Sample records for geobacillus sp strain

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

    PubMed Central

    Bhalla, Aditya; Kainth, Amoldeep Singh

    2013-01-01

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

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

    PubMed

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

    2013-01-01

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

  3. Highly Thermostable Xylanase Production from A Thermophilic Geobacillus sp. Strain WSUCF1 Utilizing Lignocellulosic Biomass.

    PubMed

    Bhalla, Aditya; Bischoff, Kenneth M; Sani, Rajesh Kumar

    2015-01-01

    Efficient enzymatic hydrolysis of lignocellulose to fermentable sugars requires a complete repertoire of biomass deconstruction enzymes. Hemicellulases play an important role in hydrolyzing hemicellulose component of lignocellulose to xylooligosaccharides and xylose. Thermostable xylanases have been a focus of attention as industrially important enzymes due to their long shelf life at high temperatures. Geobacillus sp. strain WSUCF1 produced thermostable xylanase activity (crude xylanase cocktail) when grown on xylan or various inexpensive untreated and pretreated lignocellulosic biomasses such as prairie cord grass and corn stover. The optimum pH and temperature for the crude xylanase cocktail were 6.5 and 70°C, respectively. The WSUCF1 crude xylanase was found to be highly thermostable with half-lives of 18 and 12?days at 60 and 70°C, respectively. At 70°C, rates of xylan hydrolysis were also found to be better with the WSUCF1 secretome than those with commercial enzymes, i.e., for WSUCF1 crude xylanase, Cellic-HTec2, and AccelleraseXY, the percent xylan conversions were 68.9, 49.4, and 28.92, respectively. To the best of our knowledge, WSUCF1 crude xylanase cocktail is among the most thermostable xylanases produced by thermophilic Geobacillus spp. and other thermophilic microbes (optimum growth temperature ?70°C). High thermostability, activity over wide range of temperatures, and better xylan hydrolysis than commercial enzymes make WSUCF1 crude xylanase suitable for thermophilic lignocellulose bioconversion processes. PMID:26137456

  4. Highly Thermostable Xylanase Production from A Thermophilic Geobacillus sp. Strain WSUCF1 Utilizing Lignocellulosic Biomass

    PubMed Central

    Bhalla, Aditya; Bischoff, Kenneth M.; Sani, Rajesh Kumar

    2015-01-01

    Efficient enzymatic hydrolysis of lignocellulose to fermentable sugars requires a complete repertoire of biomass deconstruction enzymes. Hemicellulases play an important role in hydrolyzing hemicellulose component of lignocellulose to xylooligosaccharides and xylose. Thermostable xylanases have been a focus of attention as industrially important enzymes due to their long shelf life at high temperatures. Geobacillus sp. strain WSUCF1 produced thermostable xylanase activity (crude xylanase cocktail) when grown on xylan or various inexpensive untreated and pretreated lignocellulosic biomasses such as prairie cord grass and corn stover. The optimum pH and temperature for the crude xylanase cocktail were 6.5 and 70°C, respectively. The WSUCF1 crude xylanase was found to be highly thermostable with half-lives of 18 and 12?days at 60 and 70°C, respectively. At 70°C, rates of xylan hydrolysis were also found to be better with the WSUCF1 secretome than those with commercial enzymes, i.e., for WSUCF1 crude xylanase, Cellic-HTec2, and AccelleraseXY, the percent xylan conversions were 68.9, 49.4, and 28.92, respectively. To the best of our knowledge, WSUCF1 crude xylanase cocktail is among the most thermostable xylanases produced by thermophilic Geobacillus spp. and other thermophilic microbes (optimum growth temperature ?70°C). High thermostability, activity over wide range of temperatures, and better xylan hydrolysis than commercial enzymes make WSUCF1 crude xylanase suitable for thermophilic lignocellulose bioconversion processes.

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

    PubMed Central

    2013-01-01

    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

  6. A modeling study by response surface methodology and artificial neural network on culture parameters optimization for thermostable lipase production from a newly isolated thermophilic Geobacillus sp. strain ARM

    PubMed Central

    Ebrahimpour, Afshin; Rahman, Raja Noor Zaliha Raja Abd; Ean Ch'ng, Diana Hooi; Basri, Mahiran; Salleh, Abu Bakar

    2008-01-01

    Background Thermostable bacterial lipases occupy a place of prominence among biocatalysts owing to their novel, multifold applications and resistance to high temperature and other operational conditions. The capability of lipases to catalyze a variety of novel reactions in both aqueous and nonaqueous media presents a fascinating field for research, creating interest to isolate novel lipase producers and optimize lipase production. The most important stages in a biological process are modeling and optimization to improve a system and increase the efficiency of the process without increasing the cost. Results Different production media were tested for lipase production by a newly isolated thermophilic Geobacillus sp. strain ARM (DSM 21496 = NCIMB 41583). The maximum production was obtained in the presence of peptone and yeast extract as organic nitrogen sources, olive oil as carbon source and lipase production inducer, sodium and calcium as metal ions, and gum arabic as emulsifier and lipase production inducer. The best models for optimization of culture parameters were achieved by multilayer full feedforward incremental back propagation network and modified response surface model using backward elimination, where the optimum condition was: growth temperature (52.3°C), medium volume (50 ml), inoculum size (1%), agitation rate (static condition), incubation period (24 h) and initial pH (5.8). The experimental lipase activity was 0.47 Uml-1 at optimum condition (4.7-fold increase), which compared well to the maximum predicted values by ANN (0.47 Uml-1) and RSM (0.476 Uml-1), whereas R2 and AAD were determined as 0.989 and 0.059% for ANN, and 0.95 and 0.078% for RSM respectively. Conclusion Lipase production is the result of a synergistic combination of effective parameters interactions. These parameters are in equilibrium and the change of one parameter can be compensated by changes of other parameters to give the same results. Though both RSM and ANN models provided good quality predictions in this study, yet the ANN showed a clear superiority over RSM for both data fitting and estimation capabilities. On the other hand, ANN has the disadvantage of requiring large amounts of training data in comparison with RSM. This problem was solved by using statistical experimental design, to reduce the number of experiments. PMID:19105837

  7. 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...

  8. A thermoalkaliphilic lipase of Geobacillus sp. T1.

    PubMed

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

    2007-05-01

    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 solubility and promoted the binding of GST moiety to the glutathione-Sepharose column. High-yield purification of T1 lipase was achieved through two-step affinity chromatography with a final specific activity and yield of 958.2 U/mg and 51.5%, respectively. The molecular mass of T1 lipase was determined to be approximately 43 kDa by gel filtration chromatography. T1 lipase had an optimum temperature and pH of 70 degrees C and pH 9, respectively. It was stable up to 65 degrees C with a half-life of 5 h 15 min at pH 9. It was stable in the presence of 1 mM metal ions Na(+), Ca(2+), Mn(2+), K(+) and Mg(2+ ), but inhibited by Cu(2+), Fe(3+) and Zn(2+). Tween 80 significantly enhanced T1 lipase activity. T1 lipase was active towards medium to long chain triacylglycerols (C10-C14) and various natural oils with a marked preference for trilaurin (C12) (triacylglycerol) and sunflower oil (natural oil). Serine and aspartate residues were involved in catalysis, as its activity was strongly inhibited by 5 mM PMSF and 1 mM Pepstatin. The T(m) for T1 lipase was around 72.2 degrees C, as revealed by denatured protein analysis of CD spectra. PMID:17426920

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

    E-print Network

    Paris-Sud XI, Université de

    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

  10. 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

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

    2009-01-01

    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

  11. Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th.

    PubMed

    Nazina, T N; Tourova, T P; Poltaraus, A B; Novikova, E V; Grigoryan, A A; Ivanova, A E; Lysenko, A M; Petrunyaka, V V; Osipov, G A; Belyaev, S S; Ivanov, M V

    2001-03-01

    Five hydrocarbon-oxidizing strains were isolated from formation waters of oilfields in Russia, Kazakhstan and China. These strains were moderately thermophilic, neutrophilic, motile, spore-forming rods, aerobic or facultatively anaerobic. The G+C content of their DNA ranged from 49.7 to 52.3 mol%. The major isoprenoid quinone was menaquinone-7; cellular fatty acid profiles consisted of significant amounts of iso-15:0, iso-16:0 and iso-17:0 fatty acids (61.7-86.8% of the total). Based on data from 16S rDNA analysis and DNA-DNA hybridization, the subsurface isolates could be divided into two groups, one of which consisted of strains UT and X and the other of which consisted of strains K, Sam and 34T. The new strains exhibited a close phylogenetic relationship to thermophilic bacilli of 'Group 5' of Ash et al. [Ash, C., Farrow, J. A. E., Wallbanks, S. & Collins, M. D. (1991). Lett Appl Microbiol 13, 202-206] and a set of corresponding signature positions of 16S rRNA. Comparative analysis of the 16S rDNA sequences and fatty acid compositions of the novel isolates and established species of thermophilic bacilli indicated that the subsurface strains represent two new species within a new genus, for which the names Geobacillus subterraneus gen. nov., sp. nov., and Geobacillus uzenensis sp. nov. are proposed. It is also proposed that Bacillus stearothermophilus, Bacillus thermoleovorans, Bacillus thermocatenulatus, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans be transferred to this new genus, with Geobacillus stearothermophilus (formerly Bacillus stearothermophilus) as the type species. PMID:11321089

  12. 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...

  13. Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies

    PubMed Central

    Brumm, Phillip J.; De Maayer, Pieter; Mead, David A.; Cowan, Don A.

    2015-01-01

    In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and ?-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, ?-mannosides, ?-1,4-glucosides and arabinan.

  14. Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies.

    PubMed

    Brumm, Phillip J; De Maayer, Pieter; Mead, David A; Cowan, Don A

    2015-01-01

    In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and ?-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, ?-mannosides, ?-1,4-glucosides and arabinan. PMID:26029180

  15. Characterization of thermostable cellulases produced by Bacillus and Geobacillus strains

    Microsoft Academic Search

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

    2010-01-01

    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,

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

    PubMed Central

    2012-01-01

    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

  17. Draft Genome Sequence of Geobacillus sp. Isolate T6, a Thermophilic Bacterium Collected from a Thermal Spring in Argentina.

    PubMed

    Ortiz, Elio M; Berretta, Marcelo F; Navas, Laura E; Benintende, Graciela B; Amadio, Ariel F; Zandomeni, Rubén O

    2015-01-01

    Geobacillus sp. isolate T6 was collected from a thermal spring in Salta, Argentina. The draft genome sequence (3,767,773 bp) of this isolate is represented by one major scaffold of 3,46 Mbp, a second one of 207 kbp, and 20 scaffolds of <13 kbp. The assembled sequences revealed 3,919 protein-coding genes. PMID:26184933

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

    PubMed

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

    2014-08-01

    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

  19. Production of a novel glycerol-inducible lipase from thermophilic Geobacillus stearothermophilus strain-5

    Microsoft Academic Search

    Mahmoud M. Berekaa; Taha I. Zaghloul; Yasser R. Abdel-Fattah; Hesham M. Saeed; Mohamed Sifour

    2009-01-01

    In a screening program for isolation of thermophilic lipase-producing bacteria, a number of thermophilic bacteria were isolated\\u000a from desert soil from Baltim, Egypt. Among 55 isolates, a potent bacterial candidate (starin-5) was characterized and identified\\u000a by biochemical and PCR techniques, based on 16S rRNA sequencing. Phylogenetic analysis revealed its closeness to geobacilli\\u000a especially the thermophilic Geobacillus stearothermophilus with optimal growth and

  20. Genetic engineering of Geobacillus spp.

    PubMed

    Kananavi?i?t?, R?ta; ?itavi?ius, Donaldas

    2015-04-01

    Members of the genus Geobacillus are thermophiles that are of great biotechnological importance, since they are sources of many thermostable enzymes. Because of their metabolic versatility, geobacilli can be used as whole-cell catalysts in processes such as bioconversion and bioremediation. The effective employment of Geobacillus spp. requires the development of reliable methods for genetic engineering of these bacteria. Currently, genetic manipulation tools and protocols are under rapid development. However, there are several convenient cloning vectors, some of which replicate autonomously, while others are suitable for the genetic modification of chromosomal genes. Gene expression systems are also intensively studied. Combining these tools together with proper techniques for DNA transfer, some Geobacillus strains were shown to be valuable producers of recombinant proteins and industrially important biochemicals, such as ethanol or isobutanol. This review encompasses the progress made in the genetic engineering of Geobacillus spp. and surveys the vectors and transformation methods that are available for this genus. PMID:25659824

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

    PubMed Central

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

    2014-01-01

    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

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

    PubMed

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

    2014-01-01

    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

  3. Studies of nitrile oxide cycloadditions, and the phenolic oxidative coupling of vanillin aldoxime by Geobacillus sp. DDS012 from Italian rye grass silage.

    PubMed

    Kelly, David R; Baker, Simon C; King, David S; de Silva, Deepa S; Lord, Gwyn; Taylor, Jason P

    2008-02-21

    During studies directed towards the discovery of nitrile hydrolysing enzymes from thermophiles, vanillin aldoxime was incubated with the thermophilic organism, Geobacillus sp. DDS012 isolated from Italian rye grass (Lolium multiflorum) silage. The predominant product was a dihydro-dimer, which could only be characterised by LC-MS. This was initially imagined to be the product of cycloaddition of vanillin aldoxime with the corresponding nitrile oxide, but preparation of the supposed adduct and model studies excluded this possibility. The rate constant for the second order dimerisation of 4-O-acetyl vanillin nitrile oxide was measured (1.21 x 10(-4) M(-1) s(-1), 0.413 M, 25 degrees C) and the (13)C-NMR signal for the nitrile oxide carbon was observed (delta(C) 34.4, br. t (1)J(13)C,(14)N circa 50 Hz). Treatment of vanillin aldoxime with potassium persulfate and iron sulfate gave material with the same LC-MS properties as the natural product, which is therefore identified as 5,5'-dehydro-di-(vanillin aldoxime) 1d formed by phenolic oxidative coupling. PMID:18264580

  4. Enhancing the cellulose-degrading activity of cellulolytic bacteria CTL-6 (Clostridium thermocellum) by co-culture with non-cellulolytic bacteria W2-10 (Geobacillus sp.).

    PubMed

    Lü, Yucai; Li, Ning; Yuan, Xufeng; Hua, Binbin; Wang, Jungang; Ishii, Masaharu; Igarashi, Yasuo; Cui, Zongjun

    2013-12-01

    The effect of a non-cellulolytic bacterium W2-10 (Geobacillus sp.) on the cellulose-degrading activity of a cellulolytic bacterium CTL-6 (Clostridium thermocellum) was determined using cellulose materials (paper and straw) in peptone cellulose solution (PCS) medium under aerobic conditions. The results indicated that in the co-culture, addition of W2-10 resulted in a balanced medium pH, and may provide the required anaerobic environment for CTL-6. Overall, addition of W2-10 was beneficial to CTL-6 growth in the adverse environment of the PCS medium. In co-culture with W2-10, the CTL-6 cellulose degradation efficiency of filter paper and alkaline-treated wheat straw significantly increased up to 72.45 and 37.79 %, respectively. The CMCase activity and biomass of CTL-6 also increased from 0.23 U ml(-1) and 45.1 ?g ml(-1) (DNA content) up to 0.47 U ml(-1) and 112.2 ?g ml(-1), respectively. In addition, co-culture resulted in accumulation of acetate and propionate up to 4.26 and 2.76 mg ml(-1). This was a respective increase of 2.58 and 4.45 times, in comparison to the monoculture with CTL-6. PMID:23975281

  5. Highly thermostable GH39 ß-xylosidase from a Geobacillus sp. strain WSUCF1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background Complete enzymatic hydrolysis of xylan to xylose requires the action of endoxylanase and ß-xylosidase. ß-xylosidases play an important part in hydrolyzing xylo-oligosaccharides to xylose. Thermostable ß-xylosidases have been a focus of attention as industrially important enzymes due to th...

  6. Cloning, Sequence Analysis and Three-dimensional Structure Prediction of DNA Pol I from Thermophilic Geobacillus sp. MKK Isolated from an Iranian Hot Spring

    Microsoft Academic Search

    Mohammad Khalaj-Kondori; Majid Sadeghizadeh; Khosro Khajeh; Hossein Naderi-Manesh; Ali Mohammad Ahadi; Abdorahman Emamzadeh

    2007-01-01

    Molecular phylogenetic analysis of a novel thermophilic eubacterium isolated from an Iranian hot spring using 16S rDNA sequence\\u000a showed that the new isolate belongs to genera Geobacillus. DNA pol I gene from this isolate was amplified, cloned, sequenced, and the three-dimensional (3D) structure of deduced amino\\u000a acid sequence was predicted. Sequence analysis revealed the gene is 2,631 bp long, encodes a

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

    SciTech Connect

    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

    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.

  8. Nitrogen Control of Atrazine Utilization in Pseudomonas sp. Strain ADP

    Microsoft Academic Search

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

    2003-01-01

    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

  9. Methylomonas sp. strain 761M: an unusual Type I methanotroph

    SciTech Connect

    Zhao, S.J.; Hanson, R.S.

    1985-01-01

    Methylomonas sp. strain 761M and strains derived from it are described as unusual type I methanotrophs that require multicarbon compounds for rapid growth. Alpha-ketoglutarate dehydrogenase is present in these strains, and they contain a functional tricarboxylic acid cycle. Methylomonas sp. strain 761M appears to be well-adapted to studies of energy and growth yields on C/sub 1/ substrates because the assimilation of C/sub 1/ units can be substantially reduced. 16 references, 2 figures, 4 tables.

  10. Draft Genome Sequence of Rhodococcus sp. Strain 311R

    PubMed Central

    Ehsani, Elham; Jauregui, Ruy; Geffers, Robert; Jareck, Michael; Boon, Nico; Pieper, Dietmar H.

    2015-01-01

    Here, we report the draft genome sequence of Rhodococcus sp. strain 311R, which was isolated from a site contaminated with alkanes and aromatic compounds. Strain 311R shares 90% of the genome of Rhodococcus erythropolis SK121, which is the closest related bacteria. PMID:25999565

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

    PubMed Central

    Che, Shuai; Song, Lai; Song, Weizhi; Yang, Meng

    2013-01-01

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

  12. Draft Genome Sequence of Rhodococcus sp. Strain 311R.

    PubMed

    Ehsani, Elham; Jauregui, Ruy; Geffers, Robert; Jareck, Michael; Boon, Nico; Pieper, Dietmar H; Vilchez-Vargas, Ramiro

    2015-01-01

    Here, we report the draft genome sequence of Rhodococcus sp. strain 311R, which was isolated from a site contaminated with alkanes and aromatic compounds. Strain 311R shares 90% of the genome of Rhodococcus erythropolis SK121, which is the closest related bacteria. PMID:25999565

  13. Rhodococcus sp. strain TM1 plays a synergistic role in the degradation of piperidine by Mycobacterium sp. strain THO100.

    PubMed

    Kim, Yong-Hak; Kang, Un-Beom; Konishi, Kyoko; Lee, Cheolju

    2006-09-01

    Mycobacterium sp. strain THO100 and Rhodococcus sp. strain TM1 were isolated from a morpholine-containing enrichment culture of activated sewage sludge. Strain THO100, but not strain TM1, was able to degrade alicyclic amines such as morpholine, piperidine, and pyrrolidine. The mixed strains THO100 and TM1 showed a better growth on piperidine as the substrate than the pure strain THO100 because strain TM1 was able to reduce the level of glutaraldehyde (GA) produced during piperidine degradation. GA was toxic to strain THO100 (IC(50) = 28.3 microM) but less toxic to strain TM1 (IC(50) = 215 microM). Strain THO100 possessed constitutive semialdehyde dehydrogenases, namely Sad1 and Sad2, whose activities toward succinic semialdehyde (SSA) were strongly inhibited by GA. The two isozymes were identified as catalase-peroxidase (KatG = Sad1) and semialdehyde dehydrogenase (Sad2) based on mass spectrometric analyses of tryptic peptides and database searches of the partial DNA sequences of their genes. In contrast, strain TM1 containing another constitutive enzyme Gad1 could oxidize both SSA and GA. This study suggested that strain TM1 possessing Gad1 played a synergistic role in reducing the toxic and inhibitory effects of GA produced in the degradation of piperidine by strain THO100. PMID:16832627

  14. Biodegradation of 4-nitrotoluene by pseudomonas sp. strain 4NT

    SciTech Connect

    Haigler, B.E.; Spain, J.C. (Tyndall Air Force Base, FL (United States))

    1993-07-01

    Nitroaromatic compounds, common intermediates or by-products in synthesis of dyes, solvents, and explosives, has resulting in their emergence as environmental contaminants. Bacterial strains able to degrade 4-nitrotoluene (4-NT) have been isolated. The present study reports the complete degradative pathway of Pseudomonas sp. strain 4NT that uses 4-NT as a sole source of carbon, nitrogen, and energy. 33 refs., 2 figs., 3 tabs.

  15. Complete Genome Assembly of Corynebacterium sp. Strain ATCC 6931

    PubMed Central

    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

    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

  16. 40 CFR 180.1120 - Streptomyces sp. strain K61; exemption from the requirement of a tolerance.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 2011-07-01 false Streptomyces sp. strain K61; exemption from the requirement...Tolerances § 180.1120 Streptomyces sp. strain K61; exemption from the requirement... The biological pesticide Streptomyces sp. strain K61 is exempted from the...

  17. 40 CFR 180.1120 - Streptomyces sp. strain K61; exemption from the requirement of a tolerance.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 2010-07-01 false Streptomyces sp. strain K61; exemption from the requirement...Tolerances § 180.1120 Streptomyces sp. strain K61; exemption from the requirement... The biological pesticide Streptomyces sp. strain K61 is exempted from the...

  18. Saturation Mutagenesis of 2,4-DNT Dioxygenase of Burkholderia sp. Strain DNT

    E-print Network

    Wood, Thomas K.

    Saturation Mutagenesis of 2,4-DNT Dioxygenase of Burkholderia sp. Strain DNT for Enhanced this study indicated that the 2,4-DNT dioxygenases of Burkholderia sp. strain DNT and B. cepacia R34 are more). Burkholderia sp. strain DNT was isolated from water samples from Waconda Bay near the Volunteer Army Ammunition

  19. Effect of salt stress on the physiology of Frankia sp strain CcI6.

    PubMed

    Oshone, Rediet; Mansour, Samira R; Tisa, Louis S

    2013-11-01

    Actinorhizal plants are able to overcome saline soils and reclaim land. Frankia sp strain CcI6 was isolated from nodules of Casuarina cunninghamiana found in Egypt. Phylogenetic analysis of Frankia sp. strain CcI6 revealed that the strain is closely related to Frankia sp. strain CcI3. The strain displays an elevated level of NaCl tolerance. Vesicle production and nitrogenase activity were also influenced by NaCl. PMID:24287648

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

    PubMed Central

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

    2009-01-01

    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

  1. Natural transformation of Thermotoga sp. strain RQ7

    PubMed Central

    2014-01-01

    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

  2. Nutritional Requirements of Methanosarcina sp. Strain TM-1.

    PubMed

    Murray, P A; Zinder, S H

    1985-07-01

    Methanosarcina sp. strain TM-1, an acetotrophic, thermophilic methanogen isolated from an anaerobic sludge digestor, was originally reported to require an anaerobic sludge supernatant for growth. It was found that the sludge supernatant could be replaced with yeast extract (1 g/liter), 6 mM bicarbonate-30% CO(2), and trace metals, with a doubling time on methanol of 14 h. For growth on either methanol or acetate, yeast extract could be replaced with CaCl(2) . 2H(2)O (13.6 muM minimum) and the vitamin p-aminobenzoic acid (PABA, ca. 3 nM minimum), with a doubling time on methanol of 8 to 9 h. Filter-sterilized folic acid at 0.3 muM could not replace PABA. The antimetabolite sulfanilamide (20 mM) inhibited growth of and methanogenesis by Methanosarcina sp. strain TM-1, and this inhibition was reversed by the addition of 0.3 muM PABA. When a defined medium buffered with 20 mM N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid was used, it was shown that Methanosarcina sp. strain TM-1 required 6 mM bicarbonate-30% CO(2) for optimal growth and methanogenesis from methanol. Cells growing on acetate were less dependent on bicarbonate-CO(2). When we used a defined medium in which the only organic compounds present were methanol or acetate, nitrilotriacetic acid (0.2 mM), and PABA, it was possible to limit batch cultures of Methanosarcina sp. strain TM-1 for nitrogen at NH(4) concentrations at or below 2.0 mM, in marked contrast with Methanosarcina barkeri 227, which fixes dinitrogen when grown under NH(4) limitation. PMID:16346841

  3. Marine Diatom, Navicula sp. Strain JPCC DA0580 and Marine Green Alga, Chlorella sp. Strain NKG400014 as Potential Sources for Biodiesel Production

    Microsoft Academic Search

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

    2010-01-01

    Marine diatom, strain JPCC DA0580, and marine green microalga strain NKG400014 were selected as high neutral lipid-producers\\u000a from marine microalgal culture collection toward biodiesel production. These strains were tentatively identified as Navicula sp. and Chlorella sp., respectively, by 18S rDNA analysis. Growth and lipid accumulation conditions of both strains were analyzed by changing\\u000a nutrient concentrations in growth media and initial

  4. Desulfurization of dibenzothiophene by Corynebacterium sp. strain SY1

    SciTech Connect

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

    1992-03-01

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

  5. Genome Sequences of the Lignin-Degrading Pseudomonas sp. Strain YS-1p and Rhizobium sp. Strain YS-1r Isolated from Decaying Wood

    PubMed Central

    Prabhakaran, Madhu; Couger, Matthew B.; Jackson, Colin A.; Weirick, Tyler

    2015-01-01

    Pseudomonas sp. strain YS-1p and Rhizobium sp. strain YS-1r were isolated from a lignin-degrading enrichment culture. The isolates degraded lignin-derived monomers, dimers, alkali lignin, and, to a smaller extent (3% to 5%), lignin in switch grass and alfalfa. Genome analysis revealed the presence of a variety of lignin-degrading genes. PMID:25744986

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

    PubMed Central

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

    1998-01-01

    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

  7. Kinetics of Acetate Utilization by Two Thermophilic Acetotrophic Methanogens: Methanosarcina sp. Strain CALS-1 and Methanothrix sp. Strain CALS-1.

    PubMed

    Min, H; Zinder, S H

    1989-02-01

    The kinetics of acetate utilization were examined for washed concentrated cell suspensions of two thermophilic acetotrophic methanogens isolated from a 58 degrees C anaerobic digestor. Progress curves for acetate utilization by cells of Methanosarcina sp. strain CALS-1 showed that the utilization rate was concentration independent (zero order) above concentrations near 3 mM and that acetate utilization ceased when a threshold concentration near 1 mM was reached. Acetate utilization by cells of Methanothrix sp. strain CALS-1 was concentration independent down to 0.1 to 0.2 mM, and threshold values of 12 to 21 muM were observed. Typical utilization rates in the concentration-independent stage were 210 and 130 nmol min mg of protein for the methanosarcina and the methanothrix, respectively. These results are in agreement with a general model in which high acetate concentrations favor Methanosarcina spp., while low concentrations favor Methanothrix spp. However, acetate utilization by these two strains did not follow simple Michaelis-Menton kinetics. PMID:16347856

  8. Niche adjustment for bioaugmentation with Pseudomonas sp. strain KC

    SciTech Connect

    Dybas, M.J.; Tatara, G.M.; Criddle, C.S. [Michigan State Univ., East Lansing, MI (United States); Knoll, W.H. [Michigan State Univ., Noblesville, IN (United States); Mayotte, T.J. [Golder Associates, Inc., East Lansing, MI (United States)

    1995-12-31

    To be effective, novel organisms introduced into the environment must be able to survive and compete with indigenous organisms. However, to minimize the possibility of ecological disturbance, colonization should ideally be constrained. A possible solution is to create a temporary niche for the introduced organism. Alkalinity addition creates just such a niche by reducing the bioavailability of essential trace metals, such as iron, thereby favoring organisms with efficient trace metal scavenging systems. The authors evaluated alkaline pH adjustment with Pseudomonas sp. strain KC, a denitrifying aquifer organism that degrades carbon tetrachloride (CT) under denitrifying conditions. They compared the kinetic parameters of strain KC with those of its potential competitors (other denitrifiers) in groundwater from a CT-contaminated aquifer at Schoolcraft, Michigan. Under moderately alkaline conditions, strain KC had a higher maximum specific growth rate and yield. With alkaline adjustment, strain KC grew and degraded CT in columns containing aquifer solids from the Schoolcraft site and in slurries of aquifer material from Hanford, Washington. Upon reducing pH, a rapid decline in the KC population followed.

  9. Decolorization of sulfonated azo dye Metanil Yellow by newly isolated bacterial strains: Bacillus sp. strain AK1 and Lysinibacillus sp. strain AK2.

    PubMed

    Anjaneya, O; Souche, S Yogesh; Santoshkumar, M; Karegoudar, T B

    2011-06-15

    Two different bacterial strains capable of decolorizing a highly water soluble azo dye Metanil Yellow were isolated from dye contaminated soil sample collected from Atul Dyeing Industry, Bellary, India. The individual bacterial strains Bacillus sp. AK1 and Lysinibacillus sp. AK2 decolorized Metanil Yellow (200 mg L(-1)) completely within 27 and 12h respectively. Various parameters like pH, temperature, NaCl and initial dye concentrations were optimized to develop an economically feasible decolorization process. The maximum concentration of Metanil Yellow (1000 mg L(-1)) was decolorized by strains AK2 and AK1 within 78 and 84 h respectively. These strains could decolorize Metanil Yellow over a broad pH range 5.5-9.0; the optimum pH was 7.2. The decolorization of Metanil Yellow was most efficient at 40°C and confirmed by UV-visible spectroscopy, TLC, HPLC and GC/MS analysis. Further, both the strains showed the involvement of azoreductase in the decolorization process. Phytotoxicity studies of catabolic products of Metanil Yellow on the seeds of chick pea and pigeon pea revealed much reduction in the toxicity of metabolites as compared to the parent dye. These results indicating the effectiveness of strains AK1 and AK2 for the treatment of textile effluents containing azo dyes. PMID:21470774

  10. Degradation of alkylphenol ethoxylates by Pseudomonas sp. strain TR01.

    PubMed

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

    1994-07-01

    An alkylphenol ethoxylate-degrading bacterium was isolated from activated sludge of a municipal sewage treatment plant by enrichment culture. This organism was found to belong to the genus Pseudomonas; since no corresponding species was identified, we designated it as Pseudomonas sp. strain TR01. This strain had an optimal temperature and pH of 30 degrees C and 7, respectively, for both growth and the degradation of Triton N-101 (a nonylphenol ethoxylate in which the average number of ethylene oxide [EO] units is 9.5). The strain was unable to mineralize Triton N-101 but was able to degrade its EO chain exclusively. The resulting dominant intermediate was identified by normal-phase high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry as a nonylphenol ethoxylate with 2 mol of EO units. A carboxylated metabolite, [(nonylphenoxy)ethoxy]acetic acid, was detected by gas chromatography-mass spectrometry. This bacterium also metabolized alcohol ethoxylates with various numbers of EO units but not polyethylene glycols whatever their degree of polymerization. By oxygen consumption assay, the alkyl group or arene corresponding to the hydrophobic part of alcohol ethoxylates or alkylphenol ethoxylates was shown to contribute to the induction of the metabolic system of the EO chain of Triton N-101, instead of the EO chain itself, which corresponds to its hydrophilic part. Thus, the isolated pseudomonad bacterium has unique substrate assimilability: it metabolizes the EO chain only when the chain linked to bulky hydrophobic groups. PMID:8074508

  11. Degradation of alkylphenol ethoxylates by Pseudomonas sp. strain TR01.

    PubMed Central

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

    1994-01-01

    An alkylphenol ethoxylate-degrading bacterium was isolated from activated sludge of a municipal sewage treatment plant by enrichment culture. This organism was found to belong to the genus Pseudomonas; since no corresponding species was identified, we designated it as Pseudomonas sp. strain TR01. This strain had an optimal temperature and pH of 30 degrees C and 7, respectively, for both growth and the degradation of Triton N-101 (a nonylphenol ethoxylate in which the average number of ethylene oxide [EO] units is 9.5). The strain was unable to mineralize Triton N-101 but was able to degrade its EO chain exclusively. The resulting dominant intermediate was identified by normal-phase high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry as a nonylphenol ethoxylate with 2 mol of EO units. A carboxylated metabolite, [(nonylphenoxy)ethoxy]acetic acid, was detected by gas chromatography-mass spectrometry. This bacterium also metabolized alcohol ethoxylates with various numbers of EO units but not polyethylene glycols whatever their degree of polymerization. By oxygen consumption assay, the alkyl group or arene corresponding to the hydrophobic part of alcohol ethoxylates or alkylphenol ethoxylates was shown to contribute to the induction of the metabolic system of the EO chain of Triton N-101, instead of the EO chain itself, which corresponds to its hydrophilic part. Thus, the isolated pseudomonad bacterium has unique substrate assimilability: it metabolizes the EO chain only when the chain linked to bulky hydrophobic groups. PMID:8074508

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

    PubMed

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

    2011-01-01

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

  13. Draft Genome Sequences of Agrobacterium nepotum Strain 39/7T and Agrobacterium sp. Strain KFB 330

    PubMed Central

    Pu?awska, Joanna; Proki?, An?elka; Ivanovi?, Milan; Zlatkovi?, Nevena; Gaši?, Katarina; Obradovi?, Aleksa

    2015-01-01

    Tumorigenic strains of Agrobacterium spp. are responsible for crown gall disease of numerous plant species. We present here draft genome sequences of nonpathogenic Agrobacterium nepotum strain 39/7T (CFBP 7436T, LMG 26435T), isolated from crown gall tumor on Prunus cerasifera, and tumorigenic Agrobacterium sp. strain KFB 330 (CFBP 8308, LMG 28674), isolated from galls on raspberry. PMID:25908139

  14. Draft Genome Sequences of Agrobacterium nepotum Strain 39/7T and Agrobacterium sp. Strain KFB 330.

    PubMed

    Kuzmanovi?, Nemanja; Pu?awska, Joanna; Proki?, An?elka; Ivanovi?, Milan; Zlatkovi?, Nevena; Gaši?, Katarina; Obradovi?, Aleksa

    2015-01-01

    Tumorigenic strains of Agrobacterium spp. are responsible for crown gall disease of numerous plant species. We present here draft genome sequences of nonpathogenic Agrobacterium nepotum strain 39/7(T) (CFBP 7436(T), LMG 26435(T)), isolated from crown gall tumor on Prunus cerasifera, and tumorigenic Agrobacterium sp. strain KFB 330 (CFBP 8308, LMG 28674), isolated from galls on raspberry. PMID:25908139

  15. Complete genome sequence of Arthrobacter sp. strain FB24

    SciTech Connect

    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

    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.

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

    PubMed

    Kudo, Toshiaki; 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; Ohkuma, Moriya

    2014-01-01

    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

  17. Draft Genome Sequence of the Electricigen Acidiphilium sp. Strain PM (DSM 24941)

    PubMed Central

    San Martin-Uriz, Patxi; Gomez, Manuel J.; Arcas, Aida; Bargiela, Rafael; Amils, Ricardo

    2011-01-01

    Acidiphilium sp. strain PM (DSM 24941) was isolated from Rio Tinto's acidic, heavy metal-rich waters. Voltammetry experiments revealed that this strain is capable of electricity production even under aerobic conditions. Here we report the draft genome sequence of Acidiphilium sp. PM and a preliminary genome analysis that reveals a versatile respiratory metabolism. PMID:21914891

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

    E-print Network

    Roegner, Matthias

    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

  19. [Geobacillus uralicus, a new species of thermophilic bacteria].

    PubMed

    Popova, N A; Nikolaev, Iu A; Turova, T P; Lysenko, A M; Osipov, G A; Verkhovtseva, N V; Panikov, N S

    2002-01-01

    The K2T strain of thermophilic spore-forming bacteria was isolated from a biofilm on the surface of a corroded pipeline in an extremely deep well (4680 m, 40-72 degrees C) in the Ural. The cells are rod-shaped, motile, gram-variable. They grow on a complex medium with tryptone and yeast extract and on a synthetic medium with glucose and mineral salts without additional growth factors. The cells use a wide range of organic substances as carbon and energy sources. They exhibit a respiratory metabolism but are also capable of anaerobic growth on a nitrate-containing medium and of fermentation. Growth occurs within the 40-75 degrees C temperature range (with an optimum of 65 degrees C) and at pH 5-9. The minimum generation time (15 min) was observed at pH 7.5. Ammonium salts and nitrates are used as nitrogen sources. The G + C content of the DNA is 54.5 mol%. From the morphological, physiological, and biochemical properties and the nucleotide sequence of the 16S rRNA gene, it was concluded that the isolate K2T represents a new species of the genus Geobacillus, Geobacillus uralicus. PMID:12138763

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

    SciTech Connect

    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

    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.

