strains. Together with the glidobactins produced by a number of beta- and gammaproteobacterial human and animal pathogens, it belongs to the syrbactins, a structurally novel class of proteasome inhibitors. In plants, proteasome inhibition by syringolin A-producing P. syringae strains leads to the suppression of host defense pathways requiring proteasome activity, such as the ones mediated by salicylic acid and jasmonic acid. Here we report the discovery of a syl-like gene cluster with some unusual features in the alphaproteobacterial endophyte Rhizobium sp. strain AP16 that encodes a putative syringolin A-like synthetase whose components share 55% to 65% sequence identity (72% to 79% similarity) at the amino acid level. As revealed by average nucleotide identity (ANI) calculations, this strain likely belongs to the same species as biocontrol strain R. rhizogenes K84 (formely known as Agrobacterium radiobacter K84), which, however, carries a nonfunctional deletion remnant of the syl-like gene cluster. Here we present a functional analysis of the syl-like gene cluster of Rhizobium sp. strain AP16 and demonstrate that this endophyte synthesizes syringolin A and some related minor variants, suggesting that proteasome inhibition by syrbactin production can be important not only for pathogens but also for endophytic bacteria in the interaction with their hosts. PMID:24727275

Bigler, Laurent; Dudler, Robert

2014-01-01

164

Identification of an Enzyme System for Daidzein-to-Equol Conversion in Slackia sp. Strain NATTS  

PubMed Central

An Escherichia coli library comprising 8,424 strains incorporating gene fragments of the equol-producing bacterium Slackia sp. strain NATTS was constructed and screened for E. coli strains having daidzein- and dihydrodaidzein (DHD)- metabolizing activity. We obtained 3 clones that functioned to convert daidzein to DHD and 2 clones that converted DHD to equol. We then sequenced the gene fragments inserted into plasmids contained by these 5 clones. All of the gene fragments were contiguous, encoding three open reading frames (ORF-1, -2, and -3). Analysis of E. coli strains containing an expression vector incorporating one of the orf-1, -2, or -3 genes revealed that (i) the protein encoded by orf-1 was involved in the conversion of cis/trans-tetrahydrodaidzein (cis/trans-THD) to equol, (ii) the protein encoded by orf-2 was involved in the conversion of DHD to cis/trans-THD, and (iii) the protein encoded by orf-3 was involved in the conversion of daidzein to DHD. ORF-1 had a primary amino acid structure similar to that of succinate dehydrogenase. ORF-2 was presumed to be an enzyme belonging to the short-chain dehydrogenase/reductase superfamily. ORF-3 was predicted to have 42% identity to the daidzein reductase of Lactococcus strain 20-92 and belonged to the NADH:flavin oxidoreductase family. These findings showed that the daidzein-to-equol conversion reaction in the Slackia sp. NATTS strain proceeds by the action of these three enzymes. PMID:22179235

Moriyama, Kaoru; Nomoto, Koji; Akaza, Hideyuki

2012-01-01

165

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

2012-05-01

166

Methanobacterium paludis sp. nov. and a novel strain of Methanobacterium lacus isolated from northern peatlands.  

PubMed

Two mesophilic, hydrogenotrophic methanogens, designated strains SWAN1T and AL-21, were isolated from two contrasting peatlands: a near circumneutral temperate minerotrophic fen in New York State, USA, and an acidic boreal poor fen site in Alaska, USA, respectively. Cells of the two strains were rod-shaped, non-motile, stained Gram-negative and resisted lysis with 0.1% SDS. Cell size was 0.6×1.5-2.8 µm for strain SWAN1T and 0.45-0.85×1.5-35 µm for strain AL-21. The strains used H2/CO2 but not formate or other substrates for methanogenesis, grew optimally around 32-37 °C, and their growth spanned through a slightly low to neutral pH range (4.7-7.1). Strain AL-21 grew optimally closer to neutrality at pH 6.2, whereas strain SWAN1T showed a lower optimal pH at 5.4-5.7. The two strains were sensitive to NaCl with a maximal tolerance at 160 mM for strain SWAN1T and 50 mM for strain AL-21. Na2S was toxic at very low concentrations (0.01-0.8 mM), resulting in growth inhibition above these values. The DNA G+C content of the genomes was 35.7 mol% for strain SWAN1T and 35.8 mol% for strain AL-21. Phylogenetic analysis of the 16S rRNA gene sequences showed that the strains are members of the genus Methanobacterium. Strain SWAN1T shared 94-97% similarity with the type strains of recognized species of the genus Methanobacterium, whereas strain AL-21 shared 99% similarity with Methanobacterium lacus 17A1T. On the basis of phenotypic, genomic and phylogenetic characteristics, strain SWAN1T (=DSM 25820T=JCM 18151T) is proposed as the type strain of a novel species, Methanobacterium paludis sp. nov., while strain AL-21 is proposed as a second strain of Methanobacterium lacus. PMID:24449792

Cadillo-Quiroz, Hinsby; Bräuer, Suzanna L; Goodson, Noah; Yavitt, Joseph B; Zinder, Stephen H

2014-05-01

167

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

168

Degradation of hydrogen sulfide by Xanthomonas sp. strain DY44 isolated from peat.  

PubMed Central

Xanthomonas sp. strain DY44, capable of degrading H2S, was isolated from dimethyl disulfide-acclimated peat. This bacterium removed H2S either as a single gas or in the presence of the sulfur-containing compounds methanethiol, dimethyl sulfide, and dimethyl disulfide. The maximum specific H2S removal rate, obtained in the late stationary phase, was 3.92 mmol g of dry cells-1 h-1 (6.7 x 10(-16) mol cell-1 h-1) at pH 7 and 30 degrees C through a batch experiment in a basal mineral medium. Since Xanthomonas sp. strain DY44 exhibited no autotrophic growth with H2S, the H2S removal was judged not to be a consequence of chemolithotrophic activity. By using X-ray photoelectron spectroscopy, the metabolic product of H2S oxidation was determined to be polysulfide, which has properties very similar to those of elemental sulfur. Autoclaved cells (120 degrees C, 20 min) did not show H2S degradation, but cells killed by gamma-irradiation and cell extracts both oxidized H2S, suggesting the existence of a heat-labile intracellular enzymatic system for H2S oxidation. When Xanthomonas sp. strain DY44 was inoculated into fibrous peat, this strain degraded H2S without lag time, suggesting that it will be a good candidate for maintaining high H2S removability in the treatment of exhaust gases. PMID:1599238

Cho, K S; Hirai, M; Shoda, M

1992-01-01

169

Degradation of hydrogen sulfide by Xanthomonas sp. strain DY44 isolated from peat.  

PubMed

Xanthomonas sp. strain DY44, capable of degrading H2S, was isolated from dimethyl disulfide-acclimated peat. This bacterium removed H2S either as a single gas or in the presence of the sulfur-containing compounds methanethiol, dimethyl sulfide, and dimethyl disulfide. The maximum specific H2S removal rate, obtained in the late stationary phase, was 3.92 mmol g of dry cells-1 h-1 (6.7 x 10(-16) mol cell-1 h-1) at pH 7 and 30 degrees C through a batch experiment in a basal mineral medium. Since Xanthomonas sp. strain DY44 exhibited no autotrophic growth with H2S, the H2S removal was judged not to be a consequence of chemolithotrophic activity. By using X-ray photoelectron spectroscopy, the metabolic product of H2S oxidation was determined to be polysulfide, which has properties very similar to those of elemental sulfur. Autoclaved cells (120 degrees C, 20 min) did not show H2S degradation, but cells killed by gamma-irradiation and cell extracts both oxidized H2S, suggesting the existence of a heat-labile intracellular enzymatic system for H2S oxidation. When Xanthomonas sp. strain DY44 was inoculated into fibrous peat, this strain degraded H2S without lag time, suggesting that it will be a good candidate for maintaining high H2S removability in the treatment of exhaust gases. PMID:1599238

Cho, K S; Hirai, M; Shoda, M

1992-04-01

170

The Glutathione/Glutaredoxin System Is Essential for Arsenate Reduction in Synechocystis sp. Strain PCC 6803? †  

PubMed Central

Arsenic resistance in Synechocystis sp. strain PCC 6803 is mediated by an operon of three genes in which arsC codes for an arsenate reductase with unique characteristics. Here we describe the identification of two additional and nearly identical genes coding for arsenate reductases in Synechocystis sp. strain PCC 6803, which we have designed arsI1 and arsI2, and the biochemical characterization of both ArsC (arsenate reductase) and ArsI. Functional analysis of single, double, and triple mutants shows that both ArsI enzymes are active arsenate reductases but that their roles in arsenate resistance are essential only in the absence of ArsC. Based on its biochemical properties, ArsC belongs to a family that, though related to thioredoxin-dependent arsenate reductases, uses the glutathione/glutaredoxin system for reduction, whereas ArsI belongs to the previously known glutaredoxin-dependent family. We have also analyzed the role in arsenate resistance of the three glutaredoxins present in Synechocystis sp. strain PCC 6803 both in vitro and in vivo. Only the dithiolic glutaredoxins, GrxA (glutaredoxin A) and GrxB (glutaredoxin B), are able to donate electrons to both types of reductases in vitro, while GrxC (glutaredoxin C), a monothiolic glutaredoxin, is unable to donate electrons to either type. Analysis of glutaredoxin mutant strains revealed that only those lacking the grxA gene have impaired arsenic resistance. PMID:19304854

López-Maury, Luis; Sánchez-Riego, Ana María; Reyes, José Carlos; Florencio, Francisco J.

2009-01-01

171

A novel dipeptidyl aminopeptidase from Pseudomonas sp. strain WO24.  

PubMed Central

An activity similar to that of dipeptidyl aminopeptidase I (DAP I) which releases dipeptide from Gly-Arg-p-nitroanilide (Gly-Arg-pNA) was detected in a Pseudomonas sp. An enzyme was isolated and purified about 400-fold by a series of column chromatographies. The enzyme, named DAP BI (DAP from bacteria, type I), was revealed to be homogeneous by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and isoelectric focusing. The molecular mass was estimated to be 82 kDa by SDS-PAGE and 65 kDa by gel filtration, suggesting that the enzyme may be a monomer. The enzyme had an isoelectric point of 4.7. It is optimally active at pH 9.0. The Km and Vmax of the enzyme for Gly-Arg-pNA were 0.25 mM and 195 micromol/min/mg, respectively. The purified enzyme did not hydrolyze Gly-Phe-pNA, which was also a substrate for DAP I, whereas it hydrolyzed Arg-Arg-4-methoxy-beta-naphthylamide (Arg-Arg-MNA), a model substrate for DAP III. The Km and Vmax for Arg-Arg-MNA were 0.019 mM and 145 micromol/min/mg, respectively. This purified enzyme can also catalyze the removal of Asp-Arg from the N termini of angiotensins I and II. The enzyme activity was completely inhibited by Zn(II) (0.5 mM), tosyl-L-Lys-chloromethyl ketone (0.1 mM), and leupeptin (0.1 mM) and partially inhibited by Co(II) (0.5 mM) and chymostatin (0.1 mM), whereas the enzyme was not affected by general serine protease inhibitors (phenylmethylsulfonyl fluoride and diisopropylfluorophosphate) and thiol protease inhibitors. The substrate specificity, classification of catalytic site, and other enzymatic properties demonstrate that this enzyme is distinct from the previously described mammalian DAPs I and III and Saccharomyces cerevisiae DAP III. These results indicate that DAP BI may be a new type of the DAP family. PMID:8631703

Ogasawara, W; Ochiai, K; Ando, K; Yano, K; Yamasaki, M; Okada, H; Morikawa, Y

1996-01-01

172

Isolation of the stable strain Labrys sp. BK-8 for l(+)-tartaric acid production.  

PubMed

A novel cis-epoxysuccinate hydrolase (CESH) producing strain of Labrys sp. BK-8 for production of l(+)-tartaric acid was isolated and identified. After optimization, a maximum activity of 3597 ± 151 U/g was achieved in batch culture in a 10 L fermentor. When Labrys sp. BK-8 was immobilized on ?-carrageenan, the immobilized cells showed a high conversion rate (>99%), enantioselectivity (EE > 99.5%) and storage stability (>90 d). A conversion rate of 97% was still achieved after 10 repeat batches. The CESH was stable over a broad range of temperatures (up to 45°C) and pH values (4.0-10.0). The Labrys sp. BK-8 isolate provides a new alternative with good stability for the industrial biosynthesis of l(+)-tartaric acid. PMID:25468422

Bao, Wenna; Pan, Haifeng; Zhang, Zhenhong; Cheng, Yongqing; Xie, Zhipeng; Zhang, Jianguo

2014-11-15

173

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

174

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

PubMed Central

Corynebacterium sp. strain C125, originally isolated on o-xylene, was selected for its ability to grow on tetralin (1,2,3,4-tetrahydronaphthalene) as the sole source of carbon and energy. The catabolism of tetralin in Corynebacterium sp. strain C125 was shown to proceed via initial hydroxylation of the benzene nucleus at positions C-5 and C-6, resulting in the formation of the corresponding cis-dihydro diol. Subsequently, the dihydro diol was dehydrogenated by a NAD-dependent dehydrogenase to 5,6,7,8-tetrahydro-1,2-naphthalene diol. The aromatic ring was cleaved in the extradiol position by a catechol-2,3-dioxygenase. The ring fission product was subject to a hydrolytic attack, resulting in the formation of a carboxylic acid-substituted cyclohexanone. This is the first report of the catabolism of tetralin via degradation of the aromatic moiety. PMID:8434923

Sikkema, J; de Bont, J A

1993-01-01

175

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

176

Desaturation, dioxygenation, and monooxygenation reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain 9816-4.  

PubMed Central

The stereospecific oxidation of indan and indene was examined with mutant and recombinant strains expressing naphthalene dioxygenase of Pseudomonas sp. strain 9816-4. Pseudomonas sp. strain 9816/11 and Escherichia coli JM109(DE3)[pDTG141] oxidized indan to (+)-(1S)-indanol, (+)-cis-(1R,2S)-indandiol, (+)-(1S)-indenol, and 1-indanone. The same strains oxidized indene to (+)-cis-(1R,2S)-indandiol and (+)-(1S)-indenol. Purified naphthalene dioxygenase oxidized indan to the same four products formed by strains 9816/11 and JM109(DE3)[pDTG141]. In addition, indene was identified as an intermediate in indan oxidation. The major products formed from indene by purified naphthalene dioxygenase were (+)-(1S)-indenol and (+)-(1R,2S)-indandiol. The results show that naphthalene dioxygenase catalyzes the enantiospecific monooxygenation of indan to (+)-(1S)-indanol and the desaturation of indan to indene, which then serves as a substrate for the formation of (+)-(1R,2S)-indandiol and (+)-(1S)-indenol. The relationship of the desaturase, monooxygenase, and dioxygenase activities of naphthalene dioxygenase is discussed with reference to reactions catalyzed by toluene dioxygenase, plant desaturases, cytochrome P-450, methane monooxygenase, and other bacterial monooxygenases. PMID:7751268

Gibson, D T; Resnick, S M; Lee, K; Brand, J M; Torok, D S; Wackett, L P; Schocken, M J; Haigler, B E

1995-01-01

177

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

PubMed Central

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 to salicylic acid through the angular dioxygenation pathway. In contrast to DBF, strain XLDN2-5 could transform DBT through the ring cleavage and sulfoxidation pathways. Sphingomonas sp. strain XLDN2-5 could cometabolically degrade DBF and DBT in the growing system using CA as a substrate. After 40 h of incubation, 90% of DBT was transformed, and CA and DBF were completely removed. These results suggested that strain XLDN2-5 might be useful in the bioremediation of environments contaminated by these compounds. PMID:17337542

Gai, Zhonghui; Yu, Bo; Li, Li; Wang, Ying; Ma, Cuiqing; Feng, Jinhui; Deng, Zixin; Xu, Ping

2007-01-01

178

Purification and Characterization of a Novel Naphthalene Dioxygenase from Rhodococcus sp. Strain NCIMB12038  

PubMed Central

We report here the characterization of the catalytic component (ISPNAR) of a new naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038. The genes encoding the two subunits of ISPNAR are not homologous to their previously characterized counterparts in Pseudomonas. The deduced amino acid sequences have only 33 and 29% identity with the corresponding subunits in Pseudomonas putida NCIB 9816-4, for which the tertiary structure has been reported. PMID:10498739

Larkin, Michael J.; Allen, Christopher C. R.; Kulakov, Leonid A.; Lipscomb, David A.

1999-01-01

179

Proposed oxidative metabolic pathway for polypropylene glycol in Sphingobium sp. strain PW-1.  

PubMed

Polypropylene glycol (PPG)-assimilating Sphingobium sp. strain PW-1 was grown on 0.5% PPG 700. PPG and its metabolites were analyzed by MALDI-TOF mass spectrometry. An oxidized form of a terminal alcohol group appeared with each molecular species as a metabolite. Cell-free extract showed PPG dehydrogenase activity. In this way, the oxidative metabolic pathway for PPG was confirmed. PMID:18391452

Hu, Xiaoping; Liu, Xin; Tani, Akio; Kimbara, Kazuhide; Kawai, Fusako

2008-04-01

180

Draft genome sequences of the biocontrol bacterium Mitsuaria sp. strain H24L5A.  

PubMed

Mitsuaria sp. strain H24L5A is a plant-associated bacterium with proven capacities to suppress plant pathogens. Here, we report the draft genome sequences and automatic annotation of H24L5A. Comparative genomic analysis indicates H24L5A's similarity to the Leptothrix and Methylibium species, as well as several genes potentially contributing to its biocontrol activities. PMID:22247532

Rong, Xiaoqing; Gurel, Fulya Baysal; Meulia, Tea; McSpadden Gardener, Brian B

2012-02-01

181

Molecular characterization of the cyanophycin synthetase from Synechocystis sp. strain PCC6308  

Microsoft Academic Search

A 3878-bp genomic region from the cyanobacterium Synechocystis sp. strain PCC6308, amplified by inverse PCR, harbored the structural genes cphA (2625 bp) and cphB (819 bp) encoding cyanophycin synthetase and cyanophycinase, respectively. Both primary structures exhibited a high degree of similarity to the corresponding translational products from other cyanobacteria. Five regions were localized in the cyanophycin synthetase consensus sequence by

Elsayed Aboulmagd; Fred Bernd Oppermann-Sanio; Alexander Steinbüchel

2000-01-01

182

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

183

Engineering the Genotype of Acinetobacter sp. Strain ADP1 To Enhance Biosynthesis of Cyanophycin  

Microsoft Academic Search

To study the importance of arginine provision and phosphate limitation for synthesis and accumulation of cyanophycin (CGP) in Acinetobacter sp. strain ADP1, genes encoding the putative arginine regulatory protein (argR) and the arginine succinyltransferase (astA) were inactivated, and the effects of these mutations on CGP synthesis were analyzed. The inactivation of these genes resulted in a 3.5- or 7-fold increase

Yasser Elbahloul; Alexander Steinbuchel

2006-01-01

184

Draft Genome Sequence of Root-Colonizing Bacterium Bacillus sp. Strain PTS-394  

PubMed Central

Here, we report the high-quality draft genome sequence of Bacillus sp. strain PTS-394, isolated from the rhizosphere of tomatoes grown on Putuo Mountain (Xiamen, Fujian province, China), which exhibited excellent colonization ability on plant roots. The 4.0-Mb genome uncovered the mechanism for its potential root colonization ability and may provide novel insights into plant-bacterium interactions. PMID:24526631

Qiao, Junqing; Liang, Xuejie; Hu, Yonghong; Du, Yan

2014-01-01

185

Characterization of the Protocatechuic Acid Catabolic Gene Cluster from Streptomyces sp. Strain 2065  

Microsoft Academic Search

Protocatechuate 3,4-dioxygenase (EC 1.13.11.3) catalyzes the ring cleavage step in the catabolism of aro- matic compounds through the protocatechuate branch of the b-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 b- and a-subunits were obtained. PCR amplification was used for the cloning of the corresponding genes, and

SAKURA G. IWAGAMI; KEQIAN YANG; JULIAN DAVIES

2000-01-01

186

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. PMID:11004166

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

2000-01-01

187

Draft Genome Sequence of Plant Growth-Promoting Rhizobacterium Pantoea sp. Strain AS-PWVM4  

PubMed Central

Nonpathogenic Pantoea spp. have been shown to confer biofertilizer and biocontrol activities, indicating their potential for increasing crop yield. Herein, we provide the high-quality genome sequence of Pantoea sp. strain AS-PWVM4, a Gram-negative motile plant growth-promoting rhizobacterium isolated from a pomegranate plant. The 4.9-Mb genome contains genes related to plant growth promotion and the synthesis of siderophores. PMID:24309733

Khatri, Indu; Kaur, Sukhvir; Devi, Usha; Kumar, Navinder; Sharma, Deepak

2013-01-01

188

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. PMID:12231684

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

1993-01-01

189

Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2  

PubMed Central

In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated Klebsiella sp. strain BRL6-2 on minimal media with alkali lignin as the sole carbon source. This organism was isolated anaerobically from tropical forest soils collected from the Bisley watershed at the Ridge site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are characterized by cycles of iron oxidation and reduction. Genome sequencing was targeted because of its ability to grow on lignin anaerobically and lignocellulolytic activity via in vitro enzyme assays. The genome of Klebsiella sp. strain BRL6-2 is 5.80 Mbp with no detected plasmids, and includes a relatively small arsenal of genes encoding lignocellulolytic carbohydrate active enzymes. The genome revealed four putative peroxidases including glutathione and DyP-type peroxidases, and a complete protocatechuate pathway encoded in a single gene cluster. Physiological studies revealed Klebsiella sp. strain BRL6-2 to be relatively stress tolerant to high ionic strength conditions. It grows in increasing concentrations of ionic liquid (1-ethyl-3-methyl-imidazolium acetate) up to 73.44 mM and NaCl up to 1.5 M.

2014-01-01

190

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. PMID:15317781

Barragán, María J. López; Carmona, Manuel; Zamarro, María T.; Thiele, Bärbel; Boll, Matthias; Fuchs, Georg; García, José L.; Díaz, Eduardo

2004-01-01

191

(gyrB, alkB r) GEOBACILLUS  

E-print Network

(gyrB, alkB r) GEOBACILLUS 03.01.03 ­ ­ 2014 #12. .. ( , , 27, ) www.bio.msu.ru. . "___" 2014 . 2 , .. #12;3 . Geobacillus (, , 2004). - , . , . Geobacillus (Nazina et al., 2001) 19 , . 2010­2012 16S . (Aeribacillus

Kaplan, Alexander

192

Iron Corrosion Induced by Nonhydrogenotrophic Nitrate-Reducing Prolixibacter sp. Strain MIC1-1.  

PubMed

Microbiologically influenced corrosion (MIC) of metallic materials imposes a heavy economic burden. The mechanism of MIC of metallic iron (Fe(0)) under anaerobic conditions is usually explained as the consumption of cathodic hydrogen by hydrogenotrophic microorganisms that accelerates anodic Fe(0) oxidation. In this study, we describe Fe(0) corrosion induced by a nonhydrogenotrophic nitrate-reducing bacterium called MIC1-1, which was isolated from a crude-oil sample collected at an oil well in Akita, Japan. This strain requires specific electron donor-acceptor combinations and an organic carbon source to grow. For example, the strain grew anaerobically on nitrate as a sole electron acceptor with pyruvate as a carbon source and Fe(0) as the sole electron donor. In addition, ferrous ion and l-cysteine served as electron donors, whereas molecular hydrogen did not. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MIC1-1 was a member of the genus Prolixibacter in the order Bacteroidales. Thus, Prolixibacter sp. strain MIC1-1 is the first Fe(0)-corroding representative belonging to the phylum Bacteroidetes. Under anaerobic conditions, Prolixibacter sp. MIC1-1 corroded Fe(0) concomitantly with nitrate reduction, and the amount of iron dissolved by the strain was six times higher than that in an aseptic control. Scanning electron microscopy analyses revealed that microscopic crystals of FePO4 developed on the surface of the Fe(0) foils, and a layer of FeCO3 covered the FePO4 crystals. We propose that cells of Prolixibacter sp. MIC1-1 accept electrons directly from Fe(0) to reduce nitrate. PMID:25548048

Iino, Takao; Ito, Kimio; Wakai, Satoshi; Tsurumaru, Hirohito; Ohkuma, Moriya; Harayama, Shigeaki

2015-03-01

193

Dynamic Metabolic and Transcriptional Profiling of Rhodococcus sp. Strain YYL during the Degradation of Tetrahydrofuran  

PubMed Central

Although tetrahydrofuran-degrading Rhodococcus sp. strain YYL possesses tetrahydrofuran (THF) degradation genes similar to those of other tetrahydrofuran-degrading bacteria, a much higher degradation efficiency has been observed in strain YYL. In this study, nuclear magnetic resonance (NMR)-based metabolomics analyses were performed to explore the metabolic profiling response of strain YYL to exposure to THF. Exposure to THF slightly influenced the metabolome of strain YYL when yeast extract was present in the medium. The metabolic profile of strain YYL over time was also investigated using THF as the sole carbon source to identify the metabolites associated with high-efficiency THF degradation. Lactate, alanine, glutarate, glutamate, glutamine, succinate, lysine, trehalose, trimethylamine-N-oxide (TMAO), NAD+, and CTP were significantly altered over time in strain YYL grown in 20 mM THF. Real-time quantitative PCR (RT-qPCR) revealed changes in the transcriptional expression levels of 15 genes involved in THF degradation, suggesting that strain YYL could accumulate several disturbances in osmoregulation (trehalose, glutamate, glutamine, etc.), with reduced glycolysis levels, an accelerated tricarboxylic acid cycle, and enhanced protein synthesis. The findings obtained through 1H NMR metabolomics analyses and the transcriptional expression of the corresponding genes are complementary for exploring the dynamic metabolic profile in organisms. PMID:24532074

He, Zhixing; Yao, Yanlai

2014-01-01

194

Monooxygenase-mediated 1,2-dichloroethane degradation by Pseudomonas sp. strain DCA1  

SciTech Connect

A bacterial strain, designated Pseudomonas sp. strain DCA1, was isolated from a 1,2-dichloroethane (DCA)-degrading biofilm. Strain DCA1 utilizes DCA as the sole carbon and energy source and does not require additional organic nutrients, such as vitamins, for optimal growth. The affinity of strain DCA1 for DCA is very high, with a K{sub m} value below the detection limit of 0.5 {micro}M. Instead of a hydrolytic dehalogenation, as in other DCA utilizers, the first step in DCA degradation in strain DCA1 is an oxidation reaction. Oxygen and NAD(P)H are required for this initial step. Propene was converted to 1,2-epoxypropane by DCA-grown cells and competitively inhibited DCA degradation. The authors concluded that a monooxygenase is responsible for the first step in DCA degradation in strain DCA1. Oxidation of DCA probably results in the formation of the unstable intermediate 1,2-dichloroethanol, which spontaneously releases chloride, yielding chloroacetaldehyde. The DCA degradation pathway is strain DCA1 proceeds from chloroacetaldehyde via chloroacetic acid and presumably glycolic acid, which is similar to degradation routes observed in other DCA-utilizing bacteria.

Hage, J.C.; Hartmans, S. [Wageningen Univ. (Netherlands)

1999-06-01

195

Draft Genome Sequence of Paenibacillus sp. Strain MSt1 with Broad Antimicrobial Activity, Isolated from Malaysian Tropical Peat Swamp Soil  

PubMed Central

We report the draft genome sequence of Paenibacillus sp. strain MSt1, which has broad-range antimicrobial activity, isolated from tropical peat swamp soil. Genes involved in antimicrobial biosynthesis are found to be present in this genome. PMID:25301658

Ong, Kuan Shion; Yule, Catherine M.; Gan, Han Ming; Lee, Sui Mae

2014-01-01

196

Draft Genome Sequence of the Arsenite-Oxidizing Strain Aliihoeflea sp. 2WW, Isolated from Arsenic-Contaminated Groundwater  

PubMed Central

Here, we report the draft genome sequence of the arsenite-oxidizing bacterium Aliihoeflea sp. strain 2WW, which consists of a 4.15-Mb chromosome and contains different genes that are involved in arsenic transformations. PMID:24356838

Cavalca, Lucia; Corsini, Anna; Andreoni, Vincenza

2013-01-01

197

Augmentation of tribenuron methyl removal from polluted soil with Bacillus sp. strain BS2 and indigenous earthworms.  

PubMed

Tribenuron methyl (TBM) is a member of the sulfonylurea herbicide family and is widely used worldwide. In this study, TBM-degrading bacteria were enriched with TBM as potential carbon, nitrogen or sulfur source, and 44 bacterial isolates were obtained. These isolates were phylogenetically diverse, and were grouped into 25 operational taxonomic units and 14 currently known genera. Three representatives, Bacillus sp. strain BS2, Microbacterium sp. strain BS3, and Cellulosimicrobium sp. strain BS11, were selected, and their growth and TBM removal from culture broth were investigated. In addition, indigenous earthworms were collected and applied to augment TBM degradation in lab-scale soil column experiments. Results demonstrated that Bacillus sp. strain BS2 and earthworms significantly increased TBM removal during soil column experiments. PMID:23513692

Tang, Qiang; Zhao, Zhiping; Liu, Yajun; Wang, Nanxi; Wang, Baojun; Wang, Yanan; Zhou, Ningyi; Liu, Shuangjiang

2012-01-01

198

Novel Antiphytopathogenic Compound 2-Heptyl-5-Hexylfuran-3-Carboxylic Acid, Produced by Newly Isolated Pseudomonas sp. Strain SJT25 ?†  

PubMed Central

Pseudomonas sp. strain SJT25, which strongly antagonizes plant pathogens, was isolated from rice rhizosphere soil by a bioactivity-guided approach. A novel antiphytopathogenic compound was isolated from the fermentation broth of Pseudomonas sp. SJT25 and identified as 2-heptyl-5-hexylfuran-3-carboxylic acid. This compound showed antimicrobial activities both in vitro and in vivo. PMID:21742907

Wang, Xiao-Ying; Xu, Yu-Quan; Lin, Shuang-Jun; Liu, Zhen-Zhen; Zhong, Jian-Jiang

2011-01-01

199

Circadian Rhythm of Nitrogenase Gene Expression in the Diazotrophic Filamentous Nonheterocystous Cyanobacterium Trichodesmium sp. Strain IMS 101  

Microsoft Academic Search

Recent studies suggested that the daily cycle of nitrogen fixation activity in the marine filamentous nonhet- erocystous cyanobacterium Trichodesmium sp. is controlled by a circadian rhythm. In this study, we evaluated the rhythm of nitrogen fixation in Trichodesmium sp. strain IMS 101 by using the three criteria for an endogenous rhythm. Nitrogenase transcript abundance oscillated with a period of approximately

YI-BU CHEN; BENNY DOMINIC; MARK T. MELLON; JONATHAN P. ZEHR

1998-01-01

200

Draft Genome Sequence of a Quorum-Sensing Bacterium, Dickeya sp. Strain 2B12, Isolated from a Freshwater Lake.  

PubMed

Dickeya sp. strain 2B12 was isolated from a freshwater lake in Malaysia. Here, we report the draft genome sequence of Dickeya sp. 2B12 sequenced by the Illumina MiSeq platform. With the genome sequence available, this genome sequence will be useful for the study of quorum-sensing activity in this isolate. PMID:25657288

Tan, Kian-Hin; Sheng, Kit-Yeng; Chang, Chien-Yi; Yin, Wai-Fong; Chan, Kok-Gan

2015-01-01

201

Draft Genome Sequence of Pedobacter sp. Strain V48, Isolated from a Coastal Sand Dune in the Netherlands.  

PubMed

Pedobacter sp. strain V48 participates in an interaction with Pseudomonas fluorescens which elicits interaction-induced phenotypes. We report the draft genome sequence of Pedobacter sp. V48, consisting of 6.46 Mbp. The sequence will contribute to improved understanding of the genus and facilitate genomic analysis of the model interspecies interaction with P. fluorescens. PMID:24578271

Bitzer, Adam S; Garbeva, Paolina; Silby, Mark W

2014-01-01

202

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

203

Draft Genome Sequence of the Microbispora sp. Strain ATCC-PTA-5024, Producing the Lantibiotic NAI-107.  