  1. Mechanism of Algal Aggregation by Bacillus sp. Strain RP1137

    PubMed Central

    Powell, Ryan J.

    2014-01-01

    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

  2. Mechanism of algal aggregation by Bacillus sp. strain RP1137.

    PubMed

    Powell, Ryan J; Hill, Russell T

    2014-07-01

    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

  3. Molecular identification of alkaliphilic and halotolerant strain Bacillus sp. FTU as Bacillus pseudofirmus FTU

    Microsoft Academic Search

    Maria S. Muntyan; Tatiana P. Tourova; Anatolij M. Lysenko; Tatiana V. Kolganova; Dagmar Fritze; Vladimir P. Skulachev

    2002-01-01

    The systematic position of the alkaliphilic and halotolerant strain Bacillus sp. FTU was refined in view of the comprehensive taxonomic revision of the group of alkaliphilic and alkalitolerant Bacillus strains. Sequence analysis of almost the entire 16S rRNA gene of Bacillus sp. FTU revealed 99.8% homology with two Bacillus pseudofirmus strains. Subsequent DNA-DNA hybridization analysis confirmed the close relationship of

  4. Changes in Sodium, Calcium, and Magnesium Ion Concentrations That Inhibit Geobacillus Biofilms Have No Effect on Anoxybacillus flavithermus Biofilms.

    PubMed

    Somerton, B; Lindsay, D; Palmer, J; Brooks, J; Flint, S

    2015-08-01

    This study investigated the effects of varied sodium, calcium, and magnesium concentrations in specialty milk formulations on biofilm formation by Geobacillus spp. and Anoxybacillus flavithermus. The numbers of attached viable cells (log CFU per square centimeter) after 6 to 18 h of biofilm formation by three dairy-derived strains of Geobacillus and three dairy-derived strains of A. flavithermus were compared in two commercial milk formulations. Milk formulation B had relatively high sodium and low calcium and magnesium concentrations compared with those of milk formulation A, but the two formulations had comparable fat, protein, and lactose concentrations. Biofilm formation by the three Geobacillus isolates was up to 4 log CFU cm(-2) lower in milk formulation B than in milk formulation A after 6 to 18 h, and the difference was often significant (P ? 0.05). However, no significant differences (P ? 0.05) were found when biofilm formations by the three A. flavithermus isolates were compared in milk formulations A and B. Supplementation of milk formulation A with 100 mM NaCl significantly decreased (P ? 0.05) Geobacillus biofilm formation after 6 to 10 h. Furthermore, supplementation of milk formulation B with 2 mM CaCl2 or 2 mM MgCl2 significantly increased (P ? 0.05) Geobacillus biofilm formation after 10 to 18 h. It was concluded that relatively high free Na(+) and low free Ca(2+) and Mg(2+) concentrations in milk formulations are collectively required to inhibit biofilm formation by Geobacillus spp., whereas biofilm formation by A. flavithermus is not impacted by typical cation concentration differences of milk formulations. PMID:26002898

  5. Methylammonium uptake by Rhizobium sp. strain 32H1.

    PubMed Central

    Gober, J W; Kashket, E R

    1983-01-01

    We present evidence that methylammonium is transported into cowpea Rhizobium sp. strain 32H1 cells by a membrane carrier whose natural substrate is ammonium. After growth in low (0.2%) oxygen, which is necessary for nitrogen fixation by these cells, respiring rhizobial cells took up [14C]methylammonium to high intracellular levels. Cells grown in atmospheric (21%) oxygen did not take up methylammonium. Uptake (transport plus metabolism) was maximal in cells harvested in the early stationary phase of batch culture and had a distinct pH optimum of 6.5 to 7.0. Uptake was inhibited by metabolic poisons that dissipate the proton motive force or inhibit ATP synthesis. Inhibition of uptake by ammonium and the counterflow phenomenon indicated that ammonium and methylammonium share a transport carrier. Of the methylammonium taken up, about 15% was accumulated to intracellular levels 20 times higher than those in the medium; most of the methylammonium was metabolized to gamma-N-methylglutamine. PMID:6826521

  6. Dynamics of genome architecture in Rhizobium sp. strain NGR234.

    PubMed

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

    2002-01-01

    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

  7. Dynamics of Genome Architecture in Rhizobium sp. Strain NGR234†

    PubMed Central

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

    2002-01-01

    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

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

    PubMed Central

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

    2014-01-01

    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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed Central

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

    2015-01-01

    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. PMID:25700412

  11. Whole-Genome Sequence of Enterobacter sp. Strain SST3, an Endophyte Isolated from Jamaican Sugarcane (Saccharum sp.) Stalk Tissue

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

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

    1991-01-01

    Rhizobium sp. strain NGR234 produces large amounts of acidic exopolysaccharide. Mutants that fail to synthesize this exopolysaccharide are also unable to nodulate the host plant Leucaena leucocephala. A hybrid strain of Rhizobium sp. strain NGR234 containing exo genes from Rhizobium meliloti was constructed. The background genetics and nod genes of Rhizobium sp. strain NGR234 are retained, but the cluster of genes involved in exopolysaccharide biosynthesis was deleted. These exo genes were replaced with genes required for the synthesis of succinoglycan exopolysaccharide from R. meliloti. As a result of the genetic manipulation, the ability of these hybrids to synthesize exopolysaccharide was restored, but the structure was that of succinoglycan and not that of Rhizobium sp. strain NGR234. The replacement genes were contained on a cosmid which encoded the entire known R. meliloti exo gene cluster, with the exception of exoB. Cosmids containing smaller portions of this exo gene cluster did not restore exopolysaccharide production. The presence of succinoglycan was indicated by staining with the fluorescent dye Calcofluor, proton nuclear magnetic resonance spectroscopy, and monosaccharide analysis. Although an NGR234 exoY mutant containing the R. meliloti exo genes produced multimers of the succinoglycan repeat unit, as does the wild-type R. meliloti, the deletion mutant of Rhizobium sp. strain NGR234 containing the R. meliloti exo genes produced only the monomer. The deletion mutant therefore appeared to lack a function that affects the multiplicity of succinoglycan produced in the Rhizobium sp. strain NGR234 background. Although these hybrid strains produced succinoglycan, they were still able to induce the development of an organized nodule structure on L. leucocephala. The resulting nodules did not fix nitrogen, but they did contain infection threads and bacteroids within plant cells. This clearly demonstrated that a heterologous acidic exopolysaccharide structure was sufficient to enable nodule development to proceed beyond the developmental barrier imposed on mutants of Rhizobium sp. strain NGR234 that are unable to synthesize any acidic exopolysaccharide. Images PMID:2022612

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

    Microsoft Academic Search

    HIDETO FUKUSHI; KATSUYA HIRAI

    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

  14. Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation

    PubMed Central

    Paul, Robin; Jinkerson, Robert E.; Buss, Kristina; Steel, Jason; Mohr, Remus; Hess, Wolfgang R.; Chen, Min

    2014-01-01

    Leptolyngbya sp. strain Heron Island is a cyanobacterium exhibiting chromatic acclimation. However, this strain has strong interactions with other bacteria, making it impossible to obtain axenic cultures for sequencing. A protocol involving an analysis of tetranucleotide frequencies, G+C content, and BLAST searches has been described for separating the cyanobacterial scaffolds from those of its cooccurring bacteria. PMID:24503993

  15. 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...

  16. Genome Sequence of an Indigoid-Producing Strain, Pseudomonas sp. PI1.

    PubMed

    Qu, Yuanyuan; Liu, Ziyan; Shen, Wenli; Li, Shuzhen; Tang, Hongzhi; Xu, Ping

    2015-01-01

    Pseudomonas sp. strain PI1 can cometabolize indole in the presence of phenol to produce various indigoids. Here, we present a 7.2-Mb draft genome sequence of strain PI1, which may provide insight into the study of phenol-indole cometabolism and its application in aromatic bioremediation and wastewater treatment processes. PMID:26067966

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

    PubMed Central

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

    2014-01-01

    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

  18. Draft Genome Sequence of the Sulfonamide Antibiotic-Degrading Microbacterium sp. Strain C448

    PubMed Central

    Martin-Laurent, Fabrice; Marti, Romain; Waglechner, Nicholas; Wright, Gerard D.

    2014-01-01

    We report the draft genome sequence of Microbacterium sp. strain C448, isolated from agricultural soil with a decade of exposure to veterinary antibiotics on the basis of using sulfamethazine and other antibiotics as the sole sources of carbon. The genome sequence revealed that strain C448 harbors several antibiotic resistance genes, including sulI. PMID:24526651

  19. 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....

  20. Reduction of Photoautotrophic Productivity in the Cyanobacterium Synechocystis sp. Strain PCC 6803 by Phycobilisome Antenna Truncation

    PubMed Central

    Page, Lawrence E.; Liberton, Michelle

    2012-01-01

    Truncation of the algal light-harvesting antenna is expected to enhance photosynthetic productivity. The wild type and three mutant strains of Synechocystis sp. strain 6803 with a progressively smaller phycobilisome antenna were examined under different light and CO2 conditions. Surprisingly, such antenna truncation resulted in decreased whole-culture productivity for this cyanobacterium. PMID:22706065

  1. Genome Sequence of an Indigoid-Producing Strain, Pseudomonas sp. PI1

    PubMed Central

    Liu, Ziyan; Shen, Wenli; Li, Shuzhen; Xu, Ping

    2015-01-01

    Pseudomonas sp. strain PI1 can cometabolize indole in the presence of phenol to produce various indigoids. Here, we present a 7.2-Mb draft genome sequence of strain PI1, which may provide insight into the study of phenol-indole cometabolism and its application in aromatic bioremediation and wastewater treatment processes. PMID:26067966

  2. Growth in Coculture Stimulates Metabolism of the Phenylurea Herbicide Isoproturon by Sphingomonas sp. Strain SRS2

    Microsoft Academic Search

    S. R. Sorensen; Zeev Ronen; Jens Aamand

    2002-01-01

    Metabolism of the phenylurea herbicide isoproturon by Sphingomonas sp. strain SRS2 was significantly enhanced when the strain was grown in coculture with a soil bacterium (designated strain SRS1). Both members of this consortium were isolated from a highly enriched isoproturon-degrading culture derived from an agricultural soil previously treated regularly with the herbicide. Based on analysis of the 16S rRNA gene,

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

    Microsoft Academic Search

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

    2008-01-01

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

  4. Draft Whole-Genome Sequence of Serratia sp. Strain TEL, Associated with Oscheius sp. TEL-2014 (Nematoda: Rhabditidae) Isolated from a Grassland in South Africa

    PubMed Central

    Featherston, Jonathan; Gray, Vincent M.

    2015-01-01

    Here, we report on the draft genome sequence of Serratia sp. strain TEL, associated with Oscheius sp. TEL-2014 (Nematoda: Rhabditidae, KM492926) isolated from a grassland in Suikerbosrand Nature Reserve near Johannesburg in South Africa. Serratia sp. strain TEL has a genome size of 5,000,541 bp with 4,647 genes and a G+C content of 59.1%. PMID:26159531

  5. Complete Genome of Serratia sp. Strain FGI 94, a Strain Associated with Leaf-Cutter Ant Fungus Gardens.

    PubMed

    Aylward, Frank O; Tremmel, Daniel M; Starrett, Gabriel J; Bruce, David C; Chain, Patrick; Chen, Amy; Davenport, Karen W; Detter, Chris; Han, Cliff S; Han, James; Huntemann, Marcel; Ivanova, Natalia N; Kyrpides, Nikos C; Markowitz, Victor; Mavrommatis, Kostas; Nolan, Matt; Pagani, Ioanna; Pati, Amrita; Pitluck, Sam; Teshima, Hazuki; Deshpande, Shweta; Goodwin, Lynne; Woyke, Tanja; Currie, Cameron R

    2013-01-01

    Serratia sp. strain FGI 94 was isolated from a fungus garden of the leaf-cutter ant Atta colombica. Analysis of its 4.86-Mbp chromosome will help advance our knowledge of symbiotic interactions and plant biomass degradation in this ancient ant-fungus mutualism. PMID:23516234

  6. Complete Genome of Serratia sp. Strain FGI 94, a Strain Associated with Leaf-Cutter Ant Fungus Gardens

    PubMed Central

    Aylward, Frank O.; Tremmel, Daniel M.; Starrett, Gabriel J.; Bruce, David C.; Chain, Patrick; Chen, Amy; Davenport, Karen W.; Detter, Chris; Han, Cliff S.; Han, James; Huntemann, Marcel; Ivanova, Natalia N.; Kyrpides, Nikos C.; Markowitz, Victor; Mavrommatis, Kostas; Nolan, Matt; Pagani, Ioanna; Pati, Amrita; Pitluck, Sam; Teshima, Hazuki; Deshpande, Shweta; Goodwin, Lynne; Woyke, Tanja

    2013-01-01

    Serratia sp. strain FGI 94 was isolated from a fungus garden of the leaf-cutter ant Atta colombica. Analysis of its 4.86-Mbp chromosome will help advance our knowledge of symbiotic interactions and plant biomass degradation in this ancient ant-fungus mutualism. PMID:23516234

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

    PubMed

    Ding, Chang; Zhao, Siyan; He, Jianzhong

    2014-11-01

    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

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

    PubMed Central

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

    2007-01-01

    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

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

    PubMed Central

    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

    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

  10. Cd, Cu, Ni, Mn and Zn resistance and bioaccumulation by thermophilic bacteria, Geobacillus toebii subsp. decanicus and Geobacillus thermoleovorans subsp. stromboliensis

    Microsoft Academic Search

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

    Bioaccumulation and heavy metal resistance of Cd2+, Cu2+, Ni2+, Zn2+ and Mn2+ ions by thermophilic Geobacillus toebii subsp. decanicus and Geobacillus thermoleovorans subsp. stromboliensis were investigated. The metal resistance from the most resistant to the most sensitive was found as Mn > Ni > Cu > Zn > Cd\\u000a for both Geobacillus thermoleovorans subsp. stromboliensis and Geobacillus toebii subsp. decanicus. It was determined that the highest metal bioaccumulation

  11. Characterization of phenanthrene degradation by strain polyporus sp. S133.

    PubMed

    Hadibarata, Tony; Tachibana, Sanro

    2010-01-01

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

  12. Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

    PubMed Central

    Harjes, Janno; Ryu, Taewoo; Abdelmohsen, Usama Ramadan; Moitinho-Silva, Lucas; Horn, Hannes; Ravasi, Timothy

    2014-01-01

    The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters. PMID:24604655

  13. Expression of the ggpS Gene, Involved in Osmolyte Synthesis in the Marine Cyanobacterium Synechococcus sp. Strain PCC 7002, Revealed Regulatory Differences between This Strain and the Freshwater Strain Synechocystis sp. Strain PCC 6803

    PubMed Central

    Engelbrecht, Friederike; Marin, Kay; Hagemann, Martin

    1999-01-01

    Synthesis of the osmolyte glucosylglycerol (GG) in the marine cyanobacterium Synechococcus sp. strain PCC 7002 was characterized. The ggpS gene, which encodes the key enzyme (GG-phosphate synthase [GgpS]) in GG biosynthesis, was cloned by using PCR. A 2,030-bp DNA sequence which contained one open reading frame (ORF) was obtained. The protein deduced from this ORF exhibited 85% similarity to the GgpS of the freshwater cyanobacterium Synechocystis sp. strain PCC 6803. The function of the protein was confirmed by generating a ggpS null mutant, which was not able to synthesize GG and thus exhibited a salt-sensitive phenotype. Expression of the ggpS gene was analyzed in salt-shocked cells by performing Northern blot and immunoblot experiments. While almost no expression was detected in cells grown in low-salt medium, immediately after a salt shock the amounts of ggpS mRNA and GgpS protein increased up to 100-fold. The finding that salt-induced expression occurred was confirmed by measuring enzyme activities, which were negligible in control cells but clearly higher in salt-treated Synechococcus sp. cells. The salt-induced increase in GgpS activity could be inhibited by adding chloramphenicol, while in protein extracts of the freshwater cyanobacterium Synechocystis sp. strain PCC 6803 a constitutive, high level of enzyme activity that was not affected by chloramphenicol was found. A comparison of GG accumulation in the two cyanobacteria revealed that in the marine strain osmolyte synthesis seemed to be regulated mainly by transcriptional control, whereas in the freshwater strain control seemed to be predominantly posttranslational. PMID:10543792

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

    PubMed Central

    Chaurasia, Akhilesh Kumar; Apte, Shree Kumar

    2011-01-01

    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

  15. Degradation of acyl-homoserine lactone molecules by Acinetobacter sp. strain C1010.

    PubMed

    Kang, Beom Ryong; Lee, Jung Hoon; Ko, Sug Ju; Lee, Yong Hwan; Cha, Jae Soon; Cho, Baik Ho; Kim, Young Cheol

    2004-11-01

    A bacterium C1010, isolated from the rhizospheres of cucumbers in fields in Korea, degraded the microbial quorum-sensing molecules, hexanoyl homoserine lactone (HHSL), and octadecanoyl homoserine lactone (OHSL). Morphological characteristics and 16S rRNA sequence analysis identified C1010 as Acinetobacter sp. strain C1010. This strain was able to degrade the acyl-homoserine lactones (AHLs) produced by the biocontrol bacterium, Pseudomonas chlororaphis O6, and a phytopathogenic bacterium, Burkholderia glumae. Co-cultivation studies showed that the inactivation of AHLs by C1010 inhibited production of phenazines by P. chlororaphis O6. In virulence tests, the C1010 strain attenuated soft rot symptom caused by Erwinia carotovora ssp. carotovora. We suggest Acinetobacter sp. strain C1010 could be a useful bacterium to manipulate biological functions that are regulated by AHLs in various Gram-negative bacteria. PMID:15644910

  16. Benomyl-resistant mutant strain of Trichoderma sp. with increased mycoparasitic activity.

    PubMed

    Olejníková, P; Ondrusová, Z; Krystofová, S; Hudecová, D

    2010-01-01

    Application of UV radiation to the strain Trichoderma sp. T-bt (isolated from lignite) resulted in the T-brm mutant which was resistant to the systemic fungicide benomyl. The tub2 gene sequence in the T-brm mutant differed from the parent as well as the collection strain (replacing tyrosine with histidine in the TUB2 protein). Under in vitro conditions this mutant exhibited a higher mycoparasitic activity toward phytopathogenic fungi. PMID:20336512

  17. Benomyl-resistant mutant strain of Trichoderma sp. with increased mycoparasitic activity

    Microsoft Academic Search

    P. Olejníková; Z. Ondrušová; S. Kryštofová; D. Hudecová

    2010-01-01

    Application of UV radiation to the strain Trichoderma sp. T-bt (isolated from lignite) resulted in the T-brm mutant which was resistant to the systemic fungicide benomyl. The\\u000a tub2 gene sequence in the T-brm mutant differed from the parent as well as the collection strain (replacing tyrosine with histidine\\u000a in the TUB2 protein). Under in vitro conditions this mutant exhibited a

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

    PubMed

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

    2014-01-01

    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

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

    PubMed Central

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

    2014-01-01

    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

  20. Genome Sequence of the Halotolerant Staphylococcus sp. Strain OJ82, Isolated from Korean Traditional Salt-Fermented Seafood

    PubMed Central

    Sung, Jung-Suk; Chun, Jongsik; Choi, Sungjong

    2012-01-01

    Staphylococcus sp. strain OJ82 was isolated from a Korean traditional fermented squid seafood, ojingeo-jeotgal. Staphylococcus sp. OJ82 could grow and show extracellular protease and ?-galactosidase activities in the presence of extremely high saline (20%). Here, we report the genome sequence of Staphylococcus sp. OJ82. PMID:23105083

  1. Genome sequence of the halotolerant Staphylococcus sp. strain OJ82, isolated from Korean traditional salt-fermented seafood.

    PubMed

    Sung, Jung-Suk; Chun, Jongsik; Choi, Sungjong; Park, Woojun

    2012-11-01

    Staphylococcus sp. strain OJ82 was isolated from a Korean traditional fermented squid seafood, ojingeo-jeotgal. Staphylococcus sp. OJ82 could grow and show extracellular protease and ?-galactosidase activities in the presence of extremely high saline (20%). Here, we report the genome sequence of Staphylococcus sp. OJ82. PMID:23105083

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

    PubMed

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

    2015-01-01

    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

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

    PubMed Central

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

    2015-01-01

    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

  4. Naturally transformable Acinetobacter sp. strain ADP1 belongs to the newly described species Acinetobacter baylyi.

    PubMed

    Vaneechoutte, Mario; Young, David M; Ornston, L Nicholas; De Baere, Thierry; Nemec, Alexandr; Van Der Reijden, Tanny; Carr, Emma; Tjernberg, Ingela; Dijkshoorn, Lenie

    2006-01-01

    Genotypic and phenotypic analyses were carried out to clarify the taxonomic position of the naturally transformable Acinetobacter sp. strain ADP1. Transfer tDNA-PCR fingerprinting, 16S rRNA gene sequence analysis, and selective restriction fragment amplification (amplified fragment length polymorphism analysis) indicate that strain ADP1 and a second transformable strain, designated 93A2, are members of the newly described species Acinetobacter baylyi. Transformation assays demonstrate that the A. baylyi type strain B2(T) and two other originally identified members of the species (C5 and A7) also have the ability to undergo natural transformation at high frequencies, confirming that these five strains belong to a separate species of the genus Acinetobacter, characterized by the high transformability of its strains that have been cultured thus far. PMID:16391138

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

    PubMed

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

    2010-09-01

    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

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

    E-print Network

    Roegner, Matthias

    Properties of Mutants of Synechocystis sp. Strain PCC 6803 Lacking Inorganic Carbon SequestrationA is the only active inorganic carbon sequestration system showed low activity of HCO3 ­ uptake and grew under the significance of carbon sequestration in dissipating excess light energy. Keywords: CO2 and HCO3 À uptake -- CO2

  7. A Novel Caffeine Dehydrogenase in Pseudomonas sp. Strain CBB1 Oxidizes Caffeine to Trimethyluric Acid?

    PubMed Central

    Yu, Chi Li; Kale, Yogesh; Gopishetty, Sridhar; Louie, Tai Man; Subramanian, Mani

    2008-01-01

    A unique heterotrimeric caffeine dehydrogenase was purified from Pseudomonas sp. strain CBB1. This enzyme oxidized caffeine to trimethyluric acid stoichiometrically and hydrolytically, without producing hydrogen peroxide. The enzyme was not NAD(P)+ dependent; coenzyme Q0 was the preferred electron acceptor. The enzyme was specific for caffeine and theobromine and showed no activity with xanthine. PMID:17981969

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

    PubMed Central

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

    2013-01-01

    Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum Actinobacteria, isolated from a restaurant chair cushion. The assembly contains 3,791,485 bp (G+C content of 73%) and is contained in 68 scaffolds. PMID:23661474

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

    SciTech Connect

    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

    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.

  10. Transformation of dibenzo-p-dioxin by pseudomonas sp. strain HH69

    SciTech Connect

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

    1990-04-01

    Dibenzo-p-dioxin was oxidatively cleaved by the dibenzofuran-degrading bacterium Pseudomonas sp. strain HH69 to produce minor amounts of 1-hydroxydibenzo-p-dioxin and catechol, while a 2-phenoxy derivative of muconic acid was formed as the major product. Upon acidic methylation, the latter yielded the dimethylester of cis,trans-2-(2-hydroxyphenoxy)-muconic acid.

  11. OXIDATION OF POLYCHLORINATED BIPHENYLS BY PSEUDOMONAS SP. STRAIN LB400 AND PSEUDOMONAS PSEUDOALCALIGENES KF707

    EPA Science Inventory

    Biphenyl-grown cells and cell extracts prepared from biphenyl-grown cells of Pseudomonas sp. strain LB400 oxidize a much wider range of chlorinated biphenyls than do analogous preparations from Pseudomonas pseudoalcaligenes KF707. These results are attributed to differences in th...

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

    EPA Science Inventory

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

  13. Oxidation of polychlorinated biphenyls by pseudomonas sp. strain LB400 and pseudomonas pseudoalcaligenes KF707

    SciTech Connect

    Gibson, D.T.; Cruden, D.L.; Haddock, J.D.; Zylstra, G.J.; Brand, J.M.

    1993-01-01

    Biphenyl-grown cells and cell extracts prepared from biphenyl-grown cells of Pseudomonas sp. strain LB400 oxidize a much wider range of chlorinated biphenyls that do analogous preparations from Pseudomonas pseudoalcaligenes KF707. These results are attributed to differences in the substrate specificity of the biphenyl 2,3-dioxygenases from both organisms.

  14. Cloning of Pseudomonas sp. strain CBS3 genes specifying dehalogenation of 4-chlorobenzoate

    SciTech Connect

    Savard, P.; Peloquin, L.; Sylvestre, M.

    1986-10-01

    Halogenated benzoates have been used as models for the study of the biodegradation of herbicides and PCBs. The degradation of 4-chlorobenzoate (4-CBA) by Pseudomonas sp. strain CBS3 is thought to proceed first by the dehalogenation of 4-CBA to 4-hydroxybenzoate (4-HBA), which is then metabolized following the protocatechuate branch of the ..beta..-ketoadipate pathway. The cloning of the 4-CBA dehalogenation system was carried out by constructing a gene bank of Pseudomonas sp. strain CBS3 in Pseudomonas putida. Hybrid plasmid pPSA843 contains a 9.5-kilobase-pair fragment derived from the chromosome of Pseudomonas sp. strain CBS3. This plasmid confers on P. putida the ability to dehalogenate 4-CBA and grow on 4-CBA as the only source of carbon. However, pPSA843 did not complement mutants of P. putida unable to grow on 4-HBA (POB/sup -/), showing that the genes involved in the metabolism of 4-HBA were not cloned. Subcloning of Pseudomonas sp. strain CBS3 genes revealed that most of the insert is required for the dehalogenation of 4-CBA, suggesting that more than one gene product is involved in this dehalogenation.

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

    EPA Science Inventory

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

  16. Genome Sequence of the Alkaline-Tolerant Cellulomonas sp. Strain FA1.

    PubMed

    Cohen, Michael F; Hu, Ping; Nguyen, My Vu; Kamennaya, Nina; Brown, Natasha; Woyke, Tanja; Kyrpides, Nikos; Holman, Hoi-Ying; Torok, Tamas

    2015-01-01

    We present the genome of the cellulose-degrading Cellulomonas sp. strain FA1 isolated from an actively serpentinizing highly alkaline spring. Knowledge of this genome will enable studies into the molecular basis of plant material degradation in alkaline environments and inform the development of lignocellulose bioprocessing procedures for biofuel production. PMID:26089422

  17. Complete Genome Sequence of Rhodococcus sp. Strain IcdP1 Shows Diverse Catabolic Potential.

    PubMed

    Qu, Jie; Miao, Li-Li; Liu, Ying; Liu, Zhi-Pei

    2015-01-01

    The complete genome sequence of Rhodococcus sp. strain IcdP1 is presented here. This organism was shown to degrade a broad range of high-molecular-weight polycyclic aromatic hydrocarbons and organochlorine pesticides. The sequence data can be used to predict genes for xenobiotic biodegradation and metabolism. PMID:26139718

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

    PubMed Central

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

    2014-01-01

    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

  19. Genome Sequence of the Electrogenic Petroleum-Degrading Thalassospira sp. Strain HJ

    PubMed Central

    Kiseleva, Larisa; Garushyants, Sofya K.; Briliute, Justina; Simpson, David J. W.; Goryanin, Igor

    2015-01-01

    We present the draft genome of the petroleum-degrading Thalassospira sp. strain HJ, isolated from tidal marine sediment. Knowledge of this genomic information will inform studies on electrogenesis and means to degrade environmental organic contaminants, including compounds found in petroleum. PMID:25977412

  20. Draft Genome Sequence of Halomonas sp. KHS3, a Polyaromatic Hydrocarbon-Chemotactic Strain

    PubMed Central

    Gasperotti, Ana Florencia; Studdert, Claudia Alicia; Revale, Santiago

    2015-01-01

    The draft genome sequence of Halomonas sp. KHS3, isolated from seawater from Mar del Plata harbor, is reported. This strain is able to grow using aromatic compounds as a carbon source and shows strong chemotactic response toward these substrates. Genes involved in motility, chemotaxis, and degradation of aromatic hydrocarbons were identified. PMID:25767220

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

    PubMed Central

    Schott, Eric J.

    2014-01-01

    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

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

    PubMed Central

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

    2014-01-01

    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

  3. Genome Sequence of the Alkaline-Tolerant Cellulomonas sp. Strain FA1

    PubMed Central

    Hu, Ping; Nguyen, My Vu; Kamennaya, Nina; Brown, Natasha; Woyke, Tanja; Kyrpides, Nikos; Holman, Hoi-Ying; Torok, Tamas

    2015-01-01

    We present the genome of the cellulose-degrading Cellulomonas sp. strain FA1 isolated from an actively serpentinizing highly alkaline spring. Knowledge of this genome will enable studies into the molecular basis of plant material degradation in alkaline environments and inform the development of lignocellulose bioprocessing procedures for biofuel production.

  4. Draft Genome Sequence of the Carbofuran-Mineralizing Novosphingobium sp. Strain KN65.2

    PubMed Central

    Nguyen, Thi Phi Oanh; De Mot, René

    2015-01-01

    Complete mineralization of the N-methylcarbamate insecticide carbofuran, including mineralization of the aromatic moiety, appears to be confined to sphingomonad isolates. Here, we report the first draft genome sequence of such a sphingomonad strain, i.e., Novosphingobium sp. KN65.2, isolated from carbofuran-exposed agricultural soil in Vietnam. PMID:26159535

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

    PubMed Central

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

    2011-01-01

    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

  6. Transformation of carbon tetrachloride by Pseudomonas sp. strain KC under denitrification conditions

    SciTech Connect

    Criddle, C.S.; DeWitt, J.T.; Grbic-Galic, D.; McCarty, P.L. (Stanford Univ., CA (USA))

    1990-11-01

    A denitrifying Pseudomonas sp. (strain KC) capable of transforming carbon tetrachloride (CT) was isolated from groundwater aquifer solids. Major products of the transformation of {sup 14}C-labeled CT by Pseudomonas strain KC under denitrification conditions were {sup 14}CO{sub 2} and an unidentified water-soluble fraction. Little or no chloroform was produced. Addition of dissolved trace metals, notably, ferrous iron and cobalt, to the growth medium appeared to enhance growth of Pseudomonas strain KC while inhibiting transformation of CT. It is hypothesized that transformation of CT by this organism is associated with the mechanism of trace-metal scavenging.

  7. Biomineralization of N,N-dimethylformamide by Paracoccus sp. strain DMF.

    PubMed

    Swaroop, Shiv; Sughosh, P; Ramanathan, Gurunath

    2009-11-15

    N,N-dimethylformamide (DMF) is a man-made compound that is widely used as a solvent for the synthesis of various organic compounds. In this study, a bacterial strain Paracoccus sp. DMF capable of using DMF as the sole carbon, nitrogen and energy source, was isolated from an enrichment culture developed using activated sludge from domestic waste water treatment unit as the source inoculum. The strain DMF was characterized by biochemical tests and 16S rDNA sequence analysis, to be belonging to the genus Paracoccus. Growth on DMF was accompanied with ammonia release and the total organic carbon (TOC) analysis indicated its extensive mineralization. Batch culture studies were conducted in the substrate range of 100-5000 mg L(-1) to determine the biokinetic constants. Strain Paracoccus sp. DMF could tolerate very high concentrations of DMF as the growth was observed even at 15000 mg L(-1). High (micro(max)) and (K(i)) showed the suitability of the strain for the treatment of DMF containing waste water. Transient accumulation of dimethylamine (DMA) in the medium during the growth on DMF and utilization of DMA and monomethylamine (MMA) as growth substrates by Paracoccus sp. strain DMF showed that the pathway of DMF degradation involves DMA and MMA as intermediates, ultimately leading to the formation of carbon dioxide (CO(2)) and ammonia (NH(3)). PMID:19592157

  8. Sequence of the Ampullariella sp. strain 3876 gene coding for xylose isomerase.

    PubMed Central

    Saari, G C; Kumar, A A; Kawasaki, G H; Insley, M Y; O'Hara, P J

    1987-01-01

    The nucleotide sequence of the gene coding for xylose isomerase from Ampullariella sp. strain 3876, a gram-positive bacterium, has been determined. A clone of a fragment of strain 3876 DNA coding for a xylose isomerase activity was identified by its ability to complement a xylose isomerase-defective Escherichia coli strain. One such complementation positive fragment, 2,922 nucleotides in length, was sequenced in its entirety. There are two open reading frames 1,182 and 1,242 nucleotides in length, on opposite strands of this fragment, each of which could code for a protein the expected size of xylose isomerase. The 1,182-nucleotide open reading frame was identified as the coding sequence for the protein from the sequence analysis of the amino-terminal region and selected internal peptides. The gene initiates with GTG and has a high guanine and cytosine content (70%) and an exceptionally strong preference (97%) for guanine or cytosine in the third position of the codons. The gene codes for a 43,210-dalton polypeptide composed of 393 amino acids. The xylose isomerase from Ampullariella sp. strain 3876 is similar in size to other bacterial xylose isomerases and has limited amino acid sequence homology to the available sequences from E. coli, Bacillus subtilis, and Streptomyces violaceus-ruber. In all cases yet studied, the bacterial gene for xylulose kinase is downstream from the gene for xylose isomerase. We present evidence suggesting that in Ampullariella sp. strain 3876 these genes are similarly arranged. PMID:3027039

  9. Secondary substrate utilization of methylene chloride by an isolated strain of Pseudomonas sp

    SciTech Connect

    LaPat-Polasko, L.T.; McCarty, P.L.; Zehnder, J.B.

    1984-04-01

    Secondary substrate utilization of methylene chloride was analyzed by using Pseudomonas sp. strain LP. Both batch and continuously fed reactors demonstrated that this strain was capable of simultaneously consuming two substrates at different concentrations: the primary substrate at the higher concentration (milligrams per liter) and the secondary substrate at the lower concentration (micrograms per liter). The rate of methylene chloride utilization at trace concentrations was greater in the presence of the primary substrate, acetate, than without it. However, when the substrate roles were changed, the acetate secondary substrate utilization rate was less when methylene chloride was present. Thus, substrate interactions are important in the kinetics of secondary substrate utilization. Pseudomonas sp. strain LP showed a preference toward degrading methylene chloride over acetate, whether it was the primary or secondary substrate, providing it was below an inhibitory concentration of ca. 10 mg/liter. 23 references.

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

    PubMed Central

    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

    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

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

    PubMed

    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

    2013-12-20

    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

  12. Engineering the genotype of Acinetobacter sp. strain ADP1 to enhance biosynthesis of cyanophycin.

    PubMed

    Elbahloul, Yasser; Steinbüchel, Alexander

    2006-02-01

    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. DeltaastA(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

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

    PubMed Central

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

    2002-01-01

    A high-rate fluidized-bed bioreactor has been treating polychlorophenol-contaminated groundwater in southern Finland at 5 to 8°C for over 6 years. We examined the microbial diversity of the bioreactor using three 16S ribosomal DNA (rDNA)-based methods: denaturing gradient gel electrophoresis, length heterogeneity-PCR analysis, and restriction fragment length polymorphism analysis. The molecular study revealed that the process was dependent on a stable bacterial community with low species diversity. The dominant organism, Novosphingobium sp. strain MT1, was isolated and characterized. Novosphingobium sp. strain MT1 degraded the main contaminants of the groundwater, 2,4,6-trichlorophenol, 2,3,4,6-tetrachlorophenol, and pentachlorophenol, at 8°C. The strain carried a homolog of the pcpB gene, coding for the pentachlorophenol-4-monooxygenase in Sphingobium chlorophenolicum. Spontaneous deletion of the pcpB gene homolog resulted in the loss of degradation ability. Phenotypic dimorphism (planktonic and sessile phenotypes), low growth rate (0.14 to 0.15 h?1), and low-copy-number 16S rDNA genes (single copy) were characteristic of strain MT1 and other MT1-like organisms isolated from the bioreactor. PMID:11772624

  14. High Genetic Diversity Among Strains of Fusarium oxysporum f. sp. vasinfectum from Cotton in Ivory Coast.

    PubMed

    Abo, Kouabenan; Klein, Keith K; Edel-Hermann, Véronique; Gautheron, Nadine; Traore, Dossahoua; Steinberg, Christian

    2005-12-01

    ABSTRACT Seventeen isolates of Fusarium oxysporum f. sp. vasinfectum from the Ivory Coast were characterized using vegetative compatibility group (VCG), restriction fragment length polymorphism of the ribosomal inter-genic spacer region (IGS), and mating type (MAT) idiomorph, and compared with a worldwide collection of the pathogen containing all available reference strains. Some of the isolates were identical to known reference strains for all three traits, whereas others had previously unknown varieties of IGS and (possibly) VCG. One or the other MAT idiomorph was present in each of the new isolates and the reference strains. The new isolates and reference strains were grouped based upon the three traits. Strains from the Ivory Coast were found in 7 of 11 groups detected, suggesting multiple sources for Fusarium wilt in the country. Despite the presence of both MAT idiomorphs among isolates, no evidence for recombination was found. PMID:18943549

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

    PubMed

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

    2014-05-01

    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

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

    PubMed Central

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

    2013-01-01

    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

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

    PubMed Central

    Bigler, Laurent; Dudler, Robert

    2014-01-01

    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

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

    PubMed

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

    1999-01-01

    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

  19. A novel dipeptidyl aminopeptidase from Pseudomonas sp. strain WO24.

    PubMed Central

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

    1996-01-01

    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

  20. Pseudomonas arsenicoxydans sp nov., an arsenite-oxidizing strain isolated from the Atacama desert.

    PubMed

    Campos, Victor L; Valenzuela, Cristian; Yarza, Pablo; Kämpfer, Peter; Vidal, Roberto; Zaror, C; Mondaca, Maria-Angelica; Lopez-Lopez, Arantxa; Rosselló-Móra, Ramon

    2010-06-01

    A Gram-negative, arsenite-oxidizing bacterial strain, designated VC-1, was isolated from sediment samples from the Camarones Valley in the Atacama Desert, Chile. Strain VC-1 was strictly aerobic, oxidase and catalase positive, rod shaped, of about 5.5 microm in length and 0.5-1.0 microm in diameter. It was motile by means of multiple polar flagella. The phylogenetic reconstruction of the 16S rRNA gene sequence, an MLSA study by concatenating six genes, and DDH studies indicated that the strain differed genotypically from its closest relatives and was therefore recognized as a new species within the genus Pseudomonas. Phenotypic analysis combining metabolic tests, fatty acid profiles and MALDI-TOF profiles of total cell extracts supported the classification of the new species for which we propose the designation Pseudomonas arsenicoxydans sp. nov. The type strain is accessible under the culture collection numbers CCUG 58201(T) and CECT 7543(T). PMID:20409659

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

    SciTech Connect

    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

    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.

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

    SciTech Connect

    Lewis, T.A.; Crawford, R.L. (Univ. of Idaho, Moscow (United States))

    1993-05-01

    Carbon tetrachloride (CT) is a carcinogenic, ozone-depleting, toxic, xenobiotic compound found in ground water, listed as a priority pollutant by the US EPA. In aqueous solution, CT is not readily hydrolyzed and has an estimated half-life of 7,000 years. Since CT resists spontaneous degradation, conditions favorable for dehalogenation must be created to effect remediation of CT contamination. This paper describes studies of CT transformation aimed at determining the potential of Pseudomonas sp. strain KC as a bioaugmentation strain and describes a search for KC-type CT transformation activity in samples from regional aquifers. 11 refs., 9 figs., 1 tab.

  3. Two distinct monooxygenases for alkane oxidation in Nocardioides sp. strain CF8.

    PubMed

    Hamamura, N; Yeager, C M; Arp, D J

    2001-11-01

    Alkane monooxygenases in Nocardioides sp. strain CF8 were examined at the physiological and genetic levels. Strain CF8 can utilize alkanes ranging in chain length from C(2) to C(16). Butane degradation by butane-grown cells was strongly inhibited by allylthiourea, a copper-selective chelator, while hexane-, octane-, and decane-grown cells showed detectable butane degradation activity in the presence of allylthiourea. Growth on butane and hexane was strongly inhibited by 1-hexyne, while 1-hexyne did not affect growth on octane or decane. A specific 30-kDa acetylene-binding polypeptide was observed for butane-, hexane-, octane-, and decane-grown cells but was absent from cells grown with octane or decane in the presence of 1-hexyne. These results suggest the presence of two monooxygenases in strain CF8. Degenerate primers designed for PCR amplification of genes related to the binuclear-iron-containing alkane hydroxylase from Pseudomonas oleovorans were used to clone a related gene from strain CF8. Reverse transcription-PCR and Northern blot analysis showed that this gene encoding a binuclear-iron-containing alkane hydroxylase was expressed in cells grown on alkanes above C(6). These results indicate the presence of two distinct monooxygenases for alkane oxidation in Nocardioides sp. strain CF8. PMID:11679317

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

    PubMed Central

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

    2007-01-01

    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

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

    PubMed Central

    2012-01-01

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

  6. The acid stress response of the cyanobacterium Synechocystis sp. strain PCC 6308

    Microsoft Academic Search

    Jean J. Huang; Nancy H. Kolodny; Jennifer T. Redfearn; Mary M. Allen

    2002-01-01

    . The cyanobacterium Synechocystis sp. strain PCC 6308 has been shown to exhibit predictable physiological responses to acid stress. Originally isolated from a Wisconsin lake, this cyanobacterium grows optimally under alkaline conditions in the laboratory. After acid stress at a pH of between 4.4 and 7.7, cells return to exponential growth following a lag phase. The organism's response to this

  7. Substantially monodispersed poly(?- l -lysine)s frequently occurred in newly isolated strains of Streptomyces sp

    Microsoft Academic Search

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

    2007-01-01

    The presence of poly(?-l-lysine) (?-PL) was found quite frequently by screening various strains of Streptomyces sp. Most of the ten newly obtained ?-PLs, when they were produced from glucose, showed a polydispersity index of M\\u000a w\\/M\\u000a n?=?1.01 using ion-pair chromatography analysis. The polymers were classified into five groups according to their chain lengths.\\u000a The average numbers of residues in the

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

    PubMed Central

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

    2000-01-01

    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

  9. Clustered Genes Required for the Synthesis of Heterocyst Envelope Polysaccharide in Anabaena sp. Strain PCC 7120

    Microsoft Academic Search

    Guocun Huang; Qing Fan; Sigal Lechno-Yossef; Elizabeth Wojciuch; C. Peter Wolk; Takakazu Kaneko; Satoshi Tabata

    2005-01-01

    As demonstrated with alr2835 (hepA) and alr2834 (hepC) mutants, heterocysts of Anabaena sp. strain PCC 7120, a filamentous cyanobacterium, must have an envelope polysaccharide layer (the Hep phenotype) to fix dinitrogen in an oxygen-containing milieu (the Fox phenotype). Transpositions presumptively responsible for a Fox phenotype were localized in open reading frames (ORFs) near hepA and hepC. A mutation in each

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

    SciTech Connect

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

    1996-09-01

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

  11. Enhanced degradation of naphthalene by immobilization of Pseudomonas sp. strain NGK1 in polyurethane foam

    Microsoft Academic Search

    S. Manohar; C. K. Kim; T. B. Karegoudar

    2001-01-01

    A Pseudomonas sp. strain NGK1 (NCIM 5120) capable of degrading naphthalene was immobilized in polyurethane foam. The naphthalene-degrading activity of the freely suspended cells was compared with that of immobilized cells in batches in shaken culture and in a continuous culture system in a packed-bed reactor. Increasing concentrations of naphthalene were better tolerated and more quickly degraded by immobilized cell

  12. Production of high yields of docosahexaenoic acid by Schizochytrium sp. strain SR21

    Microsoft Academic Search

    T. Yaguchi; S. Tanaka; T. Yokochi; T. Nakahara; T. Higashihara

    1997-01-01

    The culture conditions for high-yield production of docosahexaenoic acid (DHA) by Schizochytrium sp. strain SR21 were investigated in a fermenter. With increasing carbon (glucose) and nitrogen (corn steep liquor and ammonium\\u000a sulfate) sources (up to 12% glucose) in the medium, DHA productivity increased without a decrease in growth rate, i.e., 2.0,\\u000a 2.7, and 3.3 g DHA\\/L\\/d with 6, 10, and

  13. Metabolism of 2,4,6-trinitrotoluene (TNT) by Desulfovibrio sp. (B strain)

    Microsoft Academic Search

    R. Boopathy; C. F. Kulpa; M. Wilson

    1993-01-01

    A sulfate-reducing bacterium, Desulfovibrio sp. (B strain) isolated from an anaerobic reactor treating furfural-containing waste-water was studied for its ability to metabolize trinitrotoluene (TNT). The result showed that this isolate could transform 100 ppm TNT within 7 to 10 days of incubation at 37°C, when grown with 30 mm pyruvate as the primary carbon source and 20 mm sulfate as

  14. Ultrastructure of the membrane systems in the unicellular cyanobacterium Synechocystis sp. strain PCC 6803

    Microsoft Academic Search

    Michelle Liberton; R. Howard Berg; John Heuser; Robin Roth; Himadri B. Pakrasi

    2006-01-01

    Summary.  Among prokaryotes, cyanobacteria are unique in having highly differentiated internal membrane systems. Like other Gram-negative\\u000a bacteria, cyanobacteria such as Synechocystis sp. strain PCC 6803 have a cell envelope consisting of a plasma membrane, peptidoglycan layer, and outer membrane. In addition,\\u000a these organisms have an internal system of thylakoid membranes where the electron transfer reactions of photosynthesis and\\u000a respiration occur. A

  15. Purification and characterization of an antimicrobial peptide produced by Pseudomonas sp. strain 4B

    Microsoft Academic Search

    Roberta Fontoura; Jordana Corralo Spada; Silvana Terra Silveira; Siu Mui Tsai; Adriano Brandelli

    2009-01-01

    An antimicrobial peptide produced by a bacterium isolated from the effluent pond of a bovine abattoir was purified and characterized.\\u000a The strain was characterized by biochemical profiling and 16S rDNA sequencing as Pseudomonas sp. The antimicrobial peptide was purified by ammonium sulfate precipitation, gel filtration, and ion exchange chromatography.\\u000a Direct activity on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was

  16. Transcriptional Organization of Genes for Protocatechuate and Quinate Degradation from Acinetobacter sp. Strain ADP1

    Microsoft Academic Search

    Sureyya Dal; Gaby Trautwein; Ulrike Gerischer

    2005-01-01

    Quinate and protocatechuate are both abundant plant products and can serve, along with a large number of other aromatic or hydroaromatic compounds, as growth substrates for Acinetobacter sp. strain ADP1. The respective genes are part of the chromosomal dca-pca-qui-pob-hca cluster encoding these pathways. The adjacent pca and qui gene clusters, which encode enzymes for protocatechuate breakdown via the -ketoadipate pathway

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

    Microsoft Academic Search

    Yasser Elbahloul; Alexander Steinbuchel

    2006-01-01

    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

  18. areABC Genes Determine the Catabolism of Aryl Esters in Acinetobacter sp. Strain ADP1

    Microsoft Academic Search

    RHEINALLT M. JONES; LAUREN S. COLLIER; ELLEN L. NEIDLE; PETER A. WILLIAMS

    1999-01-01

    Acinetobacter sp. strain ADP1 is able to grow on a range of esters of aromatic alcohols, converting them to the corresponding aromatic carboxylic acids by the sequential action of three inducible enzymes: an areA- encoded esterase, an areB-encoded benzyl alcohol dehydrogenase, and an areC-encoded benzaldehyde dehy- drogenase. The are genes, adjacent to each other on the chromosome and transcribed in

  19. Conversion of the Pseudomonas aeruginosa Quinolone Signal and Related Alkylhydroxyquinolines by Rhodococcus sp. Strain BG43

    PubMed Central

    Müller, Christine; Birmes, Franziska S.; Niewerth, Heiko

    2014-01-01

    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 Rhodococcus erythropolis, was isolated from soil by enrichment on the Pseudomonas quinolone signal [PQS; 2-heptyl-3-hydroxy-4(1H)-quinolone], a quorum sensing signal employed by the opportunistic pathogen Pseudomonas aeruginosa. The isolate, termed Rhodococcus sp. strain BG43, cometabolically degraded PQS and 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

  20. Conversion of the Pseudomonas aeruginosa Quinolone Signal and Related Alkylhydroxyquinolines by Rhodococcus sp. Strain BG43.

    PubMed

    Müller, Christine; Birmes, Franziska S; Niewerth, Heiko; Fetzner, Susanne

    2014-12-01

    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 Rhodococcus erythropolis, was isolated from soil by enrichment on the Pseudomonas quinolone signal [PQS; 2-heptyl-3-hydroxy-4(1H)-quinolone], a quorum sensing signal employed by the opportunistic pathogen Pseudomonas aeruginosa. The isolate, termed Rhodococcus sp. strain BG43, cometabolically degraded PQS and 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

  1. Hydrogen production of a salt tolerant strain Bacillus sp. B2 from marine intertidal sludge.

    PubMed

    Liu, Hongyan; Wang, Guangce

    2012-01-01

    To isolate a salt tolerant hydrogen-producing bacterium, we used the sludge from the intertidal zone of a bathing beach in Tianjin as inoculum to enrich hydrogen-producing bacteria. The sludge was treated by heat-shock pretreatment with three different temperature (80, 100 and 121°C) respectively. A hydrogen-producing bacterium was isolated from the sludge pretreated at 80°C by sandwich plate technique and identified using microscopic examination and 16S rDNA gene sequence analysis. The isolated bacterium was named as Bacillus sp. B2. The present study examined the hydrogen-producing ability of Bacillus sp. B2. The strain was able to produce hydrogen over a wide range of initial pH from 5.0 to 10.0, with an optimum at pH 7.0. The level of hydrogen production was also affected by the salt concentration. Strain B2 has unique capability to adapt high salt concentration. It could produce hydrogen at the salt concentration from 4 to 60‰. The maximum of hydrogen-producing yield of strain B2 was 1.65 ± 0.04 mol H(2)/mol glucose (mean ± SE) at an initial pH value of 7.0 in marine culture conditions. Hydrogen production under fresh culture conditions reached a higher level than that in marine ones. As a result, it is likely that Bacillus sp. B2 could be applied to biohydrogen production using both marine and fresh organic waste. PMID:22806777

  2. Monooxygenase-Mediated 1,2-Dichloroethane Degradation by Pseudomonas sp. Strain DCA1

    PubMed Central

    Hage, Jacobus C.; Hartmans, Sybe

    1999-01-01

    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 Km value below the detection limit of 0.5 ?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. We 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 in strain DCA1 proceeds from chloroacetaldehyde via chloroacetic acid and presumably glycolic acid, which is similar to degradation routes observed in other DCA-utilizing bacteria. PMID:10347028

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

    SciTech Connect

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

    1999-06-01

    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.

  4. Complete Genome Sequence of the Cyanogenic Phosphate-Solubilizing Pseudomonas sp. Strain CCOS 191, a Close Relative of Pseudomonas mosselii

    PubMed Central

    Pothier, Joël F.; Ruinelli, Michela; Blom, Jochen; Frasson, David; Koechli, Chantal; Fabbri, Carlotta; Brandl, Helmut; Duffy, Brion; Sievers, Martin

    2015-01-01

    We sequenced the complete genome of the isolate Pseudomonas sp. CCOS 191. This strain is able to dissolve phosphate minerals and form cyanide. The genome sequence is used to establish the phylogenetic relationship of this species. PMID:26067963

  5. Complete Genome Sequence of the Cyanogenic Phosphate-Solubilizing Pseudomonas sp. Strain CCOS 191, a Close Relative of Pseudomonas mosselii.

    PubMed

    Smits, Theo H M; Pothier, Joël F; Ruinelli, Michela; Blom, Jochen; Frasson, David; Koechli, Chantal; Fabbri, Carlotta; Brandl, Helmut; Duffy, Brion; Sievers, Martin

    2015-01-01

    We sequenced the complete genome of the isolate Pseudomonas sp. CCOS 191. This strain is able to dissolve phosphate minerals and form cyanide. The genome sequence is used to establish the phylogenetic relationship of this species. PMID:26067963

  6. Draft Genome Sequence of Salimicrobium sp. Strain MJ3, Isolated from Myulchi-Jeot, Korean Fermented Seafood

    PubMed Central

    Lee, Se Hee; Jung, Ji Young

    2012-01-01

    Salimicrobium sp. strain MJ3 was isolated from myulchi-jeot, traditional fermented seafood made from anchovy in South Korea. Here we announce the draft genome sequence of Salimicrobium sp. MJ3 with 2,717,782 bp, which consists of 45 contigs (>500 bp in size), and provide a description of their annotation. PMID:23144427

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

    Microsoft Academic Search

    Munees Ahemad

    2011-01-01

    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.

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

    PubMed Central

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

    2012-01-01

    Background Bacteriocins are antimicrobial peptides that are produced by bacteria as a defense mechanism in complex environments. Identification and characterization of novel bacteriocins in novel strains of bacteria is one of the important fields in bacteriology. Methodology/Findings The strain GI-9 was identified as Brevibacillus sp. by 16 S rRNA gene sequence analysis. The bacteriocin produced by strain GI-9, namely, laterosporulin was purified from supernatant of the culture grown under optimal conditions using hydrophobic interaction chromatography and reverse-phase HPLC. The bacteriocin was active against a wide range of Gram-positive and Gram-negative bacteria. MALDI-TOF experiments determined the precise molecular mass of the peptide to be of 5.6 kDa and N-terminal sequencing of the thermo-stable peptide revealed low similarity with existing antimicrobial peptides. The putative open reading frame (ORF) encoding laterosporulin and its surrounding genomic region was fished out from the draft genome sequence of GI-9. Sequence analysis of the putative bacteriocin gene did not show significant similarity to any reported bacteriocin producing genes in database. Conclusions We have identified a bacteriocin producing strain GI-9, belonging to the genus Brevibacillus sp. Biochemical and genomic characterization of laterosporulin suggests it as a novel bacteriocin with broad spectrum antibacterial activity. PMID:22403615

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

    PubMed Central

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

    1996-01-01

    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

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

    PubMed

    Wang, J; Li, G; Lu, H; Zheng, Z; Huang, Y; Su, W

    2000-12-15

    The diterpenoid taxol is an important anticancer agent used widely in the clinic. The purpose of this work was to identify a taxol-producing endophytic fungus (strain TF5) isolated from Taxus mairei and study its anticancer activities. Strain TF5 was identified as a Tubercularia sp. according to the morphology of the fungal culture, the mechanism of spore production and the characteristics of the spores. Strain TF5 produced taxol, when grown in potato dextrose liquid medium and analyzed by thin layer chromatography, high performance liquid chromatography, ultraviolet and mass spectrometry. The fungal taxol, which was isolated from the organic extract of the TF5 culture, had strong cytotoxic activity towards KB and P388 cancer cells in vitro, tested by the MTT assay. Observed with immunofluorescence and electron microscopy, the fungal taxol enhanced microtubule stability and bundling in culture cells and induced tubulin polymerization in vitro similar to the authentic taxol. PMID:11111032

  11. Effects of modified Phycobilin biosynthesis in the Cyanobacterium Synechococcus sp. Strain PCC 7002.

    PubMed

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

    2011-04-01

    The pathway for phycocyanobilin biosynthesis in Synechococcus sp. strain PCC 7002 comprises two enzymes: heme oxygenase and phycocyanobilin synthase (PcyA). The phycobilin content of cells can be modified by overexpressing genes encoding alternative enzymes for biliverdin reduction. Overexpression of the pebAB and HY2 genes, encoding alternative ferredoxin-dependent biliverdin reductases, caused unique effects due to the overproduction of phycoerythrobilin and phytochromobilin, respectively. Colonies overexpressing pebAB became reddish brown and visually resembled strains that naturally produce phycoerythrin. This was almost exclusively due to the replacement of phycocyanobilin by phycoerythrobilin on the phycocyanin ?-subunit. This phenotype was unstable, and such strains rapidly reverted to the wild-type appearance, presumably due to strong selective pressure to inactivate pebAB expression. Overproduction of phytochromobilin, synthesized by the Arabidopsis thaliana HY2 product, was tolerated much better. Cells overexpressing HY2 were only slightly less pigmented and blue-green than the wild type. Although the pcyA gene could not be inactivated in the wild type, pcyA was easily inactivated when cells expressed HY2. These results indicate that phytochromobilin can functionally substitute for phycocyanobilin in Synechococcus sp. strain PCC 7002. Although functional phycobilisomes were assembled in this strain, the overall phycobiliprotein content of cells was lower, the efficiency of energy transfer by these phycobilisomes was lower than for wild-type phycobilisomes, and the absorption cross-section of the cells was reduced relative to that of the wild type because of an increased spectral overlap of the modified phycobiliproteins with chlorophyll a. As a result, the strain producing phycobiliproteins carrying phytochromobilin grew much more slowly at low light intensity. PMID:21296968

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

    PubMed Central

    Trautner, Christoph

    2013-01-01

    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

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

    PubMed

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

    2010-07-01

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

  14. Taxonomic re-evaluation of 'Nocardiopsis' sp. K-252T (= NRRL 15532T): a proposal to transfer this strain to the genus Nonomuraea as Nonomuraea longicatena sp. nov.

    PubMed

    Chiba, S; Suzuki, M; Ando, K

    1999-10-01

    Re-evaluation of the taxonomic position of strain K-252T, which produces the compound K-252a, showed that the strain does not belong to the genus Nocardiopsis suggested previously. Strain K-252T formed aerial mycelia with long spore chains, and hyphal fragmentation was not observed. The cell wall chemotype of the strain was III/B, the major menaquinone was MK-9 (III, VIII-H4), the phospholipid pattern was PIV and the major cellular fatty acids were 10Me-C17:0, iso-C16:0 and C16:0. Phylogenetic analysis of the 16S rRNA sequence showed that strain K-252T was clustered in the Nonomuraea group. Furthermore, on the basis of DNA-DNA reassociation and phenotypic data, strain K-252T (= NRRL 15532T) was classified as a new species of the genus Nonomuraea. This strain is proposed as Nonomuraea longicatena sp. nov. PMID:10555344

  15. Desulfurization of diesel oils by a newly isolated dibenzothiophene-degrading Nocardia sp. strain CYKS2.

    PubMed

    Chang, J H; Rhee, S K; Chang, Y K; Chang, H N

    1998-01-01

    A dibenzothiophene (DBT)-degrading bacterial strain was isolated from dyeing industry wastewater and identified as Nocardia sp. CYKS2. The newly isolated bacterial strain Nocardia sp. CYKS2 was able to convert DBT to 2-hydroxybiphenyl (2-HBP) as the dead-end metabolite through a sulfur-specific pathway. Other organic sulfur compounds, such as thiophene derivatives, thiazole derivatives, sulfides, and disulfides were also desulfurized by Nocardia sp. CYKS2. In batch culture, 0.2 mM DBT was completely desulfurized in 60 h. After DBT was depleted, neither cell growth nor 2-HBP production was observed. When a model oil which DBT was dissolved in hexadecane was treated with growing cells, DBT was desulfurized from 10 mM to about 2 mM in 80 h. In this case, desulfurization rate was 0.279 mg-sulfur/(L-dispersion.h), which was about 2.5 times higher than that in the previous case of batch culture. When diesel oil was treated, the sulfur content decreased from 0.3 to 0.24 wt % in 48 h. A volumetric phase ratio of oil to water was 1/10 in this case. The sulfur decreased from 0.3 to 0.2 wt % in 48 h, when the volumetric phase ratio was 1/20. The desulfurization rates were 0.909 and 0.992 mg-sulfur/(L-dispersion.h), respectively. PMID:9841646

  16. Modular system for assessment of glycosyl hydrolase secretion in Geobacillus thermoglucosidasius.

    PubMed

    Bartosiak-Jentys, Jeremy; Hussein, Ali H; Lewis, Claire J; Leak, David J

    2013-07-01

    The facultatively anaerobic, thermophilic bacterium Geobacillus thermoglucosidasius is being developed as an industrial micro-organism for cellulosic bioethanol production. Process improvement would be gained by enhanced secretion of glycosyl hydrolases. Here we report the construction of a modular system for combining promoters, signal peptide encoding regions and glycosyl hydrolase genes to facilitate selection of the optimal combination in G. thermoglucosidasius. Initially, a minimal three-part E. coli-Geobacillus sp. shuttle vector pUCG3.8 was constructed using Gibson isothermal DNA assembly. The three PCR amplicons contained the pMB1 E. coli origin of replication and multiple cloning site (MCS) of pUC18, the Geobacillus sp. origin of replication pBST1 and the thermostable kanamycin nucleotidyltransferase gene (knt), respectively. G. thermoglucosidasius could be transformed with pUCG3.8 at an increased efficiency [2.8×10(5) c.f.u. (µg DNA)(-1)] compared to a previously reported shuttle vector, pUCG18. A modular cassette for the inducible expression and secretion of proteins in G. thermoglucosidasius, designed to allow the simple interchange of parts, was demonstrated using the endoglucanase Cel5A from Thermotoga maritima as a secretion target. Expression of cel5A was placed under the control of a cellobiose-inducible promoter (P?glu) together with a signal peptide encoding sequence from a G. thermoglucosidasius C56-YS93 endo-?-1,4-xylanase. The interchange of parts was demonstrated by exchanging the cel5A gene with the 3' region of a gene with homology to celA from Caldicellulosiruptor saccharolyticus and substituting P?glu for the synthetic, constitutive promoter PUp2n38, which increased Cel5A activity five-fold. Cel5A and CelA activities were detected in culture supernatants indicating successful expression and secretion. N-terminal protein sequencing of Cel5A carrying a C-terminal FLAG epitope confirmed processing of the signal peptide sequence. PMID:23704786

  17. Chemoheterotrophic Growth of the Cyanobacterium Anabaena sp. Strain PCC 7120 Dependent on a Functional Cytochrome c Oxidase

    PubMed Central

    Stebegg, Ronald; Wurzinger, Bernhard; Mikulic, Markus

    2012-01-01

    Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium commonly used as a model organism for studying cyanobacterial cell differentiation and nitrogen fixation. For many decades, this cyanobacterium was considered an obligate photo-lithoautotroph. We now discovered that this strain is also capable of mixotrophic, photo-organoheterotrophic, and chemo-organoheterotrophic growth if high concentrations of fructose (at least 50 mM and up to 200 mM) are supplied. Glucose, a substrate used by some facultatively organoheterotrophic cyanobacteria, is not effective in Anabaena sp. PCC 7120. The gtr gene from Synechocystis sp. PCC 6803 encoding a glucose carrier was introduced into Anabaena sp. PCC 7120. Surprisingly, the new strain containing the gtr gene did not grow on glucose but was very sensitive to glucose, with a 5 mM concentration being lethal, whereas the wild-type strain tolerated 200 mM glucose. The Anabaena sp. PCC 7120 strain containing gtr can grow mixotrophically and photo-organoheterotrophically, but not chemo-organoheterotrophically with fructose. Anabaena sp. PCC 7120 contains five respiratory chains ending in five different respiratory terminal oxidases. One of these enzymes is a mitochondrial-type cytochrome c oxidase. As in almost all cyanobacteria, this enzyme is encoded by three adjacent genes called coxBAC1. When this locus was disrupted, the cells lost the capability for chemo-organoheterotrophic growth. PMID:22730128

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

    PubMed Central

    Marshall, Christopher W.; May, Harold D.

    2015-01-01

    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

  19. Draft Genome Sequence of a Sulfur-Oxidizing Autotroph, Sulfuricella sp. Strain T08, Isolated from a Freshwater Lake

    PubMed Central

    Kojima, Hisaya; Fukui, Manabu

    2015-01-01

    Sulfuricella sp. strain T08 is a sulfur-oxidizing autotroph newly isolated from a freshwater lake in Japan. Strain T08 is the second isolate of the genus Sulfuricella. Here, we report the annotated draft genome sequence of the isolate. PMID:25999549

  20. Draft Genome Sequence of the Aquatic Phosphorus-Solubilizing and -Mineralizing Bacterium Bacillus sp. Strain CPSM8

    PubMed Central

    Maitra, Nilanjan; Whitman, William B.; Ayyampalayam, Saravanaraj; Samanta, Srikanta; Sarkar, Keka; Bandopadhyay, Chinmay; Aftabuddin, M.; Sharma, Anil P.

    2014-01-01

    Bacillus sp. strain CPSM8 is an efficient solubilizer and mineralizer of phosphorus. Here, we present the 4.39-Mb draft genome sequence of the strain, providing insight into the phosphorus-releasing genes related to productivity in aquatic habitats. PMID:24482525

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

    PubMed

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

    2013-01-01

    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

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

    PubMed Central

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

    2012-01-01

    Methylobacterium sp. strain GXF4 is an isolate from grapevine. Here we present the sequence, assembly, and annotation of its genome, which may shed light on its role as a grapevine xylem inhabitant. To our knowledge, this is the first genome announcement of a plant xylem-associated strain of the genus Methylobacterium. PMID:22933776

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

    PubMed

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

    2015-01-01

    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

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

    PubMed Central

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

    2015-01-01

    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

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

    PubMed Central

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

    2014-01-01

    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

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

    PubMed

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

    2014-01-01

    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

  7. Draft Genome Sequence of Frankia sp. Strain CN3, an Atypical, Noninfective (Nod–) Ineffective (Fix–) Isolate from Coriaria nepalensis

    PubMed Central

    Ghodhbane-Gtari, Faten; Beauchemin, Nicholas; Bruce, David; Chain, Patrick; Chen, Amy; Walston Davenport, Karen; Deshpande, Shweta; Detter, Chris; Furnholm, Teal; Goodwin, Lynne; Gtari, Maher; Han, Cliff; Han, James; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos; Land, Miriam L.; Markowitz, Victor; Mavrommatis, Kostas; Nolan, Matt; Nouioui, Imen; Pagani, Ioanna; Pati, Amrita; Pitluck, Sam; Santos, Catarina L.; Sen, Arnab; Sur, Saubashya; Szeto, Ernest; Tavares, Fernando; Teshima, Hazuki; Thakur, Subarna; Wall, Luis; Woyke, Tanja

    2013-01-01

    We report here the genome sequence of Frankia sp. strain CN3, which was isolated from Coriaria nepalensis. This genome sequence is the first from the fourth lineage of Frankia, strains of which are unable to reinfect actinorhizal plants. At 10 Mb, it represents the largest Frankia genome sequenced to date. PMID:23516212

  8. Gene Amplification Involves Site-specific Short Homology-independent Illegitimate Recombination in Acinetobacter sp. Strain ADP1

    Microsoft Academic Search

    Andrew B Reams; Ellen L Neidle

    2004-01-01

    A system for studying gene amplification in the bacterium Acinetobacter sp. strain ADP1 was used to isolate 105 spontaneous mutants. The method selects for the elevated expression of neighboring transcriptional units in a parent strain lacking its normal transcriptional activators. Gene amplification can compensate for the activator loss by increasing the copy number of seven weakly expressed genes. Mutant colonies

  9. Pseudomonas sp. strain 273, and aerobic {alpha},{omega}-dichloroalkane-degrading bacterium

    SciTech Connect

    Wischnak, C.; Mueller, R. [Technische Univ. Hamburg-Harburg (Germany). Arbeitsbereich Biotechnologie II; Loeffler, F.E. [Technische Univ. Hamburg-Harburg (Germany). Arbeitsbereich Biotechnologie II]|[Michigan State Univ., East Lansing, MI (United States). Center for Microbial Ecology; Li, J.; Urbance, J.W. [Michigan State Univ., East Lansing, MI (United States). Center for Microbial Ecology

    1998-09-01

    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 C{sub 5} to C{sub 12} {alpha},{omega}-dichloroalkanes in the presence of oxygen. No dehalogenation occurred under anaerobic conditions. The best substrates for dehalogenation and growth were C{sub 9} to C{sub 12} 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.

  10. Degradation of ethyl mercaptan and its major intermediate diethyl disulfide by Pseudomonas sp. strain WL2.

    PubMed

    Wang, Xiangqian; Wu, Chao; Liu, Nan; Li, Sujing; Li, Wei; Chen, Jianmeng; Chen, Dongzhi

    2015-04-01

    A Pseudomonas sp. strain WL2 that is able to efficiently metabolize ethyl mercaptan (EM) into diethyl disulfide (DEDS) through enzymatic oxidation was isolated from the activated sludge of a pharmaceutical wastewater plant. One hundred percent removal of 113.5 mg L(-1) EM and 110.3 mg L(-1) DEDS were obtained within 14 and 32 h, respectively. A putative EM degradation pathway that involved the catabolism via DEDS was proposed, which indicated DEDS were further mineralized into carbon dioxide (CO2), bacterial cells, and sulfate (SO4 (2-)) through the transformation of element sulfur and ethyl aldehyde. Degradation kinetics for EM and DEDS with different initial concentrations by strain WL2 were evaluated using Haldane-Andrews model with maximum specific degradation rates of 3.13 and 1.33 g g(-1) h(-1), respectively, and maximum degradation rate constants of 0.522 and 0.175 h(-1) using pseudo-first-order kinetic model were obtained. Results obtained that aerobic degradation of EM by strain WL2 was more efficient than those from previous studies. Substrate range studies of strain WL2 demonstrated its ability to degrade several mercaptans, disulfides, aldehydes, and methanol. All the results obtained highlight the potential of strain WL2 for the use in the biodegradation of volatile organic sulfur compounds (VOSCs). PMID:25398287

  11. Metabolic Engineering of Synechocystis sp. Strain PCC 6803 for Isobutanol Production

    PubMed Central

    Varman, Arul M.; Xiao, Yi; Pakrasi, Himadri B.

    2013-01-01

    Global warming and decreasing fossil fuel reserves have prompted great interest in the synthesis of advanced biofuels from renewable resources. In an effort to address these concerns, we performed metabolic engineering of the cyanobacterium Synechocystis sp. strain PCC 6803 to develop a strain that can synthesize isobutanol under both autotrophic and mixotrophic conditions. With the expression of two heterologous genes from the Ehrlich pathway, the engineered strain can accumulate 90 mg/liter of isobutanol from 50 mM bicarbonate in a gas-tight shaking flask. The strain does not require any inducer (i.e., isopropyl ?-d-1-thiogalactopyranoside [IPTG]) or antibiotics to maintain its isobutanol production. In the presence of glucose, isobutanol synthesis is only moderately promoted (titer = 114 mg/liter). Based on isotopomer analysis, we found that, compared to the wild-type strain, the mutant significantly reduced its glucose utilization and mainly employed autotrophic metabolism for biomass growth and isobutanol production. Since isobutanol is toxic to the cells and may also be degraded photochemically by hydroxyl radicals during the cultivation process, we employed in situ removal of the isobutanol using oleyl alcohol as a solvent trap. This resulted in a final net concentration of 298 mg/liter of isobutanol under mixotrophic culture conditions. PMID:23183979

  12. Complete Genomic Sequence of the Filamentous Nitrogen-fixing Cyanobacterium Anabaena sp. Strain PCC 7120

    Microsoft Academic Search

    Takakazu Kaneko; Yasukazu Nakamura; C. Peter Wolk; Tanya Kuritz; Shigemi Sasamoto; Akiko Watanabe; Mayumi Iriguchi; Atsuko Ishikawa; Kumiko Kawashima; Takaharu Kimura; Yoshie Kishida; Mitsuyo Kohara; Midori Matsumoto; Ai Matsuno; Akiko Muraki; Naomi Nakazaki; Sayaka Shimpo; Masako Sugimoto; Masaki Takazawa; Manabu Yamada; Miho Yasuda; Satoshi Tabata

    2001-01-01

    The nucleotide sequence of the entire genome of a filamentous cyanobacterium, Anabaena sp. strain PCC 7120, was determined. The genome of Anabaena consisted of a single chromosome (6,413,771 bp) and six plasmids, designated pCC7120? (408,101 bp), pCC7120? (186,614 bp), pCC7120? (101,965 bp), pCC7120? (55,414 bp), pCC7120? (40,340 bp), and pCC7120? (5,584 bp). The chromosome bears 5368 po- tential protein-encoding genes,

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

    PubMed Central

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

    2011-01-01

    Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium. PMID:21551312

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

    Microsoft Academic Search

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

    2009-01-01

    This study evaluates the potential of bio-augmentation to improve the degradation of recalcitrant nonylphenol during the wastewater\\u000a treatment in membrane bioreactors (MBR). One MBR containing activated sludge was bio-augmented using multistep inoculation\\u000a with freeze dried Sphingomonas sp. strain TTNP3, whereas a second control reactor contained activated sludge solely. The 14C-labeled-nonylphenol isomer (4-[1-ethyl-1,3-dimethylpentyl]phenol) was applied as a single pulse. Bio-augmentation resulted

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

    PubMed Central

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

    2014-01-01

    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

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

    SciTech Connect

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

    2011-01-01

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

  17. Bradyrhizobium sp. Strains That Nodulate the Leguminous Tree Acacia albida Produce Fucosylated and Partially Sulfated Nod Factors

    PubMed Central

    Ferro, Myriam; Lorquin, Jean; Ba, Salif; Sanon, Kadidia; Promé, Jean-Claude; Boivin, Catherine

    2000-01-01

    We determined the structures of Nod factors produced by six different Bradyrhizobium sp. strains nodulating the legume tree Acacia albida (syn. Faidherbia albida). Compounds from all strains were found to be similar, i.e., O-carbamoylated and substituted by an often sulfated methyl fucose and different from compounds produced by Rhizobium-Mesorhizobium-Sinorhizobium strains nodulating other species of the Acaciae tribe. PMID:11055966

  18. Dependence of linkage of alleles on their physical distance in natural transformation of Acinetobacter sp. strain ADP1

    Microsoft Academic Search

    Ulrike Gerischer; Nicholas L. Ornston

    2001-01-01

    The interdependence of genetic linkage in transformation and physical distance was studied in the bacterium Acinetobacter sp. strain ADP1. Transformation experiments were performed using 17 strains containing different mutations within the 21-kb pca-qui-pob gene cluster as recipients for the DNA of one of two strains carrying a mutation causing a temperature-sensitive phenotype. The different phenotypes of the transformants (temperature-sensitive or

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

    Microsoft Academic Search

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

    2005-01-01

    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

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

    SciTech Connect

    Spain, J.C.; Gibson, D.T.