PubMed

We report the draft genome sequence of Microbispora sp. strain ATCC-PTA-5024, a soil isolate that produces NAI-107, a new lantibiotic with the potential to treat life-threatening infections caused by multidrug-resistant Gram-positive pathogens. The draft genome of strain Microbispora sp. ATCC-PTA-5024 consists of 8,543,819 bp, with a 71.2% G+C content and 7,860 protein-coding genes. PMID:24459268

Sosio, Margherita; Gallo, Giuseppe; Pozzi, Roberta; Serina, Stefania; Monciardini, Paolo; Bera, Agnieska; Stegmann, Evi; Weber, Tilmann

2014-01-01

204

Evaluation of insecticidal activity of a bacterial strain, Serratia sp. EML-SE1 against diamondback moth  

Microsoft Academic Search

To identify novel bioinsecticidal agents, a bacterial strain, Serratia sp. EML-SE1, was isolated from a dead larva of the lepidopteran diamondback moth (Plutella xylostella) collected from a cabbage field in Korea. In this study, the insecticidal activity of liquid cultures in Luria-Bertani broth\\u000a (LBB) and nutrient broth (NB) of a bacterial strain, Serratia sp. EML-SE1 against thirty 3rd and 4th

Hyung Uk Jeong; Hye Yeon Mun; Hyung Keun Oh; Seung Bum Kim; Kwang Yeol Yang; Iksoo Kim; Hyang Burm Lee

2010-01-01

205

Degradation of Chlorinated Dibenzofurans and Dibenzo-p-Dioxins by Sphingomonas sp. Strain RW1  

PubMed Central

The ability of the dibenzofuran- and dibenzo-p-dioxin-mineralizing bacterium Sphingomonas sp. strain RW1 (R.-M. Wittich, H. Wilkes, V. Sinnwell, W. Francke, and P. Fortnagel, Appl. Environ. Microbiol. 58:1005-1010, 1992) to oxidize chlorinated derivatives of dibenzofuran and dibenzo-p-dioxin was analyzed. Strain RW1 degraded several mono- and dichlorinated dibenzofurans and dibenzo-p-dioxins, but it did not degrade more highly chlorinated congeners. Most mono- and dichlorinated dibenzofurans and dibenzo-p-dioxins investigated in this study were degraded to the corresponding mono- and dichlorinated salicylates and catechols, respectively, together with salicylate and catechol. This indicates an initial dioxygenolytic attack on the substituted as well as on the nonsubstituted aromatic nucleus of most of the target compounds. Strain RW1 could not grow at the expense of monochlorinated dibenzo-p-dioxins and dibenzofurans as carbon sources, with the exception of 4-chlorodibenzofuran, which was stoichiometrically converted to 3-chlorosalicylate. PMID:16535225

Wilkes, H.; Wittich, R.; Timmis, K. N.; Fortnagel, P.; Francke, W.

1996-01-01

206

The sll1951 Gene Encodes the Surface Layer Protein of Synechocystis sp. Strain PCC 6803  

PubMed Central

Sll1951 is the surface layer (S-layer) protein of the cyanobacterium Synechocystis sp. strain PCC 6803. This large, hemolysin-like protein was found in the supernatant of a strain that was deficient in S-layer attachment. An sll1951 deletion mutation was introduced into Synechocystis and was easily segregated to homozygosity under laboratory conditions. By thin-section and negative-stain transmission electron microscopy, a ?30-nm-wide S-layer lattice covering the cell surface was readily visible in wild-type cells but was absent in the ?sll1951 strain. Instead, the ?sll1951 strain displayed a smooth lipopolysaccharide surface as its most peripheral layer. In the presence of chaotropic agents, the wild type released a large (>150-kDa) protein into the medium that was identified as Sll1951 by mass spectrometry of trypsin fragments; this protein was missing in the ?sll1951 strain. In addition, Sll1951 was prominent in crude extracts of the wild type, indicating that it is an abundant protein. The carotenoid composition of the cell wall fraction of the ?sll1951 strain was similar to that of the wild type, suggesting that the S-layer does not contribute to carotenoid binding. Although the photoautotrophic growth rate of the ?sll1951 strain was similar to that of the wild-type strain, the viability of the ?sll1951 strain was reduced upon exposure to lysozyme treatment and hypo-osmotic stress, indicating a contribution of the S-layer to the integrity of the Synechocystis cell wall. This work identifies the S-layer protein in Synechocystis and shows that, at least under laboratory conditions, this very abundant, large protein has a supportive but not a critical role in the function of the cyanobacterium. PMID:24078613

Trautner, Christoph

2013-01-01

207

Survival of the anaerobic fungus Orpinomyces sp. strain C1A after prolonged air exposure  

PubMed Central

Anaerobic fungi are efficient plant biomass degraders and represent promising agents for a variety of biotechnological applications. We evaluated the tolerance of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, to air exposure in liquid media using soluble (cellobiose) and insoluble (dried switchgrass) substrates. Strain C1A grown on cellobiose survived for 11, and 13.5?hours following air exposure when grown under planktonic, and immobilized conditions, respectively. When grown on switchgrass media, strain C1A exhibited significantly enhanced air tolerance and survived for 168?hours. The genome of strain C1A lacked a catalase gene, but contained superoxide dismutase and glutathione peroxidase genes. Real time PCR analysis indicated that superoxide dismutase, but not glutathione peroxidase, exhibits a transient increase in expression level post aeration. Interestingly, the C1A superoxide dismutase gene of strain C1A appears to be most closely related to bacterial SODs, which implies its acquisition from a bacterial donor via cross kingdom horizontal gene transfer during Neocallimastigomycota evolution. We conclude that strain C1A utilizes multiple mechanisms to minimize the deleterious effects of air exposure such as physical protection and the production of oxidative stress enzymes. PMID:25367149

Struchtemeyer, Christopher G.; Ranganathan, Abhaya; Couger, M. B.; Liggenstoffer, Audra S.; Youssef, Noha H.; Elshahed, Mostafa S.

2014-01-01

208

Survival of the anaerobic fungus Orpinomyces sp. strain C1A after prolonged air exposure.  

PubMed

Anaerobic fungi are efficient plant biomass degraders and represent promising agents for a variety of biotechnological applications. We evaluated the tolerance of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, to air exposure in liquid media using soluble (cellobiose) and insoluble (dried switchgrass) substrates. Strain C1A grown on cellobiose survived for 11, and 13.5 hours following air exposure when grown under planktonic, and immobilized conditions, respectively. When grown on switchgrass media, strain C1A exhibited significantly enhanced air tolerance and survived for 168 hours. The genome of strain C1A lacked a catalase gene, but contained superoxide dismutase and glutathione peroxidase genes. Real time PCR analysis indicated that superoxide dismutase, but not glutathione peroxidase, exhibits a transient increase in expression level post aeration. Interestingly, the C1A superoxide dismutase gene of strain C1A appears to be most closely related to bacterial SODs, which implies its acquisition from a bacterial donor via cross kingdom horizontal gene transfer during Neocallimastigomycota evolution. We conclude that strain C1A utilizes multiple mechanisms to minimize the deleterious effects of air exposure such as physical protection and the production of oxidative stress enzymes. PMID:25367149

Struchtemeyer, Christopher G; Ranganathan, Abhaya; Couger, M B; Liggenstoffer, Audra S; Youssef, Noha H; Elshahed, Mostafa S

2014-01-01

209

Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae  

PubMed Central

Here we present the draft genome of Tatumella sp. strain UCD-D_suzukii, the first member of this genus to be sequenced. The genome contains 3,602,931 bp in 72 scaffolds. This strain was isolated from Drosophila suzukii larvae as part of a larger project to study the microbiota of D. suzukii. PMID:24762940

Dunitz, Madison I.; James, Pamela M.; Jospin, Guillaume; Coil, David A.; Chandler, James Angus

2014-01-01

210

Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae.  

PubMed

Here we present the draft genome of Tatumella sp. strain UCD-D_suzukii, the first member of this genus to be sequenced. The genome contains 3,602,931 bp in 72 scaffolds. This strain was isolated from Drosophila suzukii larvae as part of a larger project to study the microbiota of D. suzukii. PMID:24762940

Dunitz, Madison I; James, Pamela M; Jospin, Guillaume; Eisen, Jonathan A; Coil, David A; Chandler, James Angus

2014-01-01

211

Draft Genome Sequence of Sulfurospirillum sp. Strain MES, Reconstructed from the Metagenome of a Microbial Electrosynthesis System  

PubMed Central

A draft genome of Sulfurospirillum sp. strain MES was isolated through taxonomic binning of a metagenome sequenced from a microbial electrosynthesis system (MES) actively producing acetate and hydrogen. The genome contains the nosZDFLY genes, which are involved in nitrous oxide reduction, suggesting the potential role of this strain in denitrification. PMID:25593246

Marshall, Christopher W.; May, Harold D.

2015-01-01

212

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

PubMed Central

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.

2013-01-01

213

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

2013-01-01

214

Draft Genome Sequence of the Cellulolytic Bacterium Clavibacter sp. CF11, a Strain Producing Cold-Active Cellulase  

PubMed Central

Clavibacter sp. strain CF11, which was isolated from soil at a tomato-planting greenhouse in Inner Mongolia, North China, has a high capability for producing cold-active cellulase at low temperatures. Here, we report the draft genome sequence of strain CF11, which comprises 2,437 protein-coding sequences and 49 RNA-coding sequences. PMID:25555737

Yuan, Bo; Zeng, Yonghui; Meng, Jianyu; Li, Heng; Li, Guojing

2015-01-01

215

Draft Genome Sequence of the Cellulolytic Bacterium Clavibacter sp. CF11, a Strain Producing Cold-Active Cellulase.  

PubMed

Clavibacter sp. strain CF11, which was isolated from soil at a tomato-planting greenhouse in Inner Mongolia, North China, has a high capability for producing cold-active cellulase at low temperatures. Here, we report the draft genome sequence of strain CF11, which comprises 2,437 protein-coding sequences and 49 RNA-coding sequences. PMID:25555737

Du, Ying; Yuan, Bo; Zeng, Yonghui; Meng, Jianyu; Li, Heng; Wang, Ruigang; Li, Guojing; Feng, Fuying

2015-01-01

216

Whole-Genome Sequence of Burkholderia sp. Strain RPE67, a Bacterial Gut Symbiont of the Bean Bug Riptortus pedestris  

PubMed Central

Burkholderia sp. strain RPE67 is a bacterial symbiont isolated from a field-collected bean bug, Riptortus pedestris. To understand the genetic basis of the insect-microbe symbiosis, we performed whole-genome sequencing of the Burkholderia strain, revealing an 8.69-Mb genome consisting of three chromosomes and three plasmids. PMID:24948758

Takeshita, Kazutaka; Shibata, Tomoko F.; Nikoh, Naruo; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Fukatsu, Takema; Shigenobu, Shuji

2014-01-01

217

Genome Sequence of Martelella sp. Strain AD-3, a Moderately Halophilic Polycyclic Aromatic Hydrocarbon-Degrading Bacterium  

PubMed Central

Martelella sp. strain AD-3, enriched from a petroleum-contaminated site with high salinity, can efficiently degrade polycyclic aromatic hydrocarbons. Here, we report the 4.75-Mb genome sequence of strain AD-3 with its genetic feature of helping to remediate environmental organic pollutants. PMID:24435873

Cui, Changzheng; Li, Pengpeng; Liu, Gao; Lin, Kuangfei; Luo, Qishi; Liu, Shanshan; Xu, Ping

2014-01-01

218

Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1  

PubMed Central

Mycobacterium sp.Spyr1 is a newly isolated strain that occurs in a creosote contaminated site in Greece. It was isolated by an enrichment method using pyrene as sole carbon and energy source and is capable of degrading a wide range of PAH substrates including pyrene, fluoranthene, fluorene, anthracene and acenapthene. Here we describe the genomic features of this organism, together with the complete sequence and annotation. The genome consists of a 5,547,747 bp chromosome and two plasmids, a larger and a smaller one with sizes of 211,864 and 23,681 bp, respectively. In total, 5,588 genes were predicted and annotated. PMID:22180818

Kallimanis, Aristeidis; Karabika, Eugenia; Mavromatis, Kostantinos; Lapidus, Alla; LaButti, Kurt M.; Liolios, Konstantinos; Ivanova, Natalia; Goodwin, Lynne; Woyke, Tanja; Velentzas, Athanasios D.; Perisynakis, Angelos; Ouzounis, Christos C.; Kyrpides, Nikos C.; Koukkou, Anna I.; Drainas, Constantin

2011-01-01

219

Two New Antibiotic Pyridones Produced by a Marine Fungus, Trichoderma sp. Strain MF106  

PubMed Central

Two unusual pyridones, trichodin A (1) and trichodin B (2), together with the known compound, pyridoxatin (3), were extracted from mycelia and culture broth of the marine fungus, Trichoderma sp. strain MF106 isolated from the Greenland Seas. The structures of the new compounds were characterized as an intramolecular cyclization of a pyridine basic backbone with a phenyl group. The structure and relative configuration of the new compounds were established by spectroscopic means. The new compound 1 and the known compound 3 showed antibiotic activities against the clinically relevant microorganism, Staphylococcus epidermidis, with IC50 values of 24 ?M and 4 ?M, respectively. PMID:24663111

Wu, Bin; Oesker, Vanessa; Wiese, Jutta; Schmaljohann, Rolf; Imhoff, Johannes F.

2014-01-01

220

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 PMID:6417112

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

1983-01-01

221

Enhanced phenol degradation by immobilized Acinetobacter sp. strain AQ5NOL 1  

Microsoft Academic Search

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\\u000a phenol degradation was achieved at gellan gum concentration of 0.75% (w\\/v), bead size of 3 mm diameter (estimated surface\\u000a area of 28.26 mm2) and bead number of 300 per 100 ml medium. At phenol concentration of 100 mg l?1,

Siti Aqlima Ahmad; Nor Aripin Shamaan; Noorliza Mat Arif; Gan Bee Koon; Mohd Yunus Abdul Shukor; Mohd Arif Syed

222

Cometabolic Degradation of Dibenzofuran by Biphenyl-Cultivated Ralstonia sp. Strain SBUG 290  

Microsoft Academic Search

Cells of the gram-negative bacterium Ralstonia sp. strain SBUG 290 grown in the presence of biphenyl are able to cooxidize dibenzofuran which has been 1,2-hydroxylated. Meta cleavage of the 1,2-dihydroxydibenzo- furan between carbon atoms 1 and 9b produced 2-hydroxy-4-(3*-oxo-3*H-benzofuran-2*-yliden)but-2-enoic acid, which was degraded completely via salicylic acid. The presence of these intermediates indicates a degradation mechanism for dibenzofuran via lateral

DORTE BECHER; MICHAEL SPECHT; ELKE HAMMER; WITTKO FRANCKE; FRIEDER SCHAUER

2000-01-01

223

Effect of pesticides on plant growth promoting traits of greengram-symbiont, Bradyrhizobium sp. strain MRM6.  

PubMed

The aim of this study was to investigate the toxicity of herbicides (metribuzin and glyphosate), insecticides (imidacloprid and thiamethoxam) and fungicides (hexaconazole, metalaxyl and kitazin) at the recommended and the higher dose rates on plant 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 was observed in plant growth promoting traits of the strain MRM6 apart from exo-polysaccharides which increased consistently on increasing pesticide concentrations. Generally, the highest toxicity to plant growth promoting characteristics of the Bradyrhizobium sp. strain MRM6 was observed when the strain MRM6 was grown with three times the recommended field rates of glyphosate, imidacloprid and hexaconazole. PMID:21359648

Ahemad, Munees; Khan, Mohammad Saghir

2011-04-01

224

Endophytic Colonization of Vitis vinifera L. by Plant Growth-Promoting Bacterium Burkholderia sp. Strain PsJN  

Microsoft Academic Search

Patterns of colonization of Vitis vinifera L. cv. Chardonnay plantlets by a plant growth-promoting bacterium, Burkholderia sp. strain PsJN, were studied under gnotobiotic conditions. Wild-type strain PsJN and genetically engineered derivatives of this strain tagged with gfp (PsJN::gfp2x) or gusA (PsJN::gusA11) genes were used to enumerate and visualize tissue colonization. The rhizospheres of 4- to 5-week-old plantlets with five developed

Stephane Compant; Birgit Reiter; Angela Sessitsch; Jerzy Nowak; Christophe Clement; E. Ait Barka

2005-01-01

225

Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana Trench  

Microsoft Academic Search

The thermophilic strains HTA426 and HTA462 isolated from the Mariana Trench were identified as Geobacillus kaustophilus and G. stearothermophilus, respectively, based on physiologic and phylogenetic analyses using 16S rDNA sequences and DNA–DNA relatedness. The genome size of HTA426 and HTA462 was estimated at 3.23–3.49 Mb and 3.7–4.49 Mb, respectively. The nucleotide sequences of three independent ?-phage inserts of G. stearothermophilus HTA462

Hideto Takami; Shinro Nishi; Jei Lu; Shigeru Shimamura; Yoshihiro Takaki

2004-01-01

226

Enzymatic transglycosylation of natural and modified nucleosides by immobilized thermostable nucleoside phosphorylases from Geobacillus stearothermophilus  

Microsoft Academic Search

Natural and modified purine nucleosides have been synthesized using the recombinant thermostable enzymes purine nucleoside\\u000a phosphorylase II (E. C. 2.4.2.1) and pyrimidine nucleoside phosphorylase (E. C. 2.4.2.2) from Geobacillus stearothermophilus B-2194. The enzymes were produced in recombinant E. coli strains and covalently immobilized on aminopropylsilochrom AP-CPG-170 after heating the cell lysates and the removal of coagulated\\u000a thermolabile proteins. The resulting

S. A. Taran; K. N. Verevkina; S. A. Feofanov; A. I. Miroshnikov

2009-01-01

227

Oxidation of substituted phenols by Pseudomonas putida F1 and Pseudomonas sp. strain JS6.  

PubMed Central

The biodegradation of benzene, toluene, and chlorobenzenes by Pseudomonas putida involves the initial conversion of the parent molecules to cis-dihydrodiols by dioxygenase enzyme systems. The cis-dihydrodiols are then converted to the corresponding catechols by dihydrodiol dehydrogenase enzymes. Pseudomonas sp. strain JS6 uses a similar system for growth on toluene or dichlorobenzenes. We tested the wild-type organisms and a series of mutants for their ability to transform substituted phenols after induction with toluene. When grown on toluene, both wild-type organisms converted methyl-, chloro-, and nitro-substituted phenols to the corresponding catechols. Mutant strains deficient in dihydrodiol dehydrogenase or catechol oxygenase activities also transformed the phenols. Oxidation of phenols was closely correlated with the induction and activity of the toluene dioxygenase enzyme system. PMID:3415220

Spain, J C; Gibson, D T

1988-01-01

228

Isolation and characterization of a Pseudomonas sp. strain PH1 utilizing meta-aminophenol.  

PubMed

Pseudomonas sp. strain PH1 was isolated from soil contaminated with pharmaceutical and dye industry waste. The isolate PH1 could use m-aminophenol as a sole source of carbon, nitrogen, and energy to support the growth. PH1 could degrade up to 0.32 mM m-aminophenol in 120 h, when provided as nitrogen source at 0.4 mM concentration with citrate (0.5 mM) as a carbon source in the growth medium. The presence of ammonium chloride as an additional nitrogen source repressed the degradation of m-aminophenol by PH1. To identify strain PH1, the 16S rDNA sequence was amplified by PCR using conserved eubacterial primers. The FASTA program was used to analyze the 16S rDNA sequence and the resulting homology patterns suggested that PH1 is a Pseudomonas. PMID:10749534

Kutty, R; Purohit, H J; Khanna, P

2000-03-01

229

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. PMID:10572142

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

1999-01-01

230

Glycogen production for biofuels by the euryhaline cyanobacteria Synechococcus sp. strain PCC 7002 from an oceanic environment  

PubMed Central

Background Oxygenic photosynthetic microorganisms such as cyanobacteria and microalgae have attracted attention as an alternative carbon source for the next generation of biofuels. Glycogen abundantly accumulated in cyanobacteria is a promising feedstock which can be converted to ethanol through saccharification and fermentation processes. In addition, the utilization of marine cyanobacteria as a glycogen producer can eliminate the need for a freshwater supply. Synechococcus sp. strain PCC 7002 is a fast-growing marine coastal euryhaline cyanobacteria, however, the glycogen yield has not yet been determined. In the present study, the effects of light intensity, CO2 concentration, and salinity on the cell growth and glycogen content were investigated in order to maximize glycogen production in Synechococcus sp. strain PCC 7002. Results The optimal culture conditions for glycogen production in Synechococcus sp. strain PCC 7002 were investigated. The maximum glycogen production of 3.5 g L?1 for 7 days (a glycogen productivity of 0.5 g L?1 d?1) was obtained under a high light intensity, a high CO2 level, and a nitrogen-depleted condition in brackish water. The glycogen production performance in Synechococcus sp. strain PCC 7002 was the best ever reported in the ?-polyglucan (glycogen or starch) production of cyanobacteria and microalgae. In addition, the robustness of glycogen production in Synechococcus sp. strain PCC 7002 to salinity was evaluated in seawater and freshwater. The peak of glycogen production of Synechococcus sp. strain PCC 7002 in seawater and freshwater were 3.0 and 1.8 g L?1 in 7 days, respectively. Glycogen production in Synechococcus sp. strain PCC 7002 maintained the same level in seawater and half of the level in freshwater compared with the optimal result obtained in brackish water. Conclusions We conclude that Synechococcus sp. strain PCC 7002 has high glycogen production activity and glycogen can be provided from coastal water accompanied by a fluctuation of salinity. This work supports Synechococcus sp. strain PCC 7002 as a promising carbohydrate source for biofuel production. PMID:24959200

2014-01-01

231

Response of Nitrosospira sp. Strain AF-Like Ammonia Oxidizers to Changes in Temperature, Soil Moisture Content, and Fertilizer Concentration?  

PubMed Central

Very little is known regarding the ecology of Nitrosospira sp. strain AF-like bacteria, a unique group of ammonia oxidizers within the Betaproteobacteria. We studied the response of Nitrosospira sp. strain AF-like ammonia oxidizers to changing environmental conditions by applying molecular methods and physiological measurements to Californian grassland soil manipulated in the laboratory. This soil is naturally high in Nitrosospira sp. strain AF-like bacteria relative to the much-better-studied Nitrosospira multiformis-like ammonia-oxidizing bacteria. Increases in temperature, soil moisture, and fertilizer interacted to reduce the relative abundance of Nitrosospira sp. strain AF-like bacteria, although they remained numerically dominant. The overall abundance of ammonia-oxidizing bacteria increased with increasing soil moisture and decreased with increasing temperature. Potential nitrification activity was altered by interactions among temperature, soil moisture, and fertilizer, with activity tending to be higher when soil moisture and temperature were increased. The increase in potential nitrification activity with increased temperature was surprising, given that the overall abundance of ammonia-oxidizing bacteria decreased significantly under these conditions. This observation suggests that (i) Nitrosospira sp. strain AF-like bacteria may respond to increased temperature with an increase in activity, despite a decrease in abundance, or (ii) that potential nitrification activity in these soils may be due to organisms other than bacteria (e.g., archaeal ammonia oxidizers), at least under conditions of increased temperature. PMID:17158615

Avrahami, Sharon; Bohannan, Brendan J. M.

2007-01-01

232

Metabolism of Dibenzofuran by Pseudomonas sp. Strain HH69 and the Mixed Culture HH27  

PubMed Central

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 (chromone), several 2-substituted chroman-4-ones, and traces of the four isomeric monohydroxydiben-zofurans were identified in the culture medium. 2,2?,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?,3-trihydroxybiphenyl is suggested as the next enzymatic step in the degradative pathway. PMID:16348159

Fortnagel, Peter; Harms, Hauke; Wittich, Rolf-Michael; Krohn, Sabine; Meyer, Holger; Sinnwell, Volker; Wilkes, Heinz; Francke, Wittko

1990-01-01

233

Biodegradation of triazine herbicide metribuzin by the strain Bacillus sp. N1.  

PubMed

By enrichment culturing of soil contaminated with metribuzin, a highly efficient metribuzin degrading bacterium, Bacillus sp. N1, was isolated. This strain grows using metribuzin at 5.0% (v/v) as the sole nitrogen source in a liquid medium. Optimal metribuzin degradation occurred at a temperature of 30ºC and at pH 7.0. With an initial concentration of 20 mg L(-1), the degradation rate was 73.5% in 120 h. If the initial concentrations were higher than 50 mg L(-1), the biodegradation rates decreased as the metribuzin concentrations increased. When the concentration was 100 mg L(-1), the degradation rate was only 45%. Degradation followed the pesticide degradation kinetic equation at initial concentrations between 5 mg L(-1) and 50 mg L(-1). When the metribuzin contaminated soil was mixed with strain N1 (with the concentration of metribuzin being 20 mg L(-1) and the inoculation rate of 10(11) g(-1) dry soil), the degradation rate of the metribuzin was 66.4% in 30 days, while the degradation rate of metribuzin was only 19.4% in the control soil without the strain N1. These results indicate that the strain N1 can significantly increase the degradation rate of metribuzin in contaminated soil. PMID:24328539

Zhang, Hao; Zhang, Yubin; Hou, Zhiguang; Wu, Xian; Gao, Henan; Sun, Fengjie; Pan, Hongyu

2014-01-01

234

Karyotype rearrangements and telomere analysis in Myzus persicae (Hemiptera, Aphididae) strains collected on Lavandula sp. plants  

PubMed Central

Abstract Karyotype analysis of nine strains of the peach-potato aphid Myzus persicae (Sulzer, 1776), collected on Lavandula sp. plants, evidenced showed that five of them had a standard 2n = 12 karyotype, one possessed a fragmentation of the X chromosome occurring at the telomere opposite to the NOR-bearing one and three strains had a chromosome number 2n = 11 due to a non-reciprocal translocation of an autosome A3 onto an A1 chromosome. Interestingly, the terminal portion of the autosome A1 involved in the translocation was the same in all the three strains, as evidenced by FISH with the histone cluster as a probe. The study of telomeres in the Myzus persicae strain with the X fission evidenced that telomerase synthesised de novo telomeres at the breakpoints resulting in the stabilization of the chromosomal fragments. Lastly, despite the presence of a conserved telomerase, aphid genome is devoid of genes coding for shelterin, a complex of proteins involved in telomere functioning frequently reported as conserved in eukaryotes. The absence of this complex, also confirmed in the genome of other arthropods, suggests that the shift in the sequence of the telomeric repeats has been accompanied by other changes in the telomere components in arthropods in respect to other metazoans. PMID:25610541

Mandrioli, Mauro; Zanasi, Federica; Manicardi, Gian Carlo

2014-01-01

235

Large-scale bioreactor production of the herbicide-degrading Aminobacter sp. strain MSH1.  

PubMed

The Aminobacter sp. strain MSH1 has potential for pesticide bioremediation because it degrades the herbicide metabolite 2,6-dichlorobenzamide (BAM). Production of the BAM-degrading bacterium using aerobic bioreactor fermentation was investigated. A mineral salt medium limited for carbon and with an element composition similar to the strain was generated. The optimal pH and temperature for strain growth were determined using shaker flasks and verified in bioreactors. Glucose, fructose, and glycerol were suitable carbon sources for MSH1 (??=?0.1 h(-1)); slower growth was observed on succinate and acetic acid (??=?0.01 h(-1)). Standard conditions for growth of the MSH1 strain were defined at pH 7 and 25 °C, with glucose as the carbon source. In bioreactors (1 and 5 L), the specific growth rate of MSH1 increased from ??=?0.1 h(-1) on traditional mineral salt medium to ??=?0.18 h(-1) on the optimized mineral salt medium. The biomass yield under standard conditions was 0.47 g dry weight biomass/g glucose consumed. An investigation of the catabolic capacity of MSH1 cells harvested in exponential and stationary growth phases showed a degradation activity per cell of about 3?×?10(-9) ?g BAM h(-1). Thus, fast, efficient, large-scale production of herbicide-degrading Aminobacter was possible, bringing the use of this bacterium in bioaugmentation field remediation closer to reality. PMID:24562459

Schultz-Jensen, Nadja; Knudsen, Berith E; Frkova, Zuzana; Aamand, Jens; Johansen, Tina; Thykaer, Jette; Sørensen, Sebastian R

2014-03-01

236

Composition of the carbohydrate granules of the cyanobacterium, Cyanothece sp. strain ATCC 51142  

NASA Technical Reports Server (NTRS)

Cyanothece sp. strain ATCC 51142 is an aerobic, unicellular, diazotrophic cyanobacterium that temporally separates O2-sensitive N2 fixation from oxygenic photosynthesis. The energy and reducing power needed for N2 fixation appears to be generated by an active respiratory apparatus that utilizes the contents of large interthylakoidal carbohydrate granules. We report here on the carbohydrate and protein composition of the granules of Cyanothece sp. strain ATCC 51142. The carbohydrate component is a glucose homopolymer with branches every nine residues and is chemically identical to glycogen. Granule-associated protein fractions showed temporal changes in the number of proteins and their abundance during the metabolic oscillations observed under diazotrophic conditions. There also were temporal changes in the protein pattern of the granule-depleted supernatant fractions from diazotrophic cultures. None of the granule-associated proteins crossreacted with antisera directed against several glycogen-metabolizing enzymes or nitrogenase, although these proteins were tentatively identified in supernatant fractions. It is suggested that the granule-associated proteins are structural proteins required to maintain a complex granule architecture.

Schneegurt, M. A.; Sherman, D. M.; Sherman, L. A.; Mitchell, C. A. (Principal Investigator)

1997-01-01

237

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

PubMed Central

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

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

2014-01-01

238

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. PMID:1575472

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

1992-01-01

239

Plasmid Localization and Organization of Melamine Degradation Genes in Rhodococcus sp. Strain Mel  

PubMed Central

Rhodococcus sp. strain Mel was isolated from soil by enrichment and grew in minimal medium with melamine as the sole N source with a doubling time of 3.5 h. Stoichiometry studies showed that all six nitrogen atoms of melamine were assimilated. The genome was sequenced by Roche 454 pyrosequencing to 13× coverage, and a 22.3-kb DNA region was found to contain a homolog to the melamine deaminase gene trzA. Mutagenesis studies showed that the cyanuric acid hydrolase and biuret hydrolase genes were clustered together on a different 17.9-kb contig. Curing and gene transfer studies indicated that 4 of 6 genes required for the complete degradation of melamine were located on an ?265-kb self-transmissible linear plasmid (pMel2), but this plasmid was not required for ammeline deamination. The Rhodococcus sp. strain Mel melamine metabolic pathway genes were located in at least three noncontiguous regions of the genome, and the plasmid-borne genes encoding enzymes for melamine metabolism were likely recently acquired. PMID:22210223

Dodge, Anthony G.; Wackett, Lawrence P.

2012-01-01

240

Characterization of the Gene Cluster Involved in Isoprene Metabolism in Rhodococcus sp. Strain AD45  

PubMed Central

The genes involved in isoprene (2-methyl-1,3-butadiene) utilization in Rhodococcus sp. strain AD45 were cloned and characterized. Sequence analysis of an 8.5-kb DNA fragment showed the presence of 10 genes of which 2 encoded enzymes which were previously found to be involved in isoprene degradation: a glutathione S-transferase with activity towards 1,2-epoxy-2-methyl-3-butene (isoI) and a 1-hydroxy-2-glutathionyl-2-methyl-3-butene dehydrogenase (isoH). Furthermore, a gene encoding a second glutathione S-transferase was identified (isoJ). The isoJ gene was overexpressed in Escherichia coli and was found to have activity with 1-chloro-2,4-dinitrobenzene and 3,4-dichloro-1-nitrobenzene but not with 1,2-epoxy-2-methyl-3-butene. Downstream of isoJ, six genes (isoABCDEF) were found; these genes encoded a putative alkene monooxygenase that showed high similarity to components of the alkene monooxygenase from Xanthobacter sp. strain Py2 and other multicomponent monooxygenases. The deduced amino acid sequence encoded by an additional gene (isoG) showed significant similarity with that of ?-methylacyl-coenzyme A racemase. The results are in agreement with a catabolic route for isoprene involving epoxidation by a monooxygenase, conjugation to glutathione, and oxidation of the hydroxyl group to a carboxylate. Metabolism may proceed by fatty acid oxidation after removal of glutathione by a still-unknown mechanism. PMID:10715003

van Hylckama Vlieg, Johan E. T.; Leemhuis, Hans; Spelberg, Jeffrey H. Lutje; Janssen, Dick B.

2000-01-01

241

Host range susceptibility of Enterococcus sp. strains isolated from diseased turbot: possible routes of infection.  

PubMed Central

Experiments were conducted to assess the pathogenicity of Enterococcus sp. strains isolated from diseased turbot for several fish species (turbot, salmon, trout, and seabream), as well as for mice. The intraperitoneal injection assays indicated that the tested strains showed host specificity for turbot, with a high degree of virulence (50% lethal dose of 10(4) cells per g of fish). The Spanish Enterococcus sp. isolates were nonpathogenic for the other fish species studied and for mice. The possible routes of infection were determined by bath exposure (with and without prior abrasion of the skin) and by intragastric inoculations with food and feces contaminated with the pathogen. The bath challenges indicated that the Enterococcus isolates were able to overcome the defense mechanisms present on the surface of the turbot only if the skin was abraded prior to the exposure. The antibacterial activities of components of a glycoprotein nature present in the turbot skin mucus are probably responsible in part for the resistance in noninjured fish to infection. On the other hand, we demonstrated the capacity of this pathogen to overcome adverse conditions in the stomachs of fish when associated with food or fecal material, since it is able to establish an infective state and to produce mortalities after 16 to 20 days postingestion. From all of these findings, we can conclude that horizontal transmissions through water and the fecal-oral route are the main avenues of infection of turbot streptococcosis. PMID:8593061

Romalde, J L; Magariños, B; Nuñez, S; Barja, J L; Toranzo, A E

1996-01-01

242

Rapid Aggregation of Biofuel-Producing Algae by the Bacterium Bacillus sp. Strain RP1137  

PubMed Central

Algal biofuels represent one of the most promising means of sustainably replacing liquid fuels. However, significant challenges remain before alga-based fuels become competitive with fossil fuels. One of the largest challenges is the ability to harvest the algae in an economical and low-energy manner. In this article, we describe the isolation of a bacterial strain, Bacillus sp. strain RP1137, which can rapidly aggregate several algae that are candidates for biofuel production, including a Nannochloropsis sp. This bacterium aggregates algae in a pH-dependent and reversible manner and retains its aggregation ability after paraformaldehyde fixation, opening the possibility for reuse of the cells. The optimal ratio of bacteria to algae is described, as is the robustness of aggregation at different salinities and temperatures. Aggregation is dependent on the presence of calcium or magnesium ions. The efficiency of aggregation of Nannochloropsis oceanica IMET1 is between 70 and 95% and is comparable to that obtained by other means of harvest; however, the rate of harvest is fast, with aggregates forming in 30 s. PMID:23892750

Powell, Ryan J.

2013-01-01

243

Biodegradation of crude oil by a newly isolated strain Rhodococcus sp. JZX-01.  

PubMed

A highly efficient oil-degrading bacteria JZX-01 was isolated from the oil-contaminated soil of the seacoast near the Boxi Offshore Oil Field of China. Morphological, physiological, and 16S rDNA gene sequence analyses indicated that JZX-01 was assigned to the genus Rhodococcus sp. This strain decomposed 65.27 ± 5.63 % of the crude oil in 9 days. Gas chromatography-mass spectrometry analysis showed that even the long-chain hydrocarbons (C31-C38) and branched alkanes (pristine and phytane), which were regarded as the stubborn ones, could be degraded. Further study showed that the bacteria still has good oil degradation ability at low temperatures as well as under high salt conditions. Moreover, JZX-01 was found to have a biosurfactant-producing capacity, which significantly favors the surface tension reduction and crude oil degradation. The promising isolated strain Rhodococcus sp. JZX-01 could be further used for the bioremediation of oil-polluted soil or seawater in a wide range of temperatures and high salt conditions. PMID:23996118

Li, Chen; Zhou, Zheng-Xi; Jia, Xiao-Qiang; Chen, Yu; Liu, Jiao; Wen, Jian-Ping

2013-12-01

244

A Gene Cluster Involved in Metal Homeostasis in the Cyanobacterium Synechocystis sp. Strain PCC 6803  

PubMed Central

A gene cluster composed of nine open reading frames (ORFs) involved in Ni2+, Co2+, and Zn2+ sensing and tolerance in the cyanobacterium Synechocystis sp. strain PCC 6803 has been identified. The cluster includes an Ni2+ response operon and a Co2+ response system, as well as a Zn2+ response system previously described. Expression of the Ni2+ response operon (nrs) was induced in the presence of Ni2+ and Co2+. Reduced Ni2+ tolerance was observed following disruption of two ORFs of the operon (nrsA and nrsD). We also show that the nrsD gene encodes a putative Ni2+ permease whose carboxy-terminal region is a metal binding domain. The Co2+ response system is composed of two divergently transcribed genes, corR and corT, mutants of which showed decreased Co2+ tolerance. Additionally, corR mutants showed an absence of Co2+-dependent induction of corT, indicating that CorR is a transcriptional activator of corT. To our knowledge, CorR is the first Co2+-sensing transcription factor described. Our data suggest that this region of the Synechocystis sp. strain PCC 6803 genome is involved in sensing and homeostasis of Ni2+, Co2+, and Zn2+. PMID:10692354

García-Domínguez, Mario; Lopez-Maury, Luis; Florencio, Francisco J.; Reyes, José C.

2000-01-01

245

Purification and Characterization of the Recombinant Thermus sp. Strain T2 ?-Galactosidase Expressed in Escherichia coli  

PubMed Central

The nucleotide sequence of the Thermus sp. strain T2 DNA coding for a thermostable ?-galactosidase was determined. The deduced amino acid sequence of the enzyme predicts a polypeptide of 474 amino acids (Mr, 53,514). The observed homology between the deduced amino acid sequences of the enzyme and ?-galactosidase from Thermus brockianus was over 70%. Thermus sp. strain T2 ?-galactosidase was expressed in its active form in Escherichia coli and purified. Native polyacrylamide gel electrophoresis and gel filtration chromatography data suggest that the enzyme is octameric. The enzyme was most active at 75°C for p-nitrophenyl-?-d-galactopyranoside hydrolysis, and it retained 50% of its initial activity after 1 h of incubation at 70°C. The enzyme was extremely stable over a broad range of pH (pH 6 to 13) after treatment at 40°C for 1 h. The enzyme acted on the terminal ?-galactosyl residue, not on the side chain residue, of the galactomanno-oligosaccharides as well as those of yeasts and Mortierella vinacea ?-galactosidase I. The enzyme has only one Cys residue in the molecule. para-Chloromercuribenzoic acid completely inhibited the enzyme but did not affect the mutant enzyme which contained Ala instead of Cys, indicating that this Cys residue is not responsible for its catalytic function. PMID:11282611

Ishiguro, Mitsunori; Kaneko, Satoshi; Kuno, Atsushi; Koyama, Yoshinori; Yoshida, Shigeki; Park, Gwi-Gun; Sakakibara, Yoshikiyo; Kusakabe, Isao; Kobayashi, Hideyuki

2001-01-01

246

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

247

Molecular structure and enzymatic function of lycopene cyclase from the cyanobacterium Synechococcus sp strain PCC7942.  

PubMed Central

A gene encoding the enzyme lycopene cyclase in the cyanobacterium Synechococcus sp strain PCC7942 was mapped by genetic complementation, cloned, and sequenced. This gene, which we have named crtL, was expressed in strains of Escherichia coli that were genetically engineered to accumulate the carotenoid precursors lycopene, neurosporene, and zeta-carotene. The crtL gene product converts the acyclic hydrocarbon lycopene into the bicyclic beta-carotene, an essential component of the photosynthetic apparatus in oxygen-evolving organisms and a source of vitamin A in human and animal nutrition. The enzyme also converts neurosporene to the monocyclic beta-zeacarotene but does not cyclize zeta-carotene, indicating that desaturation of the 7-8 or 7'-8' carbon-carbon bond is required for cyclization. The bleaching herbicide 2-(4-methylphenoxy)triethylamine hydrochloride (MPTA) effectively inhibits both cyclization reactions. A mutation that confers resistance to MPTA in Synechococcus sp PCC7942 was identified as a point mutation in the promoter region of crtL. The deduced amino acid sequence of lycopene cyclase specifies a polypeptide of 411 amino acids with a molecular weight of 46,125 and a pI of 6.0. An amino acid sequence motif indicative of FAD utilization is located at the N terminus of the polypeptide. DNA gel blot hybridization analysis indicated a single copy of crtL in Synechococcus sp PCC7942. Other than the FAD binding motif, the predicted amino acid sequence of the cyanobacterial lycopene cyclase bears little resemblance to the two known lycopene cyclase enzymes from nonphotosynthetic bacteria. Preliminary results from DNA gel blot hybridization experiments suggest that, like two earlier genes in the pathway, the Synechococcus gene encoding lycopene cyclase is homologous to plant and algal genes encoding this enzyme. PMID:7919981

Cunningham, F X; Sun, Z; Chamovitz, D; Hirschberg, J; Gantt, E

1994-01-01

248

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

249

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. PMID:15466039

Yoshida, Masahiro; Fukuhara, Nobuhiro; Oikawa, Tadao

2004-01-01

250

Cloning and Expression of the Benzoate Dioxygenase Genes from Rhodococcus sp. Strain 19070  

PubMed Central

The bopXYZ genes from the gram-positive bacterium Rhodococcus sp. strain 19070 encode a broad-substrate-specific benzoate dioxygenase. Expression of the BopXY terminal oxygenase enabled Escherichia coli to convert benzoate or anthranilate (2-aminobenzoate) to a nonaromatic cis-diol or catechol, respectively. This expression system also rapidly transformed m-toluate (3-methylbenzoate) to an unidentified product. In contrast, 2-chlorobenzoate was not a good substrate. The BopXYZ dioxygenase was homologous to the chromosomally encoded benzoate dioxygenase (BenABC) and the plasmid-encoded toluate dioxygenase (XylXYZ) of gram-negative acinetobacters and pseudomonads. Pulsed-field gel electrophoresis failed to identify any plasmid in Rhodococcus sp. strain 19070. Catechol 1,2- and 2,3-dioxygenase activity indicated that strain 19070 possesses both meta- and ortho-cleavage degradative pathways, which are associated in pseudomonads with the xyl and ben genes, respectively. Open reading frames downstream of bopXYZ, designated bopL and bopK, resembled genes encoding cis-diol dehydrogenases and benzoate transporters, respectively. The bop genes were in the same order as the chromosomal ben genes of P. putida PRS2000. The deduced sequences of BopXY were 50 to 60% identical to the corresponding proteins of benzoate and toluate dioxygenases. The reductase components of these latter dioxygenases, BenC and XylZ, are 201 residues shorter than the deduced BopZ sequence. As predicted from the sequence, expression of BopZ in E. coli yielded an approximately 60-kDa protein whose presence corresponded to increased cytochrome c reductase activity. While the N-terminal region of BopZ was approximately 50% identical in sequence to the entire BenC or XylZ reductases, the C terminus was unlike other known protein sequences. PMID:11375157

Haddad, Sandra; Eby, D. Matthew; Neidle, Ellen L.

2001-01-01

251

Cloning and expression of the benzoate dioxygenase genes from Rhodococcus sp. strain 19070.  

PubMed

The bopXYZ genes from the gram-positive bacterium Rhodococcus sp. strain 19070 encode a broad-substrate-specific benzoate dioxygenase. Expression of the BopXY terminal oxygenase enabled Escherichia coli to convert benzoate or anthranilate (2-aminobenzoate) to a nonaromatic cis-diol or catechol, respectively. This expression system also rapidly transformed m-toluate (3-methylbenzoate) to an unidentified product. In contrast, 2-chlorobenzoate was not a good substrate. The BopXYZ dioxygenase was homologous to the chromosomally encoded benzoate dioxygenase (BenABC) and the plasmid-encoded toluate dioxygenase (XylXYZ) of gram-negative acinetobacters and pseudomonads. Pulsed-field gel electrophoresis failed to identify any plasmid in Rhodococcus sp. strain 19070. Catechol 1,2- and 2,3-dioxygenase activity indicated that strain 19070 possesses both meta- and ortho-cleavage degradative pathways, which are associated in pseudomonads with the xyl and ben genes, respectively. Open reading frames downstream of bopXYZ, designated bopL and bopK, resembled genes encoding cis-diol dehydrogenases and benzoate transporters, respectively. The bop genes were in the same order as the chromosomal ben genes of P. putida PRS2000. The deduced sequences of BopXY were 50 to 60% identical to the corresponding proteins of benzoate and toluate dioxygenases. The reductase components of these latter dioxygenases, BenC and XylZ, are 201 residues shorter than the deduced BopZ sequence. As predicted from the sequence, expression of BopZ in E. coli yielded an approximately 60-kDa protein whose presence corresponded to increased cytochrome c reductase activity. While the N-terminal region of BopZ was approximately 50% identical in sequence to the entire BenC or XylZ reductases, the C terminus was unlike other known protein sequences. PMID:11375157

Haddad, S; Eby, D M; Neidle, E L

2001-06-01

252

Molecular cloning of a malyl coenzyme A lyase gene from Pseudomonas sp. strain AM1, a facultative methylotroph.  

PubMed

A genomic library containing HindIII partial digests of Pseudomonas sp. strain AM1 DNA was constructed in the broad-host-range cosmid pVK100. PCT57, a Pseudomonas sp. strain AM1 methanol mutant deficient in malyl coenzyme A lyase activity, was complemented to a methanol-positive phenotype by mobilization of the pVK100 library into PCT57 recipients with the ColE1/RK2 mobilizing plasmid pRK2013. Six different complemented isolates all contained a recombinant plasmid carrying the same 19.6-kilobase-pair Pseudomonas sp. strain AM1 DNA insert. Subcloning and complementation analysis demonstrated that the gene deficient in PCT57 (mcl-1) was located in a 1.6-kilobase-pair region within a 7.4-kilobase-pair EcoRI-HindIII fragment. PMID:6094488

Fulton, G L; Nunn, D N; Lidstrom, M E

1984-11-01

253

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

2013-10-01

254

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

2012-05-10

255

Degradation of 1,2-Dibromoethane by Mycobacterium sp. Strain GP1  

PubMed Central

The newly isolated bacterial strain GP1 can utilize 1,2-dibromoethane as the sole carbon and energy source. On the basis of 16S rRNA gene sequence analysis, the organism was identified as a member of the subgroup which contains the fast-growing mycobacteria. The first step in 1,2-dibromoethane metabolism is catalyzed by a hydrolytic haloalkane dehalogenase. The resulting 2-bromoethanol is rapidly converted to ethylene oxide by a haloalcohol dehalogenase, in this way preventing the accumulation of 2-bromoethanol and 2-bromoacetaldehyde as toxic intermediates. Ethylene oxide can serve as a growth substrate for strain GP1, but the pathway(s) by which it is further metabolized is still unclear. Strain GP1 can also utilize 1-chloropropane, 1-bromopropane, 2-bromoethanol, and 2-chloroethanol as growth substrates. 2-Chloroethanol and 2-bromoethanol are metabolized via ethylene oxide, which for both haloalcohols is a novel way to remove the halide without going through the corresponding acetaldehyde intermediate. The haloalkane dehalogenase gene was cloned and sequenced. The dehalogenase (DhaAf) encoded by this gene is identical to the haloalkane dehalogenase (DhaA) of Rhodococcus rhodochrous NCIMB 13064, except for three amino acid substitutions and a 14-amino-acid extension at the C terminus. Alignments of the complete dehalogenase gene region of strain GP1 with DNA sequences in different databases showed that a large part of a dhaA gene region, which is also present in R. rhodochrous NCIMB 13064, was fused to a fragment of a haloalcohol dehalogenase gene that was identical to the last 42 nucleotides of the hheB gene found in Corynebacterium sp. strain N-1074. PMID:10094681

Poelarends, Gerrit J.; van Hylckama Vlieg, Johan E. T.; Marchesi, Julian R.; Freitas Dos Santos, Luisa M.; Janssen, Dick B.

1999-01-01

256

Targeted Gene Disruption of the Cyclo (L-Phe, L-Pro) Biosynthetic Pathway in Streptomyces sp. US24 Strain  

PubMed Central

We have previously isolated a new actinomycete strain from Tunisian soil called Streptomyces sp. US24, and have shown that it produces two bioactive molecules including a Cyclo (L-Phe, L-Pro) diketopiperazine (DKP). To identify the structural genes responsible for the synthesis of this DKP derivative, a PCR amplification (696?bp) was carried out using the Streptomyces sp. US24 genomic DNA as template and two degenerate oligonucleotides designed by analogy with genes encoding peptide synthetases (NRPS). The detection of DKP derivative biosynthetic pathway of the Streptomyces sp. US24 strain was then achieved by gene disruption via homologous recombination using a suicide vector derived from the conjugative plasmid pSET152 and containing the PCR product. Chromatography analysis, biological tests and spectroscopic studies of supernatant cultures of the wild-type Streptomyces sp. US24 strain and three mutants obtained by this gene targeting disruption approach showed that the amplified DNA fragment is required for Cyclo (L-Phe, L-Pro) biosynthesis in Streptomyces sp. US24 strain. This DKP derivative seems to be produced either directly via a nonribosomal pathway or as a side product in the course of nonribosomal synthesis of a longer peptide. PMID:17710112

Sioud, Samiha; Karray-Rebai, Ines; Aouissaoui, Hedi; Aigle, Bertrand; Bejar, Samir; Mellouli, Lotfi

2007-01-01

257

Biosynthesis of polyunsaturated fatty acids in the oleaginous marine diatom Fistulifera sp. strain JPCC DA0580.  

PubMed

Studies of polyunsaturated fatty acid (PUFA) biosynthesis in microalgae are of great importance for many reasons, including the production of biofuel and variable omega 3-long chain PUFAs. The elucidation of the PUFA biosynthesis pathway is necessary for bioengineering to increase or decrease PUFA content in certain microalgae. In this study, we identified the PUFA synthesis pathway in the oleaginous marine diatom, Fistulifera sp. strain JPCC DA0580, a promising candidate for biodiesel production. The data revealed not only the presence of the desaturases and elongases involved in eicosapentaenoic acid (EPA) synthesis, but also the unexpected localization of ?3-desaturase expression in the chloroplast. This suggests that this microalga might perform the final step of EPA synthesis in the chloroplast and not in the endoplasmic reticulum (ER) like other diatoms. The detailed fatty acid profile suggests that the EPA was synthesized only through the ?6-pathway in this strain, which was also different from other diatoms. Finally, the transcriptome analysis demonstrated an overall down-regulation of desaturases and elongases over incubation time. These genetic features might explain the decrease of PUFA percentage over incubation time in this strain. The important insights into metabolite synthesis acquired here will be useful for future metabolic engineering to control PUFA content in this diatom. PMID:24335525

Liang, Yue; Maeda, Yoshiaki; Sunaga, Yoshihiko; Muto, Masaki; Matsumoto, Mitsufumi; Yoshino, Tomoko; Tanaka, Tsuyoshi

2013-12-01

258

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

2012-03-14

259

Modification of norfloxacin by a Microbacterium sp. strain isolated from a wastewater treatment plant.  

PubMed

Antimicrobial residues found in municipal wastewater may increase selective pressure on microorganisms for development of resistance, but studies with mixed microbial cultures derived from wastewater have suggested that some bacteria are able to inactivate fluoroquinolones. Medium containing N-phenylpiperazine and inoculated with wastewater was used to enrich fluoroquinolone-modifying bacteria. One bacterial strain isolated from an enrichment culture was identified by 16S rRNA gene sequence analysis as a Microbacterium sp. similar to a plant growth-promoting bacterium, Microbacterium azadirachtae (99.70%), and a nematode pathogen, "M. nematophilum" (99.02%). During growth in medium with norfloxacin, this strain produced four metabolites, which were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and nuclear magnetic resonance (NMR) analyses as 8-hydroxynorfloxacin, 6-defluoro-6-hydroxynorfloxacin, desethylene norfloxacin, and N-acetylnorfloxacin. The production of the first three metabolites was enhanced by ascorbic acid and nitrate, but it was inhibited by phosphate, amino acids, mannitol, formate, and thiourea. In contrast, N-acetylnorfloxacin was most abundant in cultures supplemented with amino acids. This is the first report of defluorination and hydroxylation of a fluoroquinolone by an isolated bacterial strain. The results suggest that some bacteria may degrade fluoroquinolones in wastewater to metabolites with less antibacterial activity that could be subject to further degradation by other microorganisms. PMID:21724893

Kim, Dae-Wi; Heinze, Thomas M; Kim, Bong-Soo; Schnackenberg, Laura K; Woodling, Kellie A; Sutherland, John B

2011-09-01

260

Modification of Norfloxacin by a Microbacterium sp. Strain Isolated from a Wastewater Treatment Plant?  

PubMed Central

Antimicrobial residues found in municipal wastewater may increase selective pressure on microorganisms for development of resistance, but studies with mixed microbial cultures derived from wastewater have suggested that some bacteria are able to inactivate fluoroquinolones. Medium containing N-phenylpiperazine and inoculated with wastewater was used to enrich fluoroquinolone-modifying bacteria. One bacterial strain isolated from an enrichment culture was identified by 16S rRNA gene sequence analysis as a Microbacterium sp. similar to a plant growth-promoting bacterium, Microbacterium azadirachtae (99.70%), and a nematode pathogen, “M. nematophilum” (99.02%). During growth in medium with norfloxacin, this strain produced four metabolites, which were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and nuclear magnetic resonance (NMR) analyses as 8-hydroxynorfloxacin, 6-defluoro-6-hydroxynorfloxacin, desethylene norfloxacin, and N-acetylnorfloxacin. The production of the first three metabolites was enhanced by ascorbic acid and nitrate, but it was inhibited by phosphate, amino acids, mannitol, formate, and thiourea. In contrast, N-acetylnorfloxacin was most abundant in cultures supplemented with amino acids. This is the first report of defluorination and hydroxylation of a fluoroquinolone by an isolated bacterial strain. The results suggest that some bacteria may degrade fluoroquinolones in wastewater to metabolites with less antibacterial activity that could be subject to further degradation by other microorganisms. PMID:21724893

Kim, Dae-Wi; Heinze, Thomas M.; Kim, Bong-Soo; Schnackenberg, Laura K.; Woodling, Kellie A.; Sutherland, John B.

2011-01-01

261

Three dehalogenases and physiological restraints in the biodegradation of haloalkanes by Arthrobacter sp. strain HA1  

SciTech Connect

Arthrobacter sp. strain HA1 utilizes 18 C{sub 2}-to-C{sub 8} 1-haloalkanes for growth and synthesizes an inducible 1-bromoalkane debrominase of unknown physiological function in addition to an inducible 1-chlorohexane halidohydrolase which dehalogenates some 50 substrates, including {alpha},{omega}-dihaloalkanes were utilized by cultures of strain HA1 under certain conditions only. Kinetics of growth and substrate utilization indicated that cells of strain HA1 growing in butanol-salts medium could be used to test whether compounds induced the 1-chlorohexane halidohydrolase. No gratuitous induction of synthesis of the enzyme was observed. Many enzyme substrates (e.g., bromobenzene) did not induce synthesis of the enzyme, though the enzyme sequence to degrade the product (phenol) was present. Some inducers (e.g., bromomethane) were enzyme substrates but not growth substrates. In an attempt to find a physiological role for the 1-bromoalkane debrominase, we observed that several long-chain haloaliphatic compounds (>C{sub 9}; e.g., 1-bromohexadecane and 1-chlorohexadecane) were utilized for growth and that induced cells could dehalogenate several 1-haloalkanes (at least C{sub 4} to C{sub 16}). The dehalogenation of the long-chain compounds could not be assayed in the cell extract, so we presume that a third haloalkane dehalogenase was present. All dehalogenations were equally active in the presence or absence of molecular oxygen and were presumed to be hydrolytic.

Scholtz, R.; Messi, F.; Leisinger, T.; Cook, A.M. (Swiss Federal Institute of Technology, Zurich (Switzerland))

1988-12-01

262

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

263

[Isolation, identification and characterization of a diethylstilbestrol-degrading bacterial strain Serratia sp].  

PubMed

Utilizing the diethylstilbestrol (DES)-degrading bacteria to biodegrade DES is a most reliable technique for cleanup of DES pollutants from the environment. However, little information is available heretofore on the isolation of DES-degrading bacteria and their DES removal performance in the environment. A novel bacterium capable of degrading DES was isolated from the activated sludge of a wastewater treatment plant. According to its morphology, physiochemical characteristics, and 16S rDNA sequence analysis, this strain was identified as Serratia sp.. The strain was an aerobic bacterium, and it could degrade 68.3% of DES (50 mg x L(-1)) after culturing for 7 days at 30 degrees C, 150 r x min(-1) in shaking flasks. The optimal conditions for DES biodegradation by the obtained strain were 30 degrees C, 40-60 mg x L(-1) DES, pH 7.0, 5% of inoculation volume, 0 g x L(-1) of added NaCl, and 10 mL of liquid medium volume in 100 mL flask. PMID:25338395

Xu, Ran-Fang; Sun, Min-Xia; Liu, Juan; Wang, Hong; Li, Xin; Zhu, Xue-Zhu; Ling, Wan-Ting

2014-08-01

264

Biosynthesis of Polyunsaturated Fatty Acids in the Oleaginous Marine Diatom Fistulifera sp. Strain JPCC DA0580  

PubMed Central

Studies of polyunsaturated fatty acid (PUFA) biosynthesis in microalgae are of great importance for many reasons, including the production of biofuel and variable omega 3-long chain PUFAs. The elucidation of the PUFA biosynthesis pathway is necessary for bioengineering to increase or decrease PUFA content in certain microalgae. In this study, we identified the PUFA synthesis pathway in the oleaginous marine diatom, Fistulifera sp. strain JPCC DA0580, a promising candidate for biodiesel production. The data revealed not only the presence of the desaturases and elongases involved in eicosapentaenoic acid (EPA) synthesis, but also the unexpected localization of ?3-desaturase expression in the chloroplast. This suggests that this microalga might perform the final step of EPA synthesis in the chloroplast and not in the endoplasmic reticulum (ER) like other diatoms. The detailed fatty acid profile suggests that the EPA was synthesized only through the ?6-pathway in this strain, which was also different from other diatoms. Finally, the transcriptome analysis demonstrated an overall down-regulation of desaturases and elongases over incubation time. These genetic features might explain the decrease of PUFA percentage over incubation time in this strain. The important insights into metabolite synthesis acquired here will be useful for future metabolic engineering to control PUFA content in this diatom. PMID:24335525

Liang, Yue; Maeda, Yoshiaki; Sunaga, Yoshihiko; Muto, Masaki; Matsumoto, Mitsufumi; Yoshino, Tomoko; Tanaka, Tsuyoshi

2013-01-01

265

Effect of enterocin EJ97 against Geobacillus   stearothermophilus vegetative cells and endospores in canned foods and beverages  

Microsoft Academic Search

Geobacillus stearothermophilus is a thermophilic bacterium typically responsible for the flat-sour spoilage of low-acid canned food with high water activity.\\u000a Control of vegetative cells and spores of G. stearothermophilus strains CECT 48 and CECT 49 by enterocin EJ97 produced by Enterococcus faecalis EJ97 is described. Both strains were highly sensitive to EJ97 in a culture medium. In samples from canned foods inoculated\\u000a with

Pilar Martínez Viedma; Hikmate Abriouel; Nabil Ben Omar; Rosario Lucas López; Antonio Gálvez

2010-01-01

266

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 0.758 g/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

2013-11-01

267

Hypervariable pili and flagella genes provide suitable new targets for DNA high-resolution melt-based genotyping of dairy Geobacillus spp.  

PubMed

Although nonpathogenic in nature, spores of Geobacillus are able to attach to surfaces, germinate, and form biofilms, allowing rapid multiplication and persistence within milk powder processing plants, causing final product contamination, and eventually leading to a loss of revenue in terms of downgraded product quality. As a result, Geobacillus spp. have been found to be common contaminants of milk powder worldwide. Genotyping methods can help in gaining insight into the ecology and transmission of these thermophilic bacteria within and between dairy processing plants. The objective of this study was to use the assembled draft genomes of two Geobacillus spp. to identify and test new hypervariable genotyping targets for differentiating closely related dairy Geobacillus isolates. The two Geobacillus spp. strains obtained from high spore count powders were obtained in 2010 (isolate 7E) and in 1995 (isolate 126) and were previously shown to be of same genotype based on a variable number tandem repeat genotyping method. Significant nucleotide sequence variation was found in genes encoding pili and flagella, which were further investigated as suitable loci for a new high-resolution melt analysis (HRMA)-based genotyping method. Three genes encoding pulG (containing prepilin-type N-terminal cleavage domain), pilT (pili retraction protein), and fliW (flagellar assembly protein) were selected as targets for the new pili/flagella gene (PilFla) HRMA genotyping method. The three-gene-based PilFla-HRMA genotyping method differentiated 35 milk powder Geobacillus spp. isolates into 19 different genotype groups (D = 0.93), which compared favorably to the previous method (which used four variable number tandem repeat loci) that generated 16 different genotype groups (D = 0.90). In conclusion, through comparative genomics of two closely related dairy Geobacillus strains, we have identified new hypervariable regions that prove to be useful targets for highly discriminatory genotyping. PMID:25285488

Chauhan, Kanika; Seale, R Brent; Deeth, Hilton C; Turner, Mark S

2014-10-01

268

Biodegradation of diphenyl ether and its monohalogenated derivatives by Sphingomonas sp. strain SS3.  

PubMed Central

The bacterium Sphingomonas sp. strain SS3, which utilizes diphenyl ether and its 4-fluoro, 4-chloro, and (to a considerably lesser extent) 4-bromo derivatives as sole sources of carbon and energy, was enriched from soil samples of an industrial waste deposit. The bacterium showed cometabolic activities toward all other isomeric monohalogenated diphenyl ethers. During diphenyl ether degradation in batch culture experiments, phenol and catechol were produced as intermediates which were then channeled into the 3-oxoadipate pathway. The initial step in the degradation follows the recently discovered mechanism of 1,2-dioxygenation, which yields unstable phenolic hemiacetals from diphenyl ether structures. Oxidation of the structure-related dibenzo-p-dioxin yielded 2-(2-hydroxyphenoxy)-muconate upon ortho cleavage of the intermediate 2,2',3-trihydroxydiphenyl ether. Formation of phenol, catechol, halophenol, and halocatechol from the conversion of monohalogenated diphenyl ethers gives evidence for a nonspecific attack of the dioxygenating enzyme system. PMID:1444384

Schmidt, S; Wittich, R M; Erdmann, D; Wilkes, H; Francke, W; Fortnagel, P

1992-01-01

269

Pseudomonas sp. strain HBP1 Prp degrades 2-isopropylphenol (ortho-cumenol) via meta cleavage.  

PubMed

Pseudomonas sp. strain HBP1 Prp grew on 2-isopropylphenol as the sole carbon and energy source with a maximal specific growth rate of 0.14 h-1 and transient accumulation of isobutyric acid. Oxygen uptake experiments with resting cells and enzyme assays with crude-cell extracts showed that 2-isopropylphenol was catabolized via a broad-spectrum meta cleavage pathway. These findings were confirmed by experiments with partially purified enzymes. Identification of 3-isopropylcatechol and 2-hydroxy-6-oxo-7-methylocta-2,4-dienoic acid as the products of the initial monooxygenase reaction and the subsequent extradiol ring cleavage dioxygenase reaction, respectively, was based on gas chromatography-mass spectrometry analysis of the corresponding trimethylsilyl derivatives. The meta cleavage product hydrolase hydrolyzed 2-hydroxy-6-oxo-7-methylocta-2,4-dienoic acid (meta cleavage product of 2-isopropylphenol) to isobutyric acid and 2-hydroxypent-2,4-dienoic acid. PMID:7811094

Reichlin, F; Kohler, H P

1994-12-01

270

Paenibacillus sp. strain HC1 xylanases responsible for degradation of rice bran hemicellulose.  

PubMed

Paenibacillus sp. strain HC1 is the first bacterium capable of growing on rice bran hemicellulose as a sole carbon source. Two xylanases (Xyl-I and -II) were purified from the bacterial culture fluid and enzymatically characterized. Xyl-I and -II showed monomer forms with molecular masses of 30 and 18kDa, respectively, and were most active at around pH 5.0 and 45 degrees C. Xylooligosaccharides were degraded to xylobiose and xylose by Xyl-I, but not by Xyl-II, suggesting that Xyl-I plays an important role in complete depolymerization of xylan. Both enzymes acted endolytically on rice bran hemicellulose, indicating that Xyl-I and -II contribute to the structure determination and practical use of the polysaccharide, an unutilized biomass in technology. PMID:16829064

Harada, Karen Mine; Tanaka, Keiko; Fukuda, Yasuki; Hashimoto, Wataru; Murata, Kousaku

2008-01-01

271

Synthetic Biology Toolbox for Controlling Gene Expression in the Cyanobacterium Synechococcus sp. strain PCC 7002.  

PubMed

The application of synthetic biology requires characterized tools to precisely control gene expression. This toolbox of genetic parts previously did not exist for the industrially promising cyanobacterium, Synechococcus sp. strain PCC 7002. To address this gap, two orthogonal constitutive promoter libraries, one based on a cyanobacterial promoter and the other ported from Escherichia coli, were built and tested in PCC 7002. The libraries demonstrated 3 and 2.5 log dynamic ranges, respectively, but correlated poorly with E. coli expression levels. These promoter libraries were then combined to create and optimize a series of IPTG inducible cassettes. The resultant induction system had a 48-fold dynamic range and was shown to out-perform Ptrc constructs. Finally, a RBS library was designed and tested in PCC 7002. The presented synthetic biology toolbox will enable accelerated engineering of PCC 7002. PMID:25216157

Markley, Andrew L; Begemann, Matthew B; Clarke, Ryan E; Gordon, Gina C; Pfleger, Brian F

2014-09-25

272

Reduction of conjugal transfer efficiency by three restriction activities of Anabaena sp. strain PCC 7120.  