    1988-06-01

    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.

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

    PubMed Central

    2009-01-01

    Background The genome of Arthrobacter sp. strain FB24 contains a chromate resistance determinant (CRD), consisting of a cluster of 8 genes located on a 10.6 kb fragment of a 96 kb plasmid. The CRD includes chrA, which encodes a putative chromate efflux protein, and three genes with amino acid similarities to the amino and carboxy termini of ChrB, a putative 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. To delineate the contribution of the CRD genes to the FB24 chromate [Cr(VI)] response, we evaluated the growth of mutant strains bearing regions of the CRD and transcript expression levels in response to Cr(VI) challenge. Results 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 possible regulatory roles. Conclusion Our findings indicate that chromate resistance in Arthrobacter sp. strain FB24 is due to chromate efflux through the ChrA transport protein. More importantly, new genes have been identified as having significant roles in chromate resistance. Collectively, the functional predictions of these additional genes suggest the involvement of a signal transduction system in the regulation of chromate efflux and warrants further study. PMID:19758450

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

    PubMed Central

    2014-01-01

    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

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

    PubMed Central

    Avrahami, Sharon; Bohannan, Brendan J. M.

    2007-01-01

    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

  4. Purification and Gene Cloning of  -Methylserine Aldolase from Ralstonia sp. Strain AJ110405 and Application of the Enzyme in the Synthesis of  -Methyl-L-Serine

    Microsoft Academic Search

    Hiroyuki Nozaki; Shinji Kuroda; Kunihiko Watanabe; Kenzo Yokozeki

    2008-01-01

    By screening microorganisms that are capable of assimilating -methyl-DL-serine, we detected -methylserine aldolase in Ralstonia sp. strain AJ110405, Variovorax paradoxus AJ110406, and Bosea sp. strain AJ110407. A homogeneous form of this enzyme was purified from Ralstonia sp. strain AJ110405, and the gene encoding the enzyme was cloned and expressed in Escherichia coli. The enzyme appeared to be a homodimer consisting

  5. Biodegradation of cypermethrin by a novel Catellibacterium sp. strain CC-5 isolated from contaminated soil.

    PubMed

    Zhao, Haoyu; Geng, Yucong; Chen, Long; Tao, Ke; Hou, Taiping

    2013-05-01

    The bacterial strain CC-5, isolated from contaminated soil and identified as Catellibacterium sp. based on morphology and partial 16S rDNA gene sequence analysis, utilized cypermethrin as its sole carbon source and degraded 97% of 100 mg·L(-1) cypermethrin within 7 days. The optimal degradation conditions were determined to be 30 °C and pH 7.0. Degradation was found to follow a first-order model at initial cypermethrin concentrations below 400 mg·L(-1). Strain CC-5 suffered substrate inhibition at high cypermethrin concentrations, and the biodegradation kinetics were successfully described by the Haldane model, with a maximal specific degradation rate of 1.36 day(-1), an inhibition constant of 164.61 mg·L(-1), and a half-saturation constant of 101.12 mg·L(-1). Inoculating cypermethrin-treated soil samples with strain CC-5 resulted in a higher rate of cypermethrin removal than that in noninoculated soil, regardless of whether the soil had previously been sterilized. These results reveal that the bacterial strain may possess potential to be used in bioremediation of pyrethroid-contaminated environment. PMID:23647343

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

    PubMed Central

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

    2014-01-01

    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

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

    SciTech Connect

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

    1990-04-01

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

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

    PubMed

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

    2014-01-01

    Karyotype analysis of nine strains of the peach-potato aphid Myzuspersicae (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 Myzuspersicae 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

  9. [Sensitivity of Staphylococcus aureus strains isolated from the patients of the SP ZOZ Hospital in Nidzica to bacteriocidal agents].

    PubMed

    Pszenna, Miros?awa; Rokosz, Alicja; Luczak, Miros?aw

    2006-01-01

    The aim of this study was to evaluate a frequency of isolation and antimicrobial susceptibility testing of Staphylococcus aureus strains isolated from clinical specimens obtained from patients hospitalized in different hospital wards (SP ZOZ) in Nidzica from 01. 09. 2000 to 31. 12. 2003. During over three years 716 Staphylococcus aureus strains were cultured out of 15517 clinical specimens supplied to the Bacteriological Laboratory of SP ZOZ in Nidzica. S. aureus strains were isolated from 4.6% of examined samples. Samples were collected from patients hospitalized in all wards (five wards). Analysis of susceptibility to antimicrobial agents of identified S. aureus strains was performed. Seventy strains (9.8%) were metihicillin-resistant (MRSA). One hundred twenty four strains (17.3%) revealed inducible resistance to macrolides, linkosamides and streptogramins B (MLS, mechanism). The greatest activity in vitro against clinical S. aureus strains showed glycopeptide antibiotic--vancomycin (100% of susceptible strains). Clinical S. aureus strains isolated from patients of hospital in Nidzica are in the majority susceptible to antibiotics/chemotherapeutics, except of penicillin. Percentage of methicillin-resistant strains (MRSA) is not high (<10). Nevertheless, constant monitoring of a drug susceptibility of nosocomial S. aureus strains is important, considering the necessity of control of current epidemiological and therapeutic situation. PMID:16871967

  10. Biosurfactant production by a CO2 sequestering Bacillus sp. strain ISTS2.

    PubMed

    Sundaram, Smita; Thakur, Indu Shekhar

    2015-07-01

    A chemolithotrophic bacterium, Bacillus sp. strain ISTS2, produced biosurfactant when enriched in the chemostat in presence of sodium bicarbonate as carbon source was evaluated for carbon dioxide (CO2) sequestration and biosurfactant production. CO2 sequestration efficiency of the bacterium was determined by enzymatic activity of carbonic anhydrase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Biosurfactant production ability at 100mM NHCO3 and 5% CO2 was screened by surface and interfacial tension measurement, emulsification stability test, hydrophobicity test, contact angle measurement, bacterial adhesion to hydrocarbon and purified by silica gel column (60-120mesh). Thin layer chromatography (TLC) and gas chromatography-mass spectrometry (GC-MS) showed that the crude biosurfactant of ISTS2 were composed of lipopeptides and free fatty acids (FA) and its hydrophobic fraction contained five kinds of fatty acids (FA) with chain lengths of C14-C19. Thus Bacillus sp. strain IST2 can be used as a cleaner bioprocess for the utilization of industrial CO2 as alternate substrate. PMID:25641713

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

    PubMed

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

    2010-01-01

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

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

    PubMed

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

    2013-12-01

    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

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

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

    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.

  14. Biodegradation and utilization of dimethylformamide by biofilm forming Paracoccus sp. strains MKU1 and MKU2.

    PubMed

    Nisha, Kamaldeen Nasrin; Devi, Venkatesan; Varalakshmi, Perumal; Ashokkumar, Balasubramaniem

    2015-07-01

    Two bacterial strains capable of degrading N,N-dimethylformamide (DMF) were isolated from the effluent and sludge samples of textile and tyre industries. The 16S rRNA gene analysis revealed that bacterial strains belonged to the genera Paracoccus and named as Paracoccus sp. MKU1 and Paracoccus sp. MKU2. The DMF degradation experiments conducted at a DMF concentration of 1% v/v and HPLC analysis revealed that MKU1 and MKU2 degraded 55% and 46% of DMF after 120h of growth. Biofilm quantification by microtiter plate assay revealed that both the bacterial isolates can form efficient biofilm on during DMF utilization. The presence of secondary carbon sources influenced the DMF degradation and biofilm formation where highest biofilm formation was observed in the presence of acetate and enhanced the DMF degradation to a maximum of 86.59% with MKU1 whereas glucose and acetate enhanced DMF degradation by MKU2 to a maximum of 82.7% and 80% respectively. PMID:25728343

  15. Achromobacter denitrificans strain SP1 efficiently remediates di(2-ethylhexyl)phthalate.

    PubMed

    Pradeep, S; Josh, M K Sarath; Binod, P; Devi, R Sudha; Balachandran, S; Anderson, Robin C; Benjamin, Sailas

    2015-02-01

    This study describes how Achromobacter denitrificans strain SP1, a novel isolate from heavily plastics-contaminated sewage sludge efficiently consumed the hazardous plasticizer, di(2-ethylhexyl)phthalate (DEHP) as carbon source supplemented in a simple basal salt medium (BSM). Response surface methodology was employed for the statistical optimization of the process parameters such as temperature (32°C), agitation (200 rpm), DEHP concentration (10 mM), time (72 h) and pH (8.0). At these optimized conditions, experimentally observed DEHP degradation was 63%, while the predicted value was 59.2%; and the correlation coefficient between them was 0.998, i.e., highly significant and fit to the predicted model. Employing GC-MS analysis, the degradation pathway was partially deduced with intermediates such as mono(2-ethylhexyl)phthalate and 2-ethyl hexanol. Briefly, this first report describes A. denitrificans strain SP1 as a highly efficient bacterium for completely remediating the hazardous DEHP (10 mM) in 96 h in BSM (50% consumed in 60 h), which offers great potentials for efficiently cleaning the DEHP-contaminated environments such as soil, sediments and water upon its deployment. PMID:25463861

  16. Growth of Acinetobacter sp. strain HO1-N on n-hexadecanol: physiological and ultrastructural characteristics.

    PubMed Central

    Singer, M E; Tyler, S M; Finnerty, W R

    1985-01-01

    The growth of Acinetobacter sp. strain HO1-N on hexadecanol results in the formation of intracytoplasmic membranes and intracellular rectangular inclusions containing one of the end products of hexadecanol metabolism, hexadecyl palmitate. The intracellular inclusions were purified and characterized as "wax ester inclusions" consisting of 85.6% hexadecyl palmitate, 4.8% hexadecanol, and 9.6% phospholipid, with a phospholipid-to-protein ratio of 0.42 mumol of lipid phosphate per mg of inclusion protein. The cellular lipids consisted of 69.8% hexadecyl palmitate, 22.8% phospholipid, 1.9% triglyceride, 4.7% mono- and diglyceride, 0.1% free fatty acid, and 0.8% hexadecanol, as compared with 98% hexadecyl palmitate and 1.9% triglyceride, which comprised the extracellular lipids. Cell-associated hexadecanol represented 0.05% of the exogenously supplied hexadecanol, with hexadecyl palmitate accounting for 14.7% of the total cellular dry weight. Acinetobacter sp. strain HO1-N possesses a mechanism for the intracellular packaging of hexadecyl palmitate in wax ester inclusions, which differ in structure and chemical composition from "hydrocarbon inclusions" isolated from hexadecane-grown cells. Images PMID:2984172

  17. Rapid aggregation of biofuel-producing algae by the bacterium Bacillus sp. strain RP1137.

    PubMed

    Powell, Ryan J; Hill, Russell T

    2013-10-01

    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

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

    PubMed Central

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

    1994-01-01

    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

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

    SciTech Connect

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

    1984-11-01

    A genomic library containing HindIII partial digest 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 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. 33 references, 3 figures, 3 tables.

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

    PubMed

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

    2001-06-01

    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

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

    PubMed Central

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

    2001-01-01

    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

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

    PubMed

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

    2013-10-01

    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

  3. Characterization of Thermostable Cellulases Produced by Bacillus and Geobacillus Strains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacterial community composition of thermophilic (60 deg C) mixed cellulose-enrichment cultures was examined by constructing a 16S rDNA clone library which demonstrated major lineages affiliated to Actinobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Firmicutes, and Proteobacteria. A tot...

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

    PubMed Central

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

    1999-01-01

    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

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

    PubMed

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

    2012-05-10

    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

  6. Metabolism of 2-methylpropene (isobutylene) by the aerobic bacterium Mycobacterium sp. strain ELW1.

    PubMed

    Kottegoda, Samanthi; Waligora, Elizabeth; Hyman, Michael

    2015-03-01

    An aerobic bacterium (Mycobacterium sp. strain ELW1) that utilizes 2-methylpropene (isobutylene) as a sole source of carbon and energy was isolated and characterized. Strain ELW1 grew on 2-methylpropene (growth rate = 0.05 h(-1)) with a yield of 0.38 mg (dry weight) mg 2-methylpropene(-1). Strain ELW1 also grew more slowly on both cis- and trans-2-butene but did not grow on any other C2 to C5 straight-chain, branched, or chlorinated alkenes tested. Resting 2-methylpropene-grown cells consumed ethene, propene, and 1-butene without a lag phase. Epoxyethane accumulated as the only detected product of ethene oxidation. Both alkene consumption and epoxyethane production were fully inhibited in cells exposed to 1-octyne, suggesting that alkene oxidation is initiated by an alkyne-sensitive, epoxide-generating monooxygenase. Kinetic analyses indicated that 1,2-epoxy-2-methylpropane is rapidly consumed during 2-methylpropene degradation, while 2-methyl-2-propen-1-ol is not a significant metabolite of 2-methylpropene catabolism. Degradation of 1,2-epoxy-2-methylpropane by 2-methylpropene-grown cells led to the accumulation and further degradation of 2-methyl-1,2-propanediol and 2-hydroxyisobutyrate, two sequential metabolites previously identified in the aerobic microbial metabolism of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA). Growth of strain ELW1 on 2-methylpropene, 1,2-epoxy-2-methylpropane, 2-methyl-1,2-propanediol, and 2-hydroxyisobutyrate was fully inhibited when cobalt ions were omitted from the growth medium, while growth on 3-hydroxybutyrate and other substrates was unaffected by the absence of added cobalt ions. Our results suggest that, like aerobic MTBE- and TBA-metabolizing bacteria, strain ELW1 utilizes a cobalt/cobalamin-dependent mutase to transform 2-hydroxyisobutyrate. Our results have been interpreted in terms of their impact on our understanding of the microbial metabolism of alkenes and ether oxygenates. PMID:25576605

  7. Cloning and characterization of Pseudomonas sp. strain DNT genes for 2,4-dinitrotoluene degradation.

    PubMed Central

    Suen, W C; Spain, J C

    1993-01-01

    The degradation of 2,4-dinitrotoluene (DNT) by Pseudomonas sp. strain DNT is initiated by a dioxygenase attack to yield 4-methyl-5-nitrocatechol (MNC) and nitrite. Subsequent oxidation of MNC by a monooxygenase results in the removal of the second molecule of nitrite, and further enzymatic reactions lead to ring fission. Initial studies on the molecular basis of DNT degradation in this strain revealed the presence of three plasmids. Mitomycin-derived mutants deficient in either DNT dioxygenase only or DNT dioxygenase and MNC monooxygenase were isolated. Plasmid profiles of mutant strains suggested that the mutations resulted from deletions in the largest plasmid. Total plasmid DNA partially digested by EcoRI was cloned into a broad-host-range cosmid vector, pCP13. Recombinant clones containing genes encoding DNT dioxygenase, MNC monooxygenase, and 2,4,5-trihydroxytoluene oxygenase were characterized by identification of reaction products and the ability to complement mutants. Subcloning analysis suggests that the DNT dioxygenase is a multicomponent enzyme system and that the genes for the DNT pathway are organized in at least three different operons. Images PMID:8449889

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

    PubMed Central

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

    2013-01-01

    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

  9. Isolation of a new strain of Picochlorum sp and characterization of its potential biotechnological applications.

    PubMed

    de la Vega, M; Díaz, E; Vila, M; León, R

    2011-01-01

    Selection of new autochthon strains is necessary, and for the moment the best strategy, to find microalgae well adapted to the local climatological conditions able to simultaneously produce several compounds of biotechnological interest and grow at high rates. We describe the isolation and characterization of a new microalgal strain isolated from the marshlands of the Odiel River in the Southwest of Spain. The new microalga belongs to the genus Picochlorum, as deduced from the analysis of its 18S rRNA encoding gene, is able to grow at a high growth rate and thrive with adverse conditions. It has an appreciable constitutive level of lutein (3.5 mg g(-1) DW) and zeaxanthin (0.4 mg g(-1) DW) which is increased to 1.8 mg g(-1) DW at high light intensities. This strain is also characterized by a very low level of linolenic acid (3.8% of total fatty acids) and no polyunsaturated fatty acids with four or more double bonds. Although the total lipid content is not particularly high, 23% of the dry weight, its fatty acid profile makes of Picochlorum sp HM1 a promising candidate for biodiesel production, and the high content in the carotenoids lutein and zeaxanthin indicates that the microalga could also be a good source for natural eye vitamin supplements, which could be obtained as co-products. PMID:21954123

  10. Copper tolerance in Frankia sp. strain EuI1c involves surface binding and copper transport.

    PubMed

    Rehan, Medhat; Furnholm, Teal; Finethy, Ryan H; Chu, Feixia; El-Fadly, Gomaah; Tisa, Louis S

    2014-09-01

    Several Frankia strains have been shown to be copper-tolerant. The mechanism of their copper tolerance was investigated for Frankia sp. strain EuI1c. Copper binding was shown by binding studies. Unusual globular structures were observed on the surface of the bacterium. These globular structures were composed of aggregates containing many relatively smaller "leaf-like" structures. Scanning electron microscopy with energy-dispersive X-ray (SEM-EDAX) analysis of these structures indicated elevated copper and phosphate levels compared to the control cells. Fourier transform infrared spectroscopy (FTIR) analysis indicated an increase in extracellular phosphate on the cell surface of copper-stressed cells. Bioinformatics' analysis of the Frankia sp. strain EuI1c genome revealed five potential cop genes: copA, copZ, copC, copCD, and copD. Experiments with Frankia sp. strain EuI1c using qRT-PCR indicated an increase in messenger RNA (mRNA) levels of the five cop genes upon Cu(2+) stress. After 5 days of Cu(2+) stress, the copA, copZ, copC, copCD, and copD mRNA levels increased 25-, 8-, 18-, 18-, and 25-fold, respectively. The protein profile of Cu(2+)-stressed Frankia sp. strain EuI1c cells revealed the upregulation of a 36.7 kDa protein that was identified as FraEuI1c_1092 (sulfate-binding periplasmic transport protein). Homologues of this gene were only present in the genomes of the Cu(2+)-resistant Frankia strains (EuI1c, DC12, and CN3). These data indicate that copper tolerance by Frankia sp. strain EuI1c involved the binding of copper to the cell surface and transport proteins. PMID:24903815

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

    PubMed

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

    2013-11-01

    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

  12. Physical mapping and characterization of a catabolic plasmid from the deep-subsurface bacterium Sphingomonas sp. strain F199.

    PubMed Central

    Stillwell, L C; Thurston, S J; Schneider, R P; Romine, M F; Fredrickson, J K; Saffer, J D

    1995-01-01

    A supercoiled 180-kb plasmid, pNL1, has been isolated from the deep-subsurface, chemoheterotrophic Sphingomonas sp. strain F199, and a physical map was generated. Analysis of a pNL1-derived cosmid library indicated that catechol 2,3-dioxygenase activity was linked to two distinct regions of the plasmid. Thus, the genes for aromatic catabolism in this Sphingomonas strain are, at least in part, plasmid encoded. PMID:7635838

  13. Regio- and stereospecific oxidation of fluorene, dibenzofuran, and dibenzothiophene by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4

    SciTech Connect

    Resnick, S.M.; Gibson, D.T. [Univ. of Iowa, Iowa City, IA (United States)

    1996-11-01

    Fluorene, dibenzofuran, dibenzothiophene, and carbazole are structural analogs differing only in the type of atom bridging the two aromatic rings. These compounds are constituents of fossil fuels. The authors have examined the oxidation of fluorene, dibenzofuran, and dibenzothiophene by mutant and recombinant strains which express NDO from Pseudomonas sp. strain NCIB 9816-4 and reports the yields, region chemistry, absolute stereochemistry, and enantiomeric purity of the isolated initial metabolites. 71 refs., 3 figs., 2 tabs.

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

    Microsoft Academic Search

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

    2011-01-01

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

  15. Biodegradation of 3-Nitrotyrosine by Burkholderia sp. Strain JS165 and Variovorax paradoxus JS171

    PubMed Central

    Nishino, Shirley F.; Spain, Jim C.

    2006-01-01

    The cascade of reactive nitrogen species generated from nitric oxide causes modification of proteins, lipids, and nucleic acids in a wide range of organisms. 3-Nitrotyrosine is one of the most common products of the action of reactive nitrogen species on proteins. Although a great deal is known about the formation of 3-nitrotyrosine, the subsequent metabolism of this compound is a mystery. Variovorax paradoxus JS171 and Burkholderia sp. strain JS165 were isolated from soil slurries when 3-nitrotyrosine was provided as the sole carbon, nitrogen, and energy source. During growth on 3-nitrotyrosine stoichiometric amounts of nitrite were released along with approximately one-half of the theoretically available ammonia. The catabolic pathway involving oxidative denitration is distinct from the pathway for tyrosine metabolism. The facile isolation and the specific, regulated pathway for 3-nitrotyrosine degradation in natural ecosystems suggest that there is a significant flux of 3-nitrotyrosine in such environments. PMID:16461647

  16. Clustered genes required for the synthesis of heterocyst envelope polysaccharide in Anabaena sp. strain PCC 7120.

    PubMed

    Huang, Guocun; Fan, Qing; Lechno-Yossef, Sigal; Wojciuch, Elizabeth; Wolk, C Peter; Kaneko, Takakazu; Tabata, Satoshi

    2005-02-01

    As demonstrated with alr2835 (hepA) and alr2834 (hepC) mutants, heterocysts of Anabaena sp. strain PCC 7120, a filamentous cyanobacterium, must have an envelope polysaccharide layer (the Hep+ phenotype) to fix dinitrogen in an oxygen-containing milieu (the Fox+ phenotype). Transpositions presumptively responsible for a Fox- phenotype were localized in open reading frames (ORFs) near hepA and hepC. A mutation in each of nine of these ORFs was complemented by a clone bearing only that single, intact ORF. Heterocysts of the nine mutants were found to lack an envelope polysaccharide layer. Complementation of mutations in alr2832 and alr2840 may have resulted from recombination. However, alr2825, alr2827, alr2831, alr2833, alr2837, alr2839, and alr2841, like hepA and hepC, are required for a Hep+ Fox+ phenotype. PMID:15659688

  17. Purification and properties of glutathione reductase from the cyanobacterium Anabaena sp. strain 7119

    SciTech Connect

    Serrano, A.; Rivas, J.; Losada, M.

    1984-04-01

    An NADPH-glutathione reductase (EC 1.6.4.2) has been purified 6000-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

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

    PubMed

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

    2009-01-01

    Extraction of 25 L fermentation broth of the newly isolated Streptomyces sp. strain TN58 and various separation and purification steps led to the isolation of five bioactive metabolites, namely brevianamide F (C1), reported from a streptomycete for the first time, N(beta)-acetyltryptamine (C2), thiazolidomycin (C3), and two rhamnopyranosides (C4 and C5). These two rhamnopyranosides were produced directly, without precursor addition. The chemical structure of these five active compounds was established on the basis of (1)H, (13)C/APT and 2D NMR spectra, ESI and EI-MS data, and by comparison with data from the literature. According to the biological studies, we show in this work that the compounds C1, C2, C4 and C5 possess antimicrobial activities. PMID:19662574

  19. Resolution of 4-chlorobenzoate dehalogenase from Pseudomonas sp. strain CBS3 into three components

    SciTech Connect

    Elsner, A.; Loeffler, F.; Miyashita, K.; Mueller, R.; Lingens, F. (Institut fuer Mikrobiologie der Universitaet Hohenheim, Stuttgart (West Germany))

    1991-01-01

    Due to their widespread use and their recalcitrance, many chlorinated compounds are found as primary pollutants in our environment. Nevertheless, several bacteria have been isolated which possess the ability to degrade chlorinated hydrocarbons. Of special interest in these bacteria are the enzymes that catalyze the release of the halogen substituent. Extracts of Pseudomonas sp. strain CBS3 grown with 4-chlorobenzoate as sole carbon source contained an enzyme that converted 4-chlorobenzoate to 4-hydroxybenzoate. This enzyme was shown to consist of three components, all necessary for the reaction. Component I, which had a molecular weight of about 3,000, was highly unstable. Components II and III were stable proteins with molecular weights of about 86,000 and 92,000.

  20. Oxidation of biphenyl by a multicomponent enzyme system from pseudomonas sp. strain LB400

    SciTech Connect

    Haddock, J.D.; Nadim, L.M.; Gibson, D.T.

    1993-01-01

    Pseudomonas sp. strain LB400 grows on biphenyl as the sole carbon and energy source. The organism also cooxidizes several chlorinated biphenyl congeners. Biphenyl dioxygenase activity in cell extract required addition of NAD(P)H as an electron donor for the conversion of biphenyl to cis-2,3-dihydroxy-2,3-dihydrobiphenyl. Incorporation of both atoms of molecular oxygen into the substrate was shown with (18)O2. The nonlinear relationship between enzyme activity and protein concentration suggested that the enzyme is composed of multiple protein components. Ion-exchange chromatography of the cell extract gave three protein fractions that were required together to restore enzymatic activity. Similarities with other multicomponent aromatic hydrocarbon dioxygenases indicated that biphenyl dioxygenase may consist of a flavoprotein and iron-sulfur proteins that constitute a short electron transport chain involved in catalyzing the incorporation of both atoms of molecular oxygen into the aromatic ring.

  1. Cell Surface-Associated Proteins in the Filamentous Cyanobacterium Anabaena sp. strain PCC 7120

    PubMed Central

    Yoshimura, Hidehisa; Ikeuchi, Masahiko; Ohomori, Masayuki

    2012-01-01

    The cell surface senses environmental changes first and transfers signals into the cell. To understand the response to environmental changes, it is necessary to analyze cell surface components, particularly cell surface-associated proteins. We therefore investigated cell surface-associated proteins from the filamentous cyanobacterium Anabaena sp. strain PCC 7120. The cell surface-associated proteins extracted by an acidic buffer were resolved by SDS-PAGE. Eighteen proteins were identified from resolved bands by amino-terminal sequencing. Analysis of cell surface-associated proteins indicated that several proteins among them were involved in nucleic acid binding, protein synthesis, proteolytic activity and electron transfer, and other proteins were involved in the stress response. PMID:23059722

  2. Degradation of 2-hydroxybiphenyl and 2,2 prime -dihydroxybiphenyl by Pseudomonas sp. strain HBP1

    SciTech Connect

    Kohler, H.P.E.; Kohler-Staub, D.; Focht, D.D. (Univ. of California, Riverside (USA))

    1988-11-01

    Pseudomonas sp. strain HBP1 was found to grow on 2-hydroxy- and 2,2{prime}-dihydroxy-biphenyl as the sole carbon and energy sources. The first step in the degradation of these compounds was catalyzed by an NADH-dependent monooxygenase. The enzyme inserted a hydroxyl group adjacent to the already existing hydroxyl group to form 2,3-dihydroxybiphenyl when acting on 2-hydroxybiphenyl and to form 2,2{prime},3-trihydroxybiphenyl when acting on 2,2{prime}-dihydroxybiphenyl. To be substrates of the monooxygenase, compounds required a 2-hydroxyphenyl-R structure, with R being a hydrophobic group (e.g., methyl, ethyl, propyl, sec-butyl, phenyl, or 2-hydroxyphenyl). Several chlorinated hydroxybiphenyls served as pseudosubstrates by effecting consumption of NADH and oxygen without being hydroxylated. Further degradation of 2,3-dihydroxy- and 2,2{prime},3-trihydroxybiphenyl involved meta cleavage, with subsequent formation of benzoate and salicylate, respectively.

  3. Purification and properties of xylanase A from alkali-tolerant Bacillus sp. strain BP-23.

    PubMed Central

    Blanco, A; Vidal, T; Colom, J F; Pastor, F I

    1995-01-01

    Xylanase A from the recently isolated Bacillus sp. strain BP-23 was purified to homogeneity. The enzyme shows a molecular mass of 32 kDa and an isoelectric point of 9.3. Optimum temperature and pH for xylanase activity were 50 degrees C and 5.5 respectively. Xylanase A was completely inhibited by N-bromosuccinimide. The main products of birchwood xylan hydrolysis were xylotetraose and xylobiose. The enzyme was shown to facilitate chemical bleaching of pulp, generating savings of 38% in terms of chlorine dioxide consumption. The amino-terminal sequence of xylanase A has a conserved sequence of five amino acids found in xylanases from family F. PMID:8534112

  4. Kinetics study of pyridine biodegradation by a novel bacterial strain, Rhizobium sp. NJUST18.

    PubMed

    Shen, Jinyou; Zhang, Xin; Chen, Dan; Liu, Xiaodong; Zhang, Libin; Sun, Xiuyun; Li, Jiansheng; Bi, Huiping; Wang, Lianjun

    2014-06-01

    Biodegradation of pyridine by a novel bacterial strain, Rhizobium sp. NJUST18, was studied in batch experiments over a wide concentration range (from 100 to 1,000 mg l(-1)). Pyridine inhibited both growth of Rhizobium sp. NJUST18 and biodegradation of pyridine. The Haldane model could be fitted to the growth kinetics data well with the kinetic constants ?* = 0.1473 h(-1), K s = 793.97 mg l(-1), K i = 268.60 mg l(-1) and S m = 461.80 mg l(-1). The true ? max, calculated from ?*, was found to be 0.0332 h(-1). Yield coefficient Y X/S depended on S i and reached a maximum of 0.51 g g(-1) at S i of 600 mg l(-1). V max was calculated by fitting the pyridine consumption data with the Gompertz model. V max increased with initial pyridine concentration up to 14.809 mg l(-1) h(-1). The q S values, calculated from [Formula: see text], were fitted with the Haldane equation, yielding q Smax = 0.1212 g g(-1) h(-1) and q* = 0.3874 g g(-1) h(-1) at S m' = 507.83 mg l(-1), K s' = 558.03 mg l(-1), and K i' = 462.15 mg l(-1). Inhibition constants for growth and degradation rate value were in the same range. Compared with other pyridine degraders, ? max and S m obtained for Rhizobium sp. NJUST18 were relatively high. High K i and K i' values and extremely high K s and K s' values indicated that NJUST18 was able to grow on pyridine within a wide concentration range, especially at relatively high concentrations. PMID:24425539

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

    PubMed

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

    2005-01-01

    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

  6. Paired cloning vectors for complementation of mutations in the cyanobacterium Anabaena sp. strain PCC 7120

    SciTech Connect

    Wolk, C. Peter Wolk [Michigan State University, East Lansing; Fan, Qing [Northwestern University, Evanston; Zhou, Ruanbao [Anhui Normal University, People's Republic of China; Huang, Guocun [University of Texas Southwestern Medical; Lechno-Yossef, Sigal [Michigan State University, East Lansing; Kuritz, Tanya [ORNL; Wojciuch, Elizabeth [Michigan State University, East Lansing

    2007-01-01

    The clones generated in a sequencing project represent a resource for subsequent analysis of the organism whose genome has been sequenced. We describe an interrelated group of cloning vectors that either integrate into the genome or replicate, and that enhance the utility, for developmental and other studies, of the clones used to determine the genomic sequence of the cyanobacterium, Anabaena sp. strain PCC 7120. One integrating vector is a mobilizable BAC vector that was used both to generate bridging clones and to complement transposon mutations. Upon addition of a cassette that permits mobilization and selection, pUC-based sequencing clones can also integrate into the genome and thereupon complement transposon mutations. The replicating vectors are based on cyanobacterial plasmid pDU1, whose sequence we report, and on broad-host-range plasmid RSF1010. The RSF1010- and pDU1-based vectors provide the opportunity to express different genes from either cell-type-specific or -generalist promoters, simultaneously from different plasmids in the same cyanobacterial cells. We show that pDU1 ORF4 and its upstream region play an essential role in the replication and copy number of pDU1, and that ORFs alr2887 and alr3546 (hetF{sub A}) of Anabaena sp. are required specifically for fixation of dinitrogen under oxic conditions.

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

    PubMed Central

    Ligon, James M.; Nakas, James P.

    1987-01-01

    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

  8. Cloning and sequencing of a bile acid-inducible operon from Eubacterium sp. strain VPI 12708.

    PubMed Central

    Mallonee, D H; White, W B; Hylemon, P B

    1990-01-01

    Two bile acid-inducible polypeptides from Eubacterium sp. strain VPI 12708 with molecular weights of 27,000 and approximately 45,000 have previously been shown to be encoded by genes residing on a 2.9-kb EcoRI fragment. We now report the cloning and sequencing of three additional overlapping DNA fragments upstream from this EcoRI fragment. Together, these four fragments contain a large segment of a bile acid-inducible operon which encodes the 27,000- and 45,000-Mr (now shown to be 47,500-Mr) polypeptides and open reading frames potentially coding for four additional polypeptides with molecular weights of 59,500, 58,000, 19,500, and 9,000 to 11,500. A bile acid-inducible polypeptide with an apparent Mr of 23,500, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, was purified to homogeneity, and the N-terminal amino acid sequence that was obtained matched the sequence deduced from the open reading frame coding for the 19,500-Mr polypeptide. A short DNA segment containing the 3' downstream end of the gene coding for the 47,500-Mr polypeptide was not successfully cloned but was directly sequenced from DNA fragments synthesized by polymerase chain reaction. The mRNA initiation site for the bile acid-inducible operon was shown by primer extension to be immediately upstream from the gene encoding the 58,000-Mr polypeptide. A potential promoter region upstream from the mRNA initiation site displayed significant homology with the promoter regions of previously identified bile acid-inducible genes from Eubacterium sp. strain VPI 12708. We hypothesize that this bile acid-inducible operon codes for most of the enzymes involved in the bile acid 7 alpha-dehydroxylation pathway in this bacterium. Images PMID:2254270

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

    SciTech Connect

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

    1987-03-01

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

  10. Structure of the detoxification catalyst mercuric ion reductase from Bacillus sp. strain RC607

    NASA Astrophysics Data System (ADS)

    Schiering, N.; Kabsch, W.; Moore, M. J.; Distefano, M. D.; Walsh, C. T.; Pai, E. F.

    1991-07-01

    SEVERAL hundred million tons of toxic mercurials are dispersed in the biosphere1. Microbes can detoxify organo-mercurials and mercury salts through sequential action of two enzymes, organomercury lyase2 and mercuric ion reductase (MerA) 3-5. The latter, a homodimer with homology to the FAD-dependent disulphide oxidoreductases6, catalyses the reaction NADPH + Hg(II) --> NADP+ + H+Hg(0), one of the very rare enzymic reactions with metal substrates. Human glutathione reductase7,8 serves as a reference molecule for FAD-dependent disulphide reductases and between its primary structure9 and that of MerA from Tn501 (Pseudomonas), Tn21 (Shigella), pI258 (Staphylococcus) and Bacillus, 25-30% of the residues have been conserved10,11. All MerAs have a C-terminal extension about 15 residues long but have very varied N termini. Although the enzyme from Streptomyces lividans has no addition, from Pseudomonas aeruginosa Tn5Ol and Bacillus sp. strain RC607 it has one and two copies respectively of a domain of 80-85 residues, highly homologous to MerP, the periplasmic component of proteins encoded by the mer operon11. These domains can be proteolytically cleaved off without changing the catalytic efficiency3. We report here the crystal structure of MerA from the Gram-positive bacterium Bacillus sp. strain RC607. Analysis of its complexes with nicotinamide dinucleotide substrates and the inhibitor Cd(II) reveals how limited structural changes enable an enzyme to accept as substrate what used to be a dangerous inhibitor. Knowledge of the mode of mercury ligation is a prerequisite for understanding this unique detoxification mechanism.