PubMed Central

The efficiency of conjugal transfer of plasmids from Escherichia coli to the cyanobacterium Anabaena sp. strain PCC 7120 was quantitated as a function of the number of restriction sites for the restriction enzymes carried by the recipient. In addition to the previously recognized isoschizomers of AvaI and AvaII, PCC 7120 was found to possess an isoschizomer of AvaIII. Plasmids modified in E. coli with methylases that protect in vitro against restriction by the three enzymes were transferred with high efficiency, nearly independent of the number of restriction sites on the plasmid. Plasmids left unprotected against one of the three restriction enzymes were transferred with lower efficiencies. For low numbers of sites, the efficiency of conjugal transfer decreased as an exponential function of the number of unprotected sites. The methods presented may be used to increase the efficiency of conjugal transfer into restriction-competent bacteria. PMID:9068647

Elhai, J; Vepritskiy, A; Muro-Pastor, A M; Flores, E; Wolk, C P

1997-01-01

273

Saccharification of corn fiber using enzymes from Aureobasidium sp. strain NRRL Y-2311-1  

SciTech Connect

Crude enzyme preparations from Aureobasidium sp. strain NRRL Y-2311-1 were characterized and tested for the capacity to saccharify corn fiber. Cultures grown on xylan, corn fiber, and alkaline hydrogen peroxide (AHP)-pretreated corn fiber produced specific levels of endoxylanase, amylase, protease, cellulose, and other activities. Using equal units of endoxylanase activity, crude enzymes from AHP-pretreated corn fiber cultures were most effective in saccharification. Multiple enzyme activities were implicated in this process. Pretreatment of corn fiber with AHP nearly doubled the susceptibility of hemicellulose to enzymatic digestion. Up to 138 mg xylose, 125 mg arabinose, and 490 mg glucose were obtained per g pretreated corn fiber under conditions tested. 31 refs., 2 figs., 4 tabs.

Leathers, T.D.; Gupta, S.C. [Dept. of Agriculture, Peoria, IL (United States)

1996-06-01

274

Catalytically important amino acid residues in endoglucanases from a mutant strain Trichoderma sp. M7.  

PubMed

Two endoglucanases, EG-III (49.7 kD) and EG-IV (47.5 kD), from a mutant strain Trichoderma sp. M7 were modified with several specific reagents. Water-soluble carbodiimide completely inactivated only one of the purified endoglucanases and kinetic analysis indicated that at least two molecules of carbodiimide bind to EG-IV for inactivation. The reaction followed pseudo-first-order kinetics with a second-order rate constant of 3.57 x 10(-5) mM(-1) x in(-1). Both endoglucanases were inhibited by iodoacetamide, but the absence of substrate protection excluded direct involvement of cysteine residues in the catalysis. N-Bromosuccinimide (NBS) showed a strong inhibitory effect on both endoglucanases, suggesting that tryptophan residues are essential for the activity and binding to the substrate, since the presence of substrates or analogs prior to NBS modification protected the enzymes against inactivation. PMID:16487064

Petrova, S D; Bakalova, N G; Kolev, D N

2006-01-01

275

Cellulose degradation by one mesophilic strain Caulobacter sp. FMC1 under both aerobic and anaerobic conditions.  

PubMed

Caulobacteria are presumed to be responsible for considerable mineralization of organic material in aquatic environments. In this study, a facultative, mesophilic and cellulolytic bacterium Caulobacter sp. FMC1 was isolated from sediments which were taken from a shallow freshwater lake and then enriched with amendment of submerged macrophyte for three months. This strain seemed to evolve a capacity to adapt redox-fluctuating environments, and could degrade cellulose both aerobically and anaerobically. Cellulose degradation percentages under aerobic and anaerobic conditions were approximately 27% and 10% after a 240-h incubation in liquid mediums containing 0.5% cellulose, respectively. Either cellulose or cellobiose alone was able to induce activities of endoglucanase, exoglucanase, and ?-1,4-glucosidase. Interestingly, ethanol was produced as the main fermentative product under anaerobic incubation on cellulose. These results could improve our understanding about cellulose-degrading process in aquatic environments, and were also useful in optimizing cellulose bioconversion process for bioethanol production. PMID:23357088

Song, Na; Cai, Hai-Yuan; Yan, Zai-Sheng; Jiang, He-Long

2013-03-01

276

Degradation of p-chlorotoluene by a mutant of Pseudomonas sp. strain JS6.  

PubMed Central

Pseudomonas sp. strain JS6 grows on chlorobenzene, p-dichlorobenzene, or toluene as a sole source of carbon and energy. It does not grow on p-chlorotoluene (p-CT). Growth on glucose in the presence of p-CT resulted in the accumulation of 4-chloro-2,3-dihydroxy-1-methylbenzene (3-chloro-6-methylcatechol), 4-chloro-2,3-dihydroxy-1-methylcyclohexa-4,6-diene (p-CT dihydrodiol), and 2-methyl-4-carboxymethylenebut-2-en-4-olide (2-methyl dienelactone). Strain JS21, a spontaneous mutant capable of growth on p-CT, was isolated from cultures of strain JS6 after extended exposure to p-CT. In addition to growing on p-CT, JS21 grew on all of the substrates that supported growth of the parent strain, including p-dichlorobenzene, chlorobenzene, benzene, toluene, benzoate, p-hydroxybenzoate, phenol, and ethylbenzene. The pathway for degradation of p-CT by JS21 was investigated by respirometry, isolation of intermediates, and assay of enzymes in cell extracts. p-CT was converted to 3-chloro-6-methylcatechol by dioxygenase and dihydrodiol dehydrogenase enzymes. 3-Chloro-6-methylcatechol underwent ortho ring cleavage catalyzed by a catechol 1,2-dioxygenase to form 2-chloro-5-methyl-cis,cis-muconate, which was converted to 2-methyl dienelactone. A dienelactone hydrolase converted 2-methyl dienelactone to 2-methylmaleylacetic acid. Preliminary results indicate that a change in wild-type induction patterns allows JS21 to grow on p-CT. PMID:2719478

Haigler, B E; Spain, J C

1989-01-01

277

Degradation of p-chlorotoluene by a mutant of Pseudomonas sp. strain JS6  

SciTech Connect

Pseudomonas sp. strain JS6 grows on chlorobenzene, p-dichlorobenzene, or toluene as a sole source of carbon and energy. It does not grow on p-chlorotoluene (p-CT). Growth on glucose in the presence of p-CT resulted in the accumulation of 4-chloro-2,3- dihydroxy-1-methyl benzene (3-chloro-6- methylcatechol), 4-chloro- 2,3-dihydroxy-1-methyl cyclohexa- 4,6-diene (p-CT dihydrodoil), and 2-methyl-4-carboxy methylenebut-2-en-4-olide (2-methyl dienelactone). Strain JS21, a spontaneous mutant capable of growth on p-CT, was isolated from cultures of strain JS6 after extended exposure to p-CT. In addition to growing on p-CT, JS21 grew on all of the substrates that supported growth of the parent strain, including p-dichlorobenzene, chlorobenzene, benzene, toluene, benzoate, p-hydroxybenzoate, phenol, and ethylbenzene. The pathway for degradation of p-CT by JS21 was investigated by respirometry, isolation of intermediates, and assay of enzymes in cell extracts. p-CT was converted to 3-chloro-6-methylcatechol by dioxygenase and dihydrodiol dehydrogenase enzymes. 3-Chloro-6-methylcatechol underwent ortho ring cleavage catalyzed by a catechol 1,2-dioxygenase to form 2-chloro-5-methyl-cis,cis-muconate, which was converted to 2-methyl dienelactone. A dienelactone hydrolase converted 2-methyl dienelactone to 2-methylmaleylacetic acid. Preliminary results indicate that a change in wild-type induction patterns allows JS21 to grow on p-CT.

Haigler, B.E.; Spain, J.C. (Air Force Engineering and Services Center, Tyndall Air Force Base, FL (USA))

1989-02-01

278

Repression of the Antifungal Activity of Pseudomonas sp. Strain DF41 by the Stringent Response ?  

PubMed Central

The stringent response (SR) enables bacteria to adapt to nutrient limitation through production of the nucleotides guanosine tetraphosphate and guanosine pentaphosphate, collectively known as (p)ppGpp. Two enzymes are responsible for the intracellular pools of (p)ppGpp: RelA acts as a synthetase, while SpoT can function as either a synthetase or a hydrolase. We investigated how the SR affects the ability of the biological control agent Pseudomonas sp. strain DF41 to inhibit the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary. Strain DF41 relA and relA spoT mutants were generated and found to exhibit increased antifungal activity. Strain DF41 produces a lipopeptide (LP) molecule that is essential for Sclerotinia biocontrol. LP production and protease activity were both elevated in the relA and relA spoT mutants. Addition of relA but not spoT in trans restored the mutant phenotype to that of the parent. Next, we investigated whether an association exists between the SR and known regulators of biocontrol, including the Gac system and RpoS. A gacS mutant of strain DF41 produced less (p)ppGpp and exhibited a 1.7-fold decrease in relA expression compared to the wild type, suggesting that relA forms part of the Gac regulon. We discovered that rpoS transcription was reduced significantly in the SR mutants. Furthermore, rpoS provided in trans restored protease activity to wild-type levels but did not attenuate antifungal activity. Finally, relA expression was decreased in the mutants, indicating that the SR is required for maximum expression of relA. PMID:21705548

Manuel, Jerrylynn; Berry, Chrystal; Selin, Carrie; Fernando, W. G. Dilantha; de Kievit, Teresa R.

2011-01-01

279

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

2011-12-01

280

Genomics of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia sp. Strain MED134?†  

PubMed Central

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

2011-01-01

281

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. PMID:23045511

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

2012-01-01

282

Regiospecific Enzymatic Oxygenation of cis -Vaccenic Acid in the Marine Phototrophic Bacterium Erythrobacter sp. strain MG3  

Microsoft Academic Search

The fatty acid composition of the marine phototrophic bacterium Erythrobacter sp. strain MG3 was analysed. The involvement of an unusual enzymatic peroxidation of the allylic carbon 10 of cis-vaccenic acid in this strain was confirmed. This process, which seems to be a characteristic of some aerobic and anaerobic\\u000a phototrophic bacteria, appeared to also act on the allylic carbon 10 of

J.-F. Rontani; M. Koblížek

2008-01-01

283

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. PMID:22347595

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

2011-01-01

284

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 PMID:16347453

Ligon, James M.; Nakas, James P.

1987-01-01

285

Compositional and toxicological evaluation of the diazotrophic cyanobacterium, Cyanothece sp. strain ATCC 51142  

NASA Technical Reports Server (NTRS)

Compositional analyses of Cyanothece sp. strain ATCC 51142 showed high protein (50-60%) and low fat (0.4-1%) content, and the ability to synthesize vitamin B12. The amino acid profile indicated that Cyanothece sp. was a balanced protein source. Fatty acids of the 18:3n-3 type were also present. Mineral analyses indicated that the cellular biomass may be a good source of Fe, Zn and Na. Caloric content was 4.5 to 5.1 kcal g dry weight-1 and the carbon content was approximately 40% on a dry weight basis. Nitrogen content was 8 to 9% on a dry weight basis and total nucleic acids were 1.3% on a dry weight basis. Short-term feeding studies in rats followed by histopathology found no toxicity or dietary incompatibility problems. The level of uric acid and allantoin in urine and tissues was low, suggesting no excess of nucleic acids, as sometimes reported in the past for a cyanobacteria-containing diet. The current work discusses the potential implications of these results for human nutrition applications.

Schneegurt, M. A.; Arieli, B.; McKeehen, J. D.; Stephens, S. D.; Nielsen, S. S.; Saha, P. R.; Trumbo, P. R.; Sherman, L. A.; Mitchell, C. A. (Principal Investigator)

1995-01-01

286

Photoheterotrophic Fluxome in Synechocystis sp. Strain PCC 6803 and Its Implications for Cyanobacterial Bioenergetics.  

PubMed

This study investigated metabolic responses in Synechocystis sp. strain PCC 6803 to photosynthetic impairment. We used 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU; a photosystem II inhibitor) to block O2 evolution and ATP/NADPH generation by linear electron flow. Based on (13)C-metabolic flux analysis ((13)C-MFA) and RNA sequencing, we have found that Synechocystis sp. PCC 6803 employs a unique photoheterotrophic metabolism. First, glucose catabolism forms a cyclic route that includes the oxidative pentose phosphate (OPP) pathway and the glucose-6-phosphate isomerase (PGI) reaction. Glucose-6-phosphate is extensively degraded by the OPP pathway for NADPH production and is replenished by the reversed PGI reaction. Second, the Calvin cycle is not fully functional, but RubisCO continues to fix CO2 and synthesize 3-phosphoglycerate. Third, the relative flux through the complete tricarboxylic acid (TCA) cycle and succinate dehydrogenase is small under heterotrophic conditions, indicating that the newly discovered cyanobacterial TCA cycle (via the ?-aminobutyric acid pathway or ?-ketoglutarate decarboxylase/succinic semialdehyde dehydrogenase) plays a minimal role in energy metabolism. Fourth, NAD(P)H oxidation and the cyclic electron flow (CEF) around photosystem I are the two main ATP sources, and the CEF accounts for at least 40% of total ATP generation from photoheterotrophic metabolism (without considering maintenance loss). This study not only demonstrates a new topology for carbohydrate oxidation but also provides quantitative insights into metabolic bioenergetics in cyanobacteria. PMID:25535269

You, Le; He, Lian; Tang, Yinjie J

2015-03-01

287

Biomass production and nutrients removal by a new microalgae strain Desmodesmus sp. in anaerobic digestion wastewater.  

PubMed

Anaerobic digestion wastewater (ADW), which contains large amount of nitrogen and phosphorus, particularly high concentration of ammonium, might lead to severely environmental pollution. A new unicellular green microalgae species from a wetland at the Olympic Forest Park, Beijing, China was screened based on its growth rates and nutrients removal capability under ADW. Results of 18s rDNA and ITS1 analysis indicated that this strain have a close relationship with Desmodesmus sp., named as EJ9-6. Desmodesmus sp. EJ9-6 could remove 100% NH4-N (68.691mg/L), TP (4.565mg/L) and PO4-P (4.053mg/L), and 75.50% TN (84.236mg/L) at 10.0% ADW, which the highest biomass production was 0.412g/L after 14d cultivation. Maximum nutrients removal was observed at 10.0% ADW with daily removal rates of TN, NH4-N, TP and PO4-P at 4.542, 5.284, 0.326 and 0.290mg/L/d, respectively. PMID:24704885

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

2014-06-01

288

Complete genome sequence of the facultative anaerobic magnetotactic bacterium Magnetospirillum sp. strain AMB-1.  

PubMed

Magnetospirillum sp. strain AMB-1 is a Gram-negative alpha-proteobacterium that synthesizes nano-sized magnetites, referred to as magnetosomes, aligned intracellularly in a chain. The potential of this nano-sized material is growing and will be applicable to broad research areas. It has been expected that genome analysis would elucidate the mechanism of magnetosome formation by magnetic bacteria. Here we describe the genome of Magnetospirillum sp. AMB-1 wild type, which consists of a single circular chromosome of 4967148 bp. For identification of genes required for magnetosome formation, transposon mutagenesis and determination of magnetosome membrane proteins were performed. Analysis of a non-magnetic transposon mutant library focused on three unknown genes from 2752 unknown genes and three genes from 205 signal transduction genes. Partial proteome analysis of the magnetosome membrane revealed that the membrane contains numerous oxidation/reduction proteins and a signal response regulator that may function in magnetotaxis. Thus, oxidation/reduction proteins and elaborate multidomain signaling proteins were analyzed. This comprehensive genome analysis will enable resolution of the mechanisms of magnetosome formation and provide a template to determine how magnetic bacteria maintain a species-specific, nano-sized, magnetic single domain and paramagnetic morphology. PMID:16303747

Matsunaga, Tadashi; Okamura, Yoshiko; Fukuda, Yorikane; Wahyudi, Aris Tri; Murase, Yaeko; Takeyama, Haruko

2005-01-01

289

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. PMID:23335774

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

2013-01-01

290

Distinct actions by Paenibacillus sp. strain E18 ?-L-arabinofuranosidases and xylanase in xylan degradation.  

PubMed

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. PMID:23335774

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

2013-03-01

291

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. PMID:16461704

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

2006-01-01

292

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

PubMed Central

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-[14C]glutamate from 2-keto-[1-14C]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 [14C]bicarbonate and L-[1-14C]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. Images PMID:2880834

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

1987-01-01

293

Reclassification of Brevibacillus brevis strains NCIMB 13288 and DSM 6472 (=NRRL NRS-887) as Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov.  

PubMed

Comparison of the hypervariable region (269-279 bases in length) at the 5' end of the 16S rDNA sequences of 29 bacterial strains that were identified previously as Brevibacillus brevis showed that 13 strains clustered with Aneurinibacillus species, eight strains clustered with Bacillus species and eight strains clustered with Brevibacillus species. Based on DNA-DNA hybridization results, 27 strains, not including [Brevibacillus brevis] NCIMB 13288 and [Brevibacillus brevis] DSM 6472, were reidentified as Aneurinibacillus migulanus, Aneurinibacillus thermoaerophilus, Bacillus methanolicus, Bacillus oleronius, Brevibacillus agri, Brevibacillus brevis and Brevibacillus parabrevis. [Brevibacillus brevis] NCIMB 13288, which was located in the Aneurinibacillus cluster, showed low DNA-DNA relatedness (<14 %) and low 16S rDNA sequence similarity (96.8-97.9 %) to other Aneurinibacillus species. [Brevibacillus brevis] DSM 6472, which was located in the Brevibacillus cluster, also showed low DNA-DNA relatedness (<12 %) and low 16S rDNA sequence similarity (95.4-98.8 %) to other Brevibacillus species. These genotypic and phylogenetic data, plus phenotypic and chemotaxonomic characteristics, suggest that [Brevibacillus brevis] NCIMB 13288 (=IAM 15048) and [Brevibacillus brevis] DSM 6472 (=NRRL NRS-887) represent novel species of the genera Aneurinibacillus and Brevibacillus, respectively, for which the names Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov. are proposed. PMID:15023954

Goto, Keiichi; Fujita, Rieko; Kato, Yuko; Asahara, Mika; Yokota, Akira

2004-03-01

294

Resolution of Culture Clostridium bifermentans DPH-1 into Two Populations, a Clostridium sp. and Tetrachloroethene-Dechlorinating Desulfitobacterium hafniense Strain JH1?  

PubMed Central

Clostridium bifermentans strain DPH-1 reportedly dechlorinates tetrachloroethene (PCE) to cis-1,2-dichloroethene. Cultivation-based approaches resolved the DPH-1 culture into two populations: a nondechlorinating Clostridium sp. and PCE-dechlorinating Desulfitobacterium hafniense strain JH1. Strain JH1 carries pceA, encoding a PCE reductive dehalogenase, and shares other characteristics with Desulfitobacterium hafniense strain Y51. PMID:18708512

Fletcher, Kelly E.; Ritalahti, Kirsti M.; Pennell, Kurt D.; Takamizawa, Kazuhiro; Löffler, Frank E.

2008-01-01

295

Draft Genome Sequence of Pseudozyma brasiliensis sp. nov. Strain GHG001, a High Producer of Endo-1,4-Xylanase Isolated from an Insect Pest of Sugarcane.  

PubMed

Here, we present the nuclear and mitochondrial genome sequences of Pseudozyma brasiliensis sp. nov. strain GHG001. P. brasiliensis sp. nov. is the closest relative of Pseudozyma vetiver. P. brasiliensis sp. nov. is capable of growing on xylose or xylan as a sole carbon source and has great biotechnological potential. PMID:24356824

Oliveira, Juliana Velasco de Castro; Dos Santos, Renato Augusto Corrêa; Borges, Thuanny A; Riaño-Pachón, Diego Mauricio; Goldman, Gustavo Henrique

2013-01-01

296

Draft Genome Sequence of Pseudozyma brasiliensis sp. nov. Strain GHG001, a High Producer of Endo-1,4-Xylanase Isolated from an Insect Pest of Sugarcane  

PubMed Central

Here, we present the nuclear and mitochondrial genome sequences of Pseudozyma brasiliensis sp. nov. strain GHG001. P. brasiliensis sp. nov. is the closest relative of Pseudozyma vetiver. P. brasiliensis sp. nov. is capable of growing on xylose or xylan as a sole carbon source and has great biotechnological potential. PMID:24356824

Oliveira, Juliana Velasco de Castro; dos Santos, Renato Augusto Corrêa; Borges, Thuanny A.

2013-01-01

297

Complete Genome Sequence of Sphingobacterium sp. Strain ML3W, Isolated from Wings of Myotis lucifugus Infected with White Nose Syndrome.  

PubMed

Sphingobacterium sp. strain ML3W was isolated from the wing of a bat infected with white nose syndrome. We report the complete 5.33-Mb genome sequence of Sphingobacterium sp. strain ML3W, obtained using Pacific Biosciences technology. Being the second complete Sphingobacterium sequence, this will increase knowledge of the genus. PMID:25614576

Smith, Stephen A; Krasucki, Stephen P; McDowell, John V; Balke, Virginia L

2015-01-01

298

Hydrolytic enzyme activity of Paenibacillus sp. strain B2 and effects of the antagonistic bacterium on cell integrity of two soil-borne pathogenic fungi  

Microsoft Academic Search

Paenibacillus sp. strain B2, isolated from the mycorrhizosphere of Sorghum bicolor and having an antagonistic activity towards soil-borne fungal pathogens, possessed extracellular cellulolytic, proteolytic, chitinolytic and pectinolytic enzyme activities. The eventual role of these lytic enzymes in cellular interactions between Paenibacillus sp. strain B2 and Phytophthora parasitica and Fusariumoxysporum was investigated by electron microscopy and molecular cytology. Electron microscopic observations

S. W Budi; D van Tuinen; C Arnould; E Dumas-Gaudot; V Gianinazzi-Pearson; S Gianinazzi

2000-01-01

299

Draft Genome Sequence of Thalassotalea sp. Strain ND16A Isolated from Eastern Mediterranean Sea Water Collected from a Depth of 1,055 Meters.  

PubMed

Thalassotalea sp. strain ND16A belongs to the family Colwelliaceae and was isolated from eastern Mediterranean Sea water at a depth of 1,055 m. Members of Colwelliaceae are ubiquitous marine heterotrophs. Here, we report the draft genome sequence of Thalassotalea sp. strain ND16A, a member of the newly described genus Thalassotalea. PMID:25428976

Stelling, Savannah C; Techtmann, Stephen M; Utturkar, Sagar M; Alshibli, Noor K; Brown, Steven D; Hazen, Terry C

2014-01-01

300

Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste  

PubMed Central

Chryseobacterium sp. strain P1-3, harboring keratin degrading activity, has recently been isolated from poultry waste. Here, we report the 4.6-Mbp draft genome sequence of the keratinolytic bacterium with a G+C content of 37.0% and 4,087 protein-coding genes. PMID:25428979

Park, Gun-Seok; Hong, Sung-Jun; Lee, Chang-Hyun; Khan, Abdur Rahim; Ullah, Ihsan; Jung, Byung Kwon; Choi, JungBae; Kwak, Yunyoung; Back, Chang-Gi; Jung, Hee-Young

2014-01-01

301

Draft Genome Sequence of Haloferax sp. Strain ATB1, Isolated from a Semi-Arid Region in the Brazilian Caatinga  

PubMed Central

Organisms in the Haloferax genus are extreme halophiles that grow in environments with pH values between 4 and 12, and temperatures between 0°C and 60°C. In the present study, a draft of the first Haloferax sp. strain ATB1 genome isolated from the region of Cariri (in Paraíba State, Brazil) is presented. PMID:25125649

Castro, Wendel de Oliveira; Torres-Ballesteros, Adriana Maria; Nakayama, Cristina Rossi; Melo, Itamar Soares; Pellizari, Vivian Helena; Silva, Artur

2014-01-01

302

HIGH LEVEL EXPRESSION AND CHARACTERIZATION OF THE CYCLOPHILIN B GENE FROM THE ANAEROBIC FUNGUS ORPINOMYCES SP. STRAIN PC-2  

Technology Transfer Automated Retrieval System (TEKTRAN)

Cyclophilins are an evolutionarily conserved family of peptidyl-prolyl cis-trans isomerases (PPIases). A cyclophilin B (CyPB) gene from anaerobic fungus Orpinomyces sp. strain PC-2 was cloned and overexpressed in Escherichia coli. It was expressed as amino terminal 6 x His-tagged recombinant prote...

303

Complete Genome Sequence of Rahnella sp. Strain Y9602, a Gammaproteobacterium Isolate from Metal- and Radionuclide-Contaminated Soil  

PubMed Central

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. PMID:22461551

Bruce, David; Detter, Chris; Goodwin, Lynne A.; Han, James; Han, Cliff S.; Held, Brittany; Land, Miriam L.; Mikhailova, Natalia; Nolan, Matt; Pennacchio, Len; Pitluck, Sam; Tapia, Roxanne; Woyke, Tanja; Sobecky, Patricia A.

2012-01-01

304

Complete genome sequence of Rahnella sp. strain Y9602, a gammaproteobacterium isolate from metal- and radionuclide-contaminated soil.  

PubMed

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. PMID:22461551

Martinez, Robert J; Bruce, David; Detter, Chris; Goodwin, Lynne A; Han, James; Han, Cliff S; Held, Brittany; Land, Miriam L; Mikhailova, Natalia; Nolan, Matt; Pennacchio, Len; Pitluck, Sam; Tapia, Roxanne; Woyke, Tanja; Sobecky, Patricia A

2012-04-01

305

Genome Sequence of Maribius sp. Strain MOLA 401, a Marine Roseobacter with a Quorum-Sensing Cell-Dependent Physiology  

PubMed Central

Maribius sp. strain MOLA401 is an alphaproteobacterium isolated from a coral reef lagoon located in New Caledonia, France. We report the genome sequence and its annotation which, interestingly, reveals the presence of genes involved in quorum sensing. This is the first report of a full genome within the genus Maribius. PMID:25278539

Doberva, Margot; Sanchez-Ferandin, Sophie; Ferandin, Yoan; Intertaglia, Laurent; Joux, Fabien; Lebaron, Philippe

2014-01-01

306

Genome Sequence of Maribius sp. Strain MOLA 401, a Marine Roseobacter with a Quorum-Sensing Cell-Dependent Physiology.  

PubMed

Maribius sp. strain MOLA401 is an alphaproteobacterium isolated from a coral reef lagoon located in New Caledonia, France. We report the genome sequence and its annotation which, interestingly, reveals the presence of genes involved in quorum sensing. This is the first report of a full genome within the genus Maribius. PMID:25278539

Doberva, Margot; Sanchez-Ferandin, Sophie; Ferandin, Yoan; Intertaglia, Laurent; Joux, Fabien; Lebaron, Philippe; Lami, Raphaël

2014-01-01

307

Draft Genome Sequence of the Aromatic Hydrocarbon-Degrading Bacterium Sphingobium sp. Strain Ant17, Isolated from Antarctic Soil  

PubMed Central

Here, we present the draft genome sequence of Sphingobium sp. strain Ant17, an aromatic hydrocarbon-degrading bacterium that was isolated from Antarctic oil-contaminated soil. An analysis of this genome can lead to insights into the mechanisms of xenobiotic degradation processes at low temperatures and potentially aid in bioremediation applications. PMID:24723703

Guerrero, Leandro D.; Makhalanyane, Thulani P.; Aislabie, Jackie M.

2014-01-01

308

Draft Genome Sequence of Novosphingobium sp. Strain MBES04, Isolated from Sunken Wood from Suruga Bay, Japan  

PubMed Central

This report describes the draft genome sequence of Novosphingobium sp. strain MBES04, isolated from sunken wood from Suruga Bay, Japan, which is capable of degrading a wide range of lignin-related aromatic monomers. The draft genome sequence contains 5,361,448 bp, with a G+C content of 65.4%. PMID:25593249

Ohta, Yukari; Kobayashi, Kiwa; Tsubouchi, Taishi; Iida, Kagami; Tanizaki, Akiko; Kurosawa, Kanako; Adachi, Akiko; Nishihara, Mizue; Sato, Reona; Hasegawa, Ryoichi; Hatada, Yuji

2015-01-01

309

Draft Genome Sequence of Cellulosimicrobium sp. Strain MM, Isolated from Arsenic-Rich Microbial Mats of a Himalayan Hot Spring.  

PubMed

Microbial mats situated at the Manikaran hot springs (>95°C) are characterized by their high arsenic content (140 ppb), qualifying as a stressed niche. Here, we report the annotated draft genome (3.85 Mb) of Cellulosimicrobium sp. strain MM, isolated from these microbial mats, consisting of 3,718 coding sequences, with an average % G+C of 74.4%. PMID:25301656

Sharma, Anukriti; Hira, Princy; Shakarad, Mallikarjun; Lal, Rup

2014-01-01

310

Draft Genome Sequence of Nitrosospira sp. Strain APG3, a Psychrotolerant Ammonia-Oxidizing Bacterium Isolated from Sandy Lake Sediment  

PubMed Central

Bacteria in the genus Nitrosospira play vital roles in the nitrogen cycle. Nitrosospira sp. strain APG3 is a psychrotolerant betaproteobacterial ammonia-oxidizing bacterium isolated from freshwater lake sediment. The draft genome revealed that it represents a new species of cluster 0 Nitrosospira, which is presently not represented by described species. PMID:24201205

Garcia, Juan C.; Le, Vang Q.; Stein, Lisa Y.; Klotz, Martin G.; Nielsen, Jeppe L.

2013-01-01

311

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

312

Genome Sequence of the Deep-Sea Denitrifier Pseudomonas sp. Strain MT-1, Isolated from the Mariana Trench  

PubMed Central

Pseudomonas sp. strain MT-1 was the first deep-sea denitrifier isolated and characterized from mud recovered from a depth of 11,000 m in the Mariana Trench. We report here the genome sequence of this bacterium, which contributes to our understanding of denitrification and bioenergetics in the deep sea. PMID:25523772

Fujinami, Shun; Oikawa, Yuji; Araki, Takuma; Shinmura, Yui; Midorikawa, Ryota; Ishizaka, Hikari; Kato, Chiaki; Horikoshi, Koki; Ito, Masahiro

2014-01-01

313

Draft Genome Sequence of Cellulosimicrobium sp. Strain MM, Isolated from Arsenic-Rich Microbial Mats of a Himalayan Hot Spring  

PubMed Central

Microbial mats situated at the Manikaran hot springs (>95°C) are characterized by their high arsenic content (140 ppb), qualifying as a stressed niche. Here, we report the annotated draft genome (3.85 Mb) of Cellulosimicrobium sp. strain MM, isolated from these microbial mats, consisting of 3,718 coding sequences, with an average % G+C of 74.4%. PMID:25301656

Sharma, Anukriti; Hira, Princy; Shakarad, Mallikarjun

2014-01-01

314

Draft Genome Sequence of Sphingomonas sp. Strain Ant20, Isolated from Oil-Contaminated Soil on Ross Island, Antarctica.  

PubMed

Here, we present the draft genome of Sphingomonas sp. strain Ant20, isolated from oil-polluted soil near Scott Base, Ross Island, Antarctica. The genome of this aromatic hydrocarbon-degrading bacterium provides valuable information on the microbially mediated biodegradation of aromatic compounds in cold-climate systems. PMID:25573925

Ronca, Sandra; Frossard, Aline; Guerrero, Leandro D; Makhalanyane, Thulani P; Aislabie, Jackie M; Cowan, Don A

2015-01-01

315

Draft Genome Sequence of Bacillus sp. Strain BSC154, Isolated from Biological Soil Crust of Moab, Utah.  

PubMed

Bacillus sp. BSC154 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and biofilm production. The BSC154 genome contains iron siderophore production, nitrate reduction, mixed acid-butanediol fermentation, and assimilatory and dissimilatory sulfate metabolism pathways. PMID:25395651

Bailey, Alexis C; Kellom, Matthew; Poret-Peterson, Amisha T; Noonan, Kathryn; Hartnett, Hilairy E; Raymond, Jason

2014-01-01

316

Draft Genome Sequence of Massilia sp. Strain BSC265, Isolated from Biological Soil Crust of Moab, Utah.  

PubMed

Massilia sp. BSC265 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and exopolysaccharide synthesis for biofilm adhesion. The BSC265 genome contains a complete dissimilatory nitrate reduction pathway as well as a TCA cycle, making it a facultative anaerobe. PMID:25395652

Bailey, Alexis C; Kellom, Matthew; Poret-Peterson, Amisha T; Noonan, Kathryn; Hartnett, Hilairy E; Raymond, Jason

2014-01-01

317

Draft Genome Sequence of Microvirga sp. Strain BSC39, Isolated from Biological Soil Crust of Moab, Utah.  