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

    PubMed Central

    Ludwig, Marcus; Bryant, Donald A.

    2012-01-01

    Synechococcus sp. strain PCC 7002 is a unicellular, euryhaline cyanobacterium. It is a model organism for studies of cyanobacterial metabolism and has great potential for biotechnological applications. It exhibits an exceptional tolerance of high-light irradiation and shows very rapid growth. The habitats from which this and closely related strains were isolated are subject to changes in several environmental factors, including light, nutrient supply, temperature, and salinity. In this study global transcriptome profiling via RNAseq has been used to perform a comparative and integrated study of global changes in cells grown at different temperatures, at different salinities, and under mixotrophic conditions, when a metabolizable organic carbon source was present. Furthermore, the transcriptomes were investigated for cells that were subjected to a heat shock and that were exposed to oxidative stress. Lower growth temperatures caused relatively minor changes of the transcriptome; the most prominent changes affected fatty acid desaturases. A heat shock caused severe changes of the transcriptome pattern; transcripts for genes associated with major metabolic pathways declined and those for different chaperones increased dramatically. Oxidative stress, however, left the transcript pattern almost unaffected. When grown at high salinity, Synechococcus sp. PCC 7002 had increased expression of genes involved in compatible solute biosynthesis and showed increased mRNA levels for several genes involved in electron transport. Transcripts of two adjacent genes dramatically increased upon growth at high salinity; the respective proteins are putatively involved in coping with oxidative stress and in triggering ion channels. Only minor changes were observed when cells were grown at low salinity or when the growth medium was supplemented with glycerol. However, the transcriptome data suggest that cells must acclimate to excess reducing equivalents when a reduced C-source is present. PMID:23087677

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

    PubMed

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

    2015-01-01

    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

  13. Taxonomic study of the Lactobacillus acidophilus group, with recognition of Lactobacillus gallinarum sp. nov. and Lactobacillus johnsonii sp. nov. and synonymy of Lactobacillus acidophilus group A3 (Johnson et al. 1980) with the type strain of Lactobacillus amylovorus (Nakamura 1981).

    PubMed

    Fujisawa, T; Benno, Y; Yaeshima, T; Mitsuoka, T

    1992-07-01

    Biochemical properties and DNA-DNA reassociation studies of Lactobacillus acidophilus strains isolated from humans and animals indicate that these include six genomospecies. Two new species can be differentiated from the established species of the genus Lactobacillus: L. gallinarum sp. nov. (type strain, ATCC 33199) and L. johnsonii sp. nov. (type strain, ATCC 33200). Furthermore, it was clarified that L. acidophilus group A3 (Johnson et al. 1980) is synonymous with L. amylovorus. PMID:1503977

  14. Draft Genome Sequence of the Polyextremophilic Exiguobacterium sp. Strain S17, Isolated from Hyperarsenic Lakes in the Argentinian Puna

    PubMed Central

    Ordoñez, Omar F.; Lanzarotti, Esteban; Kurth, Daniel; Gorriti, Marta F.; Revale, Santiago; Cortez, Néstor; Vazquez, Martin P.; Farías, María E.

    2013-01-01

    Exiguobacterium sp. strain S17 is a moderately halotolerant, arsenic-resistant bacterium that was isolated from Laguna Socompa stromatolites in the Argentinian Puna. The draft genome sequence suggests potent enzyme candidates that are essential for survival under multiple environmental extreme conditions, such as high levels of UV radiation, elevated salinity, and the presence of critical arsenic concentrations. PMID:23887911

  15. Pandoraea sp. Strain E26: Discovery of Its Quorum-Sensing Properties via Whole-Genome Sequence Analysis

    PubMed Central

    Yin, Wai-Fong; Tee, Kok Keng; Chang, Chien-Yi; Priya, Kumutha

    2015-01-01

    We report the draft genome sequence of Pandoraea sp. strain E26 isolated from a former landfill site, sequenced by the Illumina MiSeq platform. This genome sequence will be useful to further understand the quorum-sensing system of this isolate. PMID:26021935

  16. Biodegradation of n-Alkylcycloalkanes and n-Alkylbenzenes via New Pathways in Alcanivorax sp. Strain MBIC 4326

    PubMed Central

    Dutta, Tapan K.; Harayama, Shigeaki

    2001-01-01

    The degradation of long-chain n-alkylbenzenes and n-alkylcyclohexanes by Alcanivorax sp. strain MBIC 4326 was investigated. The alkyl side chain of these compounds was mainly processed by ?-oxidation. In the degradation of n-alkylcyclohexanes, cyclohexanecarboxylic acid was formed as an intermediate. This compound was further transformed to benzoic acid via 1-cyclohexene-1-carboxylic acid. PMID:11282659

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

    PubMed

    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

    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

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

    Microsoft Academic Search

    Robert J Martinez; David Bruce; J. Chris Detter; Lynne A. Goodwin; James Han; Cliff Han; Brittany Held; Natalia Mikhailova; Matt Nolan; Len Pennacchio; Sam Pitluck; Roxanne Tapia; Tanja Woyke; Patricia A. Sobeckya

    2012-01-01

    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.

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

    PubMed

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

    2014-01-01

    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

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

    PubMed

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

    2014-01-01

    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

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

    PubMed

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

    2014-01-01

    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

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

    PubMed

    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; Elias, Dwayne A

    2014-01-01

    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

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

    PubMed

    Nielsen, Tue Kjærgaard; Kot, Witold; Sørensen, Sebastian R; Hansen, Lars Hestbjerg

    2015-01-01

    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

  4. Draft Genome Sequence of Pseudomonas sp. Strain 10-1B, a Polycyclic Aromatic Hydrocarbon Degrader in Contaminated Soil.

    PubMed

    Bello-Akinosho, Maryam; Adeleke, Rasheed; Swanevelder, Dirk; Thantsha, Mapitsi

    2015-01-01

    Pseudomonas sp. strain 10-1B was isolated from artificially polluted soil after selective enrichment. Its draft genome consists of several predicted genes that are involved in the hydroxylation of the aromatic ring, which is the rate-limiting step in the biodegradation of polycyclic aromatic hydrocarbons. PMID:25953172

  5. OXIDATION OF POLYCHLORINATED BIPHENYLS BY PSEUDOMONAS SP. STRAIN LB400 AND PSEUDOMONAS PSEUDOAL-CALIGENES KF707

    EPA Science Inventory

    Biphenyl-grown cells and cell extracts prepared from biphenyl-grown cells of Pseudomonas sp. strain LB400 oxidize a much wider range of chlorinated biphenyls than do analogous preparations from Pseudomonas pseudoalcaligenes KF707. hese results are attributed to differences in the...

  6. Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets

    PubMed Central

    Davenport, Karen W.; Li, Po-E; Ahmed, Sanaa A.; Daligault, Hajnalka; Gleasner, Cheryl D.; Kunde, Yuliya; McMurry, Kim; Lo, Chien-Chi; Reitenga, Krista G.; Daughton, Ashlynn R.; Shen, Xiaohong; Frietze, Seth; Wang, Dongping; Drautz-Moses, Daniela I.; Schuster, Stephan; Chain, Patrick S.; Han, Cliff

    2015-01-01

    We report here the genome sequence of Thauera sp. strain SWB20, isolated from a Singaporean wastewater treatment facility using gel microdroplets (GMDs) and single-cell genomics (SCG). This approach provided a single clonal microcolony that was sufficient to obtain a 4.9-Mbp genome assembly of an ecologically relevant Thauera species. PMID:25792053

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

    PubMed Central

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

    2013-01-01

    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

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

    PubMed Central

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

    2015-01-01

    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

  9. Pandoraea sp. Strain E26: Discovery of Its Quorum-Sensing Properties via Whole-Genome Sequence Analysis.

    PubMed

    Chan, Kok-Gan; Yin, Wai-Fong; Tee, Kok Keng; Chang, Chien-Yi; Priya, Kumutha

    2015-01-01

    We report the draft genome sequence of Pandoraea sp. strain E26 isolated from a former landfill site, sequenced by the Illumina MiSeq platform. This genome sequence will be useful to further understand the quorum-sensing system of this isolate. PMID:26021935

  10. Whole-Genome Sequence of Aquamicrobium sp. Strain SK-2, a Polychlorinated Biphenyl-Utilizing Bacterium Isolated from Sewage Sludge.

    PubMed

    Chang, Young-Cheol; Sawada, Ken; Kim, Eun-Sook; Jung, Kweon; Kikuchi, Shintaro

    2015-01-01

    Here, we report the whole-genome sequence of Aquamicrobium sp. strain SK-2, a bacterium which can use 2,2',4,4',5,5'-hexachlorobiphenyl as the sole carbon source for its growth. An approximately 9.23-Mb genome sequence of SK-2 will greatly facilitate research efforts regarding the study of the polychlorinated biphenyl (PCB) degradation mechanism. PMID:25977427

  11. Functional nodFE genes are present in Sinorhizobium sp. strain MUS10, a symbiont of tropical legume Sesbania rostrata

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sinorhizobium sp. strain MUS10, a rhizobium from the Indian subcontinent, forms nitrogen-fixing nodules on the stems and roots of tropical legume Sesbania rostrata. The structure of Nod factors (NFs) of MUS10 are similar to those of Azorhizobium caulinodans, S. saheli bv sesbaniae and S. terangae bv...

  12. Application of waste frying oils in the biosynthesis of biodemulsifier by a demulsifying strain Alcaligenes sp. S-XJ-1

    Microsoft Academic Search

    Jia Liu; Kaiming Peng; Xiangfeng Huang; Lijun Lu; Hang Cheng; Dianhai Yang; Qi Zhou; Huiping Deng

    2011-01-01

    Exploration of biodemulsifiers has become a new research aspect. Using waste frying oils (WFOs) as carbon source to synthesize biodemulsifiers has a potential prospect to decrease production cost and to improve the application of biodemulsifiers in the oilfield. In this study, a demulsifying strain, Alcaligenes sp. S-XJ-1, was investigated to synthesize a biodemulsifier using waste frying oils as carbon source.

  13. Complete Genome Sequence of Cyanobacterium Geminocystis sp. Strain NIES-3708, Which Performs Type II Complementary Chromatic Acclimation.

    PubMed

    Hirose, Yuu; Katayama, Mitsunori; Ohtsubo, Yoshiyuki; Misawa, Naomi; Iioka, Erica; Suda, Wataru; Oshima, Kenshiro; Hanaoka, Mitsumasa; Tanaka, Kan; Eki, Toshihiko; Ikeuchi, Masahiko; Kikuchi, Yo; Ishida, Makoto; Hattori, Masahira

    2015-01-01

    To explore the variation of the light-regulated genes during complementary chromatic acclimation (CCA), we determined the complete genome sequence of the cyanobacterium Geminocystis sp. strain NIES-3708. Within the light-regulated operon for CCA, we found genes for phycoerythrin but not phycocyanin, suggesting that this cyanobacterium modulates phycoerythrin composition only (type II CCA). PMID:25953174

  14. Degradation of chlorobenzenes at nanomolar concentrations by Burkholderia sp. strain PS14 in liquid cultures and in soil

    SciTech Connect

    Rapp, P.; Timmis, K.N. [GBF-National Research Centre for Biotechnology, Braunschweig (Germany). Div. of Microbiology

    1999-06-01

    The utilization of 1,2,4,5-tetrachloro-, 1,2,4-trichloro-, the three isomeric dichlorobenzenes and fructose as the sole carbon and energy sources of nanomolar concentrations was studied in batch experiments with Burkholderia sp. strain PS14. In liquid culture, all chlorobenzenes were metabolized within 1 h from their initial concentration of 500 nM to below their detection limits of 0.5 nM for 1,2,4,5-tetrachloro- and 1,2,4-trichlorobenzene and 7.5 nM for the three dichlorobenzene isomers, with 63% mineralization during this time. In soil microcosms, Burkholderia sp. strain PS14 metabolized tetrachlorobenzene present at 64.8 ppb and trichlorobenzene present at 54.4 ppb over a 72-h incubation period to below the detection limits of 0.108 and 0.09 ppb, respectively, with approximately 80% mineralization. A high sorptive capacity of Burkholderia sp. strain PS14 for 1,2,4,5-tetrachlorobenzene was found at very low cell density. The results demonstrate that Burkholderia sp. strain PS14 exhibits a very high affinity for chlorobenzenes at nanomolar concentrations.

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

    PubMed Central

    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

    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

  16. Draft Genome Sequence of Potassium-Dependent Alkaliphilic Bacillus sp. Strain TS-2, Isolated from a Jumping Spider.

    PubMed

    Fujinami, Shun; Takeda, Kiyoko; Onodera, Takefumi; Satoh, Katsuya; Sano, Motohiko; Narumi, Issay; Ito, Masahiro

    2014-01-01

    The potassium-dependent alkaliphilic Bacillus sp. strain TS-2 was isolated from the mashed extract of a jumping spider, and its draft genome sequence was obtained. Comparative genomic analysis with a previously sequenced sodium-dependent alkaliphilic Bacillus species may reveal potassium-dependent alkaline adaptation mechanisms. PMID:24855304

  17. Cloning and Characterization of Benzoate Catabolic Genes in the Gram-Positive Polychlorinated Biphenyl Degrader Rhodococcus sp. Strain RHA1

    Microsoft Academic Search

    WATARU KITAGAWA; KEISUKE MIYAUCHI; EIJI MASAI; MASAO FUKUDA

    2001-01-01

    Benzoate catabolism is thought to play a key role in aerobic bacterial degradation of biphenyl and poly- chlorinated biphenyls (PCBs). Benzoate catabolic genes were cloned from a PCB degrader, Rhodococcus sp. strain RHA1, by using PCR amplification and temporal temperature gradient electrophoresis separation. A nucleotide sequence determination revealed that the deduced amino acid sequences encoded by the RHA1 benzoate catabolic

  18. Draft Genome Sequence of Vibrio sp. Strain Vb278, an Antagonistic Bacterium Isolated from the Marine Sponge Sarcotragus spinosulus

    PubMed Central

    Gonçalves, Ana C. S.; Franco, Telma; Califano, Gianmaria; Dowd, Scot E.; Pohnert, Georg

    2015-01-01

    We report here the draft genome sequence of Vibrio sp. Vb278, a biofilm-producing strain isolated from the marine sponge Sarcotragus spinosulus, showing in vitro antibacterial activity. The annotated genome displays a range of symbiotic factors and the potential for the biosynthesis of several biologically active natural products. PMID:26021918

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

    PubMed

    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

    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

  20. Differential Degradation of Bicyclics with Aromatic and Alicyclic Rings by Rhodococcus sp. Strain DK17 ?

    PubMed Central

    Kim, Dockyu; Yoo, Miyoun; Choi, Ki Young; Kang, Beom Sik; Kim, Tai Kyoung; Hong, Soon Gyu; Zylstra, Gerben J.; Kim, Eungbin

    2011-01-01

    The metabolically versatile Rhodococcus sp. strain DK17 is able to grow on tetralin and indan but cannot use their respective desaturated counterparts, 1,2-dihydronaphthalene and indene, as sole carbon and energy sources. Metabolite analyses by gas chromatography-mass spectrometry and nuclear magnetic resonance spectrometry clearly show that (i) the meta-cleavage dioxygenase mutant strain DK180 accumulates 5,6,7,8-tetrahydro-1,2-naphthalene diol, 1,2-indene diol, and 3,4-dihydro-naphthalene-1,2-diol from tetralin, indene, and 1,2-dihydronaphthalene, respectively, and (ii) when expressed in Escherichia coli, the DK17 o-xylene dioxygenase transforms tetralin, indene, and 1,2-dihydronaphthalene into tetralin cis-dihydrodiol, indan-1,2-diol, and cis-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene, respectively. Tetralin, which is activated by aromatic hydroxylation, is degraded successfully via the ring cleavage pathway to support growth of DK17. Indene and 1,2-dihydronaphthalene do not serve as growth substrates because DK17 hydroxylates them on the alicyclic ring and further metabolism results in a dead-end metabolite. This study reveals that aromatic hydroxylation is a prerequisite for proper degradation of bicyclics with aromatic and alicyclic rings by DK17 and confirms the unique ability of the DK17 o-xylene dioxygenase to perform distinct regioselective hydroxylations. PMID:21965391

  1. Enhancement of the potential to utilize octopine in the nonfluorescent Pseudomonas sp. strain 92

    SciTech Connect

    Gill, S.S.; Boivin, R.; Dion, P. (Univ. Laval, Quebec City, Quebec (Canada))

    1991-08-01

    The nonfluorescent Pseudomonas sp. strain 92 requires the presence of a supplementary carbon source for growth on octopine, whereas the spontaneous mutant RB100 has acquired the capacity to utilize this opine as the sole carbon and nitrogen source. Insertional mutagenesis of RB100 with transposon Tn5 generated mutants which were unable to grow on octopine and others which grew slowly on this substrate. Both types of mutants yielded revertants that had regained the ability to utilize octopine. Some of the revertants had lost the transposon, whereas in others the transposon was retained but with rearrangements of the insertion site. Genes of octopine catabolism from strain 92 were cloned on a cosmid vector to generate pK3. The clone pK3 conferred the ability to utilize octopine as the sole carbon and nitrogen source on the host Pseudomonas putida KT2440. Although they conferred an equivalent growth phenotype, the mutant genes carried by RB100 and the cloned genes on pK3 differed in their regulation. Utilization of ({sup 14}C)octopine was inducible by octopine in RB100 and was constitutive in KT2440(pK3).

  2. Molecular and biochemical characterization of the tetralin degradation pathway in Rhodococcus sp. strain TFB

    PubMed Central

    Tomás?Gallardo, Laura; Santero, Eduardo; Camafeita, Emilio; Calvo, Enrique; Schlömann, Michael; Floriano, Belén

    2009-01-01

    Summary The tetralin biodegradation pathway in Rhodococcus sp. strain TFB, a Gram?positive bacterium resistant to genetic manipulation, was characterized using a proteomic approach. Relative protein expression in cell free extracts from tetralin? and glucose?grown cells was compared using the 2D?DIGE technique. Identification of proteins specifically expressed in tetralin?grown cells was used to characterize a complete set of genes involved in tetralin degradation by reverse genetics. We propose a tetralin degradation pathway analogous to that described for Sphingomonas macrogolitabida strain TFA. TFB thn genes are organized into three operons; two contain all of the structural genes and are transcribed in the same direction, while the third operon, thnST, is transcribed in the opposite direction and encodes a two?component regulatory system, whose transcription is higher in tetralin?grown cells. In addition to tetralin induction, TFB thn structural genes are subject to glucose repression. Primer extension assays and translational thnA1::gfp and thnS::gfp fusions were used to characterize putative promoter regions. A mutational analysis of the thnA1 promoter region allowed us to define nucleotides within the cis regulatory elements that are important for the control of thn gene expression. PMID:21261920

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

    PubMed Central

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

    2013-01-01

    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

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

    PubMed Central

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

    2001-01-01

    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

  5. Defluorination of organofluorine sulfur compounds by Pseudomonas sp. strain D2

    SciTech Connect

    Key, B.D.; Criddle, C.S. [Michigan State Univ., East Lansing, MI (United States)] [Michigan State Univ., East Lansing, MI (United States); Howell, R.D. [3M Environmental Technology and Safety Services, St. Paul, MN (United States)] [3M Environmental Technology and Safety Services, St. Paul, MN (United States)

    1998-08-01

    Little is known of the potential for biodegradation of fluorinated sulfonates. Because of the apparent stability of fluorinated organics, their bioactivity, and their potential for accumulation in the environment, it is important to understand their environmental fate and the mechanisms by which they might be degraded. To evaluate this potential, the following model compounds were selected: difluoromethane sulfonate (DFMS), trifluoromethane sulfonate (TFMS), 2,2,2-trifluoroethane sulfonate (TES), perfluorooctane sulfonate (PFOS), and 1H,1H,2H,2H-perfluorooctane sulfonate (H-PFOS). A laboratory isolate designated Pseudomonas sp. strain D2 completely defluorinated DFMS under aerobic sulfur-limiting conditions in a defined mineral medium. Strain D2 utilized DFMS as the sole source of sulfur, but not as a source of carbon or energy. DFMS utilization was inhibited by other forms of sulfur, and noncompetitive inhibition kinetics were observed, with K{sub i}-values of 3--4 {micro}M for sulfate, sulfite, methane sulfonate, and cystine. Strain D2 was subsequently used to evaluate degradation of other fluorinated sulfonates. Growth and defluorination were only observed for those compounds containing hydrogen (TES and H-PFOS). TFMS and PFOS were not degraded. TES was completely defluorinated, and H-PFOS was partially defluorinated. No volatile transformation products were detected for TES or DFMS, but six volatile products were detected for H-PFOS. All of the volatile products contained oxygen and fluorine, but not sulfur. This is the first report of defluorination of fluorinated sulfonates, a linkage between sulfur assimilation and defluorination, and generation of volatile fluorinated biotransformation products.

  6. Characterization and purification of bile salt hydrolase from Lactobacillus sp. strain 100-100

    SciTech Connect

    Lundeen, S.G.; Savage, D.C. (Univ. of Tennessee, Knoxville (USA))

    1990-08-01

    The authors have characterized and purified the bile salt hydrolase from Lactobacillus sp. strain 100-100. Bile salt hydrolase from cells of the strain was purified with column and high-performance liquid chromatography. The activity was assayed in whole cells and cell-free extracts with either a radiochemical assay involving ({sup 14}C)taurocholic acid or a nonradioactive assay involving trinitrobenzene sulfonate. The activity was detectable only in stationary-phase cells. Within 20 min after conjugated bile acids were added to stationary-phase cultures of strain 100-100, the activity in whole cells increased to levels three- to fivefold higher than in cells from cultures grown in medium free of bile salts. In cell-free extracts, however, the activity was about equal whether or not the cells have been grown with bile salts present. When supernatant solutions from cultures grown in medium containing taurocholic acid were used to suspend cells grown in medium free of the bile salt, the bile salt hydrolase activity detected in whole cells increased two- to threefold. Two forms of the hydrolase were purified from the cells and designated hydrolases A and B. They eluted from anion-exchange high-performance liquid chromatography in two sets of fractions, A at 0.15 M NaCl and B at 0.18 M NaCl. Their apparent molecular weights in nondenaturing polyacrylamide gel electrophoresis were 115,000 and 105,000, respectively. However, discrepancies existed in the apparent molecular weights and number of peptides detected in sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the two forms. Whether the enzyme exists in two forms in the cells remains to be determined.

  7. Lauric Acid Production in a Glycogen-Less Strain of Synechococcus sp. PCC 7002

    PubMed Central

    Work, Victoria H.; Melnicki, Matthew R.; Hill, Eric A.; Davies, Fiona K.; Kucek, Leo A.; Beliaev, Alexander S.; Posewitz, Matthew C.

    2015-01-01

    The cyanobacterium Synechococcus sp. Pasteur culture collection 7002 was genetically engineered to synthesize biofuel-compatible medium-chain fatty acids (FAs) during photoautotrophic growth. Expression of a heterologous lauroyl-acyl carrier protein (C12:0-ACP) thioesterase with concurrent deletion of the endogenous putative acyl-ACP synthetase led to secretion of transesterifiable C12:0 FA in CO2-supplemented batch cultures. When grown at steady state over a range of light intensities in a light-emitting diode turbidostat photobioreactor, the C12-secreting mutant exhibited a modest reduction in growth rate and increased O2 evolution relative to the wild-type (WT). Inhibition of (i) glycogen synthesis by deletion of the glgC-encoded ADP-glucose pyrophosphorylase (AGPase) and (ii) protein synthesis by nitrogen deprivation were investigated as potential mechanisms for metabolite redistribution to increase FA synthesis. Deletion of AGPase led to a 10-fold decrease in reducing carbohydrates and secretion of organic acids during nitrogen deprivation consistent with an energy spilling phenotype. When the carbohydrate-deficient background (?glgC) was modified for C12 secretion, no increase in C12 was achieved during nutrient replete growth, and no C12 was recovered from any strain upon nitrogen deprivation under the conditions used. At steady state, the growth rate of the ?glgC strain saturated at a lower light intensity than the WT, but O2 evolution was not compromised and became increasingly decoupled from growth rate with rising irradiance. Photophysiological properties of the ?glgC strain suggest energy dissipation from photosystem II and reconfiguration of electron flow at the level of the plastoquinone pool. PMID:25964950

  8. Alginate-dependent gene expression mechanism in Sphingomonas sp. strain A1.

    PubMed

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

    2014-07-01

    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

  9. Activation of dormant bacterial genes by Nonomuraea sp. strain ATCC 39727 mutant-type RNA polymerase.

    PubMed

    Talà, Adelfia; Wang, Guojun; Zemanova, Martina; Okamoto, Susumu; Ochi, Kozo; Alifano, Pietro

    2009-02-01

    There is accumulating evidence that the ability of actinomycetes to produce antibiotics and other bioactive secondary metabolites has been underestimated due to the presence of cryptic gene clusters. The activation of dormant genes is therefore one of the most important areas of experimental research for the discovery of drugs in these organisms. The recent observation that several actinomycetes possess two RNA polymerase beta-chain genes (rpoB) has opened up the possibility, explored in this study, of developing a new strategy to activate dormant gene expression in bacteria. Two rpoB paralogs, rpoB(S) and rpoB(R), provide Nonomuraea sp. strain ATCC 39727 with two functionally distinct and developmentally regulated RNA polymerases. The product of rpoB(R), the expression of which increases after transition to stationary phase, is characterized by five amino acid substitutions located within or close to the so-called rifampin resistance clusters that play a key role in fundamental activities of RNA polymerase. Here, we report that rpoB(R) markedly activated antibiotic biosynthesis in the wild-type Streptomyces lividans strain 1326 and also in strain KO-421, a relaxed (rel) mutant unable to produce ppGpp. Site-directed mutagenesis demonstrated that the rpoB(R)-specific missense H426N mutation was essential for the activation of secondary metabolism. Our observations also indicated that mutant-type or duplicated, rpoB often exists in nature among rare actinomycetes and will thus provide a basis for further basic and applied research. PMID:19047343

  10. Characterization of Amphora sp., a newly isolated diatom wild strain, potentially usable for biodiesel production.

    PubMed

    Chtourou, Haifa; Dahmen, Ines; Jebali, Ahlem; Karray, Fatma; Hassairi, Ilem; Abdelkafi, Slim; Ayadi, Habib; Sayadi, Sami; Dhouib, Abdelhafidh

    2015-07-01

    Microalgae as feedstock for biofuel production have attracted serious consideration as an important sustainable source of energy. For biodiesel production with microalgae, a series of consecutive processes should be performed as selection of adequate microalgal strains, mass culture, cell harvesting, oil extraction and transesterification. The aim of this study was to investigate the growth and lipid accumulation of a new isolated marine microalgal strain by optimizing culture medium composition and applying different stressful culture conditions. Microalga CTM 20023 was isolated from the evaporating salt-ponds at Sfax, Tunisia, using serial-dilution technique from enriched cultures. Phylogenetic analysis based on SSU rDNA and rbcL-3P sequences attributed this isolate to a new species of the Amphora genus. This wild strain possesses rapid gravity sedimentation of 2.91 m h(-1), suitable for an easy and low-cost biomass harvest. The optimization of the composition of the culture medium through statistical experimental designs improved the specific growth rate of Amphora sp. from 0.149 to 0.262 day(-1) and increased its 15-day culture biomass production from 465 to 2200 mg L(-1) (dw) and its lipid content from 140 to 370 mg g(-1) (dw). Highest biomass productivity of 178 mg L(-1) day(-1) was achieved at the 10th day of culture. Highest lipid content of 530 mg g(-1) (dw) was obtained under phosphorus starvation and 64.34 % of these lipids were saturated fatty acids. A first growth stage, in optimized condition, would thus offer the maximum productivity for an algal biomass feed stream, followed by second stressful stage for lipid accumulation, thus suitable for biodiesel production. PMID:25716001

  11. Bioenergetic properties of the thermoalkaliphilic Bacillus sp. strain TA2.A1.

    PubMed

    Olsson, Karen; Keis, Stefanie; Morgan, Hugh W; Dimroth, Peter; Cook, Gregory M

    2003-01-01

    The thermoalkaliphilic Bacillus sp. strain TA2.A1 was able to grow in pH-controlled batch culture containing a nonfermentable growth substrate from pH 7.5 to 10.0 with no significant change in its specific growth rate, demonstrating that this bacterium is a facultative alkaliphile. Growth at pH 10.0 was sensitive to the protonophore carbonyl cyanide m-chlorophenylhydrazone, suggesting that a proton motive force (Deltap) generated via aerobic respiration was an obligate requirement for growth of strain TA2.A1. Strain TA2.A1 exhibited intracellular pH homeostasis as the external pH increased from 7.5 to 10.0; however, the maximum DeltapH generated over this pH range was only 1.1 units at an external pH of 9.5. The membrane potential (Deltapsi) was maintained between -114 mV and -150 mV, and little significant change was observed over the pH range for growth. In contrast, the Deltap declined from -164 mV at pH 7.5 to approximately -78 mV at pH 10.0. An inwardly directed sodium motive force (DeltapNa(+)) of -100 mV at pH 10.0 indicated that cellular processes (i.e., solute transport) dependent on a sodium gradient would not be affected by the adverse Deltap. The phosphorylation potential of strain TA2.A1 was maintained between -300 mV and -418 mV, and the calculated H(+)/ATP stoichiometry of the ATP synthase increased from 2.0 at pH 7.5 to 5.7 at pH 10.0. Based on these data, vigorous growth of strain TA2.A1 correlated well with the DeltapNa(+), phosphorylation potential, and the ATP/ADP ratio, but not with Deltap. This communication represents the first report on the bioenergetics of an extremely thermoalkaliphilic aerobic bacterium. PMID:12511491

  12. Inoculation of Burkholderia cepacia, Pseudomonas fluorescens and Enterobacter sp. on Sorghum bicolor: Root colonization and plant growth promotion of dual strain inocula

    Microsoft Academic Search

    Luigi Chiarini; Annamaria Bevivino; Silvia Tabacchioni; Claudia Dalmastri

    1998-01-01

    Burkholderia cepacia strain PHP7 was tested for its ability to colonize roots and to promote the growth of Sorghum bicolor alone or in combination with Enterobacter sp. strain BB23T4d or Pseudomonas fluorescnes strain A23T3c. All three strains were able to colonize the root system of sorghum but only B. cepacia and P. fluorescens promoted plant growth in single strain inoculation

  13. Isolation and Characterization of a Novel Imidacloprid-Degrading Mycobacterium sp. Strain MK6 from an Egyptian Soil.

    PubMed

    Kandil, Mahrous M; Trigo, Carmen; Koskinen, William C; Sadowsky, Michael J

    2015-05-20

    Thus far, only a small number and types of bacteria with limited ability in degrading imidacloprid have been reported. Also, genes regulating imidacloprid (IMDA) degradation have yet to be discovered. To study this in more detail, an enrichment technique was used to isolate consortia and pure cultures of IMDA-degrading bacteria. Through this approach, we successfully isolated a novel bacterium capable of completely degrading IMDA as a sole nitrogen source. The bacterium was subsequently identified as Mycobacterium sp. strain MK6 by sequence analysis of its 16S rRNA gene (Genbank accession number KR052814 ). BLASTn searches indicated that 16S rRNA gene from Mycobacterium sp. strain MK6 was 99% identical to several Mycobacterium spp. Mycobacterium sp. strain MK6 transformed 99.7% added IMDA (150 ?g mL(-1)) in <2 weeks (t1/2 = 1.6 days) to 6-chloronicotinic acid (6-CNA) as its major metabolite. Although the isolated strain and mixed bacterial consortia were able to degrade IMDA, they failed to grow further on 6-CNA, indicating a lack of IMDA mineralization to carbon dioxide. Small amounts of the desnitro-olefin and desnitro-degradates of IMDA were observed during the incubation but did not accumulate in culture medium. PMID:25932751

  14. Biotransformation of Direct Blue 1 by a moderately halophilic bacterium Marinobacter sp. strain HBRA and toxicity assessment of degraded metabolites.

    PubMed

    Arun Prasad, A S; Satyanarayana, V S V; Bhaskara Rao, K V

    2013-11-15

    The ability of halophiles to survive in the extreme salt concentrations has gained them the importance of being used in the treatment of industrial waste waters. A moderately halophilic bacterial strain with the ability to degrade the complex azo dye Direct Blue-1 (DB-1) was isolated from sea water and identified as Marinobacter sp. strain HBRA. Complete decolorization of DB-1 (100 mg L(-1)) was achieved in 6h at 37 °C, pH 8 and with 70 g L(-1) NaCl. Decolorization was analyzed by UV-vis spectrophotometer. The FT-IR spectrum revealed that Marinobacter sp. strain HBRA specifically targeted azo bond (NN) at 1631 cm(-1) to break down Direct Blue-1. Formation of metabolites at different retention times in HPLC indicated degradation. Biotransformation pathway for DB-1 was proposed based on LC-MS. Phytotoxicity study revealed the less toxic nature of the metabolites compared to the dye. Genotoxicity with Allium cepa confirmed the cytotoxic nature of DB-1 by inducing several chromosomal abnormalities compared to the negligible effects of degraded metabolites. The current study is the first report on the detoxification of DB-1 by Marinobacter sp. strain HBRA. PMID:24121630

  15. Genomic and Transcriptomic Analyses of the Facultative Methanotroph Methylocystis sp. Strain SB2 Grown on Methane or Ethanol

    PubMed Central

    Vorobev, Alexey; Jagadevan, Sheeja; Jain, Sunit; Anantharaman, Karthik; Dick, Gregory J.; Vuilleumier, Stéphane

    2014-01-01

    A minority of methanotrophs are able to utilize multicarbon compounds as growth substrates in addition to methane. The pathways utilized by these microorganisms for assimilation of multicarbon compounds, however, have not been explicitly examined. Here, we report the draft genome of the facultative methanotroph Methylocystis sp. strain SB2 and perform a detailed transcriptomic analysis of cultures grown with either methane or ethanol. Evidence for use of the canonical methane oxidation pathway and the serine cycle for carbon assimilation from methane was obtained, as well as for operation of the complete tricarboxylic acid (TCA) cycle and the ethylmalonyl-coenzyme A (EMC) pathway. Experiments with Methylocystis sp. strain SB2 grown on methane revealed that genes responsible for the first step of methane oxidation, the conversion of methane to methanol, were expressed at a significantly higher level than those for downstream oxidative transformations, suggesting that this step may be rate limiting for growth of this strain with methane. Further, transcriptomic analyses of Methylocystis sp. strain SB2 grown with ethanol compared to methane revealed that on ethanol (i) expression of the pathway of methane oxidation and the serine cycle was significantly reduced, (ii) expression of the TCA cycle dramatically increased, and (iii) expression of the EMC pathway was similar. Based on these data, it appears that Methylocystis sp. strain SB2 converts ethanol to acetyl-coenzyme A, which is then funneled into the TCA cycle for energy generation or incorporated into biomass via the EMC pathway. This suggests that some methanotrophs have greater metabolic flexibility than previously thought and that operation of multiple pathways in these microorganisms is highly controlled and integrated. PMID:24610846

  16. Cloning of a novel arylamidase gene from Paracoccus sp. strain FLN-7 that hydrolyzes amide pesticides.

    PubMed

    Zhang, Jun; Yin, Jin-Gang; Hang, Bao-Jian; Cai, Shu; He, Jian; Zhou, Shun-Gui; Li, Shun-Peng

    2012-07-01

    The bacterial isolate Paracoccus sp. strain FLN-7 hydrolyzes amide pesticides such as diflubenzuron, propanil, chlorpropham, and dimethoate through amide bond cleavage. A gene, ampA, encoding a novel arylamidase that catalyzes the amide bond cleavage in the amide pesticides was cloned from the strain. ampA contains a 1,395-bp open reading frame that encodes a 465-amino-acid protein. AmpA was expressed in Escherichia coli BL21 and homogenously purified using Ni-nitrilotriacetic acid affinity chromatography. AmpA is a homodimer with an isoelectric point of 5.4. AmpA displays maximum enzymatic activity at 40°C and a pH of between 7.5 and 8.0, and it is very stable at pHs ranging from 5.5 to 10.0 and at temperatures up to 50°C. AmpA efficiently hydrolyzes a variety of secondary amine compounds such as propanil, 4-acetaminophenol, propham, chlorpropham, dimethoate, and omethoate. The most suitable substrate is propanil, with K(m) and k(cat) values of 29.5 ?M and 49.2 s(-1), respectively. The benzoylurea insecticides (diflubenzuron and hexaflumuron) are also hydrolyzed but at low efficiencies. No cofactor is needed for the hydrolysis activity. AmpA shares low identities with reported arylamidases (less than 23%), forms a distinct lineage from closely related arylamidases in the phylogenetic tree, and has different biochemical characteristics and catalytic kinetics with related arylamidases. The results in the present study suggest that AmpA is a good candidate for the study of the mechanism for amide pesticide hydrolysis, genetic engineering of amide herbicide-resistant crops, and bioremediation of amide pesticide-contaminated environments. PMID:22544249

  17. Characterization of a New Providencia sp. Strain X1 Producing Multiple Xylanases on Wheat Bran

    PubMed Central

    Kumar, Sharad; Singh, Sudheer Kumar; Kumar, Mahadeo

    2013-01-01

    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

  18. Isolation and characterization of multiple adenylate cyclase genes from the cyanobacterium Anabaena sp. strain PCC 7120.