PubMed

Microvirga sp. BSC39 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and exopolysaccharide synthesis for biofilm adhesion. The BSC39 genome contains iron siderophore uptake and hydrolysis enzymes; however, it lacks siderophore synthesis pathways, suggesting the uptake of siderophores produced by neighboring microbes. PMID:25395650

Bailey, Alexis C; Kellom, Matthew; Poret-Peterson, Amisha T; Noonan, Kathryn; Hartnett, Hilairy E; Raymond, Jason

2014-01-01

318

Involvement of nitric oxide synthase in sucrose-enhanced hydrogen peroxide tolerance of Rhodococcus sp. strain APG1,  

E-print Network

Involvement of nitric oxide synthase in sucrose-enhanced hydrogen peroxide tolerance of Rhodococcus Lancaster, Jr. Abstract Hydrogen peroxide (H2O2) tolerance of Rhodococcus sp. strain APG1, previously; Hydrogen peroxide tolerance; Plant­microorganism interaction; Endophytic colonization Bacteria colonize

Cohen, Michael F.

319

Draft Genome Sequence of Massilia sp. Strain BSC265, Isolated from Biological Soil Crust of Moab, Utah  

PubMed Central

Massilia sp. BSC265 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and exopolysaccharide synthesis for biofilm adhesion. The BSC265 genome contains a complete dissimilatory nitrate reduction pathway as well as a TCA cycle, making it a facultative anaerobe. PMID:25395652

Bailey, Alexis C.; Kellom, Matthew; Poret-Peterson, Amisha T.; Noonan, Kathryn; Hartnett, Hilairy E.

2014-01-01

320

Draft Genome Sequence of Frankia sp. Strain BMG5.12, a Nitrogen-Fixing Actinobacterium Isolated from Tunisian Soils  

PubMed Central

Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different families of actinorhizal plants. We report a draft genome sequence for Frankia sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from Tunisian soils with the ability to infect Elaeagnus angustifolia and Myrica gale. PMID:23846272

Nouioui, Imen; Beauchemin, Nicholas; Cantor, Michael N.; Chen, Amy; Detter, J. Chris; Furnholm, Teal; Ghodhbane-Gtari, Faten; Goodwin, Lynne; Gtari, Maher; Han, Cliff; Han, James; Huntemann, Marcel; Hua, Susan Xinyu; Ivanova, Natalia; Kyrpides, Nikos; Markowitz, Victor; Mavrommatis, Kostas; Mikhailova, Natalia; Nordberg, Henrik P.; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Sen, Arnab; Sur, Saubashya; Szeto, Ernest; Thakur, Subarna; Wall, Luis; Wei, Chia-Lin; Woyke, Tanja

2013-01-01

321

Draft Genome Sequence of Sphingomonas sp. Strain Ant20, Isolated from Oil-Contaminated Soil on Ross Island, Antarctica  

PubMed Central

Here, we present the draft genome of Sphingomonas sp. strain Ant20, isolated from oil-polluted soil near Scott Base, Ross Island, Antarctica. The genome of this aromatic hydrocarbon-degrading bacterium provides valuable information on the microbially mediated biodegradation of aromatic compounds in cold-climate systems. PMID:25573925

Ronca, Sandra; Frossard, Aline; Guerrero, Leandro D.; Makhalanyane, Thulani P.; Aislabie, Jackie M.

2015-01-01

322

Complete Genome Sequence of Pelosinus sp. Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology  

PubMed Central

Pelosinus species can reduce metals such as Fe(III), U(VI), and Cr(VI) and have been isolated from diverse geographical regions. Five draft genome sequences have been published. We report the complete genome sequence for Pelosinus sp. strain UFO1 using only PacBio DNA sequence data and without manual finishing. PMID:25189589

Brown, Steven D.; Utturkar, Sagar M.; Magnuson, Timothy S.; Ray, Allison E.; Poole, Farris L.; Lancaster, W. Andrew; Thorgersen, Michael P.; Adams, Michael W. W.

2014-01-01

323

Draft Genome Sequence of Novosphingobium sp. Strain MBES04, Isolated from Sunken Wood from Suruga Bay, Japan.  

PubMed

This report describes the draft genome sequence of Novosphingobium sp. strain MBES04, isolated from sunken wood from Suruga Bay, Japan, which is capable of degrading a wide range of lignin-related aromatic monomers. The draft genome sequence contains 5,361,448 bp, with a G+C content of 65.4%. PMID:25593249

Ohta, Yukari; Nishi, Shinro; Kobayashi, Kiwa; Tsubouchi, Taishi; Iida, Kagami; Tanizaki, Akiko; Kurosawa, Kanako; Adachi, Akiko; Nishihara, Mizue; Sato, Reona; Hasegawa, Ryoichi; Hatada, Yuji

2015-01-01

324

Draft Genome Sequence of MCPA-Degrading Sphingomonas sp. Strain ERG5, Isolated from a Groundwater Aquifer in Denmark  

PubMed Central

Sphingomonas sp. strain ERG5 was isolated from a bacterial community, originating from a groundwater aquifer polluted with low pesticide concentrations. This bacterium degrades 2-methyl-4-chlorophenoxyacetic acid (MCPA) in a wide spectrum of concentrations and has been shown to function in bioaugmented sand filters. Genes associated with MCPA degradation are situated on a putative conjugative plasmid. PMID:25676756

Nielsen, Tue Kjærgaard; Sørensen, Sebastian R.; Hansen, Lars Hestbjerg

2015-01-01

325

Draft Genome Sequence and Description of Janthinobacterium sp. Strain CG3, a Psychrotolerant Antarctic Supraglacial Stream Bacterium.  

PubMed

Here we present the draft genome sequence of Janthinobacterium sp. strain CG3, a psychrotolerant non-violacein-producing bacterium that was isolated from the Cotton Glacier supraglacial stream. The genome sequence of this organism will provide insight as to the mechanisms necessary for bacteria to survive in UV-stressed icy environments. PMID:24265494

Smith, Heidi; Akiyama, Tatsuya; Foreman, Christine; Franklin, Michael; Woyke, Tanja; Teshima, Hazuki; Davenport, Karen; Daligault, Hajnalka; Erkkila, Tracy; Goodwin, Lynne; Gu, Wei; Xu, Yan; Chain, Patrick

2013-01-01

326

Draft Genome Sequence of Pseudomonas sp. Strain Ant30-3, a Psychrotolerant Bacterium with Biodegradative Attribute Isolated from Antarctica.  

PubMed

Pseudomonas sp. strain Ant30-3, isolated from fuel-contaminated Antarctic soil, exhibited distinctive psychrotolerant attributes and the potential for degrading aromatic hydrocarbon compounds at cold temperatures. We report here the 6.14-Mb draft genome of Ant30-3, which will provide insights into the genomic basis for the psychrotolerant and biodegradative properties of this bacterium. PMID:24903870

Koo, Hyunmin; Basu, Malay K; Crowley, Michael; Aislabie, Jackie; Bej, Asim K

2014-01-01

327

Draft Genome Sequence of Nitrosospira sp. Strain APG3, a Psychrotolerant Ammonia-Oxidizing Bacterium Isolated from Sandy Lake Sediment.  

PubMed

Bacteria in the genus Nitrosospira play vital roles in the nitrogen cycle. Nitrosospira sp. strain APG3 is a psychrotolerant betaproteobacterial ammonia-oxidizing bacterium isolated from freshwater lake sediment. The draft genome revealed that it represents a new species of cluster 0 Nitrosospira, which is presently not represented by described species. PMID:24201205

Garcia, Juan C; Urakawa, Hidetoshi; Le, Vang Q; Stein, Lisa Y; Klotz, Martin G; Nielsen, Jeppe L

2013-01-01

328

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

2013-01-01

329

Complete Genomic Sequence of the Equol-Producing Bacterium Eggerthella sp. Strain YY7918, Isolated from Adult Human Intestine  

PubMed Central

Eggerthella sp. strain YY7918 was isolated from the intestinal flora of a healthy human. It metabolizes daidzein (a soybean isoflavonoid) and produces S-equol, which has stronger estrogenic activities than daidzein. Here, we report the finished and annotated genomic sequence of this organism. PMID:21914883

Yokoyama, Shin-ichiro; Oshima, Kenshiro; Nomura, Izumi; Hattori, Masahira; Suzuki, Tohru

2011-01-01

330

Topoisomerase i inhibitors from the Streptomyces sp. strain KM86-9B isolated from a marine sponge  

Microsoft Academic Search

The crude extract ofStreptomyces sp. strain KM86-9B, isolated from a marine sponge, displayed significant inhibition on topoisomerase I activity. Investigation\\u000a of the causative components by bioactivity-directed fractionation resulted in the isolation of a series of iso- and anteiso-fatty\\u000a acids.

Hong Kum Lee; Deuk-Soo Lee; Junghyun Lim; Jung Sun Kim; Kwang Sik Im; Jee H. Jung

1998-01-01

331

Genome Sequence of the Deep-Sea Denitrifier Pseudomonas sp. Strain MT-1, Isolated from the Mariana Trench.  

PubMed

Pseudomonas sp. strain MT-1 was the first deep-sea denitrifier isolated and characterized from mud recovered from a depth of 11,000 m in the Mariana Trench. We report here the genome sequence of this bacterium, which contributes to our understanding of denitrification and bioenergetics in the deep sea. PMID:25523772

Fujinami, Shun; Oikawa, Yuji; Araki, Takuma; Shinmura, Yui; Midorikawa, Ryota; Ishizaka, Hikari; Kato, Chiaki; Horikoshi, Koki; Ito, Masahiro; Tamegai, Hideyuki

2014-01-01

332

Draft Genome Sequence of Pseudomonas sp. Strain Ant30-3, a Psychrotolerant Bacterium with Biodegradative Attribute Isolated from Antarctica  

PubMed Central

Pseudomonas sp. strain Ant30-3, isolated from fuel-contaminated Antarctic soil, exhibited distinctive psychrotolerant attributes and the potential for degrading aromatic hydrocarbon compounds at cold temperatures. We report here the 6.14-Mb draft genome of Ant30-3, which will provide insights into the genomic basis for the psychrotolerant and biodegradative properties of this bacterium. PMID:24903870

Basu, Malay K.; Crowley, Michael; Aislabie, Jackie; Bej, Asim K.

2014-01-01

333

Acetylcholinesterase Inhibitors from a Marine Fungus Talaromyces sp. Strain LF458.  

PubMed

Two new oxaphenalenone dimers, talaromycesone A (1) and talaromycesone B (2), and a new isopentenyl xanthenone, talaroxanthenone (3), together with six known diphenyl ether derivatives, e.g., ?(1',3'),-1'-dehydroxypenicillide (4), 1',2'-dehydropenicillide (5), vermixocin A (6), vermixocin B (7), 3'-methoxy-1'2'-dehydropenicillide (8), and AS-186c (9), were isolated from the culture broth and mycelia of a marine fungus Talaromyces sp. strain LF458. Compound 2 represents the first example of 1-nor oxaphenalenone dimer carbon skeleton. All isolated compounds were subjected to bioactivity assays. Compounds 1, 2, and 9 exhibited potent antibacterial activities with IC50 3.70, 17.36, and 1.34 ?M, respectively, against human pathogenic Staphylococcus strains. Compounds 1, 3, and 9 displayed potent acetylcholinesterase inhibitory activities with IC50 7.49, 1.61, and 2.60 ?M, respectively. Interestingly, phosphodiesterase PDE-4B2 was inhibited by compounds 3 (IC50?7.25 ?M) and 9 (IC50?2.63 ?M). PMID:25108548

Wu, Bin; Ohlendorf, Birgit; Oesker, Vanessa; Wiese, Jutta; Malien, Susann; Schmaljohann, Rolf; Imhoff, Johannes F

2014-08-10

334

Biodegradation of benazolin-ethyl by strain Methyloversatilis sp. cd-1 isolated from activated sludge.  

PubMed

Benazolin-ethyl has been used on a wide range of weeds present in various crops since 1964. Because benazolin-ethyl is a potential hazard to the environment and human health, it is important to remove this herbicide from the environment. However, to the best of our knowledge, no report is available in the literature regarding the microbial degradation of benazolin-ethyl by bacteria. In this study, one strain named cd-1, which is capable of degrading benazolin-ethyl, was isolated from benazolin-ethyl wastewater treatment pool. The isolate was identified as Methyloversatilis sp. according to its morphological, physiological, biochemical properties, and 16S rRNA gene sequences analysis. This strain utilizes benazolin-ethyl as the sole carbon source. and degrades 100 mg l?¹ benazolin-ethyl to non-detectable level within 48 h. Three metabolites were identified as benazolin, 7-chloro-3-methylbenzo[d]thiazol-2(3H)-one, and 2-chloro-6-(methyleneamino)benzenethiol based on the MS/MS and GC/MS analyses. The first step involved in the degradation of benazolin-ethyl was the cleavage of the ester bond to form benazolin. Benazolin was subsequently subjected to demethylation for decomposition into 7-chloro-3-methylbenzo[d]thiazol-2(3H)-one and methanol. The last step was to form 2-chloro-6-(methyleneamino)benzenethiol. PMID:20848105

Cai, Tianming; Qian, Lihua; Cai, Shu; Chen, Liwei

2011-02-01

335

Using Transcriptomics To Improve Butanol Tolerance of Synechocystis sp. Strain PCC 6803  

PubMed Central

Cyanobacteria are emerging as promising hosts for production of advanced biofuels such as n-butanol and alkanes. However, cyanobacteria suffer from the same product inhibition problems as those that plague other microbial biofuel hosts. High concentrations of butanol severely reduce growth, and even small amounts can negatively affect metabolic processes. An understanding of how cyanobacteria are affected by their biofuel product can enable identification of engineering strategies for improving their tolerance. Here we used transcriptome sequencing (RNA-Seq) to assess the transcriptome response of Synechocystis sp. strain PCC 6803 to two concentrations of exogenous n-butanol. Approximately 80 transcripts were differentially expressed at 40 mg/liter butanol, and 280 transcripts were different at 1 g/liter butanol. Our results suggest a compromised cell membrane, impaired photosynthetic electron transport, and reduced biosynthesis. Accumulation of intracellular reactive oxygen species (ROS) scaled with butanol concentration. Using the physiology and transcriptomics data, we selected several genes for overexpression in an attempt to improve butanol tolerance. We found that overexpression of several proteins, notably, the small heat shock protein HspA, improved tolerance to butanol. Transcriptomics-guided engineering created more solvent-tolerant cyanobacteria strains that could be the foundation for a more productive biofuel host. PMID:24056459

Anfelt, Josefine; Hallström, Björn; Nielsen, Jens; Uhlén, Mathias

2013-01-01

336

HcwA, an Autolysin, Is Required for Heterocyst Maturation in Anabaena sp. Strain PCC 7120  

PubMed Central

In many filamentous cyanobacteria, vegetative cells can differentiate into heterocysts, cells that are specialized for aerobic fixation of N2. Synthesis of the heterocyst envelope polysaccharide is dependent on the gene hepA in Anabaena sp. strain PCC 7120. In search of genes that are involved in the regulation of hepA, we transposon mutagenized strain DR1069, which bears a chromosomal hepA::luxAB fusion. One resulting mutant, designated HNL3, grows normally in medium with nitrate and shows poor induction of hepA in response to nitrogen deprivation. In HNL3, transposon Tn5-1058 is inserted within gene hcwA, a constitutively expressed open reading frame whose predicted product resembles N-acetylmuramoyl-l-alanine amidases. Reconstruction of the mutation confirmed that the mutant phenotype resulted from the insertion of the transposon. The induction of hepA in HNL3 is partially restored upon recombination of HNL3 with plasmid-borne, wild-type hcwA. Moreover, HcwA expressed in Escherichia coli exhibits wall-lytic activity. These results suggest that the degradation, or possibly reconstruction, of the cell peptidoglycan layer is a prerequisite for heterocyst maturation. PMID:11698373

Zhu, Jinsong; Jäger, Karin; Black, Todd; Zarka, Kelly; Koksharova, Olga; Wolk, C. Peter

2001-01-01

337

A cold-adapted esterase from psychrotrophic Pseudoalteromas sp. strain 643A.  

PubMed

A psychrotrophic bacterium producing a cold-adapted esterase upon growth at low temperatures was isolated from the alimentary tract of Antarctic krill Euphasia superba Dana, and classified as Pseudoalteromonas sp. strain 643A. A genomic DNA library of strain 643A was introduced into Escherichia coli TOP10F', and screening on tributyrin-containing agar plates led to the isolation of esterase gene. The esterase gene (estA, 621 bp) encoded a protein (EstA) of 207 amino acid residues with molecular mass of 23,036 Da. Analysis of the amino acid sequence of EstA suggests that it is a member of the GDSL-lipolytic enzymes family. The purification and characterization of native EstA esterase were performed. The enzyme displayed 20-50% of maximum activity at 0-20 degrees C. The optimal temperature for EstA was 35 degrees C. EstA was stable between pH 9 and 11.5. The enzyme showed activity for esters of short- to medium-chain (C(4) and C(10)) fatty acids, and exhibited no activity for long-chain fatty acid esters like that of palmitate and stearate. EstA was strongly inhibited by phenylmethylsulfonyl fluoride, 2-mercaptoethanol, dithiothreitol and glutathione. Addition of selected divalent ions e.g. Mg(2+), Co(2+) and Cu(2+) led to the reduction of enzymatic activity and the enzyme was slightly activated ( approximately 30%) by Ca(2+) ions. PMID:17516048

Cie?li?ski, Hubert; Bia?kowska, Aneta M; D?ugo?ecka, Anna; Daroch, Maurycy; Tkaczuk, Karolina L; Kalinowska, Halina; Kur, Józef; Turkiewicz, Marianna

2007-07-01

338

Anilofos Tolerance and Its Mineralization by the Cyanobacterium Synechocystis sp. Strain PUPCCC 64  

PubMed Central

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

2013-01-01

339

A novel bacterium Saprospira sp. strain PdY3 forms bundles and lyses cyanobacteria.  

PubMed

A helical filamentous cyanobactericidal bacterium was isolated from Dianchi Lake, a eutrophic freshwater lake in Kunming City of the Yunnan Province in China using a special solid medium. This species was designated strain PdY3. This bacterium was identified as a novel Saprospira sp. on the basis of its morphological characteristics and 16S rDNA sequence. Strain PdY3 showed apparent group behavior on the solid medium, forming orderly, bundle-like group structures. These bundles moved as groups. Individuals in a bundle responded to the bundle as a whole. PdY3 also showed group behavior and formed a three-dimensional reticular structure when co-cultured with Anabaena in liquid media. This helical bacterium lysed cyanobacteria through direct contact and its group behavior greatly accelerated the cyanobactericidal process. Our experiments showed that PdY3 caused lysis of 64% of Anabaena cells within 1 day and that its cyanobactericidal range was broad. These results underscore potential application of Saprospira on the control of blooms of cyanobacteria. PdY3 group behavior might allow a more efficient capture of bacterial prey. PMID:16368567

Shi, Miao; Zou, Li; Liu, Xinyao; Gao, Yin; Zhang, Zhongkai; Wu, Weizhong; Wen, Donghui; Chen, Zhangliang; An, Chengcai

2006-01-01

340

Alginate-Dependent Gene Expression Mechanism in Sphingomonas sp. Strain A1  

PubMed Central

Sphingomonas sp. strain A1, a Gram-negative bacterium, directly incorporates alginate polysaccharide into the cytoplasm through a periplasmic alginate-binding protein-dependent ATP-binding cassette transporter. The polysaccharide is degraded to monosaccharides via the formation of oligosaccharides by endo- and exotype alginate lyases. The strain A1 proteins for alginate uptake and degradation are encoded in both strands of a genetic cluster in the bacterial genome and inducibly expressed in the presence of alginate. Here we show the function of the alginate-dependent transcription factor AlgO and its mode of action on the genetic cluster and alginate oligosaccharides. A putative gene within the genetic cluster seems to encode a transcription factor-like protein (AlgO). Mutant strain A1 (?AlgO mutant) cells with a disrupted algO gene constitutively produced alginate-related proteins. DNA microarray analysis indicated that wild-type cells inducibly transcribed the genetic cluster only in the presence of alginate, while ?AlgO mutant cells constitutively expressed the genetic cluster. A gel mobility shift assay showed that AlgO binds to the specific intergenic region between algO and algS (algO-algS). Binding of AlgO to the algO-algS intergenic region diminished with increasing alginate oligosaccharides. These results demonstrated a novel alginate-dependent gene expression mechanism. In the absence of alginate, AlgO binds to the algO-algS intergenic region and represses the expression of both strands of the genetic cluster, while in the presence of alginate, AlgO dissociates from the algO-algS intergenic region via binding to alginate oligosaccharides produced through the lyase reaction and subsequently initiates transcription of the genetic cluster. This is the first report on the mechanism by which alginate regulates the expression of the gene cluster. PMID:24816607

Hayashi, Chie; Takase, Ryuichi; Momma, Keiko; Maruyama, Yukie; Murata, Kousaku

2014-01-01

341

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. PMID:24031289

Menocci, Vivian; Goulart, Antonio José; Adalberto, Paulo Roberto; Tavano, Olga Luisa; Marques, Daniela Parreira; Contiero, Jonas; Monti, Rubens

2008-01-01

342

Geobacter lovleyi sp. nov. Strain SZ, a Novel Metal-Reducing and Tetrachloroethene-Dechlorinating Bacterium†  

PubMed Central

A bacterial isolate, designated strain SZ, was obtained from noncontaminated creek sediment microcosms based on its ability to derive energy from acetate oxidation coupled to tetrachloroethene (PCE)-to-cis-1,2-dichloroethene (cis-DCE) dechlorination (i.e., chlororespiration). Hydrogen and pyruvate served as alternate electron donors for strain SZ, and the range of electron acceptors included (reduced products are given in brackets) PCE and trichloroethene [cis-DCE], nitrate [ammonium], fumarate [succinate], Fe(III) [Fe(II)], malate [succinate], Mn(IV) [Mn(II)], U(VI) [U(IV)], and elemental sulfur [sulfide]. PCE and soluble Fe(III) (as ferric citrate) were reduced at rates of 56.5 and 164 nmol min?1 mg of protein?1, respectively, with acetate as the electron donor. Alternate electron acceptors, such as U(VI) and nitrate, did not inhibit PCE dechlorination and were consumed concomitantly. With PCE, Fe(III) (as ferric citrate), and nitrate as electron acceptors, H2 was consumed to threshold concentrations of 0.08 ± 0.03 nM, 0.16 ± 0.07 nM, and 0.5 ± 0.06 nM, respectively, and acetate was consumed to 3.0 ± 2.1 nM, 1.2 ± 0.5 nM, and 3.6 ± 0.25 nM, respectively. Apparently, electron acceptor-specific acetate consumption threshold concentrations exist, suggesting that similar to the hydrogen threshold model, the measurement of acetate threshold concentrations offers an additional diagnostic tool to delineate terminal electron-accepting processes in anaerobic subsurface environments. Genetic and phenotypic analyses classify strain SZ as the type strain of the new species, Geobacter lovleyi sp. nov., with Geobacter (formerly Trichlorobacter) thiogenes as the closest relative. Furthermore, the analysis of 16S rRNA gene sequences recovered from PCE-dechlorinating consortia and chloroethene-contaminated subsurface environments suggests that Geobacter lovleyi belongs to a distinct, dechlorinating clade within the metal-reducing Geobacter group. Substrate versatility, consumption of electron donors to low threshold concentrations, and simultaneous reduction of electron acceptors suggest that strain SZ-type organisms have desirable characteristics for bioremediation applications. PMID:16597982

Sung, Youlboong; Fletcher, Kelly E.; Ritalahti, Kirsti M.; Apkarian, Robert P.; Ramos-Hernández, Natalia; Sanford, Robert A.; Mesbah, Noha M.; Löffler, Frank E.

2006-01-01

343

Isolation and characterization of a Cr(VI)-reduction Ochrobactrum sp. strain CSCr-3 from chromium landfill.  

PubMed

A strain CSCr-3 with high Cr(VI)-reducing ability under alkaline conditions was isolated from a chromium landfill and identified as Ochrobactrum sp. on the basis of 16S rRNA gene sequence analysis. The cells were rod shaped, Gram-negative and motile. The physiological characteristics and Cr(VI)-reduction of the strain were also studied. The results showed that the Ochrobactrum sp. strain CSCr-3 was tolerant to very high concentration of Cr(VI) (800 mg/L) and capable of reducing different forms of Cr(VI) (chromate and dichromate), under a wide range of temperatures (25-40 degrees C) and pH (7-11) with optimum at 35 degrees C and initial pH 10. Higher rates of Cr(VI)-reduction were observed with higher initial cell and Cr(VI) concentrations. Strain CSCr-3 could reduce Cr(VI) very efficiently over a wide range of Cr(VI) concentrations (100-800 mg/L). The addition of glucose caused a dramatic increase in Cr(VI)-reduction by Ochrobactrum sp. CSCr-3, while the presence of sulfate or nitrate had no influence. The presence of other metals, such as Cu, Co, Mn, etc., significantly stimulated Cr(VI)-reduction ability by the strain CSCr-3. The results obtained in this study have significance for the bioremediation of chromate pollution. PMID:18722054

He, Zhiguo; Gao, Fengling; Sha, Tao; Hu, Yuehua; He, Chao

2009-04-30

344

The pacL gene of Synechococcus sp. strain PCC 7942 encodes a Ca(2+)-transporting ATPase.  

PubMed

An ATP-dependent Ca2+ uptake activity was identified in plasma membrane vesicles prepared from Synechococcus sp. strain PCC 7942. This activity was insensitive to agents which collapse pH gradients and membrane potentials but sensitive to vanadate, indicating that the activity is catalyzed by a P-type Ca(2+)-ATPase. A gene was cloned from Synechococcus sp. strain PCC 7942 by using a degenerate oligonucleotide based on a sequence conserved among P-type ATPases. This gene (pacL) encodes a product similar in structure to eukaryotic Ca(2+)-ATPases. We have shown that pacL encodes a Ca(2+)-ATPase by demonstrating that a strain in which pacL is disrupted has no Ca(2+)-ATPase activity associated with its plasma membrane. In addition, Ca(2+)-ATPase activity was restored to the delta pacL strain by introducing pacL into a second site in the Synechococcus sp. strain PCC 7942 chromosome. PMID:8021228

Berkelman, T; Garret-Engele, P; Hoffman, N E

1994-07-01

345

Isolation and characterization of 3-N-trimethylamino-1-propanol-degrading Rhodococcus sp. strain A2.  

PubMed

The aerobic degradation of 3-N-trimethylamino-1-propanol (homocholine) as a sole source of carbon and nitrogen has been found for a Rhodococcus sp. bacterium isolated from soil. The isolate was identified as Rhodococcus sp. strain A2 based on its phenotypic features, physiological and biochemical characteristics, and results of phylogenetic analysis. The washed cells of strain A2 completely degraded homocholine within 6 h, with concomitant formation of several metabolites. Analysis of the metabolites using capillary electrophoresis, fast atom bombardment-MS, and GC-MS showed that trimethylamine was the major metabolite, in addition to beta-alanine betaine (beta-AB) and trimethylaminopropionaldehyde. Therefore, the possible degradation pathway of homocholine in the isolated strain is through consequent oxidation of the alcohol group (-OH) to aldehyde (-CHO) and acid (-COOH). Thereafter, the cleavage of beta-AB C-N bonds yielded trimethylamine and alkyl chain. PMID:19486158

Mohamed Ahmed, Isam Ali; Arima, Jiro; Ichiyanagi, Tsuyoshi; Sakuno, Emi; Mori, Nobuhiro

2009-06-01

346

Draft Genome Sequence of Marine Cyanobacterium Synechococcus sp. Strain NKBG042902, Which Harbors a Homogeneous Plasmid Available for Metabolic Engineering  

PubMed Central

The marine cyanobacterium Synechococcus sp. strain NKBG042902 was isolated from coastal areas in Japan. Strain NKBG042902 has four plasmids: pSY8, pSY9, pSY10, and pSY11. Moreover, the hybrid plasmid pUSY02 containing pSY11 and Escherichia coli plasmid pUC18 was constructed for this strain. The genetic manipulation technique using pUSY02 was established for this strain and used in metabolic engineering. Here, we report the draft genome sequence of this strain, which has 77 contigs comprising a total length of 3,319,479 bp, with a G+C content of 49.4%. PMID:25059865

Honda, Toru; Liang, Yue; Arai, Daichi; Ito, Yasuhito; Yoshino, Tomoko

2014-01-01

347

Identification of Sesquiterpene Synthases from Nostoc punctiforme PCC 73102 and Nostoc sp. Strain PCC 7120? †  

PubMed Central

Cyanobacteria are a rich source of natural products and are known to produce terpenoids. These bacteria are the major source of the musty-smelling terpenes geosmin and 2-methylisoborneol, which are found in many natural water supplies; however, no terpene synthases have been characterized from these organisms to date. Here, we describe the characterization of three sesquiterpene synthases identified in Nostoc sp. strain PCC 7120 (terpene synthase NS1) and Nostoc punctiforme PCC 73102 (terpene synthases NP1 and NP2). The second terpene synthase in N. punctiforme (NP2) is homologous to fusion-type sesquiterpene synthases from Streptomyces spp. shown to produce geosmin via an intermediate germacradienol. The enzymes were functionally expressed in Escherichia coli, and their terpene products were structurally identified as germacrene A (from NS1), the eudesmadiene 8a-epi-?-selinene (from NP1), and germacradienol (from NP2). The product of NP1, 8a-epi-?-selinene, so far has been isolated only from termites, in which it functions as a defense compound. Terpene synthases NP1 and NS1 are part of an apparent minicluster that includes a P450 and a putative hybrid two-component protein located downstream of the terpene synthases. Coexpression of P450 genes with their adjacent located terpene synthase genes in E. coli demonstrates that the P450 from Nostoc sp. can be functionally expressed in E. coli when coexpressed with a ferredoxin gene and a ferredoxin reductase gene from Nostoc and that the enzyme oxygenates the NS1 terpene product germacrene A. This represents to the best of our knowledge the first example of functional expression of a cyanobacterial P450 in E. coli. PMID:18658271

Agger, Sean A.; Lopez-Gallego, Fernando; Hoye, Thomas R.; Schmidt-Dannert, Claudia

2008-01-01

348

Staurosporine from the endophytic Streptomyces sp. strain CNS-42 acts as a potential biocontrol agent and growth elicitor in cucumber.  

PubMed

Chinese medicinal plants and their surrounding rhizospheric soil serve as promising sources of actinobacteria. A total of 180 actinobacteria strains were isolated from the rhizosphere soil, leaves, stems, and roots of nine selected plants and have been identified as potential biocontrol agents against Fusarium oxysporum f. sp. cucumerinum. An endophytic strain CNS-42 isolated from Alisma orientale showed the largest zone of inhibition demonstrating a potent effect against F. oxysporum f. sp. cucumerinum and a broad antimicrobial activity against bacteria, yeasts, and other pathogenic fungi. The in vivo biocontrol assays showed that the disease severity index was significantly reduced (P < 0.05), and plant shoot fresh weight and height increased greatly (P < 0.05) in plantlets treated with strain CNS-42 compared to the negative control. This isolate was identified as Streptomyces sp. based on cultural, physiological, morphological characteristics, and 16S rRNA gene analysis. Further bioassay-guided isolation and purification revealed that staurosporine was responsible for its antifungal and plant growth promoting activities and the latter property of staurosporine is reported for the first time. The in vivo assay was further performed and indicated that staurosporine showed good growth promoting effect on the plant shoot biomass of cucumber. This is the first critical evidence identifying CNS-42 as a biocontrol agent for the soil borne pathogen, F. oxysporum f. sp. cucumerinum. PMID:25035061

Li, Xiaolin; Huang, Pei; Wang, Qian; Xiao, Lie; Liu, Miaomiao; Bolla, Krishna; Zhang, Bo; Zheng, Linyong; Gan, Bingcheng; Liu, Xueting; Zhang, Lixin; Zhang, Xiaoping

2014-09-01

349

Characterization of a New Providencia sp. Strain X1 Producing Multiple Xylanases on Wheat Bran  

PubMed Central

Providencia sp. strain X1 showing the highest xylanase activity among six bacterial isolates was isolated from saw-dust decomposing site. Strain X1 produced cellulase-free extracellular xylanase, which was higher in wheat bran medium than in xylan medium, when cultivated at pH 8.0 and 35°C. Zymogram analysis of crude preparation of enzymes obtained while growing on wheat bran and birchwood xylan revealed the presence of seven and two distinct xylanases with estimated molecular weight of 33; 35; 40; 48; 60; 75; and 95?kDa and 33 and 44?kDa, respectively. The crude xylanases were produced on wheat bran medium and showed optimum activity at pH 9.0 and 60°C. The thermotolerance studies showed activity retention of 100% and 85% at 40°C and 60°C after 30 min preincubation at pH 9.0. It was tolerant to lignin, ferulic acid, syringic acid, and guaiacol and retained 90% activity after ethanol treatment. The enzyme preparation was also tolerant to methanol and acetone and showed good activity retention in the presence of metal ions such as Fe2+, Mg2+, Zn2+, and Ca2+. The crude enzyme preparation was classified as endoxylanase based on the product pattern of xylan hydrolysis. Pretreatment of kraft pulp with crude xylanases for 3?h at 60°C led to a decrease in kappa number by 28.5%. The properties of present xylanases make them potentially useful for industrial applications. PMID:24348154

Kumar, Sharad; Singh, Sudheer Kumar; Kumar, Mahadeo

2013-01-01

350

Cloning of a Novel Arylamidase Gene from Paracoccus sp. Strain FLN-7 That Hydrolyzes Amide Pesticides  

PubMed Central

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 Km and kcat 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; Li, Shun-Peng

2012-01-01

351

Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization.  

PubMed Central

Pseudomonas sp. strain ADP metabolizes atrazine to carbon dioxide and ammonia via the intermediate hydroxyatrazine. The genetic potential to produce hydroxyatrazine was previously attributed to a 1.9-kb AvaI DNA fragment from strain ADP (M. L. de Souza, L. P. Wackett, K. L. Boundy-Mills, R. T. Mandelbaum, and M. J. Sadowsky, Appl. Environ. Microbiol. 61:3373-3378, 1995). In this study, sequence analysis of the 1.9-kb AvaI fragment indicated that a single open reading frame, atzA, encoded an activity transforming atrazine to hydroxyatrazine. The open reading frame for the chlorohydrolase was determined by sequencing to be 1,419 nucleotides and encodes a 473-amino-acid protein with a predicted subunit molecular weight of 52,421. The deduced amino acid sequence matched the first 10 amino acids determined by protein microsequencing. The protein AtzA was purified to homogeneity by ammonium sulfate precipitation and anion-exchange chromatography. The subunit and holoenzyme molecular weights were 60,000 and 245,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration chromatography, respectively. The purified enzyme in H2(18)O yielded [18O]hydroxyatrazine, indicating that AtzA is a chlorohydrolase and not an oxygenase. The most related protein sequence in GenBank was that of TrzA, 41% identity, from Rhodococcus corallinus NRRL B-15444R. TrzA catalyzes the deamination of melamine and the dechlorination of deethylatrazine and desisopropylatrazine but is not active with atrazine. AtzA catalyzes the dechlorination of atrazine, simazine, and desethylatrazine but is not active with melamine, terbutylazine, or desethyldesisopropylatrazine. Our results indicate that AtzA is a novel atrazine-dechlorinating enzyme with fairly restricted substrate specificity and contributes to the microbial hydrolysis of atrazine to hydroxyatrazine in soils and groundwater. PMID:8759853

de Souza, M L; Sadowsky, M J; Wackett, L P

1996-01-01

352

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. PMID:15516593

Warren, René; 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

353

Gene replacement of adenylate kinase in the gram-positive thermophile Geobacillus stearothermophilus disrupts adenine nucleotide homeostasis and reduces cell viability  

Microsoft Academic Search

Thermophilic bacteria are of great value for industry and research communities. Unfortunately, the cellular processes and mechanisms of these organisms remain largely understudied. In the present study, we investigate how the inactivation of adenylate kinase (AK) affects the adenine nucleotide homeostasis of a gram-positive moderate thermophile, Geobacillus stearothermophilus strain NUB3621-R. AK plays a major role in the adenine nucleotide homeostasis

Rafael Couñago; Yousif Shamoo

2005-01-01

354

Metabolism of Naphthalene, 1-Naphthol, Indene, and Indole by Rhodococcus sp. Strain NCIMB 12038  

PubMed Central

The regulation of naphthalene and 1-naphthol metabolism in a Rhodococcus sp. (NCIMB 12038) has been investigated. The microorganism utilizes separate pathways for the degradation of these compounds, and they are regulated independently. Naphthalene metabolism was inducible, but not by salicylate, and 1-naphthol metabolism, although constitutive, was also repressed during growth on salicylate. The biochemistry of naphthalene degradation in this strain was otherwise identical to that found in Pseudomonas putida, with salicylate as a central metabolite and naphthalene initially being oxidized via a naphthalene dioxygenase enzyme to cis-(1R,2S)-1,2-dihydroxy-1,2-dihydronaphthalene (naphthalene cis-diol). A dioxygenase enzyme was not expressed under growth conditions which facilitate 1-naphthol degradation. However, biotransformations with indene as a substrate suggested that a monooxygenase enzyme may be involved in the degradation of this compound. Indole was transformed to indigo by both naphthalene-grown NCIMB 12038 and by cells grown in the absence of an inducer. Therefore, the presence of a naphthalene dioxygenase enzyme activity was not necessary for this reaction. Thus, the biotransformation of indole to indigo may be facilitated by another type of enzyme (possibly a monooxygenase) in this organism. PMID:16535479

Boyd, C.; Larkin, M. J.; Reid, K. A.; Sharma, N. D.; Wilson, K.

1997-01-01

355

Dependence of tetrachloroethylene dechlorination on methanogenic substrate consumption by Methanosarcina sp. strain DCM.  

PubMed Central

Tetrachloroethylene (perchloroethylene, PCE) is a suspected carcinogen and a common groundwater contaminant. Although PCE is highly resistant to aerobic biodegradation, it is subject to reductive dechlorination reactions in a variety of anaerobic habitats. The data presented here clearly establish that axenic cultures of Methanosarcina sp. strain DCM dechlorinate PCE to trichloroethylene and that this is a biological reaction. Growth on methanol, acetate, methylamine, and trimethylamine resulted in PCE dechlorination. The reductive dechlorination of PCE occurred only during methanogenesis, and no dechlorination was noted when CH4 production ceased. There was a clear dependence of the extent of PCE dechlorination on the amount of methanogenic substrate (methanol) consumed. The amount of trichloroethylene formed per millimole of CH4 formed remained essentially constant for a 20-fold range of methanol concentrations and for growth on acetate, methylamine, and trimethylamine. These results suggest that the reducing equivalents for PCE dechlorination are derived from CH4 biosynthesis and that the extent of chloroethylene dechlorination can be enhanced by stimulating methanogenesis. It is proposed that electrons transferred during methanogenesis are diverted to PCE by a reduced electron carrier involved in methane formation. Images PMID:3223763

Fathepure, B Z; Boyd, S A

1988-01-01

356

Oxidative Pathway for the Biodegradation of Nitrobenzene by Comamonas sp. Strain JS765  

PubMed Central

Previous studies have shown that the biodegradation of nitrobenzene by Pseudomonas pseudoalcaligenes JS45 proceeds by the reduction of nitrobenzene through nitrosobenzene and hydroxylaminobenzene, followed by rearrangement to 2-aminophenol, which then undergoes meta ring cleavage. We report here the isolation of a Comamonas sp. that uses an oxidative pathway for the complete mineralization of nitrobenzene. The isolate, designated strain JS765, uses nitrobenzene as a sole source of carbon, nitrogen, and energy. Nitrobenzene-grown cells oxidized nitrobenzene, with the stoichiometric release of nitrite. Extracts of nitrobenzene-grown JS765 showed high levels of catechol 2,3-dioxygenase activity that were not abolished by heating the cell extracts to 60(deg)C for 10 min. The ring cleavage product had an absorbance maximum at 375 nm, consistent with that of 2-hydroxymuconic semialdehyde. Both NAD-dependent dehydrogenase and NAD-independent hydrolase activities towards 2-hydroxymuconic semialdehyde were induced in extracts of nitrobenzene-grown cells. Catechol accumulated in the reaction mixture when cells preincubated with 3-chlorocatechol were incubated with nitrobenzene. Conversion of nitrobenzene to catechol by induced cells in the presence of 3-chlorocatechol and (sup18)O(inf2) demonstrated the simultaneous incorporation of two atoms of oxygen, which indicated that the initial reaction was dioxygenation. The results indicate that the catabolic pathway involves an initial dioxygenase attack on nitrobenzene with the release of nitrite and formation of catechol, which is subsequently degraded by a meta cleavage pathway. PMID:16535050

Nishino, S. F.; Spain, J. C.

1995-01-01

357

Kinetics of biotransformation of 1,1,1-trichloroethane by Clostridium sp. strain TCAIIB.  

PubMed Central

Batch experiments were conducted to examine the effects of high concentrations of 1,1,1-trichloroethane (TCA) on the biotransformation of TCA by Clostridium sp. strain TCAIIB. The biotic dehalogenation of TCA to 1,1-dichloroethane by nongrowing cells was measured at 35 degrees C, and the data were used to obtain the kinetic parameters of the Monod relationship half-velocity coefficient Ks (31 microM) and the coefficient of maximum rate of TCA biotransformation (kTCA; 0.28 mumol per mg per day). The yield of biomass decreased with an increase in the TCA concentration, although TCA concentrations up to 750 microM did not completely inhibit bacterial growth. Also, kTCA was higher in the presence of high concentrations of TCA. A mathematical model based on a modified Monod equation was used to describe the biotransformation of TCA. The abiotic transformation of TCA to 1,1-dichloroethene was measured at 35 degrees C, and the first-order formation rate coefficient for 1,1-dichloroethene (ke) was determined to be 0.86 per year. PMID:2729986

Gälli, R; McCarty, P L

1989-01-01

358

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. PMID:15968060

Navarro-Llorens, Juana María; Patrauchan, Marianna A.; Stewart, Gordon R.; Davies, Julian E.; Eltis, Lindsay D.; Mohn, William W.

2005-01-01

359

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. PMID:23028517

Li, Xinliang; Zhang, Xuwang; Zhou, Jiti

2012-01-01

360

Reduction of molybdate to molybdenum blue by Enterobacter sp. strain Dr.Y13.  

PubMed

Extensive use of metals in various industrial applications has caused substantial environmental pollution. Molybdenum-reducing bacteria isolated from soils can be used to remove molybdenum from contaminated environments. In this work we have isolated a local bacterium with the capability to reduce soluble molybdate to the insoluble molybdenum blue. We studied several factors that would optimize molybdate reduction. Electron donor sources such as glucose, sucrose, lactose, maltose and fructose (in decreasing efficiency) supported molybdate reduction after 24 h of incubation with optimum glucose concentration for molybdate reduction at 1.5% (w/v). The optimum pH, phosphate and molybdate concentrations, and temperature for molybdate reduction were pH 6.5, 5.0, 25 to 50 mM and 37 degrees C, respectively. The Mo-blue produced by cellular reduction exhibited a unique absorption spectrum with a maximum peak at 865 nm and a shoulder at 700 nm. Metal ions such as chromium, cadmium, copper, silver and mercury caused approximately 73, 71, 81, 77 and 78% inhibition of the molybdenum-reducing activity, respectively. All of the respiratory inhibitors tested namely rotenone, azide, cyanide and antimycin A did not show any inhibition to the molybdenum-reducing activity suggesting components of the electron transport system are not responsible for the reducing activity. The isolate was tentatively identified as Enterobacter sp. strain Dr.Y13 based on carbon utilization profiles using Biolog GN plates and partial 16S rDNA molecular phylogeny. PMID:19455513

Shukor, M Y; Rahman, M F; Shamaan, N A; Syed, M A

2009-09-01

361

Cloning of a gene from Pseudomonas sp. strain PG2982 conferring increased glyphosate resistance.  

PubMed Central

A plasmid carrying a 2.4-kilobase-pair fragment of DNA from Pseudomonas sp. strain PG2982 has been isolated which was able to increase the glyphosate resistance of Escherichia coli cells. The increase in resistance was dependent on the presence of a plasmid-encoded protein with a molecular weight of approximately 33,000, the product of a translational fusion between a gene on the vector, pACYC184, and the insert DNA. An overlapping region of the PG2982 chromosome carrying the entire gene (designated igrA) was cloned, and a plasmid (pPG18) carrying the gene was also able to increase glyphosate resistance in E. coli. A protein with a molecular weight of approximately 40,000 was encoded by the PG2982 DNA contained in pPG18. This plasmid was not able to complement a mutation in the gene for 5-enolpyruvylshikimate-3-phosphate synthase (aroA) in E. coli, and modification of glyphosate by E. coli cells containing the plasmid could not be demonstrated. The nucleotide sequence of the PG2982 DNA contained an open reading frame able to encode a protein with a calculated molecular weight of 39,396. Images PMID:2268152

Fitzgibbon, J E; Braymer, H D

1990-01-01

362

Purification and Characterization of Hydroxyquinol 1,2-Dioxygenase from Azotobacter sp. Strain GP1  

PubMed Central

Hydroxyquinol 1,2-dioxygenase was purified from cells of the soil bacterium Azotobacter sp. strain GP1 grown with 2,4,6-trichlorophenol as the sole source of carbon. The presumable function of this dioxygenase enzyme in the degradative pathway of 2,4,6-trichlorophenol is discussed. The enzyme was highly specific for 6-chlorohydroxyquinol (6-chloro-1,2,4-trihydroxybenzene) and hydroxyquinol (1,2,4-trihydroxybenzene) and was found to perform ortho cleavage of the hydroxyquinol compounds, yielding chloromaleylacetate and maleylacetate, respectively. With the conversion of 1 mol of 6-chlorohydroxyquinol, the consumption of 1 mol of O(inf2) and the formation of 1 mol of chloromaleylacetate were observed. Catechol was not accepted as a substrate. The enzyme has to be induced, and no activity was found in cells grown on succinate. The molecular weight of native hydroxyquinol 1,2-dioxygenase was estimated to 58,000, with a sedimentation coefficient of 4.32. The subunit molecular weight of 34,250 indicates a dimeric structure of the dioxygenase enzyme. The addition of Fe(sup2+) ions significantly activated enzyme activity, and metal-chelating agents inhibited it. Electron paramagnetic resonance data are consistent with high-spin iron(III) in a rhombic environment. The NH(inf2)-terminal amino acid sequence was determined for up to 40 amino acid residues and compared with sequences from literature data for other catechol and chlorocatechol dioxygenases. PMID:16535063

Latus, M.; Seitz, H.; Eberspacher, J.; Lingens, F.

1995-01-01

363

Spirocyclic Drimanes from the Marine Fungus Stachybotrys sp. Strain MF347  

PubMed Central

A novel spirocyclic drimane coupled by two drimane fragment building blocks 2 and a new drimane 1 were identified in mycelia and culture broth of Stachybotrys sp. MF347. Their structures were established by spectroscopic means. This is the first example of spirocyclic drimane coupled by a spirodihydrobenzofuranlactam unit and a spirodihydroisobenzofuran unit; and the connecting position being N-C instead of an N and N connecting unit. Strain MF347 produced also the known spirocyclic drimanes stachybocin A (12) and stachybocin B (11) featured by two sesquiterpene-spirobenzofuran structural units connected by a lysine residue; the known spirocyclic drimanes chartarlactam O (5); chartarlactam K (6); F1839A (7); stachybotrylactam (8); stachybotramide (9); and 2?-acetoxystachybotrylactam acetate (10); as well as ilicicolin B (13), a known sesquiterpene. The relative configuration of two known spirobenzofuranlactams (3 and 4) was determined. All compounds were subjected to biological activity tests. The spirocyclic drimane 2, 11, and 12, as well as the sesquiterpene 13, exhibited antibacterial activity against the clinically relevant methicillin-resistant Staphylococcus aureus (MRSA). PMID:24694571

Wu, Bin; Oesker, Vanessa; Wiese, Jutta; Malien, Susann; Schmaljohann, Rolf; Imhoff, Johannes F.

2014-01-01

364

Discovery and characterization of a 5-hydroxymethylfurfural oxidase from Methylovorus sp. strain MP688.  

PubMed

In the search for useful and renewable chemical building blocks, 5-hydroxymethylfurfural (HMF) has emerged as a very promising candidate, as it can be prepared from sugars. HMF can be oxidized to 2,5-furandicarboxylic acid (FDCA), which is used as a substitute for petroleum-based terephthalate in polymer production. On the basis of a recently identified bacterial degradation pathway for HMF, candidate genes responsible for selective HMF oxidation have been identified. Heterologous expression of a protein from Methylovorus sp. strain MP688 in Escherichia coli and subsequent enzyme characterization showed that the respective gene indeed encodes an efficient HMF oxidase (HMFO). HMFO is a flavin adenine dinucleotide-containing oxidase and belongs to the glucose-methanol-choline-type flavoprotein oxidase family. Intriguingly, the activity of HMFO is not restricted to HMF, as it is active with a wide range of aromatic primary alcohols and aldehydes. The enzyme was shown to be relatively thermostable and active over a broad pH range. This makes HMFO a promising oxidative biocatalyst that can be used for the production of FDCA from HMF, a reaction involving both alcohol and aldehyde oxidations. PMID:24271187

Dijkman, Willem P; Fraaije, Marco W

2014-02-01

365

Discovery and Characterization of a 5-Hydroxymethylfurfural Oxidase from Methylovorus sp. Strain MP688  

PubMed Central

In the search for useful and renewable chemical building blocks, 5-hydroxymethylfurfural (HMF) has emerged as a very promising candidate, as it can be prepared from sugars. HMF can be oxidized to 2,5-furandicarboxylic acid (FDCA), which is used as a substitute for petroleum-based terephthalate in polymer production. On the basis of a recently identified bacterial degradation pathway for HMF, candidate genes responsible for selective HMF oxidation have been identified. Heterologous expression of a protein from Methylovorus sp. strain MP688 in Escherichia coli and subsequent enzyme characterization showed that the respective gene indeed encodes an efficient HMF oxidase (HMFO). HMFO is a flavin adenine dinucleotide-containing oxidase and belongs to the glucose-methanol-choline-type flavoprotein oxidase family. Intriguingly, the activity of HMFO is not restricted to HMF, as it is active with a wide range of aromatic primary alcohols and aldehydes. The enzyme was shown to be relatively thermostable and active over a broad pH range. This makes HMFO a promising oxidative biocatalyst that can be used for the production of FDCA from HMF, a reaction involving both alcohol and aldehyde oxidations. PMID:24271187

Dijkman, Willem P.

2014-01-01

366

Kinetics of molybdenum reduction to molybdenum blue by Bacillus sp. strain A.rzi.  

PubMed

Molybdenum is very toxic to agricultural animals. Mo-reducing bacterium can be used to immobilize soluble molybdenum to insoluble forms, reducing its toxicity in the process. In this work the isolation of a novel molybdate-reducing Gram positive bacterium tentatively identified as Bacillus sp. strain A.rzi from a metal-contaminated soil is reported. The cellular reduction of molybdate to molybdenum blue occurred optimally at 4 mM phosphate, using 1% (w/v) glucose, 50 mM molybdate, between 28 and 30 °C and at pH 7.3. The spectrum of the Mo-blue product showed a maximum peak at 865 nm and a shoulder at 700 nm. Inhibitors of bacterial electron transport system (ETS) such as rotenone, sodium azide, antimycin A, and potassium cyanide could not inhibit the molybdenum-reducing activity. At 0.1 mM, mercury, copper, cadmium, arsenic, lead, chromium, cobalt, and zinc showed strong inhibition on molybdate reduction by crude enzyme. The best model that fitted the experimental data well was Luong followed by Haldane and Monod. The calculated value for Luong's constants p max, K(s), S(m), and n was 5.88 ?mole Mo-blue hr(-1), 70.36 mM, 108.22 mM, and 0.74, respectively. The characteristics of this bacterium make it an ideal tool for bioremediation of molybdenum pollution. PMID:24369531

Othman, A R; Bakar, N A; Halmi, M I E; Johari, W L W; Ahmad, S A; Jirangon, H; Syed, M A; Shukor, M Y

2013-01-01

367

Biogenic Production of Photosensitive Arsenic-Sulfide Nanotubes by Shwanella sp. strain HN-41  

SciTech Connect

This paper describes the novel production of extensive filamentous, arsenic-sulfide (As-S) nanotubes (20 - 100 nm dia. X ?30 ?m length) resulting from the dissimilatoryreduction of thiosulfate and arsenate by the bacterium Shewanella sp. HN-41. While there have been several reports of bacterial-produced nanowires composed entirely of biological macromolecules, here we report for the first time the biogenic formation ofphotosensitive and electroconductive nanotubes comprised of crystalline As-S and bacterial extracellular polymeric substances (EPS). To our knowledge, there have been no previous reports of the synthesis of such a material either by chemical or biological means. The biogenic As-S nanotubes reported here represent a significant advancement as building blocks for the production of nanodevices because of their high aspect ratios and unique size dependent properties. We characterized the structural evolution of the bacterial As-S nanotubes formed by strain HN-41 using XAFS spectra as well as XRD analyses, as a function of time and extent of bacterial reduction. In addition, we characterized the electrical and photoconductive properties of the As-S nanotubes. Upon aging, the As-S nanotubes behaved as metals and semiconductors in terms of their electrical and photoconductive properties, respectively. These results indicate that the dissimilatory bacterium Shewanella may be an excellent biological tool to bioengineer As-S nanotubes, which may provide useful materials for novel nano- and optoelectronic devices.

Lee, Ji-Hoon; Kim, Min-Gyu; Yoo, Bongyoung; Myung, Nosang V.; Maeng, Jongsun; Lee, Takhe; Dohnalkova, Alice; Fredrickson, Jim K.; Sadowsky, Michael J.; Hur, Hor-Gil

2007-12-18

368

Metabolism of butyl benzyl phthalate by Gordonia sp. strain MTCC 4818.  

PubMed

The microbial degradative characteristics of butyl benzyl phthalate (BBP) were investigated by the Gordonia sp. strain MTCC 4818 isolated from creosote-contaminated soil. The test organism can utilize a number of phthalate esters as sole sources of carbon and energy, where BBP was totally degraded within 4 days under shake culture conditions. High performance liquid chromatography profile of the metabolites isolated from spent culture indicated the accumulation of two major products apart from phthalic acid (PA), which were characterized by gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy as mono-n-butyl phthalate (MBuP) and monobenzyl phthalate (MBzP). Neither of the metabolites, MBuP, MBzP or PA, supported growth of the test organism, while in resting cell transformation, the monoesters were hydrolyzed to PA to a very minor extent, which was found to be a dead-end product in the degradation process. On the other hand, the test organism grew well on benzyl alcohol and butanol, the hydrolyzed products of BBP. The esterase(s) was found to be inducible in nature and can hydrolyze in vitro the seven different phthalate diesters tested to their corresponding monoesters irrespective of their support to the growth of the test organism. PMID:12943660

Chatterjee, Subhankar; Dutta, Tapan K

2003-09-12

369

Isomaltulose Synthase from Klebsiella sp. Strain LX3: Gene Cloning and Characterization and Engineering of Thermostability  

PubMed Central

The gene (palI) encoding isomaltulose synthase (PalI) from a soil bacterial isolate, Klebsiella sp. strain LX3, was cloned and characterized. PalI converts sucrose into isomaltulose, trehalulose, and trace amounts of glucose and fructose. Sequence domain analysis showed that PalI contains an ?-amylase domain and (?/?)8-barrel structures, suggesting that it belongs to the ?-amylase family. Sequence alignment indicated that the five amino acid residues of catalytic importance in ?-amylases and glucosyltransferases (Asp241, Glu295, Asp369, His145, and His368) are conserved in PalI. Purified recombinant PalI displayed high catalytic efficiency, with a Km of 54.6 ± 1.7 mM for sucrose, and maximum activity (approximately 328.0 ± 2.5 U/mg) at pH 6.0 and 35°C. PalI activity was strongly inhibited by Fe3+ and Hg2+ and was enhanced by Mn2+ and Mg2+. The half-life of PalI was 1.8 min at 50°C. Replacement of selected amino acid residues by proline significantly increased the thermostability of PalI. Simultaneous replacement of Glu498 and Arg310 with proline resulted in an 11-fold increase in the half-life of PalI at 50°C. PMID:12039719

Zhang, Daohai; Li, Xianzhen; Zhang, Lian-Hui

2002-01-01

370

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 PMID:6425264

Serrano, A; Rivas, J; Losada, M

1984-01-01

371

Xylanase production by Burkholderia sp. DMAX strain under solid state fermentation using distillery spent wash.  

PubMed

Xylanase production by a newly isolated strain of Burkholderia sp. was studied under solid state fermentation using anaerobically treated distillery spent wash. Response surface methodology (RSM) involving Box-Behnken design was employed for optimizing xylanase production. The interactions between distillery effluent concentration, initial pH, moisture ratio and inoculum size were investigated and modeled. Under optimized conditions, xylanase production was found to be in the range of 5200-5600 U/g. The partially purified enzyme recovered after ammonium sulphate fractionation showed maximum activity at 50 degrees C and pH 8.6. Kinetic parameters like Km and Vmax for xylan were found to be 12.75 mg/ml and 165 micromol/mg/min. In the presence of metal ions such as Ca2+, Co2+, Mn2+, Ba2+, Mg2+ and protein disulphide reducing agents such as beta-mercaptoethanol and dithiotheritol (DTT) the activity of enzyme increased, where as strong inhibition of enzyme activity was observed in the presence of Cu2+, Ag+, Fe2+ and SDS. The crude enzyme hydrolysed lignocellulosic substrate, wheat bran as well as industrial pulp. PMID:18374565

Mohana, Sarayu; Shah, Amita; Divecha, Jyoti; Madamwar, Datta

2008-11-01

372

Kinetics of Molybdenum Reduction to Molybdenum Blue by Bacillus sp. Strain A.rzi  

PubMed Central

Molybdenum is very toxic to agricultural animals. Mo-reducing bacterium can be used to immobilize soluble molybdenum to insoluble forms, reducing its toxicity in the process. In this work the isolation of a novel molybdate-reducing Gram positive bacterium tentatively identified as Bacillus sp. strain A.rzi from a metal-contaminated soil is reported. The cellular reduction of molybdate to molybdenum blue occurred optimally at 4?mM phosphate, using 1% (w/v) glucose, 50?mM molybdate, between 28 and 30°C and at pH 7.3. The spectrum of the Mo-blue product showed a maximum peak at 865?nm and a shoulder at 700?nm. Inhibitors of bacterial electron transport system (ETS) such as rotenone, sodium azide, antimycin A, and potassium cyanide could not inhibit the molybdenum-reducing activity. At 0.1?mM, mercury, copper, cadmium, arsenic, lead, chromium, cobalt, and zinc showed strong inhibition on molybdate reduction by crude enzyme. The best model that fitted the experimental data well was Luong followed by Haldane and Monod. The calculated value for Luong's constants pmax, Ks, Sm, and n was 5.88??mole Mo-blue hr?1, 70.36?mM, 108.22?mM, and 0.74, respectively. The characteristics of this bacterium make it an ideal tool for bioremediation of molybdenum pollution. PMID:24369531

Othman, A. R.; Bakar, N. A.; Halmi, M. I. E.; Johari, W. L. W.; Ahmad, S. A.; Jirangon, H.; Syed, M. A.; Shukor, M. Y.

2013-01-01

373

Low-Temperature Lipase from Psychrotrophic Pseudomonas sp. Strain KB700A  

PubMed Central

We have previously reported that a psychrotrophic bacterium, Pseudomonas sp. strain KB700A, which displays sigmoidal growth even at ?5°C, produced a lipase. A genomic DNA library of strain KB700A was introduced into Escherichia coli TG1, and screening on tributyrin-containing agar plates led to the isolation of the lipase gene. Sequence analysis revealed an open reading frame (KB-lip) consisting of 1,422 nucleotides that encoded a protein (KB-Lip) of 474 amino acids with a molecular mass of 49,924 Da. KB-Lip showed 90% identity with the lipase from Pseudomonas fluorescens and was found to be a member of Subfamily I.3 lipase. Gene expression and purification of the recombinant protein were performed. KB-Lip displayed high lipase activity in the presence of Ca2+. Addition of EDTA completely abolished lipase activity, indicating that KB-Lip was a Ca2+-dependent lipase. Addition of Mn2+ and Sr2+ also led to enhancement of lipase activity but to a much lower extent than that produced by Ca2+. The optimal pH of KB-Lip was 8 to 8.5. The addition of detergents enhanced the enzyme activity. When p-nitrophenyl esters and triglyceride substrates of various chain-lengths were examined, the lipase displayed highest activity towards C10 acyl groups. We also determined the positional specificity and found that the activity was 20-fold higher toward the 1(3) position than toward the 2 position. The optimal temperature for KB-Lip was 35°C, lower than that for any previously reported Subfamily I.3 lipase. The enzyme was also thermolabile compared to these lipases. Furthermore, KB-Lip displayed higher levels of activity at low temperatures than did other enzymes from Subfamily I.3, indicating that KB-Lip has evolved to function in cold environments, in accordance with the temperature range for growth of its psychrotrophic host, strain KB700A. PMID:11526006

Rashid, Naeem; Shimada, Yuji; Ezaki, Satoshi; Atomi, Haruyuki; Imanaka, Tadayuki

2001-01-01

374

Isolation of Paenibacillus sp. and Variovorax sp. strains from decaying woods and characterization of their potential for cellulose deconstruction  

PubMed Central

Prospection of cellulose-degrading bacteria in natural environments allows the identification of novel cellulases and hemicellulases that could be useful in second-generation bioethanol production. In this work, cellulolytic bacteria were isolated from decaying native forest soils by enrichment on cellulose as sole carbon source. There was a predominance of Gram positive isolates that belonged to the phyla Proteobacteria and Firmicutes. Many primary isolates with cellulolytic activity were not pure cultures. From these consortia, isolation of pure constituents was attempted in order to test the hypothesis whether microbial consortia are needed for full degradation of complex substrates. Two isolates, CB1-2-A-5 and VG-4-A-2, were obtained as the pure constituents of CB1-2 and VG-4 consortia, respectively. Based on 16S RNA sequence, they could be classified as Variovorax paradoxus and Paenibacillus alvei. Noteworthy, only VG-4 consortium showed measurable xylan degrading capacity and signs of filter paper degradation. However, no xylan or filter paper degrading capacities were observed for the pure cultures isolated from it, suggesting that other members of this consortium were necessary for these hydrolyzing activities. Our results indicated that Paenibacillus sp. and Variovorax sp. as well as VG-4 consortium, might be a useful source of hydrolytic enzymes. Moreover, although Variovorax sp. had been previously identified in metagenomic studies of cellulolytic communities, this is the first report on the isolation and characterization of this microorganism as a cellulolytic genus. PMID:23301200

Ghio, Silvina; Lorenzo, Gonzalo Sabarís Di; Lia, Verónica; Talia, Paola; Cataldi, Angel; Grasso, Daniel; Campos, Eleonora

2012-01-01

375

Molecular cloning and characterization of thermostable esterase and lipase from Geobacillus thermoleovorans YN isolated from desert soil in Egypt  

Microsoft Academic Search

Genes encoding an esterase (EstA) and lipase (LipA) from Geobacillus thermoleovorans YN, a strain isolated from Egyptian desert soil, were cloned and the respective proteins were expressed in Escherichia coli and characterized. Whereas LipA was cloned directly by PCR amplification from genomic DNA, a genomic library composed of 3000 clones was screened on tributyrin agar plates to find EstA. An

Nadia A. Soliman; Michael Knoll; Yasser R. Abdel-Fattah; Rolf D. Schmid; Stefan Lange

2007-01-01

376

Inactivation of Geobacillus stearothermophilus in canned food and coconut milk samples by addition of enterocin AS48  

Microsoft Academic Search

The cyclic bacteriocin enterocin AS-48 was tested on a cocktail of two Geobacillus stearothermophilus strains in canned food samples (corn and peas), and in coconut milk. AS-48 (7?g\\/g) reduced viable cell counts below detection levels in samples from canned corn and peas stored at 45°C for 30 days. In coconut milk, bacterial inactivation by AS-48 (1.75?g\\/ml) was even faster. In

Pilar Martínez Viedma; Hikmate Abriouel; Nabil Ben Omar; Rosario Lucas López; Eva Valdivia; Antonio Gálvez

2009-01-01

377

DNA Microarray Analysis of Redox-Responsive Genes in the Genome of the Cyanobacterium Synechocystis sp. Strain PCC 6803  

PubMed Central

Whole-genome DNA microarrays were used to evaluate the effect of the redox state of the photosynthetic electron transport chain on gene expression in Synechocystis sp. strain PCC 6803. Two specific inhibitors of electron transport, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), were added to the cultures, and changes in accumulation of transcripts were examined. About 140 genes were highlighted as reproducibly affected by the change in the redox state of the photosynthetic electron transport chain. It was shown that some stress-responsive genes but not photosynthetic genes were under the control of the redox state of the plastoquinone pool in Synechocystis sp. strain PCC 6803. PMID:12591891

Hihara, Yukako; Sonoike, Kintake; Kanehisa, Minoru; Ikeuchi, Masahiko

2003-01-01

378

Biodegradation and detoxification of bisphenol A with one newly-isolated strain Bacillus sp. GZB: kinetics, mechanism and estrogenic transition.  