    PubMed Central

    Katayama, M; Ohmori, M

    1997-01-01

    Adenylate cyclase genes, designated cyaA, cyaB1, cyaB2, cyaC, and cyaD, were isolated from the filamentous cyanobacterium Anabaena sp. strain PCC 7120 by complementation of a strain of Escherichia coli defective for the presence of cya. These genes encoded polypeptides consisting of 735, 859, 860, 1,155, and 546 amino acid residues, respectively. Deduced amino acid sequences of the regions near the C-terminal ends of these cya genes were similar to those of catalytic domains of eukaryotic adenylate cyclases. The remaining part of each cya gene towards its N-terminal end showed a characteristic structure. CyaA had two putative membrane-spanning regions. Both CyaB1 and CyaB2 had regions that were very similar to the cyclic GMP (cGMP)-binding domain of cGMP-stimulated cGMP phosphodiesterase. CyaC consisted of four distinct domains forming sequentially from the N terminus: a response regulator-like domain, a histidine kinase-like domain, a response regulator-like domain, and the catalytic domain of adenylate cyclase. CyaD contained the forkhead-associated domain in its N-terminal region. Expression of these genes was examined by reverse transcription-PCR. The transcript of cyaC was shown to be predominant in this cyanobacterium. The cellular cyclic AMP level in the disruptant of the cyaC mutant was much lower than that in the wild type. PMID:9171404

  19. Cloning of a Novel Arylamidase Gene from Paracoccus sp. Strain FLN-7 That Hydrolyzes Amide Pesticides

    PubMed Central

    Zhang, Jun; Yin, Jin-Gang; Hang, Bao-Jian; Cai, Shu; Li, Shun-Peng

    2012-01-01

    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

  20. Reinvestigation of Brevibacterium sp. Strain KY-4313 as a Source of Canthaxanthin

    PubMed Central

    Nelis, H. J.; De Leenheer, A. P.

    1989-01-01

    The hydrocarbon-utilizing Brevibacterium sp. strain KY-4313 was reevaluated for its potential to produce canthaxanthin, a carotenoid pigment of strong commercial interest. Three approaches were used to optimize the canthaxanthin yield from this organism, i.e., the preparation of mutants, the addition of supposedly carotenogenic chemicals to the growth medium, and growth promotion. Following treatment of the parent strain with N-nitrosomethylurea, a presumed mutant was isolated which showed a 32% increase in cellular canthaxanthin content. No effective carotenogenic chemicals were found in connection with hydrocarbon fermentations, in which mainly growth promotion through periodic medium renewal proved conducive to enhanced pigment production. Carotenogenesis could be stimulated in brain heart infusion broth by adding alcohols or retinol. Improved growth in this medium was generally not associated with higher canthaxanthin yields. Both superior growth and pigment levels were obtained in a newly designed medium based on fumaric acid-molasses. The maximum yields of canthaxanthin in shake flasks were (in milligrams per liter) 4.2 (brain heart infusion broth plus propanol-zinc sulfate), 3.6 (hydrocarbon medium), and 9.3 (fumaric acid-molasses), which represent a significant improvement over the originally reported optimal result (1 mg/liter). The corresponding yields of echinenone, the direct precursor of canthaxanthin, were 1.2, 1.6, and 2.3 mg/liter, respectively. Two-liter hydrocarbon batch fermentations involving medium renewal maximally produced 7.2 mg of canthaxanthin and 3.7 mg of echinenone per liter. PMID:16348027

  1. Cloning of a gene from Pseudomonas sp. strain PG2982 conferring increased glyphosate resistance.

    PubMed Central

    Fitzgibbon, J E; Braymer, H D

    1990-01-01

    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

  2. Inhibitor studies of dissimilative Fe(III) reduction by Pseudomonas sp. strain 200 ("Pseudomonas ferrireductans")

    PubMed Central

    Arnold, R G; DiChristina, T J; Hoffmann, M R

    1986-01-01

    Aerobic respiration and dissimilative iron reduction were studied in pure, batch cultures of Pseudomonas sp. strain 200 ("Pseudomonas ferrireductans"). Specific respiratory inhibitors were used to identify elements of electron transport chains involved in the reduction of molecular oxygen and Fe(III). When cells were grown at a high oxygen concentration, dissimilative iron reduction occurred via an abbreviated electron transport chain. The induction of alternative respiratory pathways resulted from growth at low oxygen tension (less than 0.01 atm [1 atm = 101.29 kPa]). Induced cells were capable of O2 utilization at moderately increased rates; dissimilative iron reduction was accelerated by a factor of 6 to 8. In cells grown at low oxygen tension, dissimilative iron reduction appeared to be uncoupled from oxidative phosphorylation. Models of induced and uninduced electron transport chains, including a mathematical treatment of chemical inhibition within the uninduced, aerobic electron transport system, are presented. In uninduced cells respiring anaerobically, electron transport was limited by ferrireductase activity. This limitation may disappear among induced cells. PMID:2428308

  3. Purification and Properties of a Xylan-Binding Endoxylanase from Alkaliphilic Bacillus sp. Strain K-1

    PubMed Central

    Ratanakhanokchai, Khanok; Kyu, Khin Lay; Tanticharoen, Morakot

    1999-01-01

    An alkaliphilic bacterium, Bacillus sp. strain K-1, produces extracellular xylanolytic enzymes such as xylanases, ?-xylosidase, arabinofuranosidase, and acetyl esterase when grown in xylan medium. One of the extracellular xylanases that is stable in an alkaline state was purified to homogeneity by affinity adsorption-desorption on insoluble xylan. The enzyme bound to insoluble xylan but not to crystalline cellulose. The molecular mass of the purified xylan-binding xylanase was estimated to be approximately 23 kDa. The enzyme was stable at alkaline pHs up to 12. The optimum temperature and optimum pH of the enzyme activity were 60°C and 5.5, respectively. Metal ions such as Fe2+, Ca2+, and Mg2+ greatly increased the xylanase activity, whereas Mn2+ strongly inhibited it. We also demonstrated that the enzyme could hydrolyze the raw lignocellulosic substances effectively. The enzymatic products of xylan hydrolysis were a series of short-chain xylooligosaccharides, indicating that the enzyme was an endoxylanase. PMID:9925602

  4. Aerobic Biodegradation of 2,4-Dinitroanisole by Nocardioides sp. Strain JS1661

    PubMed Central

    Fida, Tekle Tafese; Palamuru, Shannu; Pandey, Gunjan

    2014-01-01

    2,4-Dinitroanisole (DNAN) is an insensitive munition ingredient used in explosive formulations as a replacement for 2,4,6-trinitrotoluene (TNT). Little is known about the environmental behavior of DNAN. There are reports of microbial transformation to dead-end products, but no bacteria with complete biodegradation capability have been reported. Nocardioides sp. strain JS1661 was isolated from activated sludge based on its ability to grow on DNAN as the sole source of carbon and energy. Enzyme assays indicated that the first reaction involves hydrolytic release of methanol to form 2,4-dinitrophenol (2,4-DNP). Growth yield and enzyme assays indicated that 2,4-DNP underwent subsequent degradation by a previously established pathway involving formation of a hydride-Meisenheimer complex and release of nitrite. Identification of the genes encoding the key enzymes suggested recent evolution of the pathway by recruitment of a novel hydrolase to extend the well-characterized 2,4-DNP pathway. PMID:25281383

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

    PubMed

    Lee, K; Gibson, D T

    1996-09-01

    Purified naphthalene dioxygenase (NDO) from Pseudomonas sp. strain NCIB 9816-4 oxidized toluene to benzyl alcohol and benzaldehyde by reactions involving benzylic monooxygenation and dioxygen-dependent alcohol oxidation, respectively. Xylene and nitrotoluene isomers were also oxidized to substituted benzyl alcohol and benzaldehyde derivatives. NDO oxidized ethylbenzene sequentially through (S)-1-phenethyl alcohol (77% enantiomeric excess) and acetophenone to 2-hydroxyacetophenone. In addition, NDO also oxidized ethylbenzene through styrene to (R)-1-phenyl-1,2-ethanediol (74% enantiomeric excess) by reactions involving desaturation and dihydroxylation, respectively. Isotope experiments with 18O2, H2 18O, and D2O suggest that 1-phenethyl alcohol is oxidized to acetophenone by a minor reaction involving desaturation followed by tautomerization. The major reaction in the conversion of 1-phenethyl alcohol and benzyl alcohol to acetophenone and benzaldehyde, respectively, probably involves monohydroxylation to form a gem-diol intermediate which stereospecifically loses the incoming hydroxyl group to leave the carbonyl product. These results are compared with similar reactions catalyzed by cytochrome P-450. PMID:8795196

  6. Isolation of a Paenibacillus sp. Strain and Structural Elucidation of Its Broad-Spectrum Lipopeptide Antibiotic

    PubMed Central

    Guo, Yaoqi; Huang, En; Yuan, Chunhua; Zhang, Liwen

    2012-01-01

    This research was initiated to search for novel antimicrobial compounds produced by food or environmental microorganisms. A new bacterial strain, designated OSY-SE, which produces a unique and potent antimicrobial agent was isolated from soil. The isolate was identified as a Paenibacillus sp. through cultural, biochemical, and genetic analyses. An antimicrobial compound was extracted from Paenibacillus OSY-SE with acetonitrile and purified using liquid chromatography. After analyses by mass spectrometry (MS) and nuclear magnetic resonance (NMR), the antimicrobial compound was determined to be a cyclic lipopeptide consisting of a C15 fatty acyl (FA) chain and 13 amino acids. The deduced sequence is FA-Orn-Val-Thr-Orn-Ser-Val-Lys-Ser-Ile-Pro-Val-Lys-Ile. The carboxyl-terminal Ile is connected to Thr by ester linkage. The new compound, designated paenibacterin, showed antagonistic activities against most Gram-positive and Gram-negative bacteria tested, including Listeria monocytogenes, methicillin-resistant Staphylococcus aureus, Escherichia coli O157:H7, and Salmonella enterica serovar Typhimurium. Paenibacterin is resistant to trypsin, lipase, ?-glucosidase, and lysozyme. Its antimicrobial activity was lost after digestion by pronase and polymyxin acylase. Paenibacterin is readily soluble in water and fairly stable to exposure to heat and a wide range of pH values. The new isolate and its antimicrobial agent are being investigated for usefulness in food and medical applications. PMID:22367082

  7. Isomaltulose synthase from Klebsiella sp. strain LX3: gene cloning and characterization and engineering of thermostability.

    PubMed

    Zhang, Daohai; Li, Xianzhen; Zhang, Lian-Hui

    2002-06-01

    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 alpha-amylase domain and (beta/alpha)(8)-barrel structures, suggesting that it belongs to the alpha-amylase family. Sequence alignment indicated that the five amino acid residues of catalytic importance in alpha-amylases and glucosyltransferases (Asp(241), Glu(295), Asp(369), His(145), and His(368)) 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 degrees 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 degrees C. Replacement of selected amino acid residues by proline significantly increased the thermostability of PalI. Simultaneous replacement of Glu(498) and Arg(310) with proline resulted in an 11-fold increase in the half-life of PalI at 50 degrees C. PMID:12039719

  8. Isomaltulose Synthase from Klebsiella sp. Strain LX3: Gene Cloning and Characterization and Engineering of Thermostability

    PubMed Central

    Zhang, Daohai; Li, Xianzhen; Zhang, Lian-Hui

    2002-01-01

    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

  9. Factors influencing substitutive transformation of carbon tetrachloride by pseudomonas sp. strain KC

    SciTech Connect

    Lewis, T.A.; Crawford, R.L. [Univ. of Idaho, Moscow, ID (United States)

    1995-12-31

    Pseudomonas sp. strain KC can transform carbon tetrachloride (CT) to carbon dioxide by an as yet unknown mechanism. In addition to CO{sub 2}, a large portion of the CT carbon atoms are found as unidentified non-volatile products. In order to assess the potential usefulness of this process as a remediation technology and to assure that other toxic compounds are not produced, experiments to investigate the transformation process were undertaken. Using L-cysteine or N,N-dimethylethylenediamine (DMED), the corresponding phosgene and thiophosgene condensation products from CT-transforming cultures of KC were observed, indicating that a radical substitution pathway was operating. Using radioisotopic tracer, it was found that the addition of DMED caused a substantial decrease in CO{sub 2} production. Other experiments were undertaken to account for the fraction of CT transformation accounted for by the sulfur and oxygen substitutive pathways. Data support a radical substitution pathway for the transformation of CT to CO{sub 2} and nonvolatile products. Furthermore, data suggest that the products of CT transformation would be fully dechlorinated due to the lability of the carbon-chlorine bonds in phosgene and thiophosgene.

  10. Inhibitor studies of dissimilative Fe(III) reduction by Pseudomonas sp. strain 200 (Pseudomonas ferrireductans)

    SciTech Connect

    Arnold, R.G.; DiChristina, T.J.; Hoffman, M.R.

    1986-08-01

    Aerobic respiration and dissimilative iron reduction were studied in pure, batch cultures of Pseudomonas sp. strain 200 (Pseudomonas ferrireductans). Specific respiratory inhibitors were used to identify elements of electron transport chains involved in the reduction of molecular oxygen and Fe(III). When cells were grown at a high oxygen concentration, dissimilative iron reduction occurred via an abbreviated electron transport chain. The induction of alternative respiratory pathways resulted from growth at low oxygen tension (<0.01 atm (1 atm = 101.29 kPa)). Induced cells were capable of O/sub 2/ utilization at moderately increased rates; dissimilative iron reduction was accelerated by a factor of 6 to 8. In cells grown at low oxygen tension, dissimilative iron reduction appeared to be uncoupled from oxidative phosphorylation. Models of induced and uninduced electron transport chains, including a mathematical treatment of chemical inhibition within the uninduced, aerobic electron transport system, are presented. In uninduced cells respiring anaerobically, electron transport was limited by ferrireductase activity. This limitation may disappear among induced cells.

  11. Spirocyclic Drimanes from the Marine Fungus Stachybotrys sp. Strain MF347

    PubMed Central

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

    2014-01-01

    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

  12. Acquired thermotolerance and heat shock in the extremely thermophilic archaebacterium Sulfolobus sp. strain B12.

    PubMed Central

    Trent, J D; Osipiuk, J; Pinkau, T

    1990-01-01

    The extreme thermophile Sulfolobus sp. strain B12 exhibits an acquired thermotolerance response. Thus, survival of cells from a 70 degrees C culture at the lethal temperature of 92 degrees C was enhanced by as much as 6 orders of magnitude over a 2-h period if the culture was preheated to 88 degrees C for 60 min or longer before being exposed to the lethal temperature. In eubacteria and eucaryotes, acquired thermotolerance correlates with the induced synthesis of a dozen or so proteins known as heat shock proteins. In this Sulfolobus species, it correlates with the preferential synthesis of primarily one major protein (55 kilodaltons) and, to a much lesser extent, two minor proteins (28 and 35 kilodaltons). Since the synthesis of all other proteins was radically reduced and these proteins were apparently not degraded or exported, their relative abundance within the cell increased during the time the cells were becoming thermotolerant. They could not yet be related to known heat shock proteins. In immunoassays, they were not cross-reactive with antibodies against heat shock proteins from Escherichia coli (DnaK and GroE), which are highly conserved between eubacteria and eucaryotes. However, it appears that if acquired thermotolerance depends on the synthesis of protective proteins, then in this extremely thermophilic archaebacterium it depends primarily on one protein. Images FIG. 2 FIG. 3 FIG. 4 PMID:2106513

  13. Acquired thermotolerance and heat shock in the extremely thermophilic archaebacterium Sulfolobus sp. strain B12.

    PubMed

    Trent, J D; Osipiuk, J; Pinkau, T

    1990-03-01

    The extreme thermophile Sulfolobus sp. strain B12 exhibits an acquired thermotolerance response. Thus, survival of cells from a 70 degrees C culture at the lethal temperature of 92 degrees C was enhanced by as much as 6 orders of magnitude over a 2-h period if the culture was preheated to 88 degrees C for 60 min or longer before being exposed to the lethal temperature. In eubacteria and eucaryotes, acquired thermotolerance correlates with the induced synthesis of a dozen or so proteins known as heat shock proteins. In this Sulfolobus species, it correlates with the preferential synthesis of primarily one major protein (55 kilodaltons) and, to a much lesser extent, two minor proteins (28 and 35 kilodaltons). Since the synthesis of all other proteins was radically reduced and these proteins were apparently not degraded or exported, their relative abundance within the cell increased during the time the cells were becoming thermotolerant. They could not yet be related to known heat shock proteins. In immunoassays, they were not cross-reactive with antibodies against heat shock proteins from Escherichia coli (DnaK and GroE), which are highly conserved between eubacteria and eucaryotes. However, it appears that if acquired thermotolerance depends on the synthesis of protective proteins, then in this extremely thermophilic archaebacterium it depends primarily on one protein. PMID:2106513

  14. Purification, biochemical characterization, and genetic cloning of the phytase produced by Burkholderia sp. strain a13.

    PubMed

    Graminho, Eduardo Rezende; Takaya, Naoki; Nakamura, Akira; Hoshino, Takayuki

    2015-01-01

    A phytase-producing bacterium, Burkholderia sp. a13 (JCM 30421), was isolated from Lake Kasumigaura by enrichment cultivation using minimum medium containing phytic acid as the sole phosphorus source. The phytase production by strain a13 was induced by the presence of phytic acid and repressed by the addition of glucose. The purified enzyme had a molecular weight of 44 kDa and a phytase activity of 174 ?mol min(-1) mg(-1). The enzyme showed broad substrate specificity, but the highest activity was observed with phytic acid. The enzyme activity was strongly inhibited by Cu(2+), Zn(2+), Hg(2+), and iodoacetic acid, indicating the requirement of a thiol group for the activity. Genetic cloning reveals that the mature portion of this enzyme consists of 428 amino acids with a calculated molecular weight of 46 kDa. The amino acid sequence showed the highest similarity to the phytase produced by Hafnia alvei with 48% identity; it also contained histidine acid phosphatase (HAP) motifs (RHGXRXP and HD), indicating the classification of this enzyme in the HAP phytase family. We have successfully expressed the cloned gene in Escherichia coli from its putative initiation codon, showing that the gene actually encodes the phytase. PMID:25833676

  15. A thermostable humic acid peroxidase from Streptomyces sp. strain AH4: purification and biochemical characterization.

    PubMed

    Fodil, Djamila; Jaouadi, Bassem; Badis, Abdelmalek; Nadia, Zaraî Jaouadi; Ferradji, Fatma Zohra; Bejar, Samir; Boutoumi, Houcine

    2012-05-01

    An extracellular thermostable humic acid peroxidase (HaP3) was isolated from a Streptomyces sp. strain AH4. MALDI-TOF MS analysis showed that the purified enzyme was a monomer with a molecular mass of 60,215.18Da. The 26N-terminal residues of HaP3 displayed high homology with Streptomyces peroxidases. Optimal peroxidase activity was obtained at pH 5 and 80°C. HaP3 was stable at pH and temperature ranges of 4-8 and 60-90°C for 72 and 4h, respectively. HaP3 catalyzed the oxidation of 2,4-dichlorophenol, commercial humic acid, guiacol, and 2,6-dichlorophenol (50mM); L-3,4-dihydroxyphenylalanine (40 mM); 4-chlorophenol, 2,4,5-trichlorophenol, and 2,4,6-trichlorophenol (30 mM) in the presence of hydrogen peroxide. Sodium azide and potassium cyanide inhibited HaP3, which indicated the presence of heme components. These properties make HaP3 a potential strong candidate for future application in the elimination of natural humic acids in drinking water. PMID:22342039

  16. Characterization of a Novel Phenol Hydroxylase in Indoles Biotranformation from a Strain Arthrobacter sp. W1

    PubMed Central

    Li, Xinliang; Zhang, Xuwang; Zhou, Jiti

    2012-01-01

    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

  17. Cloning and analysis of s-triazine catabolic genes from Pseudomonas sp. strain NRRLB-12227.

    PubMed Central

    Eaton, R W; Karns, J S

    1991-01-01

    Pseudomonas sp. strain NRRLB-12227 degrades the s-triazine melamine by a six-step pathway which allows it to use melamine and pathway intermediates as nitrogen sources. With the plasmid pLG221, mutants defective in five of the six steps of the pathway were generated. Tn5-containing-EcoRI fragments from these mutants were cloned and identified by selection for Tn5-encoded kanamycin resistance in transformants. A restriction fragment from ammelide-negative mutant RE411 was used as a probe in colony hybridization experiments to identify cloned wild-type s-triazine catabolic genes encoding ammeline aminohydrolase, ammelide aminohydrolase, and cyanuric acid amidohydrolase. These genes were cloned from total cellular DNA on several similar, but not identical, HindIII fragments, as well as on a PstI fragment and a BglII fragment. Restriction mapping and Southern hybridization analyses of these cloned DNA fragments suggested that these s-triazine catabolic genes may be located on a transposable element, the ends of which are identical 2.2-kb insertion sequences. Images PMID:1846859

  18. Utilization of Ganglioside-Degrading Paenibacillus sp. Strain TS12 for Production of Glucosylceramide

    PubMed Central

    Sumida, Tomomi; Sueyoshi, Noriyuki; Ito, Makoto

    2002-01-01

    Gangliosides, sialic acid-containing glycosphingolipids, are membrane constituents of vertebrates and are known to have important roles in cellular differentiation, adhesion, and recognition. We report here the isolation of a bacterium capable of degrading gangliotetraose-series gangliosides and a new method for the production of glucosylceramide with this bacterium. GM1a ganglioside was found to be sequentially degraded by Paenibacillus sp. strain TS12, which was isolated from soil, as follows: GM1a ? asialo GM1 ? asialo GM2 ? lactosylceramide ? glucosylceramide. TS12 was found to produce a series of ganglioside-degrading enzymes, such as sialidases, ?-galactosidases, and ?-hexosaminidases. TS12 also produced ?-glucosidases, but glucosylceramide was somewhat resistant to the bacterial enzyme under the conditions used. Taking advantage of the specificity, we developed a new method for the production of glucosylceramide using TS12 as a biocatalyst. The method involves the conversion of crude bovine brain gangliosides to glucosylceramide by coculture with TS12 and purification of the product by chromatography with Wakogel C-300 HG. PMID:12406710

  19. Microbial System for Polysaccharide Depolymerization: Enzymatic Route for Xanthan Depolymerization by Bacillus sp. Strain GL1

    PubMed Central

    Nankai, Hirokazu; Hashimoto, Wataru; Miki, Hikaru; Kawai, Shigeyuki; Murata, Kousaku

    1999-01-01

    An enzymatic route for the depolymerization of a heteropolysaccharide (xanthan) in Bacillus sp. strain GL1, which was closely related to Brevibacillus thermoruber, was determined by analyzing the structures of xanthan depolymerization products. The bacterium produces extracellular xanthan lyase catalyzing the cleavage of the glycosidic bond between pyruvylated mannosyl and glucuronyl residues in xanthan side chains (W. Hashimoto et al., Appl. Environ. Microbiol. 64:3765–3768, 1998). The modified xanthan after the lyase reaction was then depolymerized by extracellular ?-d-glucanase to a tetrasaccharide, without the terminal mannosyl residue of the side chain in a pentasaccharide, a repeating unit of xanthan. The tetrasaccharide was taken into cells and converted to a trisaccharide (unsaturated glucuronyl-acetylated mannosyl-glucose) by ?-d-glucosidase. The trisaccharide was then converted to the unsaturated glucuronic acid and a disaccharide (mannosyl-glucose) by unsaturated glucuronyl hydrolase. Finally, the disaccharide was hydrolyzed to mannose and glucose by ?-d-mannosidase. This is the first complete report on xanthan depolymerization by bacteria. Novel ?-d-glucanase, one of the five enzymes involved in the depolymerization route, was purified from the culture fluid. This enzyme was a homodimer with a subunit molecular mass of 173 kDa and was most active at pH 6.0 and 45°C. The enzyme specifically acted on xanthan after treatment with xanthan lyase and released the tetrasaccharide. PMID:10347037

  20. Metabolism of T-2 toxin in Curtobacterium sp. strain 114-2.

    PubMed

    Ueno, Y; Nakayama, K; Ishii, K; Tashiro, F; Minoda, Y; Omori, T; Komagata, K

    1983-07-01

    The metabolic pathway of T-2 toxin in Curtobacterium sp. strain 114, one of the T-2 toxin-assimilating soil bacteria, was investigated by thin-layer and gas-liquid chromatographic analyses. T-2 toxin added to the basal medium as a single carbon and energy source was biotransformed into HT-2 toxin and an unknown metabolite. Infrared, mass spectrum, proton magnetic resonance, and other physico-chemical analyses identified this new metabolite as T-2 triol. T-2 toxin was first deacetylated by the bacterium into HT-2 toxin, and this metabolite was then biotransformed into T-2 triol without formation of neosolaniol and T-2 tetraol. No trichothecenes remained in the culture medium after prolonged culture. Some properties of T-2 toxin-hydrolyzing enzymes were observed with whole cells, the cell-free soluble fraction, and the culture filtrate. Besides T-2 toxin, trichothecenes such as diacetoxyscirpenol, neosolaniol, nivalenol, and fusarenon-X were also assimilated by this bacterium. PMID:6614901

  1. NADP-dependent glutamate dehydrogenase from a facultative methylotroph, Pseudomonas sp. strain AM1.

    PubMed Central

    Bellion, E; Tan, F

    1984-01-01

    The NADP-dependent glutamate dehydrogenase (EC 1.4.1.4.) elaborated by the methylotrophic bacterium Pseudomonas sp. strain AM1 when growing on succinate and ammonium chloride was studied. The enzyme, which has a pH optimum of 9.0, was purified 140-fold and shown to have Km values of 20.2 mM, 0.76 mM, 0.033 mM, and 31.6 mM for ammonia, alpha-ketoglutarate, NADPH, and glutamate, respectively. The native molecular weight was determined by polyacrylamide gel electrophoresis to be 190,000, and electrophoresis under denaturing conditions in the presence of sodium dodecyl sulfate revealed a minimum molecular weight of 50,000. The enzyme was highly specific; NADH was unable to replace NADPH in the reaction, various alpha-keto acids could not replace alpha-ketoglutarate, and neither methylamine nor hydroxylamine could substitute for ammonia. Glutamate dehydrogenase was synthesized by the bacteria only when ammonia was its nitrogen source and was repressed if methylamine or nitrate were provided as sources of nitrogen instead of ammonia. PMID:6693348

  2. Trehalose promotes Rhodococcus sp. strain YYL colonization in activated sludge under tetrahydrofuran (THF) stress

    PubMed Central

    He, Zhixing; Zhang, Kai; Wang, Haixia; Lv, Zhenmei

    2015-01-01

    Few studies have focused on the role of compatible solutes in changing the microbial community structure in bioaugmentation systems. In this study, we investigated the influence of trehalose as a biostimulant on the microbial community in tetrahydrofuran (THF)-treated wastewater bioaugmentation systems with Rhodococcus sp. YYL. Functional gene profile changes were used to study the variation in the microbial community. Soluble di-iron monooxygenases (SDIMO), particularly group-5 SDIMOs (i.e., tetrahydrofuran and propane monooxygenases), play a significant role in the initiation of the ring cleavage of tetrahydrofuran. Group-5 SDIMOs genes are enriched upon trehalose addition, and exogenous tetrahydrofuran monooxygenase (thmA) genes can successfully colonize bioaugmentation systems. Cytochrome P450 monooxygenases (P450s) have a significant role in catalyzing the region- and stereospecific oxidation of non-activated hydrocarbons, and THF was reported to inhibit P450s in the environment. The CYP153 family was chosen as a representative P450 to study the inhibitory effects of THF. The results demonstrated that CYP153 family genes exhibited significant changes upon THF treatment and that trehalose helped maintain a rich diversity and high abundance of CYP153 family genes. Biostimulation with trehalose could alleviate the negative effects of THF stress on microbial diversity in bioaugmentation systems. Our results indicated that trehalose as a compatible solute plays a significant role for environmental strains under extreme conditions. PMID:26029182

  3. Metabolism of T-2 toxin in Curtobacterium sp. strain 114-2.

    PubMed Central

    Ueno, Y; Nakayama, K; Ishii, K; Tashiro, F; Minoda, Y; Omori, T; Komagata, K

    1983-01-01

    The metabolic pathway of T-2 toxin in Curtobacterium sp. strain 114, one of the T-2 toxin-assimilating soil bacteria, was investigated by thin-layer and gas-liquid chromatographic analyses. T-2 toxin added to the basal medium as a single carbon and energy source was biotransformed into HT-2 toxin and an unknown metabolite. Infrared, mass spectrum, proton magnetic resonance, and other physico-chemical analyses identified this new metabolite as T-2 triol. T-2 toxin was first deacetylated by the bacterium into HT-2 toxin, and this metabolite was then biotransformed into T-2 triol without formation of neosolaniol and T-2 tetraol. No trichothecenes remained in the culture medium after prolonged culture. Some properties of T-2 toxin-hydrolyzing enzymes were observed with whole cells, the cell-free soluble fraction, and the culture filtrate. Besides T-2 toxin, trichothecenes such as diacetoxyscirpenol, neosolaniol, nivalenol, and fusarenon-X were also assimilated by this bacterium. PMID:6614901

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

    PubMed Central

    Lee, K; Gibson, D T

    1996-01-01

    Purified naphthalene dioxygenase (NDO) from Pseudomonas sp. strain NCIB 9816-4 oxidized toluene to benzyl alcohol and benzaldehyde by reactions involving benzylic monooxygenation and dioxygen-dependent alcohol oxidation, respectively. Xylene and nitrotoluene isomers were also oxidized to substituted benzyl alcohol and benzaldehyde derivatives. NDO oxidized ethylbenzene sequentially through (S)-1-phenethyl alcohol (77% enantiomeric excess) and acetophenone to 2-hydroxyacetophenone. In addition, NDO also oxidized ethylbenzene through styrene to (R)-1-phenyl-1,2-ethanediol (74% enantiomeric excess) by reactions involving desaturation and dihydroxylation, respectively. Isotope experiments with 18O2, H2 18O, and D2O suggest that 1-phenethyl alcohol is oxidized to acetophenone by a minor reaction involving desaturation followed by tautomerization. The major reaction in the conversion of 1-phenethyl alcohol and benzyl alcohol to acetophenone and benzaldehyde, respectively, probably involves monohydroxylation to form a gem-diol intermediate which stereospecifically loses the incoming hydroxyl group to leave the carbonyl product. These results are compared with similar reactions catalyzed by cytochrome P-450. PMID:8795196

  5. Characterization of a sodium dodecyl sulphate-degrading Pseudomonas sp. strain DRY15 from Antarctic soil.

    PubMed

    Halmi, M I E; Hussin, W S W; Aqlima, A; Syed, M A; Ruberto, L; MacCormack, W P; Shukor, M Y

    2013-11-01

    A bacterium capable of biodegrading surfactant sodium dodecyl sulphate (SDS) was isolated from Antarctic soil. The isolate was tentatively identified as Pseudomonas sp. strain DRY15 based on carbon utilization profiles using Biolog GN plates and partial 16S rDNA molecular phylogeny. Growth characteristic studies showed that the bacterium grew optimally at 10 degrees C, 7.25 pH, 1 g l(-1) SDS as a sole carbon source and 2 g l(-1) ammonium sulphate as nitrogen source. Growth was completely inhibited at 5 g l(-1) SDS. At a tolerable initial concentration of 2 g l(-1), approximately 90% of SDS was degraded after an incubation period of eight days. The best growth kinetic model to fit experimental data was the Haldane model of substrate inhibition with a correlation coefficient value of 0.97. The maximum growth rate was 0.372 hr(-1) while the saturation constant or half velocity constant (Ks) and inhibition constant (Ki), were 0.094% and 11.212 % SDS, respectively. Other detergent tested as carbon sources at 1 g l(-1) was Tergitol NP9, Tergitol 15S9, Witconol 2301 (methyl oleate), sodium dodecylbenzene sulfonate (SDBS), benzethonium chloride, and benzalkonium chloride showed Tergitol NP9, Tergitol 15S9, Witconol 2301 and the anionic SDBS supported growth with the highest growth exhibited by SDBS. PMID:24555340

  6. Low-Temperature Lipase from Psychrotrophic Pseudomonas sp. Strain KB700A

    PubMed Central

    Rashid, Naeem; Shimada, Yuji; Ezaki, Satoshi; Atomi, Haruyuki; Imanaka, Tadayuki

    2001-01-01

    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

  7. Construction of carotenoid biosynthetic pathways through chromosomal integration in methane-utilizing bacterium Methylomonas sp. strain 16a.

    PubMed

    Ye, Rick W; Kelly, Kristen

    2012-01-01

    Methylomonas sp. strain 16a is an obligate methanotrophic bacterium that uses methane or methanol as the sole energy and carbon source. In order to engineer a stable strain to produce carotenoids, integration of genes or gene clusters in various nonessential locations in the chromosome is used. Construction of a canthaxanthin-producing strain involves the integration of canthaxanthin biosynthetic genes including the crtW gene for the ?-carotenoid ketolase. Addition of the crtZ gene that encodes the ?-carotenoid hydroxylase in this strain leads to the production of astaxanthin. Further increase in titer and yield for astaxanthin is obtained by integration of another set of astaxanthin biosynthetic gene cluster in a separate location of the chromosome. PMID:22623303

  8. Cloning and expression of Vitreoscilla hemoglobin gene in Burkholderia sp. strain DNT for enhancement of 2,4-dinitrotoluene degradation

    SciTech Connect

    Patel, S.M.; Stark, B.C.; Hwang, K.W.; Dikshit, K.L.; Webster, D.A.

    2000-02-01

    The gene (vgb) encoding the hemoglobin (VHb) of Vitreoscilla sp. was cloned into a broad host range vector and stably transformed into Burkholderia (formerly Pseudomonas) sp. strain DNT, which is able to degrade and metabolize 1,4-dinitrotoluene (DNT). Vgb was stably maintained and expressed in functional form in this recombinant strain (YV1). When growth of YV1, in both tryptic soy broth and minimal salts broth containing DNT and yeast extract, was compared with that of the untransformed strain, YV1 grew significantly better on a cell mass basis (A{sub 600}) and reached slightly higher maximum viable cell numbers. YV1 also had roughly twice the respiration as strain DNT on a cell mass basis, and in DNT-containing medium, YV1 degraded DNT faster than the untransformed strain. YV1 cells pregrown in medium containing DNT plus succinate showed the fastest degradation: 100% of the initial 200 ppm DNT was removed from the medium within 3 days.

  9. Draft Genome Sequence of a Sulfide-Oxidizing, Autotrophic Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi).

    PubMed

    Thiel, Vera; Hamilton, Trinity L; Tomsho, Lynn P; Burhans, Richard; Gay, Scott E; Schuster, Stephan C; Ward, David M; Bryant, Donald A

    2014-01-01

    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

  10. The Actinorhizal Root-Nodule Symbiont Frankia Sp. Strain CpI1 Has Two Glutamine Synthetases

    Microsoft Academic Search

    Janet Edmands; Nancy A. Noridge; David R. Benson

    1987-01-01

    Frankia sp. strain CpI1 has two glutamine synthetases. Glutamine synthetase I (GSI) is present during growth on ammonium or N2 and is similar to classical prokaryotic glutamine synthetases, Gel-filtration chromatography gave a molecular weight estimate of about 680,000 for the GSI holoenzyme, and denaturing polyacrylamide gel electrophoresis yielded a subunit molecular weight of about 59,000, indicating that GSI is most

  11. Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-Respiring Bacterium Isolated from Japanese Paddy Soil

    PubMed Central

    Ehara, Ayaka; Suzuki, Haruo

    2015-01-01

    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

  12. Identification and molecular characterization of the eugenol hydroxylase genes (ehyA\\/ehyB) of Pseudomonas sp. strain HR199

    Microsoft Academic Search

    Horst Priefert; Jörg Overhage; Alexander Steinbüchel

    1999-01-01

    The gene loci ehyA and ehyB, which are involved in the bioconversion of eugenol to coniferyl alcohol by Pseudomonas sp. strain HR199 (DSM 7063), were identified as the structural genes of a eugenol hydroxylase that represents an enzyme of\\u000a the flavocytochrome c class. These genes were localized downstream of the eugenol catabolism genes vanA and vanB, encoding vanillate-O-demethylase, on an

  13. On the Origins of Cyanuric Acid Hydrolase: Purification, Substrates, and Prevalence of AtzD from Pseudomonas sp. Strain ADP

    PubMed Central

    Fruchey, Isaac; Shapir, Nir; Sadowsky, Michael J.; Wackett, Lawrence P.

    2003-01-01

    Cyanuric acid hydrolase (AtzD) from Pseudomonas sp. strain ADP was purified to homogeneity. Of 22 cyclic amides and triazine compounds tested, only cyanuric acid and N-methylisocyanuric acid were substrates. Other cyclic amidases were found not to hydrolyze cyanuric acid. Ten bacteria that use cyanuric acid as a sole nitrogen source for growth were found to contain either atzD or trzD, but not both genes. PMID:12788776

  14. Circadian Clocks of Synechocystis sp. Strain PCC 6803, Thermosynechococcus elongatus, Prochlorococcus spp., Trichodesmium spp. and Other Species

    Microsoft Academic Search

    Setsuyuki Aoki; Kiyoshi Onai

    The cyanobacterium Synechococcus elongatus PCC 7942 has been established as the model system for studying the molecular\\u000a mechanisms of the cir-cadian clock in cyanobacteria. This chapter mainly focuses on other cyanobacteria, such as SynechocystisL sp. strain PCC 6803, Thermosynechococcus elongatus and the genera Trichodesmium and Prochlorococcus. Here, we describe the research background, current status, possible problems and perspectives for studying

  15. Deletion analysis of the C-terminal region of the a-amylase of Bacillus sp. strain TS23

    Microsoft Academic Search

    Huei-Fen Lo; Long-Liu Lin; Wen-Ying Chiang; Meng-Chun Chie; Wen-Hwei Hsu; Chen-Tien Chang

    2002-01-01

    The !-amylase from Bacillus sp. strain TS-23 is a secreted starch hydrolase with a domain organization similar to that of other microbial !-amylases and an additional functionally unknown domain (amino acids 517-613) in the C-terminal region. By sequence comparison, we found that this latter domain contained a sequence motif typical for raw-starch binding. To investigate the functional role of the

  16. X-ray Crystal Structure of Benzoate 1,2Dioxygenase Reductase from Acinetobacter sp. Strain ADP1

    Microsoft Academic Search

    Andreas Karlsson; Zanna M. Beharry; D. Matthew Eby; Eric D. Coulter; Ellen L. Neidle; Donald M. Kurtz Jr; Hans Eklund; S. Ramaswamy

    2002-01-01

    One of the major processes for aerobic biodegradation of aromatic compounds is initiated by Rieske dioxygenases. Benzoate dioxygenase contains a reductase component, BenC, that is responsible for the two-electron transfer from NADH via FAD and an iron–sulfur cluster to the terminal oxygenase component. Here, we present the structure of BenC from Acinetobacter sp. strain ADP1 at 1.5Å resolution. BenC contains

  17. Multiple Operons Connected with Catabolism of Aromatic Compounds in Acinetobacter sp. Strain ADP1 are under Carbon Catabolite Repression

    Microsoft Academic Search

    Sureyya Dal; Iris Steiner; Ulrike Gerischer

    Repression of enzymes contributing to degrada- tion of aromatic compounds via the b-ketoadipate pathway in the presence of additional carbon sources (carbon catabolite repression) in the bacterium Acinetobacter sp. strain ADP1 is de- scribed. The phenomenon was investigated on the level of specific activity of protocatechuate 3,4- dioxygenase and p-hydroxybenzoate hydroxylase participating in catabolism of protocatechuate and p-hydroxybenzoate. Strong repression

  18. Transcription of ppk from Acinetobacter sp. Strain ADP1, Encoding a Putative Polyphosphate Kinase, Is Induced by Phosphate Starvation

    Microsoft Academic Search

    WALTER GEIßDORFER; ANDREAS RATAJCZAK; WOLFGANG HILLEN

    1998-01-01

    Polyphosphate kinase (Ppk) catalyzes the formation of polyphosphate from ATP. We cloned the ppk gene (2,073 bp) from Acinetobacter sp. strain ADP1; this gene encodes a putative polypeptide of 78.6 kDa with extensive homology to polyphosphate kinase from Escherichia coli and other bacteria. Chromosomal disruption of ppk by inserting a transcriptionally fused lacZ does not affect growth under conditions of

  19. Toxicity Caused by Hydroxycinnamoyl-Coenzyme A Thioester Accumulation in Mutants of Acinetobacter sp. Strain ADP1

    Microsoft Academic Search

    Donna Parke; L. Nicholas Ornston

    2004-01-01

    Hydroxycinnamates, aromatic compounds that play diverse roles in plants, are dissimilated by enzymes encoded by the hca genes in the nutritionally versatile, naturally transformable bacterium Acinetobacter sp. strain ADP1. A key step in the hca-encoded pathway is activation of the natural substrates caffeate, p-coumarate, and ferulate by an acyl:coenzyme A (acyl:CoA) ligase encoded by hcaC. As described in this paper,

  20. Isolation of a gene (pbsC) required for siderophore biosynthesis in fluorescent Pseudomonas sp. strain M114

    Microsoft Academic Search

    Claire Adams; David N. Dowling; Dan J. O'Sullivan; Fergal O'Gara

    1994-01-01

    An iron-regulated gene, pbsC, required for siderophore production in fluorescent Pseudomonas sp. strain M114 has been identified. A kanamycin-resistance cassette was inserted at specific restriction sites within a 7 kb genomic fragment of M114 DNA and by marker exchange two siderophore-negative mutants, designated M1 and M2, were isolated. The nucleotide sequence of approximately 4 kb of the region flanking the

  1. Cloning and Nucleotide Sequences of Carbazole Degradation Genes from Marine Bacterium Neptuniibacter sp. Strain CAR-SF

    Microsoft Academic Search

    Hiroshi Nagashima; Azham Bin Zulkharnain; Rintaro Maeda; Hiroyuki Fuse; Kenichi Iwata; Toshio Omori

    2010-01-01

    The marine bacterium Neptuniibacter sp. strain CAR-SF utilizes carbazole as its sole carbon and nitrogen sources. Two sets of clustered genes related to carbazole\\u000a degradation, the upper and lower pathways, were obtained. The marine bacterium genes responsible for the upper carbazole degradation\\u000a pathway, carAa, carBa, carBb, and carC, encode the terminal oxygenase component of carbazole 1,9a-dioxygenase, the small and large

  2. Thermostable Chitosanase from Bacillus sp. Strain CK4: Cloning and Expression of the Gene and Characterization of the Enzyme

    PubMed Central

    Yoon, Ho-Geun; Kim, Hee-Yun; Lim, Young-Hee; Kim, Hye-Kyung; Shin, Dong-Hoon; Hong, Bum-Shik; Cho, Hong-Yon

    2000-01-01

    A thermostable chitosanase gene from the environmental isolate Bacillus sp. strain CK4, which was identified on the basis of phylogenetic analysis of the 16S rRNA gene sequence and phenotypic analysis, was cloned, and its complete DNA sequence was determined. The thermostable chitosanase gene was composed of an 822-bp open reading frame which encodes a protein of 242 amino acids and a signal peptide corresponding to a 30-kDa enzyme. The deduced amino acid sequence of the chitosanase from Bacillus sp. strain CK4 exhibits 76.6, 15.3, and 14.2% similarities to those from Bacillus subtilis, Bacillus ehemensis, and Bacillus circulans, respectively. C-terminal homology analysis shows that Bacillus sp. strain CK4 belongs to cluster III with B. subtilis. The gene was similar in size to that of the mesophile B. subtilis but showed a higher preference for codons ending in G or C. The enzyme contains 2 additional cysteine residues at positions 49 and 211. The recombinant chitosanase has been purified to homogeneity by using only two steps with column chromatography. The half-life of the enzyme was 90 min at 80°C, which indicates its usefulness for industrial applications. The enzyme had a useful reactivity and a high specific activity for producing functional oligosaccharides as well, with trimers through hexamers as the major products. PMID:10966383

  3. Monitoring and control of pseudomonas sp. strain KC for in-situ bioaugmentation of carbon tetrachloride contaminated sites

    SciTech Connect

    Criddle, C.S.; Dybas, M.J.; Tatara, G.M. [Michigan State Univ., East Lansing, MI (United States)] [and others

    1995-10-01

    Pseudomonas sp. strain KC converts carbon tetrachloride (CT) to carbon dioxide, formate, and non-volatile product(s) without the production of chloroform under denitrifying conditions. Most other organisms that transform CT under such conditions do so slowly and/or produce chloroform, making strain KC an attractive candidate for bioaugmentation applications. For strain KC, the mechanism of CT transformation involves secretion of a low molecular weight factor under iron-limiting conditions. The secreted factor fortuitously transforms CT and is activated for transformation by live whole cells. To determine whether the capabilities of strain KC can be applied for in-situ remediation of CT contamination, the Michigan Department of Natural Resources is supporting a field experiment in a CT-contaminated aquifer at Schoolcraft, MI. The present report describes laboratory work funded by the Great Lakes and Mid-Atlantic Hazardous Substance Research Center in support of the field project. These laboratory efforts have focused on: (1) isolation and identification of the secreted factor, (2) development and testing of a laboratory-scale model aquifer and numerical simulator to describe establishment and maintenance of a CT-transforming zone, (3) development and testing of a gene probe for detection and monitoring of strain KC, (4) identification of characteristic biochemical markers for strain KC, and (5) identification of key transport and retention mechanisms for strain KC.

  4. Novel Tripartite Aromatic Acid Transporter Essential for Terephthalate Uptake in Comamonas sp. Strain E6

    PubMed Central

    Hosaka, Masaru; Kamimura, Naofumi; Toribami, Shotaro; Mori, Kosuke; Kasai, Daisuke; Fukuda, Masao

    2013-01-01

    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

  5. Localization and Characterization of the Carbon Tetrachloride Transformation Activity of Pseudomonas sp. Strain KC

    PubMed Central

    Dybas, M. J.; Tatara, G. M.; Criddle, C. S.

    1995-01-01

    Previous research has established that Pseudomonas sp. strain KC rapidly transforms carbon tetrachloride (CT) to carbon dioxide (45 to 55%), a nonvolatile fraction (45 to 55%), and a cell-associated fraction ((equiv)5%) under denitrifying, iron-limited conditions. The present study provides additional characterization of the nonvolatile fraction, demonstrates that electron transfer plays a role in the transformation, and establishes the importance of both extracellular and intracellular factors. Experiments with (sup14)C-labeled CT indicate that more than one nonvolatile product is produced during CT transformation by strain KC. One of these products, accounting for about 20% of the [(sup14)C]CT transformed, was identified as formate on the basis of its elution time from an ion-exchange column, its boiling point, and its conversion to (sup14)CO(inf2) when incubated with formate dehydrogenase. Production of formate requires transfer of two electrons to the CT molecule. The role of electron transfer was also supported by experiments demonstrating that stationary-phase cells that do not transform CT can be stimulated to transform CT when supplemented with acetate (electron donor), nitrate (electron acceptor), or a protonophore (carbonyl cyanide m-chlorophenylhydrazone). The location of transformation activity was also evaluated. By themselves, washed cells did not transform CT to a significant degree. Occasionally, CT transformation was observed by cell-free culture supernatant, but this activity was not reliable. Rapid and reliable CT transformation was only obtained when washed whole cells were reconstituted with culture supernatant, indicating that both extracellular and intracellular factors are normally required for CT transformation. Fractionation of culture supernatant by ultrafiltration established that the extracellular factor or factors are small, with an apparent molecular mass of less than 500 Da. The extracellular factor or factors were stable after lyophilization to powder and were extractable with acetone. Addition of micromolar levels of iron inhibited CT transformation in whole cultures, but the level of iron needed to inhibit CT transformation was over 100-fold higher for washed cells reconstituted with a 10,000-Da supernatant filtrate. Thus, the inhibitory effects of iron are exacerbated by a supernatant factor or factors with a molecular mass greater than 10,000 Da. PMID:16534941

  6. FORMALDEHYDE GAS INACTIVATION OF BACILLUS ANTHRACIS, BACILLUS SUBTILIS AND GEOBACILLUS STEAROTHERMOPHILUS SPORES ON INDOOR SURFACE MATERIALS.

    EPA Science Inventory

    Research evaluated the decontamination of Bacillus anthracis, Bacillus subtilis, and Geobacillus stearothermophilus spores on indoor surface material using formaldehyde gas. Spores were dried on seven types of indoor surfaces and exposed to 1100 ppm formaldehyde gas for 10 hr. Fo...

  7. AmyM, a Novel Maltohexaose-Forming ?-Amylase from Corallococcus sp. strain EGB.

    PubMed

    Li, Zhoukun; Wu, Jiale; Zhang, Biying; Wang, Fei; Ye, Xianfeng; Huang, Yan; Huang, Qiang; Cui, Zhongli

    2015-03-01

    A novel ?-amylase, AmyM, was purified from the culture supernatant of Corallococcus sp. strain EGB. AmyM is a maltohexaose-forming exoamylase with an apparent molecular mass of 43 kDa. Based on the results of matrix-assisted laser desorption ionization-time of flight mass spectrometry and peptide mass fingerprinting of AmyM and by comparison to the genome sequence of Corallococcus coralloides DSM 2259, the AmyM gene was identified and cloned into Escherichia coli. amyM encodes a secretory amylase with a predicted signal peptide of 23 amino acid residues, which showed no significant identity with known and functionally verified amylases. amyM was expressed in E. coli BL21(DE3) cells with a hexahistidine tag. The signal peptide efficiently induced the secretion of mature AmyM in E. coli. Recombinant AmyM (rAmyM) was purified by Ni-nitrilotriacetic acid (NTA) affinity chromatography, with a specific activity of up to 14,000 U/mg. rAmyM was optimally active at 50°C in Tris-HCl buffer (50 mM; pH 7.0) and stable at temperatures of <50°C. rAmyM was stable over a wide range of pH values (from pH 5.0 to 10.0) and highly tolerant to high concentrations of salts, detergents, and various organic solvents. Its activity toward starch was independent of calcium ions. The Km and Vmax of recombinant AmyM for soluble starch were 6.61 mg ml(-1) and 44,301.5 ?mol min(-1) mg(-1), respectively. End product analysis showed that maltohexaose accounted for 59.4% of the maltooligosaccharides produced. These characteristics indicate that AmyM has great potential in industrial applications. PMID:25576603

  8. Maleylacetate reductase of Pseudomonas sp. strain B13: specificity of substrate conversion and halide elimination.

    PubMed Central

    Kaschabek, S R; Reineke, W

    1995-01-01

    Maleylacetate reductase (EC 1.3.1.32) plays a major role in the degradation of chloroaromatic compounds by channelling maleylacetate and some chlorinated derivatives into the 3-oxoadipate pathway. Several substituted maleylacetates were prepared in situ by alkaline or enzymatic hydrolysis of dienelactones as the precursor. The conversion of these methyl-, chloro-, fluoro-, and bromo-substituted maleylacetates by malelacetate reductase from 3-chlorobenzoate-grown cells of Pseudomonas sp. strain B13 was studied. Two moles of NADH per mole of substrate was consumed for the conversion of maleylacetates which contain a halogen substituent in the 2 position. In contrast, only 1 mol of NADH was necessary to convert 1 mol of substrates without a halogen substituent in the 2 position. The conversion of 2-fluoro-, 2-chloro-, 2,3-dichloro-, 2,5-dichloro-, 2,3,5-trichloro-, 2-bromo-, 2,3-dibromo-, 2,5-dibromo-, 2-bromo-5-chloro-, 2-chloro-3-methyl-, and 2-chloro-5-methylmaleylacetate was accompanied by the elimination of halide from the 2 position and the temporary occurrence of the corresponding dehalogenated maleylacetate as an intermediate consuming the second mole equivalent of NADH. The properties of the halogen substituents influenced the affinity to the enzyme in the following manner. Km values increased with increasing van der Waals radii and with decreasing electronegativity of the halogen substituents (i.e., low steric hindrance and high electronegativity positively influenced the binding).The Km values obtained with 2-methyl-,3-methyl-, and 5-methylmaleylacetate showed that a methyl substituent negatively affected the affinity in the following order: 2 position >/ = 3 position >> 5 position. A reaction mechanism explaining the exclusive elimination of halogen substituents from the 2 position is proposed. PMID:7814320

  9. Purification, Characterization, and Substrate Specificities of Multiple Xylanases from Streptomyces sp. Strain B-12-2

    PubMed Central

    Elegir, Graziano; Szakács, George; Jeffries, Thomas W.

    1994-01-01

    The endoxylanase complex from Streptomyces sp. strain B-12-2 was purified and characterized. The organism forms five distinct xylanases in the absence of significant cellulase activity when grown on oat spelt xylan. This is the largest number of endoxylanases yet reported for a streptomycete. On the basis of their physiochemical characteristics, they can be divided into two groups: the first group (xyl 1a and xyl 1b) consists of low-molecular-mass (26.4 and 23.8 kDa, respectively) neutral- to high-pI (6.5 and 8.3, respectively) endoxylanases. Group 1 endoxylanases are unable to hydrolyze aryl-?-d-cellobioside, have low levels of activity against xylotetraose (X4) and limited activity against xylopentaose, produce little or no xylose, and form products having a higher degree of polymerization with complex substrates. These enzymes apparently carry out transglycosylation. The second group (xyl 2, xyl 3, and xyl 4) consists of high-molecular-mass (36.2, 36.2, and 40.5 kDa, respectively), low-pI (5.4, 5.0, and 4.8, respectively) xylanases. Group 2 endoxylanases are able to hydrolyze aryl-?-d-cellobioside, show higher levels of activity against X4, and hydrolyze xylopentaose completely with the formation of xylobiose and xylotriose plus limited amounts of X4 and xylose. The enzymes display intergroup synergism when acting on kraft pulp. Despite intragroup similarities, each enzyme exhibited a unique action pattern and physiochemical characteristic. xyl 2 was highly glycosylated, and xyl 1b (but no other enzyme) was completely inhibited by p-hydroxymercuribenzoate. Images PMID:16349337

  10. Two Novel Phycoerythrin-Associated Linker Proteins in the Marine Cyanobacterium Synechococcus sp. Strain WH8102

    PubMed Central

    Six, Christophe; Thomas, Jean-Claude; Thion, Laurent; Lemoine, Yves; Zal, Frank; Partensky, Frédéric

    2005-01-01

    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

  11. Characterization and Evolution of Anthranilate 1,2-Dioxygenase from Acinetobacter sp. Strain ADP1

    PubMed Central

    Eby, D. Matthew; Beharry, Zanna M.; Coulter, Eric D.; Kurtz, Donald M.; Neidle, Ellen L.

    2001-01-01

    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

  12. 3,4-Dihydroxyxanthone dioxygenase from Arthrobacter sp. strain GFB100.

    PubMed

    Chen, C M; Tomasek, P H

    1991-08-01

    Bacterial extradiol ring-fission dioxygenases play a critical role in the transformation of multiring aromatic compounds to more readily biodegradable aromatic or aliphatic intermediates. Arthrobacter sp. strain GFB100 utilizes an extradiol meta-fission dioxygenase, 3,4-dihydroxyxanthone dioxygenase (DHXD), in the catabolism of the three-ring oxygen heterocyclic compound xanthone. In this paper, we show that DHXD is a cytosolic enzyme, induced by growth on xanthone and maximally expressed during the stationary phase of growth. In addition, we characterize the DHXD activity in terms of its basic enzymological properties. 1,10-Phenanthroline and H2O2 treatments eliminated DHXD activity, indicating that the enzyme required Fe2+ ions for activity. Other divalent cations were either inhibitory or had no effect on activity. DHXD had a temperature optimum of 30 degrees C and a pH optimum of 7.0. DHXD followed typical saturation kinetics and had an apparent Km of 10 microM for 3,4-dihydroxyxanthone. The dye celestine blue served as a noncompetitive DHXD inhibitor (Ki, 5 microM). Several other structural analogs served neither as substrates nor inhibitors. DHXD was thermally labile at temperatures above 40 degrees C. The half-life for thermal DHXD inactivation was 5 min at 40 degrees C. DHXD activity was completely stable through one freeze-thaw cycle, and about 80% of the DHXD activity remained after 2 days of incubation at 0 degree C. The apparent tight binding of the Fe2+ cofactor to DHXD may be a factor contributing to the stability of this extradiol dioxygenase when it is stored. PMID:1768091

  13. Heterologous Expression and Characterization of the Manganese-Oxidizing Protein from Erythrobacter sp. Strain SD21

    PubMed Central

    Nakama, Katherine; Medina, Michael; Lien, Ahn; Ruggieri, Jordan; Collins, Krystle

    2014-01-01

    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

  14. Initiation and ontogeny of vesicles in cultured Frankia sp. strain HFPArI3.

    PubMed Central

    Fontaine, M S; Lancelle, S A; Torrey, J G

    1984-01-01

    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

  15. Transcriptomic and Proteomic Profiling of Anabaena sp. Strain 90 under Inorganic Phosphorus Stress.

    PubMed

    Teikari, Jonna; Österholm, Julia; Kopf, Matthias; Battchikova, Natalia; Wahlsten, Matti; Aro, Eva-Mari; Hess, Wolfgang R; Sivonen, Kaarina

    2015-08-01

    Inorganic phosphorus (Pi) is one of the main growth-limiting factors of diazotrophic cyanobacteria. Due to human activity, the availability of Pi has increased in water bodies, resulting in eutrophication and the formation of massive cyanobacterial blooms. In this study, we examined the molecular responses of the cyanobacterium Anabaena sp. strain 90 to phosphorus deprivation, aiming at the identification of candidate genes to monitor the Pi status in cyanobacteria. Furthermore, this study increased the basic understanding of how phosphorus affects diazotrophic and bloom-forming cyanobacteria as a major growth-limiting factor. Based on RNA sequencing data, we identified 246 differentially expressed genes after phosphorus starvation and 823 differentially expressed genes after prolonged Pi limitation, most of them related to central metabolism and cellular growth. The transcripts of the genes related to phosphorus transport and assimilation (pho regulon) were most upregulated during phosphorus depletion. One of the most increased transcripts encodes a giant protein of 1,869 amino acid residues, which contains, among others, a phytase-like domain. Our findings predict its crucial role in phosphorus starvation, but future studies are still needed. Using two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we found 43 proteins that were differentially expressed after prolonged phosphorus stress. However, correlation analysis unraveled an association only to some extent between the transcriptomic and proteomic abundances. Based on the present results, we suggest that the method used for monitoring the Pi status in cyanobacterial bloom should contain wider combinations of pho regulon genes (e.g., PstABCS transport systems) in addition to the commonly used alkaline phosphatase gene alone. PMID:26025890

  16. Molecular Characterization of a Novel Peroxidase from the Cyanobacterium Anabaena sp. Strain PCC 7120 ?

    PubMed Central

    Ogola, Henry Joseph Oduor; Kamiike, Takaaki; Hashimoto, Naoya; Ashida, Hiroyuki; Ishikawa, Takahiro; Shibata, Hitoshi; Sawa, Yoshihiro

    2009-01-01

    The open reading frame alr1585 of Anabaena sp. strain PCC 7120 encodes a heme-dependent peroxidase (Anabaena peroxidase [AnaPX]) belonging to the novel DyP-type peroxidase family (EC 1.11.1.X). We cloned and heterologously expressed the active form of the enzyme in Escherichia coli. The purified enzyme was a 53-kDa tetrameric protein with a pI of 3.68, a low pH optima (pH 4.0), and an optimum reaction temperature of 35°C. Biochemical characterization revealed an iron protoporphyrin-containing heme peroxidase with a broad specificity for aromatic substrates such as guaiacol, 4-aminoantipyrine and pyrogallol. The enzyme efficiently catalyzed the decolorization of anthraquinone dyes like Reactive Blue 5, Reactive Blue 4, Reactive Blue 114, Reactive Blue 119, and Acid Blue 45 with decolorization rates of 262, 167, 491, 401, and 256 ?M·min?1, respectively. The apparent Km and kcat/Km values for Reactive Blue 5 were 3.6 ?M and 1.2 × 107 M?1 s?1, respectively, while the apparent Km and kcat/Km values for H2O2 were 5.8 ?M and 6.6 × 106 M?1 s?1, respectively. In contrast, the decolorization activity of AnaPX toward azo dyes was relatively low but was significantly enhanced 2- to ?50-fold in the presence of the natural redox mediator syringaldehyde. The specificity and catalytic efficiency for hydrogen donors and synthetic dyes show the potential application of AnaPX as a useful alternative of horseradish peroxidase or fungal DyPs. To our knowledge, this study represents the only extensive report in which a bacterial DyP has been tested in the biotransformation of synthetic dyes. PMID:19801472

  17. Characterization and evolution of anthranilate 1,2-dioxygenase from Acinetobacter sp. strain ADP1.

    PubMed

    Eby, D M; Beharry, Z M; Coulter, E D; Kurtz, D M; Neidle, E L

    2001-01-01

    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 O(2) and consumption of one NADH. The terminal oxygenase component formed an alpha(3)beta(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 O(2) consumption. Anthranilate conversion to catechol was stoichiometrically coupled to NADH oxidation and O(2) 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 degrees C) or nonpermissive (39 degrees 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 alpha and beta 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

  18. Draft Genome Sequence of Psychrotrophic Acinetobacter sp. Strain MN12 (MTCC 10786), Which Produces a Low-Temperature-Active and Alkaline-Stable Peptidase

    PubMed Central

    Swarnkar, Mohit Kumar; Salwan, Richa

    2014-01-01

    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

  19. Biotransformation of eugenol to vanillin by a mutant of Pseudomonas sp. strain HR199 constructed by disruption of the vanillin dehydrogenase ( vdh ) gene

    Microsoft Academic Search

    J. Overhage; H. Priefert; J. Rabenhorst; A. Steinbüchel

    1999-01-01

    The catabolism of eugenol in Pseudomonas sp. strain HR199 (DSM7063) proceeds via coniferyl alcohol, coniferyl aldehyde, ferulic acid, vanillin, vanillate and protocatechuate,\\u000a which is further degraded by the ortho-cleavage pathway. The vanillin dehydrogenase of Pseudomonas sp. strain HR199, which catalyses the NAD+-dependent oxidation of vanillin to vanillate, was inactivated by the insertion of omega elements into the vdh gene, which

  20. Cold-adapted and rhizosphere-competent strain of Rahnella sp. with broad-spectrum plant growth-promotion potential.

    PubMed

    Vyas, Pratibha; Joshi, Robin; Sharma, K C; Rahi, Praveen; Gulati, Ashu; Gulati, Arvind

    2010-12-01

    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

  1. Physical and Metabolic Interactions of Pseudomonas sp. Strain JA5-B45 and Rhodococcus sp. Strain F9-D79 during Growth on Crude Oil and Effect of a Chemical Surfactant on Them

    PubMed Central

    Van Hamme, Jonathan D.; Ward, Owen P.

    2001-01-01

    Methods to enhance crude oil biodegradation by mixed bacterial cultures, for example, (bio)surfactant addition, are complicated by the diversity of microbial populations within a given culture. The physical and metabolic interactions between Rhodococcus sp. strain F9-D79 and Pseudomonas sp. strain JA5-B45 were examined during growth on Bow River crude oil. The effects of a nonionic chemical surfactant, Igepal CO-630 (nonylphenol ethoxylate), also were evaluated. Strain F9-D79 grew attached to the oil-water interface and produced a mycolic acid-containing capsule. Crude oil emulsification and surface activity were associated with the cellular fraction. Strain JA5-B45 grew in the aqueous phase and was unable to emulsify oil, but cell-free supernatants mediated kerosene-water emulsion formation. In coculture, stable emulsions were formed and strain JA5-B45 had an affinity for the capsule produced by strain F9-D79. Igepal CO-630 inhibited F9-D79 cells from adhering to the interface, and cells grew dispersed in the aqueous phase as 0.5-?m cocci rather than 2.5-?m rods. The surfactant increased total petroleum hydrocarbon removal by strain JA5-B45 from 4 to 22% and included both saturated compounds and aromatics. In coculture, TPH removal increased from 13 to 40% following surfactant addition. The culture pH normally increased from 7.0 to between 7.5 and 8.5, although addition of Igepal CO-630 to F9-D79 cultures resulted in a drop to pH 5.5. We suggest a dual role for the nonylphenol ethoxylate surfactant in the coculture: (i) to improve hydrocarbon uptake by strain JA5-B45 through emulsification and (ii) to prevent strain F9-D79 from adhering to the oil-water interface, indirectly increasing hydrocarbon availability. These varied effects on hydrocarbon biodegradation could explain some of the known diversity of surfactant effects. PMID:11571196

  2. Involvement of an Extracellular Protease in Algicidal Activity of the Marine Bacterium Pseudoalteromonas sp. Strain A28

    PubMed Central

    Lee, Sun-og; Kato, Junichi; Takiguchi, Noboru; Kuroda, Akio; Ikeda, Tsukasa; Mitsutani, Atsushi; Ohtake, Hisao

    2000-01-01

    The marine bacterium Pseudoalteromonas sp. strain A28 was able to kill the diatom Skeletonema costatum strain NIES-324. The culture supernatant of strain A28 showed potent algicidal activity when it was applied to a paper disk placed on a lawn of S. costatum NIES-324. The condensed supernatant, which was prepared by subjecting the A28 culture supernatant to ultrafiltration with a 10,000-Mw-cutoff membrane, showed algicidal activity, suggesting that strain A28 produced extracellular substances capable of killing S. costatum cells. The condensed supernatant was then found to have protease and DNase activities. Two Pseudoalteromonas mutants lacking algicidal activity, designated NH1 and NH2, were selected after N-methyl-N?-nitrosoguanidine mutagenesis. The culture supernatants of NH1 and NH2 showed less than 15% of the protease activity detected with the parental strain, A28. The protease was purified to homogeneity from A28 culture supernatants by using ion-exchange chromatography followed by preparative gel electrophoresis. Paper-disk assays revealed that the purified protease had potent algicidal activity. The purified protease had a molecular mass for 50 kDa, and the N-terminal amino acid sequence was determined to be Ala-Thr-Pro-Asn-Asp-Pro. The optimum pH and temperature of the protease were found to be 8.8 and 30°C, respectively, by using succinyl-Ala-Ala-Pro-Phe-p-nitroanilide as a substrate. The protease activity was strongly inhibited by phenylmethylsulfonyl fluoride, diisopropyl fluorophosphate, antipain, chymostatin, and leupeptin. No significant inhibition was detected with EDTA, EGTA, phenanthroline or tetraethylenepentamine. These results suggest that Pseudoalteromonas sp. strain A28 produced an extracellular serine protease which was responsible for the algicidal activity of this marine bacterium. PMID:11010878

  3. Genome Analysis Coupled with Physiological Studies Reveals a Diverse Nitrogen Metabolism in Methylocystis sp. Strain SC2

    PubMed Central

    Blom, Jochen; Liesack, Werner

    2013-01-01

    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

  4. Complete Genome Sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and "Thermoanaerobacter cellulolyticus".

    PubMed

    Lee, Laura L; Izquierdo, Javier A; Blumer-Schuette, Sara E; Zurawski, Jeffrey V; Conway, Jonathan M; Cottingham, Robert W; Huntemann, Marcel; Copeland, Alex; Chen, I-Min A; Kyrpides, Nikos; Markowitz, Victor; Palaniappan, Krishnaveni; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Andersen, Evan; Pati, Amrita; Stamatis, Dimitrios; Reddy, T B K; Shapiro, Nicole; Nordberg, Henrik P; Cantor, Michael N; Hua, Susan X; Woyke, Tanja; Kelly, Robert M

    2015-01-01

    The genus Caldicellulosiruptor contains extremely thermophilic, cellulolytic bacteria capable of lignocellulose deconstruction. Currently, complete genome sequences for eleven Caldicellulosiruptor species are available. Here, we report genome sequences for three additional Caldicellulosiruptor species: Rt8.B8 DSM 8990 (New Zealand), Wai35.B1 DSM 8977 (New Zealand), and "Thermoanaerobacter cellulolyticus" strain NA10 DSM 8991 (Japan). PMID:25977428

  5. Degradation of recalcitrant aliphatic and aromatic hydrocarbons by a dioxin-degrader Rhodococcus sp. strain p52.

    PubMed

    Yang, Hai-Yan; Jia, Rui-Bao; Chen, Bin; Li, Li

    2014-09-01

    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

  6. Stimulation of 16-dehydroprogesterone and progesterone reductases of Eubacterium sp. strain 144 by hemin and hydrogen or pyruvate.

    PubMed Central

    Glass, T L; Burley, C Z

    1985-01-01

    Suspensions of Eubacterium sp. strain 144, prepared from cells grown with 16-dehydroprogesterone, catalyzed the reduction of this steroid to 17-isoprogesterone at a very low rate. Modifications of the assay to optimize the pH (5.5) and increase the steroid solubility (10% [vol/vol] methanol) did not significantly enhance the reaction. However, growth of strain 144 in the presence of hemin was found to stimulate 16-dehydroprogesterone reductase during the initial 30 min of incubation, giving a biphasic time course. These biphasic kinetics could be eliminated by providing the cells with an exogenous electron donor. Strain 144 used either H2 or pyruvate for this purpose, and 17-isoprogesterone formation was nearly complete after 20 to 30 min of incubation. However, under these conditions, strain 144 further converted 17-isoprogesterone to products which lacked UV absorbance (254 nm). When progesterone was used as a substrate, it was found that strain 144 could reduce the C4-C5 double bond of this steroid by a progesterone reductase to give mostly 5 beta-pregnadione and some 5 alpha-pregnadione. Furthermore, the 3-keto group of 5 beta-pregnadione steroid was also reduced to a hydroxy function. The maximum activities of both 16-dehydroprogesterone and progesterone reductases in cell suspensions required the growth of strain 144 with hemin and 16-dehydroprogesterone and the presence of H2 or pyruvate. PMID:3859246

  7. Genome Sequence of Blattabacterium sp. Strain BGIGA, Endosymbiont of the Blaberus giganteus Cockroach

    PubMed Central

    Huang, Charlie Y.; Moran, Nancy A.

    2012-01-01

    Cockroaches harbor the obligate flavobacterial endosymbiont Blattabacterium sp., which resides within the host's bacteriocytes and can recycle ammonia and urea nitrogenous wastes into amino acids for the host. We report the complete genome sequence of the Blattabacterium sp. associated with the giant roach Blaberus giganteus. PMID:22843586

  8. Expression and Characterization of Geobacillus stearothermophilus SR74 Recombinant ?-Amylase in Pichia pastoris

    PubMed Central

    Gandhi, Sivasangkary; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Raja Abd; Chor Leow, Thean; Oslan, Siti Nurbaya

    2015-01-01

    Geobacillus stearothermophilus SR74 is a locally isolated thermophilic bacteria producing thermostable and thermoactive ?-amylase. Increased production and commercialization of thermostable ?-amylase strongly warrant the need of a suitable expression system. In this study, the gene encoding the thermostable ?-amylase in G. stearothermophilus SR74 was amplified, sequenced, and subcloned into P. pastoris GS115 strain under the control of a methanol inducible promoter, alcohol oxidase (AOX). Methanol induced recombinant expression and secretion of the protein resulted in high levels of extracellular amylase production. YPTM medium supplemented with methanol (1% v/v) was the best medium and once optimized, the maximum recombinant ?-amylase SR74 achieved in shake flask was 28.6?U?mL?1 at 120?h after induction. The recombinant 59?kDa ?-amylase SR74 was purified 1.9-fold using affinity chromatography with a product yield of 52.6% and a specific activity of 151.8?U?mg?1. The optimum pH of ?-amylase SR74 was 7.0 and the enzyme was stable between pH 6.0–8.0. The purified enzyme was thermostable and thermoactive, exhibiting maximum activity at 65°C with a half-life (t1/2) of 88?min at 60°C. In conclusion, thermostable ?-amylase SR74 from G. stearothermophilus SR74 would be beneficial for industrial applications, especially in liquefying saccrification.