PubMed

A facultative anaerobic bacterial strain, Bacillus sp. GZB, was isolated and identified to effectively degrade bisphenol A (BPA) under anaerobic and aerobic conditions. Under anaerobic condition, Fe(3+) can be used as an electron acceptor for Bacillus sp. GZB, while 5 mg L(-1) BPA can be fully removed and 51% was mineralized under optimal aerobic conditions. Additionally, seven metabolites were identified by GC-MS, four of which were doubly confirmed by authentic standards (two synthesized) and three of four initial degradation intermediates were also quantified during BPA aerobic degradation. The evolution of 1-(4-hydroxyphenyl)ethanone showed a similar tendency with estrogenic activity changing during BPA biodegradation course, indicating its potential estrogenicity. The estrogenicity temporary increase first and decline ultimately during BPA degradation revealing the GZB can effectively detoxify BPA as well as its estrogenic intermediates. This was the first study to report a facultative anaerobic strain can degrade BPA with or without of oxygen. PMID:22507902

Li, Guiying; Zu, Lei; Wong, Po-Keung; Hui, Xinping; Lu, Yu; Xiong, Jukun; An, Taicheng

2012-06-01

379

Genome sequence of Nitrosomonas sp. strain AL212, an ammonia-oxidizing bacterium sensitive to high levels of ammonia.  

PubMed

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 K(m)), 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. PMID:21868805

Suwa, Yuichi; 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

2011-09-01

380

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

2011-09-01

381

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

2013-01-01

382

Draft Genome Sequence of a Sulfide-Oxidizing, Autotrophic Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi)  

PubMed Central

The draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain MS-G (Chloroflexi), isolated from Mushroom Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 4,784,183 bp in 251 contigs. The draft genome is predicted to encode 4,059 protein coding genes, 49 tRNA encoding genes, and 3 rRNA operons. PMID:25189583

Thiel, Vera; Hamilton, Trinity L.; Tomsho, Lynn P.; Burhans, Richard; Gay, Scott E.; Schuster, Stephan C.; Ward, David M.

2014-01-01

383

Transformation of Isopropylamine to L-Alaninol by Pseudomonas sp. Strain KIE171 Involves N-Glutamylated Intermediates  

Microsoft Academic Search

Pseudomonas sp. strain KIE171 was able to grow with isopropylamine or L-alaninol (S-()-2-amino-1- propanol) as the sole carbon source, but not with D-alaninol. To investigate the hypothesis that L-alaninol is an intermediate in the degradation of isopropylamine, two mini-Tn5 mutants unable to utilize both isopro- pylamine and L-alaninol were isolated. Whereas mutant KIE171-BI transformed isopropylamine to L-alaninol, mutant KIE171-BII failed

S. I. de Azevedo Wasch; Jan R. van der Ploeg; Tere Maire; Alice Lebreton; Andreas Kiener; Thomas Leisinger

2002-01-01

384

Hydrogen production from organic substrates in an aerobic nitrogen-fixing marine unicellular cyanobacterium Synechococcus sp. strain Miami BG 043511  

Microsoft Academic Search

Synechococcus sp. strain Miami BG 043511 exhibits very high H[sub 2] photoproduction from water, but the H[sub 2] photo-production capability is lost rapidly with the age of the batch culture. The decrease of the capability coincides with the decrease of cellular glucose content. However, H[sub 2] photoproduction capability can be restored by the addition of organic substrates. Among 40 organic

Yao-Hua Luo; Akira Mitsui

1994-01-01

385

Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-Respiring Bacterium Isolated from Japanese Paddy Soil  

PubMed Central

Here, we report a draft genome sequence of Geobacter sp. strain OR-1, an arsenate-respiring bacterium isolated from Japanese paddy soil. It contained two distinct arsenic islands, one including genes for a respiratory arsenate reductase (Arr) as well as for arsenic resistance (arsD-arsA-acr3-arsR-arrA-arrB) and the second containing only genes for arsenic resistance. PMID:25635012

Ehara, Ayaka; Suzuki, Haruo

2015-01-01

386

Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-Respiring Bacterium Isolated from Japanese Paddy Soil.  

PubMed

Here, we report a draft genome sequence of Geobacter sp. strain OR-1, an arsenate-respiring bacterium isolated from Japanese paddy soil. It contained two distinct arsenic islands, one including genes for a respiratory arsenate reductase (Arr) as well as for arsenic resistance (arsD-arsA-acr3-arsR-arrA-arrB) and the second containing only genes for arsenic resistance. PMID:25635012

Ehara, Ayaka; Suzuki, Haruo; Amachi, Seigo

2015-01-01

387

Draft Genome Sequence of Marine Bacterium Streptomyces sp. Strain CNQ431, a Producer of the Cytokine Inhibitor Splenocin.  

PubMed

Currently, corticosteroids are the most potent anti-inflammatory drugs on the market. Here, we announce the draft genome sequence of the marine-derived Streptomyces sp. strain CNQ431, which produces cytokine inhibitors, termed splenocins, which display potent suppression of cytokine production at a comparable level to that of corticosteroids. The genome is approximately 498,750 bp with 72.03% G+C content. PMID:25614558

Yu, Mingjia; Dai, Zheng; Qu, Xudong; Gao, Xu

2015-01-01

388

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

2013-10-18

389

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

390

Alpha-tocopherol is essential for acquired chill-light tolerance in the cyanobacterium Synechocystis sp. strain PCC 6803.  

PubMed

Unlike Escherichia coli, the cyanobacterium Synechocystis sp. strain PCC 6803 is insensitive to chill (5 degrees C) in the dark but rapidly losses viability when exposed to chill in the light (100 micromol photons m(-2) s(-1)). Preconditioning at a low temperature (15 degrees 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 alpha-tocopherol after exposure to chill-light stress. Mutants unable to synthesize alpha-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 P(petE) controlled the level of alpha-tocopherol and ACLT. We conclude that alpha-tocopherol is essential for ACLT of Synechocystis sp. strain PCC 6803. The role of alpha-tocopherol in ACLT may be based largely on a nonantioxidant activity that is not possessed by other tocopherols or pathway intermediates. PMID:18165303

Yang, Yang; Yin, Chuntao; Li, Weizhi; Xu, Xudong

2008-03-01

391

A novel thermostable nitrilase superfamily amidase from Geobacillus pallidus showing acyl transfer activity  

Microsoft Academic Search

An amidase (EC 3.5.1.4) in branch 2 of the nitrilase superfamily, from the thermophilic strain Geobacillus pallidus RAPc8, was produced at high expression levels (20 U\\/mg) in small-scale fermentations of Escherichia coli. The enzyme was purified to 90% homogeneity with specific activity of 1,800 U\\/mg in just two steps, namely, heat-treatment\\u000a and gel permeation chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and

H. S. Makhongela; A. E. Glowacka; V. B. Agarkar; B. T. Sewell; B. Weber; R. A. Cameron; D. A. Cowan; S. G. Burton

2007-01-01

392

Novel Tripartite Aromatic Acid Transporter Essential for Terephthalate Uptake in Comamonas sp. Strain E6  

PubMed Central

It has been suggested that a novel type of aromatic acid transporter, which is similar to the tripartite tricarboxylate transporter (TTT), is involved in terephthalate (TPA) uptake by Comamonas sp. strain E6. This suggestion was based on the presence of the putative TPA-binding protein gene, tphC, in the TPA catabolic operon. The tphC gene is essential for growth on TPA and is similar to the genes encoding TTT-like substrate-binding proteins. Here we identified two sets of E6 genes, tctBA and tpiBA, which encode TTT-like cytoplasmic transmembrane proteins. Disruption of tctA showed no influence on TPA uptake but resulted in a complete loss of the uptake of citrate. This loss suggests that tctA is involved in citrate uptake. On the other hand, disruption of tpiA or tpiB demonstrated that both genes are essential for TPA uptake. Only when both tphC and tpiBA were introduced with the TPA catabolic genes into cells of a non-TPA-degrading Pseudomonas strain did the resting cells of the transformant acquire the ability to convert TPA. From all these results, it was concluded that the TPA uptake system consists of the TpiA-TpiB membrane components and TPA-binding TphC. Interestingly, not only was the tpiA mutant of E6 unable to grow on TPA or isophthalate, it also showed significant growth delays on o-phthalate and protocatechuate. These results suggested that the TpiA-TpiB membrane components are able to interact with multiple substrate-binding proteins. The tpiBA genes were constitutively transcribed as a single operon in E6 cells, whereas the transcription of tphC was positively regulated by TphR. TPA uptake by E6 cells was completely inhibited by a protonophore, carbonyl cyanide m-chlorophenyl hydrazone, indicating that the TPA uptake system requires a proton motive force. PMID:23913423

Hosaka, Masaru; Kamimura, Naofumi; Toribami, Shotaro; Mori, Kosuke; Kasai, Daisuke; Fukuda, Masao

2013-01-01

393

Characterisation and molecular dynamic simulations of J15 asparaginase from Photobacterium sp. strain J15.  

PubMed

Genome mining revealed a 1011 nucleotide-long fragment encoding a type I L-asparaginase (J15 asparaginase) from the halo-tolerant Photobacterium sp. strain J15. The gene was overexpressed in pET-32b (+) vector in E. coli strain Rosetta-gami B (DE3) pLysS and purified using two-step chromatographic methods: Ni(2+)-Sepharose affinity chromatography and Q-Sepharose anion exchange chromatography. The final specific activity and yield of the enzyme achieved from these steps were 20 U/mg and 49.2%, respectively. The functional dimeric form of J15-asparaginase was characterised with a molecular weight of ~70 kDa. The optimum temperature and pH were 25°C and pH 7.0, respectively. This protein was stable in the presence of 1 mM Ni(2+) and Mg(2+), but it was inhibited by Mn(2+), Fe(3+) and Zn(2+)at the same concentration. J15 asparaginase actively hydrolysed its native substrate, L-asparagine, but had low activity towards L-glutamine.The melting temperature of J15 asparaginase was ~51°C, which was determined using denatured protein analysis of CD spectra. The Km, Kcat, Kcat/Km of J15 asparaginase were 0.76 mM, 3.2 s(-1), and 4.21 s(-1)mM(-1), respectively. Conformational changes of the J15 asparaginase 3D structure at different temperatures (25°C, 45°C, and 65°C) were analysed using Molecular Dynamic simulations. From the analysis, residues Tyr24, His22, Gly23, Val25 and Pro26 may be directly involved in the 'open' and 'closed' lid-loop conformation, facilitating the conversion of substrates during enzymatic reactions. The properties of J15 asparaginase, which can work at physiological pH and has low glutaminase activity, suggest that this could be a good candidate for reducing toxic effects during cancer treatment. PMID:25337608

Yaacob, Mohd Adilin; Hasan, Wan Atiqah Najiah Wan; Ali, Mohd Shukuri Mohamad; Rahman, Raja Noor Zaliha Raja Abdul; Salleh, Abu Bakar; Basri, Mahiran; Leow, Thean Chor

2014-10-22

394

Initiation and ontogeny of vesicles in cultured Frankia sp. strain HFPArI3.  

PubMed Central

Removal of combined nitrogen from the medium of Frankia sp. strain HFPArI3 induced the formation of specialized structures, called vesicles, which are the proposed site of nitrogen fixation. After 5 to 6 h of culture on N-free medium, newly formed vesicles, termed provesicles, arose from the tips of some hyphae. These structures were spherical, phase dark, ca. 1.5 to 2.0 micron in diameter, and were not associated with acetylene reduction (nitrogenase) activity. Provesicles reached their greatest frequency after ca. 24 h of N-free culture. Provesicles increased in size to become mature vesicles which first appeared after 18 to 20 h of N-free culture. They were ca. 2.5 micron in diameter, phase bright, and reached their greatest frequency after 5 to 6 days, at which time nitrogenase activity peaked. Some vesicles eventually became damaged structurally and took on the appearance of ghosts. Transmission electron micrographs revealed an increase in size from provesicle to mature vesicle. Also evident with the micrographs were the presence of a septum between the young provesicle and parental hypha, the presence of glycogen in some young vesicles, the development of internal septations as vesicles matured, and the degradation of cytoplasm and internal septae in ghost vesicles. The extent to which the formation of vesicles is reversible by the addition of NH4+ was investigated. Commitment times of 3.2 and 6.5 h were obtained for provesicles and vesicles, respectively. A concentration-dependent inhibition of nitrogenase by NH4+ was demonstrated. The structure of preexisting vesicles was also affected by addition of NH4+ to the culture medium. Images PMID:6594327

Fontaine, M S; Lancelle, S A; Torrey, J G

1984-01-01

395

Expanding the Direct HetR Regulon in Anabaena sp. Strain PCC 7120  

PubMed Central

In response to a lack of environmental combined nitrogen, the filamentous cyanobacterium Anabaena sp. strain PCC 7120 differentiates nitrogen-fixing heterocyst cells in a periodic pattern. HetR is a transcription factor that coordinates the regulation of this developmental program. An inverted repeat-containing sequence in the hepA promoter required for proheterocyst-specific transcription was identified based on sequence similarity to a previously characterized binding site for HetR in the promoter of hetP. The binding affinity of HetR for the hepA site is roughly an order of magnitude lower than that for the hetP binding site. A BLAST search of the Anabaena genome identified 166 hepA-like sites that occur as single or tandem sites (two binding sites separated by 13 bp). The vast majority of these sites are present in predicted intergenic regions. HetR bound five representative single binding sites in vitro, and binding was abrogated by transversions in the binding sites that conserved the inverted repeat nature of the sites. Binding to four representative tandem sites was not observed. Transcriptional fusions of the green fluorescent protein gene gfp with putative promoter regions associated with the representative binding sites indicated that HetR could function as either an activator or repressor and that activation was cell-type specific. Taken together, we have expanded the direct HetR regulon and propose a model in which three categories of HetR binding sites, based on binding affinity and nucleotide sequence, contribute to three of the four phases of differentiation. PMID:24375104

Videau, Patrick; Ni, Shuisong; Rivers, Orion S.; Ushijima, Blake; Feldmann, Erik A.; Cozy, Loralyn M.; Kennedy, Michael A.

2014-01-01

396

Characterization and Evolution of Anthranilate 1,2-Dioxygenase from Acinetobacter sp. Strain ADP1  

PubMed Central

The two-component anthranilate 1,2-dioxygenase of the bacterium Acinetobacter sp. strain ADP1 was expressed in Escherichia coli and purified to homogeneity. This enzyme converts anthranilate (2-aminobenzoate) to catechol with insertion of both atoms of O2 and consumption of one NADH. The terminal oxygenase component formed an ?3?3 hexamer of 54- and 19-kDa subunits. Biochemical analyses demonstrated one Rieske-type [2Fe-2S] center and one mononuclear nonheme iron center in each large oxygenase subunit. The reductase component, which transfers electrons from NADH to the oxygenase component, was found to contain approximately one flavin adenine dinucleotide and one ferredoxin-type [2Fe-2S] center per 39-kDa monomer. Activities of the combined components were measured as rates and quantities of NADH oxidation, substrate disappearance, product appearance, and O2 consumption. Anthranilate conversion to catechol was stoichiometrically coupled to NADH oxidation and O2 consumption. The substrate analog benzoate was converted to a nonaromatic benzoate 1,2-diol with similarly tight coupling. This latter activity is identical to that of the related benzoate 1,2-dioxygenase. A variant anthranilate 1,2-dioxygenase, previously found to convey temperature sensitivity in vivo because of a methionine-to-lysine change in the large oxygenase subunit, was purified and characterized. The purified M43K variant, however, did not hydroxylate anthranilate or benzoate at either the permissive (23°C) or nonpermissive (39°C) growth temperatures. The wild-type anthranilate 1,2-dioxygenase did not efficiently hydroxylate methylated or halogenated benzoates, despite its sequence similarity to broad-substrate specific dioxygenases that do. Phylogenetic trees of the ? and ? subunits of these terminal dioxygenases that act on natural and xenobiotic substrates indicated that the subunits of each terminal oxygenase evolved from a common ancestral two-subunit component. PMID:11114907

Eby, D. Matthew; Beharry, Zanna M.; Coulter, Eric D.; Kurtz, Donald M.; Neidle, Ellen L.

2001-01-01

397

The clc Element of Pseudomonas sp. Strain B13, a Genomic Island with Various Catabolic Properties  

PubMed Central

Pseudomonas sp. strain B13 is a bacterium known to degrade chloroaromatic compounds. The properties to use 3- and 4-chlorocatechol are determined by a self-transferable DNA element, the clc element, which normally resides at two locations in the cell's chromosome. Here we report the complete nucleotide sequence of the clc element, demonstrating the unique catabolic properties while showing its relatedness to genomic islands and integrative and conjugative elements rather than to other known catabolic plasmids. As far as catabolic functions, the clc element harbored, in addition to the genes for chlorocatechol degradation, a complete functional operon for 2-aminophenol degradation and genes for a putative aromatic compound transport protein and for a multicomponent aromatic ring dioxygenase similar to anthranilate hydroxylase. The genes for catabolic functions were inducible under various conditions, suggesting a network of catabolic pathway induction. For about half of the open reading frames (ORFs) on the clc element, no clear functional prediction could be given, although some indications were found for functions that were similar to plasmid conjugation. The region in which these ORFs were situated displayed a high overall conservation of nucleotide sequence and gene order to genomic regions in other recently completed bacterial genomes or to other genomic islands. Most notably, except for two discrete regions, the clc element was almost 100% identical over the whole length to a chromosomal region in Burkholderia xenovorans LB400. This indicates the dynamic evolution of this type of element and the continued transition between elements with a more pathogenic character and those with catabolic properties. PMID:16484212

Gaillard, Muriel; Vallaeys, Tatiana; Vorhölter, Frank Jörg; Minoia, Marco; Werlen, Christoph; Sentchilo, Vladimir; Pühler, Alfred; van der Meer, Jan Roelof

2006-01-01

398

Heterologous expression and characterization of the manganese-oxidizing protein from Erythrobacter sp. strain SD21.  

PubMed

The manganese (Mn)-oxidizing protein (MopA) from Erythrobacter sp. strain SD21 is part of a unique enzymatic family that is capable of oxidizing soluble Mn(II). This enzyme contains two domains, an animal heme peroxidase domain, which contains the catalytic site, followed by a C-terminal calcium binding domain. Different from the bacterial Mn-oxidizing multicopper oxidase enzymes, little is known about MopA. To gain a better understanding of MopA and its role in Mn(II) oxidation, the 238-kDa full-length protein and a 105-kDa truncated protein containing only the animal heme peroxidase domain were cloned and heterologously expressed in Escherichia coli. Despite having sequence similarity to a peroxidase, hydrogen peroxide did not stimulate activity, nor was activity significantly decreased in the presence of catalase. Both pyrroloquinoline quinone (PQQ) and hemin increased Mn-oxidizing activity, and calcium was required. The Km for Mn(II) of the full-length protein in cell extract was similar to that of the natively expressed protein, but the Km value for the truncated protein in cell extract was approximately 6-fold higher than that of the full-length protein, suggesting that the calcium binding domain may aid in binding Mn(II). Characterization of the heterologously expressed MopA has provided additional insight into the mechanism of bacterial Mn(II) oxidation, which will aid in understanding the role of MopA and Mn oxidation in bioremediation and biogeochemical cycling. PMID:25172859

Nakama, Katherine; Medina, Michael; Lien, Ahn; Ruggieri, Jordan; Collins, Krystle; Johnson, Hope A

2014-11-01

399

Initiation and ontogeny of vesicles in cultured Frankia sp. strain HFPArI3  

SciTech Connect

Removal of combined nitrogen from the medium of Frankia sp. strain HFPArI3 induced the formation of specialized structures, called vesicles, which are the proposed site of nitrogen fixation. After 5 to 8 h of culture on N-free medium, newly formed vesicles, termed provesicles arose from tips of some hyphae. These structures were spherical, phase dark, ca. 1.5 to 2.0 ..mu..m in diameter, and were not associated with acetylene reduction (nitrogenase) activity. Provesicles reached their greatest frequency after ca. 24 h of N-free culture. Provesicles increased in size to become mature vesicles which first appeared after 18 to 20 h of N-free culture. They were ca. 2.5 ..mu..m in diameter, phase bright, and reached their greatest frequency after 5 to 6 days, at which time nitrogenase activity peaked. Some vesicles eventually became damaged structurally and took on the appearance of ghosts. Transmission electron micrographs revealed an increase in size from provesicle to mature vesicle. Also evident with the micrographs were the presence of a septum between the young provesicle and parental hypha, the presence of glycogen in some young vesicles, the development of internal septations as vesicles matured, and the degradation of cytoplasm and internal septae in ghost vesicles. The extent to which the formation of vesicles is reversible by the addition of NH/sub 4//sup +/ was investigated. Commitment times of 3.2 and 6.5 h were obtained for provesicles and vesicles, respectively. A concentration-dependent inhibition of nitrogenase by NH/sub 4//sup +/ was demonstrated. The structure of preexisting vesicles was also affected by addition of NH/sub 4//sup +/ to the culture medium.

Fontaine, M.S.; Lancelle, S.A.; Torrey, J.G.

1984-12-01

400

Characterization of an acetyl xylan esterase from the anaerobic fungus Orpinomyces sp. strain PC-2  

SciTech Connect

A 1,067-bp cDNA, designated axeA, coding for an acetyl xylan esterase (AxeA) was cloned from the anaerobic rumen fungus Orpinomyces sp. strain PC-2. The gene had an open reading frame of 939 bp encoding a polypeptide of 313 amino acid residues with a calculated mass of 34,845 Da. An active esterase using the original start codon of the cDNA was synthesized in Escherichia coli. Two active forms of the esterase were purified from recombinant E. coli cultures. The size difference of 8 amino acids was a result of cleavages at two different sites within the signal peptide. The enzyme released acetate from several acetylated substrates, including acetylated xylan. The activity toward acetylated xylan was tripled in the presence of recombinant xylanase A from the same fungus. Using p-nitrophenyl acetate as a substrate, the enzyme had a K{sub m} of 0.9 mM and a V{sub max} of 785 {micro}mol min{sup {minus}} mg{sup {minus}1}. It had temperature and pH optima of 30 C and 9.0, respectively. AxeA had 56% amino acid identity with BnaA, an acetyl xylan esterase of Neocallimastix patriciarum, but the Orpinomyces AxeA was devoid of a noncatalytic repeated peptide domain (NCRPD) found at the carboxy terminus of the Neocallimastix BnaA. The NCRPD found in many glycosyl hydrolases and esterases of anaerobic fungi has been postulated to function as a docking domain for cellulase-hemicellulase complexes, similar to the dockerin of the cellulosome of Clostridium thermocellum.

Blum, D.L.; Li, X.L.; Chen, H.; Ljungdahl, L.G.

1999-09-01

401

Two Novel Phycoerythrin-Associated Linker Proteins in the Marine Cyanobacterium Synechococcus sp. Strain WH8102  

PubMed Central

The recent availability of the whole genome of Synechococcus sp. strain WH8102 allows us to have a global view of the complex structure of the phycobilisomes of this marine picocyanobacterium. Genomic analyses revealed several new characteristics of these phycobilisomes, consisting of an allophycocyanin core and rods made of one type of phycocyanin and two types of phycoerythrins (I and II). Although the allophycocyanin appears to be similar to that found commonly in freshwater cyanobacteria, the phycocyanin is simpler since it possesses only one complete set of ? and ? subunits and two rod-core linkers (CpcG1 and CpcG2). It is therefore probably made of a single hexameric disk per rod. In contrast, we have found two novel putative phycoerythrin-associated linker polypeptides that appear to be specific for marine Synechococcus spp. The first one (SYNW2000) is unusually long (548 residues) and apparently results from the fusion of a paralog of MpeC, a phycoerythrin II linker, and of CpeD, a phycoerythrin-I linker. The second one (SYNW1989) has a more classical size (300 residues) and is also an MpeC paralog. A biochemical analysis revealed that, like MpeC, these two novel linkers were both chromophorylated with phycourobilin. Our data suggest that they are both associated (partly or totally) with phycoerythrin II, and we propose to name SYNW2000 and SYNW1989 MpeD and MpeE, respectively. We further show that acclimation of phycobilisomes to high light leads to a dramatic reduction of MpeC, whereas the two novel linkers are not significantly affected. Models for the organization of the rods are proposed. PMID:15716439

Six, Christophe; Thomas, Jean-Claude; Thion, Laurent; Lemoine, Yves; Zal, Frank; Partensky, Frédéric

2005-01-01

402

Characterization of the Response to Zinc Deficiency in the Cyanobacterium Anabaena sp. Strain PCC 7120  

PubMed Central

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.

2012-01-01

403

Genome Sequence of Thermotoga sp Strain RQ2, a Hyperthermophilic Bacterium Isolated from a Geothermally Heated Region of the Seafloor near Ribeira Quente, the Azores  

SciTech Connect

Thermotoga sp. strain RQ2 is probably a strain of Thermotoga maritima. Its complete genome sequence allows for an examination of the extent and consequences of gene flow within Thermotoga species and strains. Thermotoga sp. RQ2 differs from T. maritima in its genes involved in myo-inositol metabolism. Its genome also encodes an apparent fructose phosphotransferase system (PTS) sugar transporter. This operon is also found in Thermotoga naphthophila strain RKU-10 but no other Thermotogales. These are the first reported PTS transporters in the Thermotogales.

Swithers, Kristen S [University of Connecticut, Storrs; DiPippo, Jonathan L [University of Connecticut, Storrs; 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, Cliff [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [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; Lykidis, A [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Stetter, Karl O [Universitat Regensburg, Regensburg, Germany; Nelson, Karen E [J. Craig Venter Institute; Gogarten, Peter [University of Connecticut, Storrs; Noll, Kenneth M [University of Connecticut, Storrs

2011-01-01

404

Draft Genome Sequence of Psychrotrophic Acinetobacter sp. Strain MN12 (MTCC 10786), Which Produces a Low-Temperature-Active and Alkaline-Stable Peptidase  

PubMed Central

We report here the draft genome sequence of Acinetobacter sp. strain MN12 (MTCC 10786), which is a psychrotrophic bacterium that produces an extracellular low-temperature-active and alkaline-stable peptidase. The draft genome assembly of Acinetobacter sp. MN12 has a size of 4.31 Mbp, with a G+C content of 40.75%. PMID:25414495

Swarnkar, Mohit Kumar; Salwan, Richa

2014-01-01

405

Draft Genome Sequence of the Obligate Halophilic Bacillus sp. Strain NSP22.2, Isolated from a Seasonal Salt Marsh of the Great Rann of Kutch, India  

PubMed Central

Here, we report the 4.0-Mbp draft genome of an obligate halophile, Bacillus sp. strain NSP22.2, isolated from a seasonal salt marsh of the Great Rann of Kutch, India. To understand the mechanism(s) of obligate halophilism and to isolate the relevant gene(s), the genome of Bacillus sp. NSP22.2 was sequenced. PMID:24356848

Pal, Kamal Krishna; Sherathia, Dharmesh; Vanpariya, Sejal; Patel, Ilaxi; Dalsania, Trupti; Savsani, Kinjal; Sukhadiya, Bhoomika; Mandaliya, Mona; Thomas, Manesh; Ghorai, Sucheta; Rupapara, Rupal; Rawal, Priya

2013-01-01

406

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

407

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

PubMed

Isocarbophos is a widely used organophosphorus insecticide that has caused environmental pollution in many areas. However, degradation of isocarbophos by pure cultures has not been extensively studied, and the degradation pathway has not been determined. In this paper, a highly effective isocarbophos-degrading strain, scl-2, was isolated from isocarbophos-polluted soil. Strain scl-2 was preliminarily identified as Arthrobacter sp. based on its morphological, physiological, and biochemical properties, as well as 16S rDNA analysis. Strain scl-2 could utilize isocarbophos as its sole source of carbon and phosphorus for growth. One hundred mg/l isocarbophos could be degraded to a nondetectable level in 18 h by scl-2 in cell culture, and isofenphos-methyl, profenofos, and phosmet could also be degraded. During the degradation of isocarbophos, the metabolites isopropyl salicylate, salicylate, and gentisate were detected and identified based on MS/MS analysis and their retention times in HPLC. Transformation of gentisate to pyruvate and fumarate via maleylpyruvate and fumarylpyruvate was detected by assaying for the activities of gentisate 1,2- dioxygenase (GDO) and maleylpyruvate isomerase. Therefore, we have identified the degradation pathway of isocarbophos in Arthrobacter sp. scl-2 for the first time. This study highlights an important potential use of the strain scl-2 for the cleanup of environmental contamination by isocarbophos and presents a mechanism of isocarbophos metabolism. PMID:19996699

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

2009-11-01

408

Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia  

PubMed Central

Burkholderia sp. strain WSM2230 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod isolated from acidic soil collected in 2001 from Karijini National Park, Western Australia, using Kennedia coccinea (Coral Vine) as a host. WSM2230 was initially effective in nitrogen-fixation with K. coccinea, but subsequently lost symbiotic competence. Here we describe the features of Burkholderia sp. strain WSM2230, together with genome sequence information and its annotation. The 6,309,801 bp high-quality-draft genome is arranged into 33 scaffolds of 33 contigs containing 5,590 protein-coding genes and 63 RNA-only encoding genes. The genome sequence of WSM2230 failed to identify nodulation genes and provides an explanation for the observed failure of the laboratory grown strain to nodulate. The genome of this strain is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. PMID:25197440

Walker, Robert; Watkin, Elizabeth; Tian, Rui; Bräu, Lambert; O’Hara, Graham; Goodwin, Lynne; Han, James; Lobos, Elizabeth; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

2013-01-01

409

Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia.  

PubMed

Burkholderia sp. strain WSM2230 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod isolated from acidic soil collected in 2001 from Karijini National Park, Western Australia, using Kennedia coccinea (Coral Vine) as a host. WSM2230 was initially effective in nitrogen-fixation with K. coccinea, but subsequently lost symbiotic competence. Here we describe the features of Burkholderia sp. strain WSM2230, together with genome sequence information and its annotation. The 6,309,801 bp high-quality-draft genome is arranged into 33 scaffolds of 33 contigs containing 5,590 protein-coding genes and 63 RNA-only encoding genes. The genome sequence of WSM2230 failed to identify nodulation genes and provides an explanation for the observed failure of the laboratory grown strain to nodulate. The genome of this strain is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. PMID:25197440

Walker, Robert; Watkin, Elizabeth; Tian, Rui; Bräu, Lambert; O'Hara, Graham; Goodwin, Lynne; Han, James; Lobos, Elizabeth; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

2014-06-15

410

Cold-adapted and rhizosphere-competent strain of Rahnella sp. with broad-spectrum plant growth-promotion potential.  

PubMed

A phosphate-solubilizing bacterial strain isolated from Hippophae rhamnoides rhizosphere was identified as Rahnella sp. based on its phenotypic features and 16S rRNA gene sequence. The bacterial strain showed the growth characteristics of a cold-adapted psychrotroph, with the multiple plant growth-promoting traits of inorganic and organic phosphate solubilization, 1-aminocyclopropane-1- carboxylate-deaminase activity, ammonia generation, and siderophore production. The strain also produced indole- 3-acetic acid, indole-3-acetaldehyde, indole-3-acetamide, indole-3-acetonitrile, indole-3-lactic acid, and indole-3- pyruvic acid in tryptophan-supplemented nutrient broth. Gluconic, citric and isocitric acids were the major organic acids detected during tricalcium phosphate solubilization. A rifampicin-resistant mutant of the strain exhibited high rhizosphere competence without disturbance to the resident microbial populations in pea rhizosphere. Seed bacterization with a charcoal-based inoculum significantly increased growth in barley, chickpea, pea, and maize under the controlled environment. Microplot testing of the inoculum at two different locations in pea also showed significant increase in growth and yield. The attributes of coldtolerance, high rhizosphere competence, and broad-spectrum plant growth-promoting activity exhibited the potential of Rahnella sp. BIHB 783 for increasing agriculture productivity. PMID:21193830

Vyas, Pratibha; Joshi, Robin; Sharma, K C; Rahi, Praveen; Gulati, Ashu; Gulati, Arvind

2010-12-01

411

Description of Lentzea flaviverrucosa sp. nov. and transfer of the type strain of Saccharothrix aerocolonigenes subsp. staurosporea to Lentzea albida.  

PubMed

A distinct actinomycete isolated from soil was subjected to polyphasic taxonomic analysis. It is demonstrated by comparative 16S rDNA gene sequencing that the organism, designated strain AS 4.0578T, represents a novel species of the genus Lentzea. The phylogenetic results also showed that it formed a monophyletic lineage distinct from the available members of the genera Lentzea, Lechevalieria and Saccharothrix. The organism was distinguished from all the validly described type strains of the genus Lentzea by a combination of phenotypic features and DNA-DNA hybridization. It is proposed, therefore, that strain AS 4.0578T (= JCM 11373T) be classified in the genus Lentzea as Lentzea flaviverrucosa sp. nov. In addition, it is proposed that Saccharothrix aerocolonigenes subsp. staurosporea NRRL 11184T be transferred to Lentzea albida on the basis of phylogenetic analysis, DNA-DNA homology, nucleotide signatures and phenotypic properties. PMID:12361291

Xie, Qiong; Wang, Yimin; Huang, Ying; Wu, Yuanliang; Ba, Fusen; Liu, Zhiheng

2002-09-01

412

Characterization of 17 strains belonging to the Mycobacterium simiae complex and description of Mycobacterium paraense sp. nov.  

PubMed

Fourteen mycobacterial strains isolated from pulmonary samples of independent patients in the state of Pará (Brazil), and three strains isolated in Italy, were characterized using a polyphasic approach. Thorough genetic investigation, including whole genome sequencing, demonstrated their belonging to the M. simiae complex with most close relation to Mycobacterium interjectum. For 14 of them evidence emerged supporting their inclusion in a previously unreported Mycobacterium species for which the name Mycobacterium paraense sp. nov. is proposed. The new species is characterized by slow growth, unpigmented or pale yellow scotochromogenic colonies, and HPLC mycolic acid profile different from other known mycobacteria. In different genetic regions high sequence microheterogeneity was detected. The type strain is IEC26 ((DSM46749T = CCUG66121T). PMID:25487637

Fusco da Costa, Ana Roberta; Fedrizzi, Tarcisio; Lopes, Maria Luiza; Pecorari, Monica; Oliveira da Costa, Wanda Lailan; Giacobazzi, Elisabetta; da Costa Bahia, Jeann Ricardo; De Sanctis, Veronica; Batista Lima, Karla Valeria; Bertorelli, Roberto; Grottola, Antonella; Fabio, Anna; Mariottini, Alessandro; Ferretti, Pamela; di Leva, Francesca; Fregni Serpini, Giulia; Tagliacuzzi, Sara; Rumpianesi, Fabio; Jousson, Olivier; Segata, Nicola; Tortoli, Enrico

2014-12-01

413

Strain and culture medium optimization for production enhancement of prodiginines from marine-derived Streptomyces sp. GQQ-10  

NASA Astrophysics Data System (ADS)

A mutant (GQQ-M6) of a Sponge-Derived streptomyces sp. GQQ-10 obtained by UV-induced mutation was used for producing prodiginines (PGs). Single factor experiments and orthogonal array design (OAD) methods were employed for medium optimization. In the single factor method, the effects of soluble starch, glucose, soybean flour, yeast extract and sodium acetate on PGs production were investigated individually. In the subsequent OAD experiments, the concentrations of these 5 key nutritional components combined with salinity were further adjusted. The mutant strain GQQ-M6 gave a 2.2-fold higher PGs production than that of the parent strain; OAD experiments offered a PGs yield of 61mg L-1, which was 10 times higher than that of the initial GQQ-10 strain under the original cultivation mode.

Li, Xueping; Zhang, Guojian; Zhu, Tianjiao; Li, Dehai; Gu, Qianqun

2012-09-01

414

Degradation of 2,4-dinitroanisole (DNAN) by metabolic cooperative activity of Pseudomonas sp. strain FK357and Rhodococcus imtechensis strain RKJ300.  

PubMed

2,4-Dinitroanisole (DNAN) is an insensitive explosive ingredient used by many defense agencies as a replacement for 2,4,6-trinitrotoluene. Although the biotransformation of DNAN under anaerobic condition has been reported, aerobic microbial degradation pathway has not been elucidated. An n-methyl-4-nitroaniline degrading bacterium Pseudomonas sp. strain FK357 transformed DNAN into 2,4-dinitrophenol (2,4-DNP) as an end product. Interestingly, when strain FK357 was co-cultured with a 2,4-DNP degrading Rhodococcus imtechensis strain RKJ300, complete and high rate of DNAN degradation was observed with no accumulation of intermediates. Enzyme assay using cell extracts of strain FK357 demonstrated that O-demethylation reaction is the first step of DNAN degradation with formation of 2,4-DNP and formaldehyde as intermediates. Subsequently, 2,4-DNP was degraded by strain RKJ300 via the formation of hydride-Meisenheimer complex. The present study clearly demonstrates that complete degradation of DNAN occurs as a result of the metabolic cooperative activity of two members within a bacterial consortium. PMID:24075532

Khan, Fazlurrahman; Pal, Deepika; Ghosh, Anuradha; Cameotra, Swaranjit Singh

2013-11-01

415

HylA, an Alternative Hydrolase for Initiation of Catabolism of the Phenylurea Herbicide Linuron in Variovorax sp. Strains  

PubMed Central

Variovorax sp. strain WDL1, which mineralizes the phenylurea herbicide linuron, expresses a novel linuron-hydrolyzing enzyme, HylA, that converts linuron to 3,4-dichloroaniline (DCA). The enzyme is distinct from the linuron hydrolase LibA enzyme recently identified in other linuron-mineralizing Variovorax strains and from phenylurea-hydrolyzing enzymes (PuhA, PuhB) found in Gram-positive bacteria. The dimeric enzyme belongs to a separate family of hydrolases and differs in Km, temperature optimum, and phenylurea herbicide substrate range. Within the metal-dependent amidohydrolase superfamily, HylA and PuhA/PuhB belong to two distinct protein families, while LibA is a member of the unrelated amidase signature family. The hylA gene was identified in a draft genome sequence of strain WDL1. The involvement of hylA in linuron degradation by strain WDL1 is inferred from its absence in spontaneous WDL1 mutants defective in linuron hydrolysis and its presence in linuron-degrading Variovorax strains that lack libA. In strain WDL1, the hylA gene is combined with catabolic gene modules encoding the downstream pathways for DCA degradation, which are very similar to those present in Variovorax sp. SRS16, which contains libA. Our results show that the expansion of a DCA catabolic pathway toward linuron degradation in Variovorax can involve different but isofunctional linuron hydrolysis genes encoding proteins that belong to evolutionary unrelated hydrolase families. This may be explained by divergent evolution and the independent acquisition of the corresponding genetic modules. PMID:23811502

Bers, K.; Batisson, I.; Proost, P.; Wattiez, R.; De Mot, R.

2013-01-01

416

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 LD?? 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

2013-09-01

417

Genome Analysis Coupled with Physiological Studies Reveals a Diverse Nitrogen Metabolism in Methylocystis sp. Strain SC2  

PubMed Central

Background Methylocystis sp. strain SC2 can adapt to a wide range of methane concentrations. This is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. To gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 Mb chromosome and two large plasmids. Principal Findings We report important features of the strain SC2 genome. Its sequence is compared with those of seven other methanotroph genomes, comprising members of the Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. While the pan-genome of all eight methanotroph genomes totals 19,358 CDS, only 154 CDS are shared. The number of core genes increased with phylogenetic relatedness: 328 CDS for proteobacterial methanotrophs and 1,853 CDS for the three alphaproteobacterial Methylocystaceae members, Methylocystis sp. strain SC2 and strain Rockwell, and Methylosinus trichosporium OB3b. The comparative study was coupled with physiological experiments to verify that strain SC2 has diverse nitrogen metabolism capabilities. In correspondence to a full complement of 34 genes involved in N2 fixation, strain SC2 was found to grow with atmospheric N2 as the sole nitrogen source, preferably at low oxygen concentrations. Denitrification-mediated accumulation of 0.7 nmol 30N2/hr/mg dry weight of cells under anoxic conditions was detected by tracer analysis. N2 production is related to the activities of plasmid-borne nitric oxide and nitrous oxide reductases. Conclusions/Perspectives Presence of a complete denitrification pathway in strain SC2, including the plasmid-encoded nosRZDFYX operon, is unique among known methanotrophs. However, the exact ecophysiological role of this pathway still needs to be elucidated. Detoxification of toxic nitrogen compounds and energy conservation under oxygen-limiting conditions are among the possible roles. Relevant features that may stimulate further research are, for example, absence of CRISPR/Cas systems in strain SC2, high number of iron acquisition systems in strain OB3b, and large number of transposases in strain Rockwell. PMID:24130670

Blom, Jochen; Liesack, Werner

2013-01-01

418

Degradation of recalcitrant aliphatic and aromatic hydrocarbons by a dioxin-degrader Rhodococcus sp. strain p52.  

PubMed

This study investigates the ability of Rhodococcus sp. strain p52, a dioxin degrader, to biodegrade petroleum hydrocarbons. Strain p52 can use linear alkanes (tetradecane, tetracosane, and dotriacontane), branched alkane (pristane), and aromatic hydrocarbons (naphthalene and phenanthrene) as sole carbon and energy sources. Specifically, the strain removes 85.7 % of tetradecane within 48 h at a degradation rate of 3.8 mg h(-1) g(-1) dry cells, and 79.4 % of tetracosane, 66.4 % of dotriacontane, and 63.9 % of pristane within 9-11 days at degradation rates of 20.5, 14.7, and 20.3 mg day(-1) g(-1) dry cells, respectively. Moreover, strain p52 consumes 100 % naphthalene and 55.3 % phenanthrene within 9-11 days at respective degradation rates of 16 and 12.9 mg day(-1) g(-1) dry cells. Metabolites of the petroleum hydrocarbons by strain p52 were analyzed. Genes encoding alkane-hydroxylating enzymes, including cytochrome P450 (CYP450) enzyme (CYP185) and two alkane-1-monooxygenases, were amplified by polymerase chain reaction. The transcriptional activities of these genes in the presence of petroleum hydrocarbons were detected by reverse transcription-polymerase chain reaction. The results revealed potential of strain p52 to degrade petroleum hydrocarbons. PMID:24859700

Yang, Hai-Yan; Jia, Rui-Bao; Chen, Bin; Li, Li

2014-09-01

419

Isolation and characterization of a novel 2-sec-butylphenol-degrading bacterium Pseudomonas sp. strain MS-1.  

PubMed

A novel bacterium capable of utilizing 2-sec-butylphenol as the sole carbon and energy source, Pseudomonas sp. strain MS-1, was isolated from freshwater sediment. Within 30 h, strain MS-1 completely degraded 1.5 mM 2-sec-butylphenol in basal salt medium, with concomitant cell growth. A pathway for the metabolism of 2-sec-butylphenol by strain MS-1 was proposed on the basis of the identification of 3 internal metabolites-3-sec-butylcatechol, 2-hydroxy-6-oxo-7-methylnona-2,4-dienoic acid, and 2-methylbutyric acid-by gas chromatography-mass spectrometry analysis. Strain MS-1 degraded 2-sec-butylphenol through 3-sec-butylcatechol along a meta-cleavage pathway. Degradation experiments with various alkylphenols showed that the degradability of alkylphenols by strain MS-1 depended strongly on the position (ortho > meta = para) of the alkyl substitute, and that strain MS-1 could degrade 2-alkylphenols with various sized and branched alkyl chain (o-cresol, 2-ethylphenol, 2-n-propylphenol, 2-isopropylphenol, 2-sec-butylphenol, and 2-tert-butylphenol), as well as a dialkylphenol (namely, 6-tert-butyl-m-cresol). PMID:19705287

Toyama, Tadashi; Maeda, Noritaka; Murashita, Manabu; Chang, Yong-Cheol; Kikuchi, Shintaro

2010-04-01

420

A short-filament mutant of Anabaena sp. strain PCC 7120 that fragments in nitrogen-deficient medium.  

PubMed Central

Strain 129 is a fragmentation mutant of the filamentous cyanobacterium Anabaena sp. strain PCC 7120. Growing with fixed nitrogen, this mutant forms filaments that are much shorter than wild-type filaments. Following starvation for fixed nitrogen, strain 129 becomes nearly unicellular and forms few heterocysts, although electron microscopy suggests that proheterocysts form while fragmentation occurs. Starvation for sulfate, phosphate, iron, and calcium does not cause this fragmentation. The affected gene in strain 129, fraC, was cloned by complementation and characterized. It encodes a unique 179-amino-acid protein rich in phenylalanine. Insertional inactivation of the chromosomal copy of fraC results in a phenotype identical to that of strain 129, while complementation using a truncated version of FraC results in only partial complementation of the original mutant. Heterocysts could be induced to form in N-replete cultures of strain 129, as in wild-type cells, by supplying extra copies of the hetR gene on a plasmid. Thus, FraC is required for the integrity of cell junctions in general but is apparently not directly involved in normal differentiation and nitrogen fixation. PMID:7883709

Bauer, C C; Buikema, W J; Black, K; Haselkorn, R

1995-01-01

421

Conversion of the Pseudomonas aeruginosa Quinolone Signal (PQS) and Related Alkylhydroxyquinolines by Rhodococcus sp. strain BG43.  

PubMed

A bacterial strain, which based on the sequences of its 16S rRNA, gyrB, catA and qsdA genes was identified as a Rhodococcus sp. closely related to R. erythropolis, was isolated from soil by enrichment on PQS (the Pseudomonas quinolone signal, 2-heptyl-3-hydroxy-4(1H)-quinolone), a quorum sensing signal employed by the opportunistic pathogen Pseudomonas aeruginosa. The isolate, termed Rhodococcus sp. BG43, cometabolically degraded PQS as well as its biosynthetic precursor 2-heptyl-4(1H)-quinolone (HHQ) to anthranilic acid. HHQ degradation was accompanied by transient formation of PQS, and HHQ hydroxylation by cell extracts required NADH, indicating that strain BG43 has a HHQ monooxygenase isofunctional to the biosynthetic enzyme PqsH of P. aeruginosa. The enzymes catalyzing HHQ hydroxylation and PQS degradation were inducible by PQS, suggesting a specific pathway. Remarkably, Rhodococcus sp. BG43 is also capable of transforming 2-heptyl-4-hydroxyquinoline-N-oxide to PQS. It thus converts an antibacterial secondary metabolite of P. aeruginosa to a quorum sensing signal molecule. PMID:25239889

Müller, Christine; Birmes, Franziska S; Niewerth, Heiko; Fetzner, Susanne

2014-09-19

422

Effect of Indoleacetic Acid and Related Indoles on Lactobacillus sp. Strain 11201 Growth, Indoleacetic Acid Catabolism, and 3-Methylindole Formation †  

PubMed Central

A study was conducted to determine the activity of the 3-methylindole (3MI)-forming enzyme in Lactobacillus sp. strain 11201. Cells were incubated anaerobically with 17 different indolic and aromatic compounds. Indoleacetic acid (IAA), 5-hydroxyindoleacetic acid, 5-methoxy-3-indoleacetic acid, indole-3-pyruvate, or indole-3-propionic acid induced 3MI-forming activity. The highest total enzyme activity induced by IAA was observed in cells incubated with an initial concentration of 1.14 mM IAA. Peak activity of the 3MI-forming enzyme occurred 4 h after bacteria were incubated with either 0.114 or 1.14 mM IAA. Enzyme activity peaked earlier (2 h) and disappeared more rapidly at 5.7 mM IAA than at other concentrations of IAA. The effects of IAA and 3MI on the growth of Lactobacillus sp. strain 11201 and formation of 3MI from IAA also were determined. Bacterial growth and 3MI formation from IAA were reduced in medium containing exogenous 3MI. The growth depression observed in medium containing 5.7 mM IAA appears to be due to the toxicity of 3MI rather than IAA. The formation of 3MI in this ruminal Lactobacillus sp. is mediated by an inducible enzyme, and as 3MI accumulates, bacterial growth and rates of 3MI formation from IAA are reduced. PMID:16348189

Honeyfield, D. C.; Carlson, J. R.

1990-01-01

423

Effect of Indoleacetic Acid and Related Indoles on Lactobacillus sp. Strain 11201 Growth, Indoleacetic Acid Catabolism, and 3-Methylindole Formation.  

PubMed

A study was conducted to determine the activity of the 3-methylindole (3MI)-forming enzyme in Lactobacillus sp. strain 11201. Cells were incubated anaerobically with 17 different indolic and aromatic compounds. Indoleacetic acid (IAA), 5-hydroxyindoleacetic acid, 5-methoxy-3-indoleacetic acid, indole-3-pyruvate, or indole-3-propionic acid induced 3MI-forming activity. The highest total enzyme activity induced by IAA was observed in cells incubated with an initial concentration of 1.14 mM IAA. Peak activity of the 3MI-forming enzyme occurred 4 h after bacteria were incubated with either 0.114 or 1.14 mM IAA. Enzyme activity peaked earlier (2 h) and disappeared more rapidly at 5.7 mM IAA than at other concentrations of IAA. The effects of IAA and 3MI on the growth of Lactobacillus sp. strain 11201 and formation of 3MI from IAA also were determined. Bacterial growth and 3MI formation from IAA were reduced in medium containing exogenous 3MI. The growth depression observed in medium containing 5.7 mM IAA appears to be due to the toxicity of 3MI rather than IAA. The formation of 3MI in this ruminal Lactobacillus sp. is mediated by an inducible enzyme, and as 3MI accumulates, bacterial growth and rates of 3MI formation from IAA are reduced. PMID:16348189

Honeyfield, D C; Carlson, J R

1990-05-01

424

Type 2 NADH Dehydrogenases in the Cyanobacterium Synechocystis sp. Strain PCC 6803 Are Involved in Regulation Rather Than Respiration  

PubMed Central

Analysis of the genome of Synechocystis sp. strain PCC 6803 reveals three open reading frames (slr0851, slr1743, and sll1484) that may code for type 2 NAD(P)H dehydrogenases (NDH-2). The sequence similarity between the translated open reading frames and NDH-2s from other organisms is low, generally not exceeding 30% identity. However, NAD(P)H and flavin adenine dinucleotide binding motifs are conserved in all three putative NDH-2s in Synechocystis sp. strain PCC 6803. The three open reading frames were cloned, and deletion constructs were made for each. An expression construct containing one of the three open reading frames, slr1743, was able to functionally complement an Escherichia coli mutant lacking both NDH-1s and NDH-2s. Therefore, slr0851, slr1743, and sll1484 have been designated ndbA, ndbB, and ndbC, respectively. Strains that lacked one or more of the ndb genes were created in wild-type and photosystem (PS) I-less backgrounds. Deletion of ndb genes led to small changes in photoautotrophic growth rates and respiratory activities. Electron transfer rates into the plastoquinone pool in thylakoids in darkness were consistent with the presence of a small amount of NDH-2 activity in thylakoids. No difference was observed between wild-type and the Ndb-less strains in the banding patterns seen on native gels when stained for either NADH or NADPH dehydrogenase activity, indicating that the Ndb proteins do not accumulate to high levels. A striking phenotype of the PS I-less background strains lacking one or more of the NDH-2s is that they were able to grow at high light intensities that were lethal to the control strain but they retained normal PS II activity. We suggest that the Ndb proteins in Synechocystis sp. strain PCC 6803 are redox sensors and that they play a regulatory role responding to the redox state of the plastoquinone pool. PMID:10383967

Howitt, Crispin A.; Udall, Pacer K.; Vermaas, Wim F. J.

1999-01-01

425

Isolation and complementation of mutants of Anabaena sp. strain PCC 7120 unable to grow aerobically on dinitrogen  

SciTech Connect

Mutants of Anabaena sp. strain PCC 7120 unable to grow aerobically on dinitrogen were isolated by mutagenesis with UV irradiation, followed by a period of incubation in yellow light and then by penicillin enrichment. A cosmid vector, pRL25C, containing replicons functional in Escherichia coli and in Anabaena species was constructed. DNA from wild-type Anabaena sp. strain PCC 7120 was partially digested with Sau3AI, and size-fractionated fragments about 40 kilobases (kb) in length were ligated into the phosphatase-treated unique BamHI site of pRL25C. A library of 1054 cosmid clones was generated in E. coli DH1 bearing helper plasmid pDS4101. A derivative of conjugative plasmid RP-4 was transferred to this library by conjugation, and the library was replicated to lawns of mutant Anabaena strains with defects in the polysaccharide layer of the envelopes of the heterocysts. Mutant EF116 was complemented by five cosmids, three of which were subjected to detailed restriction mapping; a 2.8-kb fragment of DNA derived from one of the cosmids was found to complement EF116. Mutant EF113 was complemented by a single cosmid, which was also restriction mapped, and was shown to be complemented by a 4.8-kb fragment of DNA derived from this cosmid.

Wolk, C.P.; Cai, Y.; Cardemil, L.; Flores, E.; Hohn, B.; Murry, M.; Schmetterer, G.; Schrautemeier, B.; Wilson, R.

1988-03-01

426

Isolation of a chlorpyrifos-degrading bacterium, Sphingomonas sp. strain Dsp-2, and cloning of the mpd gene.  

PubMed

A highly effective chlorpyrifos-degrading bacterium strain Dsp-2 was isolated from the polluted treatment system of a chlorpyrifos manufacturer. This strain was preliminarily identified as Sphingomonas sp. based on its morphological, physiological and biochemical tests as well as 16S rDNA analysis. It utilized chlorpyrifos as its sole source of carbon for growth, by hydrolyzing chlorpyrifos to 3,5,6-trichloro-2-pyridinol (TCP). It could also utilize parathion, parathion-methyl, fenitrothion and profenofos, but not phoxin and triazophos. Bioremediation of chlorpyrifos-contaminated soil was examined using Dsp-2. Dsp-2 addition to soil treated with 100mgkg(-1) chlorpyrifos resulted in a higher degradation rate than control soils without inoculation. The moderate pH, moisture and inoculum density could have promoted degradation. The gene encoding the chlorpyrifos hydrolytic enzyme was cloned by PCR. Although BLAST sequence search results indicated that this gene has 99% similarity to mpd (a gene encoding the parathion-methyl hydrolyzing enzyme in Plesiomonas sp. M6), its hydrolytic efficiency for chlorpyrifos was significantly greater than the wild-type mpd from strain M6. PMID:17306510

Li, Xiaohui; He, Jian; Li, Shunpeng

2007-03-01

427

Transcriptional analysis of the multicopy hao gene coding for hydroxylamine oxidoreductase in Nitrosomonas sp. strain ENI-11.  

PubMed

The nitrifying bacterium Nitrosomonas sp. strain ENI-11 has three copies of the gene encoding hydroxylamine oxidoreductase (hao(1), hao(2), and hao(3)) on its genome. Broad-host-range reporter plasmids containing transcriptional fusion genes between hao copies and lacZ were constructed to analyze the expression of each hydroxylamine oxidoreductase gene (hao) copy individually and quantitatively. beta-Galactosidase assays of ENI-11 harboring reporter plasmids revealed that all hao copies were transcribed in the wild-type strain. Promoter analysis of hao copies revealed that transcription of hao(3) was highest among the hao copies. Expression levels of hao(1) and hao(2) were 40% and 62% of that of hao(3) respectively. Transcription of hao(1) was negatively regulated, whereas a portion of hao(3) transcription was read through transcription from the rpsT promoter. When energy-depleted cells were incubated in the growth medium, only hao(3) expression increased. This result suggests that it is hao(3) that is responsible for recovery from energy-depleted conditions in Nitrosomonas sp. strain ENI-11. PMID:16926500

Hirota, Ryuichi; Kuroda, Akio; Ikeda, Tsukasa; Takiguchi, Noboru; Ohtake, Hisao; Kato, Junichi

2006-08-01

428

Evaluation of insecticidal activity of a bacterial strain, Serratia sp. EML-SE1 against diamondback moth.  

PubMed

To identify novel bioinsecticidal agents, a bacterial strain, Serratia sp. EML-SE1, was isolated from a dead larva of the lepidopteran diamondback moth (Plutella xylostella) collected from a cabbage field in Korea. In this study, the insecticidal activity of liquid cultures in Luria-Bertani broth (LBB) and nutrient broth (NB) of a bacterial strain, Serratia sp. EML-SE1 against thirty 3rd and 4th instar larvae of the diamondback moth was investigated on a Chinese cabbage leaf housed in a round plastic cage (Ø 10 x 6 cm). 72 h after spraying the cabbage leaf with LBB and NB cultures containing the bacterial strain, the mortalities of the larvae were determined to be 91.7% and 88.3%, respectively. In addition, the insecticidal activity on potted cabbage containing 14 leaves in a growth cage (165 x 83 x 124 cm) was found to be similar to that of the plastic cage experiment. The results of this study provided valuable information on the insecticidal activity of the liquid culture of a Serratia species against the diamondback moth. PMID:20799099

Jeong, Hyung Uk; Mun, Hye Yeon; Oh, Hyung Keun; Kim, Seung Bum; Yang, Kwang Yeol; Kim, Iksoo; Lee, Hyang Burm

2010-08-01

429

Genetic, physiological and biochemical characterization of Bacillus sp . strain RMB7 exhibiting plant growth promoting and broad spectrum antifungal activities.  

PubMed

BackgroundPlant growth promoting rhizobacteria (PGPR) are functionally diverse group of bacteria having immense potential as biofertilizers and biopesticides. Depending upon their function, they may serve as partial replacements for chemical fertilizer or pesticides as an eco-friendly and cost-effective alternatives as compared to their synthetic counterparts. Therefore, isolation, characterization and practical evaluation of PGPRs having the aforementioned multifaceted beneficial characteristics, are essentially required. This study describes the detailed polyphasic characterization of Bacillus sp. strain RMB7 having profound broad spectrum antifungal activity and plant growth promoting potential.ResultsBased on 16S rRNA gene sequencing, strain RMB7 was identified as Bacillus specie. This strain exhibited the production of 8 mg. L¿1of indole-3-acetic acid (IAA) in tryptophan-supplemented medium. It was able to solubilize 50.6 mg. L¿1 tri-calcium phosphate, reduced 601¿mol acetylene h¿1/vial and inhibited >70% growth of nine fungal phytopathogens tested in vitro. Under natural pathogen pressure, inoculation with strain RMB7 and RMB7-supernatant conferred resistance by arugula plant against Pythium irregulare with a concurrent growth improvement over non-inoculated plants. The T-RFLP analysis based on 16S rRNA gene showed that inoculation with RMB7 or its supernatant have a major impact on the indigenous rhizosphere bacterial population. Mass spectrometric analysis revealed the production of lipopeptide surfactins as well as iturin A presence in crude extract of RMB7. PCR-amplification further confirmed the presence of genes involved in the biosynthesis of these two bioactive lipopeptide compounds.ConclusionsThe data show that Bacillus sp. strain RMB7 has multifaceted beneficial characteristics. It may be an ideal plant growth promoting as well as biocontrol agent, for its integrated use in disease and nutrient management strategies. PMID:25338952

Ali, Saira; Hameed, Sohail; Imran, Asma; Iqbal, Mazhar; Lazarovits, George

2014-10-24

430

Metabolism of the Aliphatic Nitramine 4-Nitro-2,4-Diazabutanal by Methylobacterium sp. Strain JS178  

PubMed Central

The aliphatic nitramine 4-nitro-2,4-diazabutanal (NDAB; C2H5N3O3) is a ring cleavage metabolite that accumulates during the aerobic degradation of the energetic compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by various Rhodococcus spp. NDAB is also produced during the alkaline hydrolysis of either RDX or octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and during the photolysis of RDX. Traces of NDAB were observed in a soil sampled from an ammunition-manufacturing facility contaminated with both HMX and RDX, suggesting natural attenuation. In this study, we report the isolation of a soil bacterium that is able to degrade NDAB under aerobic conditions. The isolate is a pink-pigmented facultative methylotroph affiliated with the genus Methylobacterium. The strain, named Methylobacterium sp. strain JS178, degrades NDAB as a sole nitrogen source, with concomitant growth and formation of 1 molar equivalent of nitrous oxide (N2O). Comparison of the growth yield of strain JS178 grown on NDAB, nitrite (NO2?), or ammonium (NH4+) as a nitrogen source revealed that 1 N equivalent is assimilated from each mole of NDAB, which completes the nitrogen mass balance. In radiotracer experiments, strain JS178 mineralized 1 C of the [14C]NDAB produced in situ from [14C]RDX by Rhodococcus sp. strain DN22. Studies on the regulation of NDAB degradation indicated that allantoin, an intermediate in the purine catabolic pathway and a central molecule in the storage and transport of nitrogen in plants, up-regulated the enzyme(s) involved in the degradation of the nitramine. The results reveal the potential for the sequential participation of rhodococci and methylobacteria to effect the complete degradation of RDX. PMID:16085803

Fournier, Diane; Trott, Sandra; Hawari, Jalal; Spain, Jim

2005-01-01

431

Draft Whole-Genome Sequence of Serratia marcescens Strain MCB, Associated with Oscheius sp. MCB (Nematoda: Rhabditidae) Isolated from South Africa  

PubMed Central

Here we report on the draft genome sequence of Serratia marcescens strain MCB associated with Oscheius sp. MCB (Nematoda: Rhabditidae) isolated from South African soil. S. marcescens strain MCB has 5,304,212-bp genome size with 4,877 genes and a G+C content of 59.1%. PMID:25237022

Gray, Vincent M.

2014-01-01

432

Draft Genome Sequence of Uncultivated Desulfosporosinus sp. Strain Tol-M, Obtained by Stable Isotope Probing Using [13C6]Toluene  

PubMed Central

A draft Desulfosporosinus genome was assembled from the metagenome of a methanogenic [13C6]toluene-degrading community. The Desulfosporosinus sp. strain Tol-M genome is distinguished from that of previously published Desulfosporosinus strain by containing bss, bbs, and bam genes encoding enzymes for anaerobic biodegradation of monoaromatic hydrocarbons and lacking dsrAB genes for dissimilatory sulfate reduction. PMID:25593260

Abu Laban, Nidal; Tan, BoonFei; Dao, Anh

2015-01-01

433

Draft Genome Sequence of Pseudoalteromonas sp. Strain NW 4327 (MTCC 11073, DSM 25418), a Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile.  

PubMed

To date, only one marine sponge pathogen (Pseudoalteromonas sp. strain NW 4327) has fulfilled Koch's postulates. We report the 4.48-Mbp draft genome sequence of this strain, which is pathogenic to the Great Barrier Reef sponge Rhopaloeides odorabile. The sequence provides valuable information on sponge-pathogen interactions, including the mode of transmission and associated virulence factors. PMID:24482504

Choudhury, Jayanta D; Pramanik, Arnab; Webster, Nicole S; Llewellyn, Lyndon E; Gachhui, Ratan; Mukherjee, Joydeep

2014-01-01

434

Draft genome sequence of Flavobacterium sp. strain F52, isolated from the rhizosphere of bell pepper (Capsicum annuum L. cv. Maccabi).  

PubMed

Here we report the draft genome sequence of Flavobacterium sp. strain F52, isolated from the rhizosphere of bell pepper (Capsicum annuum L. cv. Maccabi). Flavobacterium spp. are ubiquitous in the rhizospheres of agricultural crops; however, little is known about their physiology. To our knowledge, this is the first published genome of a root-associated Flavobacterium strain. PMID:22965088

Kolton, Max; Green, Stefan J; Harel, Yael Meller; Sela, Noa; Elad, Yigal; Cytryn, Eddie

2012-10-01

435

High-Quality Draft Genome Sequence of Pseudomonas sp. BRG100, a Strain with Bioherbicidal Properties against Setaria viridis (Green Foxtail) and Other Pests of Agricultural Significance.  

PubMed

Pseudomonas sp. BRG100 inhibits the growth of certain agricultural pests and is a potentially useful biopesticide for weeds and plant diseases. We have sequenced the 6.25-Mbp genome of this strain and assembled it into 4 scaffolds. Genome sequence comparisons revealed that this strain may represent a novel species of Pseudomonas. PMID:25278538

Dumonceaux, Tim J; Town, Jennifer; Links, Matthew G; Boyetchko, Sue

2014-01-01

436

Draft Genome Sequence of Pseudoalteromonas sp. Strain NW 4327 (MTCC 11073, DSM 25418), a Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile  

PubMed Central

To date, only one marine sponge pathogen (Pseudoalteromonas sp. strain NW 4327) has fulfilled Koch’s postulates. We report the 4.48-Mbp draft genome sequence of this strain, which is pathogenic to the Great Barrier Reef sponge Rhopaloeides odorabile. The sequence provides valuable information on sponge-pathogen interactions, including the mode of transmission and associated virulence factors. PMID:24482504

Choudhury, Jayanta D.; Pramanik, Arnab; Webster, Nicole S.; Llewellyn, Lyndon E.; Gachhui, Ratan

2014-01-01

437

Draft Genome Sequence of Flavobacterium sp. Strain F52, Isolated from the Rhizosphere of Bell Pepper (Capsicum annuum L. cv. Maccabi)  

PubMed Central

Here we report the draft genome sequence of Flavobacterium sp. strain F52, isolated from the rhizosphere of bell pepper (Capsicum annuum L. cv. Maccabi). Flavobacterium spp. are ubiquitous in the rhizospheres of agricultural crops; however, little is known about their physiology. To our knowledge, this is the first published genome of a root-associated Flavobacterium strain. PMID:22965088

Kolton, Max; Green, Stefan J.; Harel, Yael Meller; Sela, Noa; Elad, Yigal

2012-01-01