  9. Polysaccharide-Degrading Thermophiles Generated by Heterologous Gene Expression in Geobacillus kaustophilus HTA426

    PubMed Central

    Yoshida, Ken-ichi; Ohshima, Toshihisa

    2013-01-01

    Thermophiles have important advantages over mesophiles as host organisms for high-temperature bioprocesses, functional production of thermostable enzymes, and efficient expression of enzymatic activities in vivo. To capitalize on these advantages of thermophiles, we describe here a new inducible gene expression system in the thermophile Geobacillus kaustophilus HTA426. Six promoter regions in the HTA426 genome were identified and analyzed for expression profiles using ?-galactosidase reporter assay. This analysis identified a promoter region upstream of a putative amylose-metabolizing gene cluster that directed high-level expression of the reporter gene. The expression was >280-fold that without a promoter and was further enhanced 12-fold by maltose addition. In association with a multicopy plasmid, this promoter region was used to express heterologous genes. Several genes, including a gene whose product was insoluble when expressed in Escherichia coli, were successfully expressed as soluble proteins, with yields of 0.16 to 59 mg/liter, and conferred new functions to G. kaustophilus strains. Remarkably, cellulase and ?-amylase genes conferred the ability to degrade cellulose paper and insoluble starch at high temperatures, respectively, generating thermophiles with the potential to degrade plant biomass. Our results demonstrate that this novel expression system expands the potential applications of G. kaustophilus. PMID:23793634

  10. Two types of novel dipeptidyl aminopeptidases from Pseudomonas sp. strain WO24.

    PubMed Central

    Ogasawara, W; Kobayashi, G; Okada, H; Morikawa, Y

    1996-01-01

    Two kinds of dipeptidyl aminopeptidase I (DAP I [cathepsin C])-like activities which hydrolyze Gly-Phe-p-nitroanilide (Gly-Phe-pNA) were detected in Pseudomonas sp. strain WO24. They were purified and characterized. The isolated enzymes, named DAP BII and DAP BIII, were revealed to be homogeneous by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and isoelectric focusing. DAP BII was estimated to have a molecular mass of 150,000 Da by gel filtration and a subunit size of 73,000 Da by SDS-PAGE, indicating it to be a homodimer. The molecular mass of DAP BIII was evaluated to be approximately 60,000 Da by gel filtration and 69,000 Da by SDS-PAGE, indicating that it is monomeric. The isoelectric points of DAP BII and DAP BIII were 6.1 and 5.0, and their optimal pHs were 8.0 and 8.5 to 9.0, respectively. The result of peptide mapping for DAP BII and DAP BIII showed that these enzymes consist of different components. Both enzymes were completely inhibited by diisopropylphosphofluoride but not by general thiol inhibitors, indicating that they are serine proteases. DAP BII and DAP BIII hydrolyzed Gly-Phe-pNA but not Gly-Arg-pNA, both of which are model substrates for mammalian DAP I. Despite these shared activities toward DAP I, DAP BII released dipeptides from Ala-Ala-pNA and Lys-Ala-4-methylcoumarinamide (a substrate for DAP II), whereas DAP BIII did not hydrolyze either of these compounds and was presumed to prefer substrates composed of bulky, hydrophobic amino acids at P1 and P1' positions. In addition, DAP BII showed no endopeptidase activity, whereas DAP BIII possessed the activity on N-terminally blocked peptide derivatives besides exopeptidase activity. Assays performed with bioactive peptides such as angiotensin I and neuromedin N as substrates indicate that DAP BII has a considerably broader substrate specificity than DAP BIII and is able to hydrolyze an X-Pro bond, an imido bond that few peptidases and no known DAPs can cleave. These characteristics, namely, substrate specificities, molecular mass, pI, peptide mapping, pH optimum, and effect of inhibitors, suggested that the two DAPs purified in this work are distinct enzymes and do not belong to any of the previously reported DAP classes. PMID:8892831

  11. Draft genome sequence of Flavobacterium sp. strain F52, isolated from the rhizosphere of bell pepper (Capsicum annuum L. cv. Maccabi).

    PubMed

    Kolton, Max; Green, Stefan J; Harel, Yael Meller; Sela, Noa; Elad, Yigal; Cytryn, Eddie

    2012-10-01

    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

  12. Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm.

    PubMed

    O'Dell, Kaela B; Woo, Hannah L; Utturkar, Sagar; Klingeman, Dawn; Brown, Steven D; Hazen, Terry C

    2015-01-01

    Halomonas sp. strain KO116 was isolated from Nile Delta Mediterranean Sea surface water enriched with insoluble organosolv lignin. It was further screened for growth on alkali lignin minimal salts medium agar. The strain tolerates the ionic liquid 1-ethyl-3-methylimidazolium acetate. Its complete genome sequence is presented in this report. PMID:25953187

  13. Draft Genome Sequence of Methylobacterium sp. Strain L2-4, a Leaf-Associated Endophytic N-Fixing Bacterium Isolated from Jatropha curcas L.

    PubMed Central

    Madhaiyan, Munusamy; Chan, Kam Lock

    2014-01-01

    Methylobacterium sp. strain L2-4 is an efficient nitrogen-fixing leaf colonizer of biofuel crop Jatropha curcas. This strain is able to greatly improve the growth and seed yield of Jatropha curcas and is the second reported genome sequence of plant growth-promoting bacteria isolated from Jatropha curcas. PMID:25502683

  14. Draft Genome Sequence of Burkholderia sp. Strain MP-1, a Methyl Parathion (MP)-Degrading Bacterium from MP-Contaminated Soil

    PubMed Central

    Liu, Xu-Yun; Luo, Xiao-Jing; Li, Chun-Xiu; Lai, Qi-Liang

    2014-01-01

    Burkholderia sp. strain MP-1 was isolated from pesticide-contaminated soil. Herein, we report the draft genome sequence of strain MP-1, which contains 168 contigs of 8,611,053 bp, with a G+C content of 62.55% and 7,631 protein-coding genes. PMID:24855293

  15. Draft Genome Sequence of Flavobacterium sp. Strain F52, Isolated from the Rhizosphere of Bell Pepper (Capsicum annuum L. cv. Maccabi)

    PubMed Central

    Kolton, Max; Green, Stefan J.; Harel, Yael Meller; Sela, Noa; Elad, Yigal

    2012-01-01

    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

  16. Endogenously Synthesized ( )-proto-Quercitol and Glycine Betaine Are Principal Compatible Solutes of Schizochytrium sp. Strain S8 (ATCC 20889) and Three New Isolates of Phylogenetically Related Thraustochytrids

    Microsoft Academic Search

    Anita N. Jakobsen; Inga M. Aasen; A. R. Strom

    2007-01-01

    betaine were the principal compatible solutes of Schizochytrium sp. strain S8 (ATCC 20889) and three new osmotolerant isolates of thraustochytrids (strains T65, T66, and T67). The compatible solutes were identified and quantified by use of nuclear magnetic resonance spectroscopy, and their identity was confirmed by mass spectroscopy and measurement of the specific optical rotation. The cellular content of compatible solutes

  17. Draft Genome Sequence of Uncultivated Desulfosporosinus sp. Strain Tol-M, Obtained by Stable Isotope Probing Using [13C6]Toluene

    PubMed Central

    Abu Laban, Nidal; Tan, BoonFei; Dao, Anh

    2015-01-01

    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

  18. Isolation and sequence analysis of polyketide synthase genes from the daunomycin-producing Streptomyces sp. strain C5.

    PubMed Central

    Ye, J; Dickens, M L; Plater, R; Li, Y; Lawrence, J; Strohl, W R

    1994-01-01

    A contiguous region of about 30 kbp of DNA putatively encoding reactions in daunomycin biosynthesis was isolated from Streptomyces sp. strain C5 DNA. The DNA sequence of an 8.1-kbp EcoRI fragment, which hybridized with actI polyketide synthase (PKS) and actIII polyketide reductase (PKR) gene probes, was determined, revealing seven complete open reading frames (ORFs), two in one cluster and five in a divergently transcribed cluster. The former two genes are likely to encode PKR and a bifunctional cyclase/dehydrase. The five latter genes encode: (i) a homolog of TcmH, an oxygenase of the tetracenomycin biosynthesis pathway; (ii) a PKS Orf1 homolog; (iii) a PKS Orf2 homolog (chain length factor); (iv) a product having moderate sequence identity with Escherichia coli beta-ketoacyl acyl carrier protein synthase III but lacking the conserved active site; and (v) a protein highly similar to several acyltransferases. The DNA within the 8.1-kbp EcoRI fragment restored daunomycin production to two dauA non-daunomycin-producing mutants of Streptomyces sp. strain C5 and restored wild-type antibiotic production to Streptomyces coelicolor B40 (act VII; nonfunctional cyclase/dehydrase), and to S. coelicolor B41 (actIII) and Streptomyces galilaeus ATCC 31671, strains defective in PKR activity. Images PMID:7928998

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

    PubMed

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

    2010-08-01

    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

  20. Endophytic colonization of Vitis vinifera L. by plant growth-promoting bacterium Burkholderia sp. strain PsJN.

    PubMed

    Compant, Stéphane; Reiter, Birgit; Sessitsch, Angela; Nowak, Jerzy; Clément, Christophe; Ait Barka, Essaïd

    2005-04-01

    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 leaves were inoculated with bacterial suspensions. Epiphytic and endophytic colonization patterns were then monitored by dilution plating assays and microscopic observation of organ sections. Bacteria were chronologically detected first on root surfaces, then in root internal tissues, and finally in the fifth internode and the tissues of the fifth leaf. Analysis of the PsJN colonization patterns showed that this strain colonizes grapevine root surfaces, as well as cell walls and the whole surface of some rhizodermal cells. Cells were also abundant at lateral root emergence sites and root tips. Furthermore, cell wall-degrading endoglucanase and endopolygalacturonase secreted by PsJN explained how the bacterium gains entry into root internal tissues. Host defense reactions were observed in the exodermis and in several cortical cell layers. Bacteria were not observed on stem and leaf surfaces but were found in xylem vessels of the fifth internode and the fifth leaf of plantlets. Moreover, bacteria were more abundant in the fifth leaf than in the fifth internode and were found in substomatal chambers. Thus, it seems that Burkholderia sp. strain PsJN induces a local host defense reaction and systemically spreads to aerial parts through the transpiration stream. PMID:15811990

  1. Evidence that some Frankia sp. strains are able to cross boundaries between Alnus and Elaeagnus host specificity groups.

    PubMed

    Bosco, M; Fernandez, M P; Simonet, P; Materassi, R; Normand, P

    1992-05-01

    Phenotypic and genotypic methods were used to prove the existence of Frankia strains isolated from an Elaeagnus sp. that are able to cross the inoculation barriers and infect Alnus spp. also. Repeated cycles of inoculation, nodulation, and reisolation were performed under axenic conditions. Frankia wild-type strain UFI 13270257 and three of its coisolates did exhibit complete infectivity and effectiveness on Elaeagnus spp. and Hippophaë rhamnoides and variable infectivity on Alnus spp. Microscopical observation of host plant roots showed that these strains are able to infect Alnus spp. by penetrating deformed root hairs. Reisolates obtained from nodules induced on monoxenic Alnus glutinosa, Alnus incana, and Elaeagnus angustifolia resembled the parent strains in host infectivity range, in planta and in vitro morphophysiology, isoenzymes, and nif and rrn restriction fragment length polymorphisms, thus fulfilling Koch's postulates on both host plant genera. Alnus and Elaeagnus group-specific polymerase chain reaction DNA amplifications, DNA-DNA hybridizations, and partial gene sequences coding for 16S rRNA provided evidence for the genetic uniformity of wild-type strains and their inclusion into one and the same genomic species, clearly belonging to the Elaeagnus group of Frankia species. PMID:1352442

  2. Cloning, characterization, and expression of a gene region from Pseudomonas sp. strain ADP involved in the dechlorination of atrazine.

    PubMed Central

    de Souza, M L; Wackett, L P; Boundy-Mills, K L; Mandelbaum, R T; Sadowsky, M J

    1995-01-01

    We previously identified a Pseudomonas sp. strain, ADP, which rapidly metabolized atrazine in liquid culture, agar plates, and soils (R. T. Mandelbaum, D. L. Allan, L. P. Wackett, Appl. Environ. Microbiol. 61:1451-1457, 1995). In this study, we report the cloning and partial characterization of a gene region from Pseudomonas sp. strain ADP that encodes atrazine degradation activity. A 22-kb EcoRI genomic DNA fragment, designated pMD1, was shown to encode atrazine dechlorination activity in Escherichia coli DH5 alpha. Atrazine degradation was demonstrated by a zone-clearing assay on agar medium containing crystalline atrazine and by chromatographic methods. A gene conferring the atrazine-clearing phenotype was subsequently subcloned as a 1.9-kb AvaI fragment in pACYC184, designated pMD4, and was expressed in E. coli. This result and random Tn5 mutagenesis established that the 1.9-kb AvaI fragment was essential for atrazine dechlorination. High-pressure liquid and thin-layer chromatographic analyses were used to rigorously establish that E. coli containing pMD4 degraded atrazine and accumulated hydroxyatrazine. Hydroxyatrazine was detected only transiently in E. coli containing pMD1. This is consistent with the idea that hydroxyatrazine is the first metabolite in atrazine degradation by Pseudomonas sp. strain ADP. A 0.6-kb ApaI-PstI fragment from pMD4, containing the putative atrazine chlorohydrolase gene, hybridized to DNA from atrazine-degrading bacteria isolated in Switzerland and Louisiana.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7574646

  3. Identification and Characterization of an Archaeal Kojibiose Catabolic Pathway in the Hyperthermophilic Pyrococcus sp. Strain ST04

    PubMed Central

    Jung, Jong-Hyun; Seo, Dong-Ho; Holden, James F.

    2014-01-01

    A unique gene cluster responsible for kojibiose utilization was identified in the genome of Pyrococcus sp. strain ST04. The proteins it encodes hydrolyze kojibiose, a disaccharide product of glucose caramelization, and form glucose-6-phosphate (G6P) in two steps. Heterologous expression of the kojibiose-related enzymes in Escherichia coli revealed that two genes, Py04_1502 and Py04_1503, encode kojibiose phosphorylase (designated PsKP, for Pyrococcus sp. strain ST04 kojibiose phosphorylase) and ?-phosphoglucomutase (PsPGM), respectively. Enzymatic assays show that PsKP hydrolyzes kojibiose to glucose and ?-glucose-1-phosphate (?-G1P). The Km values for kojibiose and phosphate were determined to be 2.53 ± 0.21 mM and 1.34 ± 0.04 mM, respectively. PsPGM then converts ?-G1P into G6P in the presence of 6 mM MgCl2. Conversion activity from ?-G1P to G6P was 46.81 ± 3.66 U/mg, and reverse conversion activity from G6P to ?-G1P was 3.51 ± 0.13 U/mg. The proteins are highly thermostable, with optimal temperatures of 90°C for PsKP and 95°C for PsPGM. These results indicate that Pyrococcus sp. strain ST04 converts kojibiose into G6P, a substrate of the glycolytic pathway. This is the first report of a disaccharide utilization pathway via phosphorolysis in hyperthermophilic archaea. PMID:24391053

  4. Characterization of a novel angular dioxygenase from fluorene-degrading Sphingomonas sp. strain LB126

    Microsoft Academic Search

    Luc Schuler; Sinead M. Ni Chadhain; Yves Jouanneau; Christine Meyer; Gerben J. Zylstra; Pascal Hols; Spiros N. Agathos

    2009-01-01

    In this study, the genes involved in the initial attack on fluorene by Sphingomonas sp. LB126 were investigated. The ? and ? subunits of a dioxygenase complex (FlnA1A2), showing 63% and 51% sequence identity respectively, with the subunits of an angular dioxygenase from Gram-positive Terrabacter sp. DBF63, were identified. When overexpressed in E. coli, FlnA1A2 was responsible for the angular

  5. Identification of a carotenoid-binding protein in the cytoplasmic membrane from the heterotrophic cyanobacterium Synechocystis sp. strain PCC6714.

    PubMed Central

    Bullerjahn, G S; Sherman, L A

    1986-01-01

    We isolated a carotenoid-binding protein from the cytoplasmic membrane of the cyanobacterium Synechocystis sp. strain PCC6714. The polypeptide demonstrated a characteristic mobility shift when electrophoresed in lithium dodecyl sulfate-polyacrylamide gels. The protein migrated with an apparent molecular mass of 35 kilodaltons when solubilized at 0 degrees C, but after solubilization at 70 degrees C, the protein migrated as a 45-kilodalton species. The carotenoid-binding protein accumulated only in autotrophically grown cells; cytoplasmic membranes prepared from photoheterotrophically grown cells lacked this component. Images PMID:3087963

  6. Draft genome sequence of Halomonas sp. strain KM-1, a moderately halophilic bacterium that produces the bioplastic poly(3-hydroxybutyrate).

    PubMed

    Kawata, Yoshikazu; Kawasaki, Kazunori; Shigeri, Yasushi

    2012-05-01

    We report the draft genome sequence of Halomonas sp. strain KM-1, which was isolated in Ikeda City, Osaka, Japan, and which produces the bioplastic poly(3-hydroxybutyrate). The total length of the assembled genome is 4,992,811 bp, and 4,220 coding sequences were predicted within the genome. Genes encoding proteins that are involved in the production and depolymerization of poly(3-hydroxybutyrate) were identified. The identification of these genes might be of use in the production of the bioplastic poly(3-hydroxybutyrate) and its monomer 3-hydroxybutyrate. PMID:22535927

  7. Draft Genome Sequence of Halomonas sp. Strain KM-1, a Moderately Halophilic Bacterium That Produces the Bioplastic Poly(3-Hydroxybutyrate)

    PubMed Central

    Kawasaki, Kazunori; Shigeri, Yasushi

    2012-01-01

    We report the draft genome sequence of Halomonas sp. strain KM-1, which was isolated in Ikeda City, Osaka, Japan, and which produces the bioplastic poly(3-hydroxybutyrate). The total length of the assembled genome is 4,992,811 bp, and 4,220 coding sequences were predicted within the genome. Genes encoding proteins that are involved in the production and depolymerization of poly(3-hydroxybutyrate) were identified. The identification of these genes might be of use in the production of the bioplastic poly(3-hydroxybutyrate) and its monomer 3-hydroxybutyrate. PMID:22535927

  8. Identification of Amycolatopsis sp. strain HR167 genes, involved in the bioconversion of ferulic acid to vanillin

    Microsoft Academic Search

    S. Achterholt; H. Priefert; A. Steinbüchel

    2000-01-01

    The gene loci ech, encoding enoyl-CoA hydratase\\/aldolase, and fcs, encoding an unusual feruloyl-CoA synthetase, which are involved in the bioconversion of ferulic acid to vanillin by the\\u000a Gram-positive bacterium Amycolatopsis sp. strain HR167, were localized on a 4,000?bp PstI fragment (P40). The nucleotide sequence of P40 was determined, revealing open reading frames of 864?bp and 1,476?bp, representing\\u000a ech and fcs,

  9. Competition for Astragalus sinicus root nodule infection between its native microsymbiont Rhizobium huakuii bv. renge B3 and Rhizobium sp. ACMP18 strain, specific for Astragalus cicer

    Microsoft Academic Search

    W. Malek; M. Inaba; H. Ono; Y. Kaneko; Y. Murooka

    1998-01-01

    Rhizobium huakuii bv. renge B3, a native symbiont of Astragalus sinicus, outcompeted Rhizobium sp. strain ACMP18, which was isolated from Astragalus cicer nodules, in the formation of root nodules on A.?sinicus when plants were co-inoculated with these strains. The strains occupying the nodules were identified by antibiotic resistance\\u000a and phage sensitivity markers and also by polymerase chain reaction (PCR) genomic

  10. Characterization of the IS895 family of insertion sequences from the cyanobacterium Anabaena sp. strain PCC 7120

    SciTech Connect

    Alam, J.; Vrba, J.M.; Martin, J.A.; Weislo, L.J.; Curtis, S.E. (North Carolina State Univ., Raleigh (United States)); Yuping Cai (Michigan State Univ. Plant Research Lab., East Lansing (United States))

    1991-09-01

    A family of repetitive elements from the cyanobacterium Anabaena sp. strain PCC 7120 was identified through the proximity of one element to the psbAI gene. Four members of this seven-member family were isolated and shown to have structures characteristic of bacterial insertion sequences. Each element is approximately 1,200 bp in length, is delimited by a 30-bp inverted repeat, and contains two open reading frames in tandem on the same DNA strand. The four copies differ from each other by small insertions or deletions, some of which alter the open reading frames. By using a system designed to trap insertion elements, one of the elements, denoted IS895, was shown to be mobile. The target site was not duplicated upon insertion of the element. Two other filamentous cyanobacterial strains were also found to contain sequences homologous to IS895.

  11. Effects of medium and trace metals on kinetics of carbon tetrachloride transformation by pseudomonas sp. strain KC

    SciTech Connect

    Tatara, G.M.; Dybas, M.J.; Criddle, C.S. (Michigan State Univ., East Lansing (United States))

    1993-07-01

    In recent years, interest has increased degradation of hazardous contaminants in situ by stimulating selected bacterial populations or by addition of novel organisms to contaminated sites. Advantages of introduced organisms include extensive study in the laboratory which improves prospects for control of their activities in the field. Chloroform (CF) is a common end product of carbon tetrachloride (CT) but is more presistant and is a suspected carcinogen. Metabolic pathways that do not produce CF are of interest. This study reports on the kinetics of CT transformation by Pseudomonas sp. strain KC and describes experiments to evaluate the role of trace metals in CT transformation kinetics. Evidence is provide that accelerated CT transformation can be obtained in iron-rich ground waters and soil slurries by adding strain KC after pH adjustment. 9 refs., 9 figs., 1 tab.

  12. Screening and genetic characterization of thermo-tolerant Synechocystis sp. PCC6803 strains created by adaptive evolution

    PubMed Central

    2014-01-01

    Background Temperature tolerance is an important aspect for commercial scale outdoor cultivation of microalgae and cyanobacteria. While various genes are known to be related to Synechocystis sp. PCC6803's heat shock response, there is very limited published data concerning the specific genes involved in long term thermal tolerance. We have previously used random mutagenesis and adaptive evolution to generate a mixture of strains of Synechocystis sp. PCC6803 with significantly increased thermal tolerance. The genetic modifications leading to the phenotypes of the newly generated strains are the focus of this work. Results We used a custom screening platform, based on 96-deepwell microplate culturing in an in house designed cultivation chamber integrated in a liquid handling robot for screening and selection; in addition we also used a more conventional system. The increased thermal tolerances of the isolated monoclonal strains were validated in larger bioreactors and their whole genomes sequenced. Comparison of the sequence information to the parental wild type identified various mutations responsible for the enhanced phenotypes. Among the affected genes identified are clpC, pnp, pyk2, sigF, nlpD, pyrR, pilJ and cya1. Conclusions The applied methods (random mutagenesis, in vivo selection, screening, validation, whole genome sequencing) were successfully applied to identify various mutations, some of which are very unlikely to have been identified by other approaches. Several of the identified mutations are found in various strains and (due to their distribution) are likely to have occurred independently. This, coupled with the relatively low number of affected genes underscores the significance of these specific mutations to convey thermal tolerance in Synechocystis. PMID:25029912

  13. Isolation and characterization of a novel 2-methyl-4-chlorophenoxyacetic acid-degrading Enterobacter sp. strain SE08.

    PubMed

    Tan, Lin; Hu, Qiulong; Xiong, Xingyao; Su, Xiaojun; Huang, Yanning; Jiang, Ziwei; Zhou, Qingming; Zhao, Songyi; Zeng, Wei-ai

    2013-10-01

    A bacterial strain (SE08) capable of utilizing 2-methyl-4-chlorophenoxy acetic acid (MCPA) as the sole carbon and energy source for growth was isolated by continuous enrichment culturing in minimal salt medium (MSM) from a long term MCPA exposed soil. This bacterial strain was identified as Enterobacter sp. based on morphological, physiological and biochemical tests, as well as 16S rRNA sequence analysis. Its ability to degrade MCPA was determined using high performance liquid chromatography. The strain SE08 can tolerate unusually high MCPA concentrations (125-2000mg/L). The influences of culturing factors (initial concentration, pH, and temperature) on the bacterial growth and substrate degradation were studied. The results showed that the optimal MCPA degradation occurred at an MCPA concentration of 500mg/L, 30°C and pH 6.0. Under these conditions, 68.5 percent of MCPA in MSM was degraded by SE08, and the OD600nm reached 0.64 after culturing for 72h. The degradation of MCPA could be enhanced by addition of both carbon and nitrogen sources. At an initial MCPA concentration of 500mg/L, when 5g/L glucose and 2.5g/L yeast extract were added into the MSM media, the MCPA degradation was significantly increased to 83.8 percent, and OD600nm was increased to 1.09 after incubation at 30°C and pH 6.0 for 72h. This is the first study showing that an Enterobacter sp. strain is capable of degrading MCPA, which might provide a new approach for the remediation of MCPA contaminated soil and contribute to the limited knowledge about the function of Enterobacter species. PMID:23856120

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

    Microsoft Academic Search

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

    2006-01-01

    A novel bacterium, strain b6T (T=type strain), was isolated from a disused mine site by growth using arsenite [As(III)] as energy source in a simple mineral\\u000a medium. Cells of strain b6T were rod-shaped, Gram-negative, non-sporulating and motile. Optimum growth occurred at temperatures between 20 and 30 °C,\\u000a and at pH between 4.0 and 7.5. Strain b6T grew chemoautotrophically on As(III), sulphur

  15. Aerobic degradation of 4-nitroaniline (4-NA) via novel degradation intermediates by Rhodococcus sp. strain FK48.

    PubMed

    Khan, Fazlurrahman; Pandey, Janmejay; Vikram, Surendra; Pal, Deepika; Cameotra, Swaranjit Singh

    2013-06-15

    An aerobic strain, Rhodococcus sp. strain FK48, capable of growing on 4-nitroaniline (4-NA) as the sole source of carbon, nitrogen, and energy has been isolated from enrichment cultures originating from contaminated soil samples. During growth studies with non- induced cells of FK48 catalyzed sequential denitrification (release of NO? substituent) and deamination (release of NH? substituent) of 4-NA. However, none of the degradation intermediates could be identified with growth studies. During resting cell studies, 4-NA-induced cells of strain FK48 transformed 4-NA via a previously unknown pathway which involved oxidative hydroxylation leading to formation of 4-aminophenol (4-AP). Subsequent degradation involved oxidated deamination of 4-AP and formation of 1,2,4-benzenetriol (BT) as the major identified terminal aromatic intermediate. Identification of these intermediates was ascertained by HPLC, and GC-MS analyses of the culture supernatants. 4-NA-induced cells of strain FK48 showed positive activity for 1,2,4-benzenetriol dioxygenase in spectrophotometric assay. This is the first conclusive study on aerobic microbial degradation of 4-NA and elucidation of corresponding metabolic pathway. PMID:23587930

  16. Metal Reduction and Iron Biomineralization by a Psychrotolerant Fe(III)-Reducing Bacterium, Shewanella sp. Strain PV-4

    PubMed Central

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

    2006-01-01

    A marine psychrotolerant, dissimilatory Fe(III)-reducing bacterium, Shewanella sp. strain PV-4, from the microbial mat at a hydrothermal vent of Loihi Seamount in the Pacific Ocean has been further characterized, with emphases on metal reduction and iron biomineralization. The strain is able to reduce metals such as Fe(III), Co(III), Cr(VI), Mn(IV), and U(VI) as electron acceptors while using lactate, formate, pyruvate, or hydrogen as an electron donor. Growth during iron reduction occurred over the pH range of 7.0 to 8.9, a sodium chloride range of 0.05 to 5%, and a temperature range of 0 to 37°C, with an optimum growth temperature of 18°C. Unlike mesophilic dissimilatory Fe(III)-reducing bacteria, which produce mostly superparamagnetic magnetite (<35 nm), this psychrotolerant bacterium produces well-formed single-domain magnetite (>35 nm) at temperatures from 18 to 37°C. The genome size of this strain is about 4.5 Mb. Strain PV-4 is sensitive to a variety of commonly used antibiotics except ampicillin and can acquire exogenous DNA (plasmid pCM157) through conjugation. PMID:16672462

  17. Microbial Community Dynamics during the Bioremediation Process of Chlorimuron-Ethyl-Contaminated Soil by Hansschlegelia sp. Strain CHL1

    PubMed Central

    Yang, Liqiang; Li, Xinyu; Li, Xu; Su, Zhencheng; Zhang, Chenggang; Zhang, Huiwen

    2015-01-01

    Long-term and excessive application of chlorimuron-ethyl has led to a series of environmental problems. Strain Hansschlegelia sp. CHL1, a highly efficient chlorimuron-ethyl degrading bacterium isolated in our previous study, was employed in the current soil bioremediation study. The residues of chlorimuron-ethyl in soils were detected, and the changes of soil microbial communities were investigated by phospholipid fatty acid (PLFA) analysis. The results showed that strain CHL1 exhibited significant chlorimuron-ethyl degradation ability at wide range of concentrations between 10?g kg-1 and 1000?g kg-1. High concentrations of chlorimuron-ethyl significantly decreased the total concentration of PLFAs and the Shannon-Wiener indices and increased the stress level of microbes in soils. The inoculation with strain CHL1, however, reduced the inhibition on soil microbes caused by chlorimuron-ethyl. The results demonstrated that strain CHL1 is effective in the remediation of chlorimuron-ethyl-contaminated soil, and has the potential to remediate chlorimuron-ethyl contaminated soils in situ. PMID:25689050

  18. Characterization of a chromosomally encoded 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase from Burkholderia sp. strain RASC.

    PubMed Central

    Suwa, Y; Wright, A D; Fukimori, F; Nummy, K A; Hausinger, R P; Holben, W E; Forney, L J

    1996-01-01

    The findings of previous studies indicate that the genes required for metabolism of the pesticide 2,4-dichlorophenoxyacetic acid (2,4-D) are typically encoded on broad-host-range plasmids. However, characterization of plasmid-cured strains of Burkholderia sp. strain RASC, as well as mutants obtained by transposon mutagenesis, suggested that the 2,4-D catabolic genes were located on the chromosome of this strain. Mutants of Burkholderia strain RASC unable to degrade 2,4-D (2,4-D- strains) were obtained by insertional inactivation with Tn5. One such mutant (d1) was shown to have Tn5 inserted in tfdARASC, which encodes 2,4-D/alpha-ketoglutarate dioxygenase. This is the first reported example of a chromosomally encoded tfdA. The tfdARASC gene was cloned from a library of wild-type Burkholderia strain RASC DNA and shown to express 2,4-D/alpha-ketoglutarate dioxygenase activity in Escherichia coli. The DNA sequence of the gene was determined and shown to be similar, although not identical, to those of isofunctional genes from other bacteria. Moreover, the gene product (TfdARASC) was purified and shown to be similar in molecular weight, amino-terminal sequence, and reaction mechanism to the canonical TfdA of Alcaligenes eutrophus JMP134. The data presented here indicate that tfdA genes can be found on the chromosome of some bacterial species and suggest that these catabolic genes are rather mobile and may be transferred by means other than conjugation. PMID:8779585

  19. Oscillating behavior of carbohydrate granule formation and dinitrogen fixation in the cyanobacterium Cyanothece sp. strain ATCC 51142

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

    It has been shown that some aerobic, unicellular, diazotrophic cyanobacteria temporally separate photosynthetic O2 evolution and oxygen-sensitive N2 fixation. Cyanothece sp. ATCC strain 51142 is an aerobic, unicellular, diazotrophic cyanobacterium that fixes N2 during discrete periods of its cell cycle. When the bacteria are maintained under diurnal light-dark cycles, N2 fixation occurs in the dark. Similar cycling is observed in continuous light, implicating a circadian rhythm. Under N2-fixing conditions, large inclusion granules form between the thylakoid membranes. Maximum granulation, as observed by electron microscopy, occurs before the onset of N2 fixation, and the granules decrease in number during the period of N2 fixation. The granules can be purified from cell homogenates by differential centrifugation. Biochemical analyses of the granules indicate that these structures are primarily carbohydrate, with some protein. Further analyses of the carbohydrate have shown that it is a glucose polymer with some characteristics of glycogen. It is proposed that N2 fixation is driven by energy and reducing power stored in these inclusion granules. Cyanothece sp. strain ATCC 51142 represents an excellent experimental organism for the study of the protective mechanisms of nitrogenase, metabolic events in cyanobacteria under normal and stress conditions, the partitioning of resources between growth and storage, and biological rhythms.

  20. Degradation of Glyoxylate and Glycolate with ATP Synthesis by a Thermophilic Anaerobic Bacterium, Moorella sp. Strain HUC22-1?

    PubMed Central

    Sakai, Shinsuke; Inokuma, Kentaro; Nakashimada, Yutaka; Nishio, Naomichi

    2008-01-01

    The thermophilic homoacetogenic bacterium Moorella sp. strain HUC22-1 ferments glyoxylate to acetate roughly according to the reaction 2 glyoxylate ? acetate + 2 CO2. A batch culture with glyoxylate and yeast extract yielded 11.7 g per mol of cells per substrate, which was much higher than that obtained with H2 plus CO2. Crude extracts of glyoxylate-grown cells catalyzed the ADP- and NADP-dependent condensation of glyoxylate and acetyl coenzyme A (acetyl-CoA) to pyruvate and CO2 and converted pyruvate to acetyl-CoA and CO2, which are the key reactions of the malyl-CoA pathway. ATP generation was also detected during the key enzyme reactions of this pathway. Furthermore, this bacterium consumed l-malate, an intermediate in the malyl-CoA pathway, and produced acetate. These findings suggest that Moorella sp. strain HUC22-1 can generate ATP by substrate-level phosphorylation during glyoxylate catabolism through the malyl-CoA pathway. PMID:18083850

  1. Characterization of the Polyurethanolytic Activity of Two Alicycliphilus sp. Strains Able To Degrade Polyurethane and N-Methylpyrrolidone?

    PubMed Central

    Oceguera-Cervantes, Alejandro; Carrillo-García, Agustín; López, Néstor; Bolaños-Nuñez, Sandra; Cruz-Gómez, M. Javier; Wacher, Carmen; Loza-Tavera, Herminia

    2007-01-01

    Two bacterial strains (BQ1 and BQ8) were isolated from decomposed soft foam. These were selected for their capacity to grow in a minimal medium (MM) supplemented with a commercial surface-coating polyurethane (PU) (Hydroform) as the carbon source (MM-PUh). Both bacterial strains were identified as Alicycliphilus sp. by comparative 16S rRNA gene sequence analysis. Growth in MM-PUh showed hyperbolic behavior, with BQ1 producing higher maximum growth (17.8 ± 0.6 mg·ml?1) than BQ8 (14.0 ± 0.6 mg·ml?1) after 100 h of culture. Nuclear magnetic resonance, Fourier transform infrared (IR) spectroscopy, and gas chromatography-mass spectrometry analyses of Hydroform showed that it was a polyester PU type which also contained N-methylpyrrolidone (NMP) as an additive. Alicycliphilus sp. utilizes NMP during the first stage of growth and was able to use it as the sole carbon and nitrogen source, with calculated Ks values of about 8 mg·ml?1. Enzymatic activities related to PU degradation (esterase, protease, and urease activities) were tested by using differential media and activity assays in cell-free supernatants of bacterial cultures in MM-PUh. Induction of esterase activity in inoculated MM-PUh, but not that of protease or urease activities, was observed at 12 h of culture. Esterase activity reached its maximum at 18 h and was maintained at 50% of its maximal activity until the end of the analysis (120 h). The capacity of Alicycliphilus sp. to degrade PU was demonstrated by changes in the PU IR spectrum and by the numerous holes produced in solid PU observed by scanning electron microscopy after bacterial culture. Changes in the PU IR spectra indicate that an esterase activity is involved in PU degradation. PMID:17693569

  2. Isolation and characterization of alkane-utilizing Nocardioides sp. strain CF8.

    PubMed

    Hamamura, N; Arp, D J

    2000-05-01

    A butane-utilizing bacterial strain CF8 was isolated and identified as a member of the genus Nocardioides from chemotaxonomic and 16S rDNA sequence analysis. Strain CF8 grew on alkanes ranging from C(2) to C(16) in addition to butane and various other substrates including primary alcohols, carboxylic acids, and phenol. Butane degradation by strain CF8 was inactivated by light, a specific inactivator of copper-containing monooxygenases. The unique thermal aggregation phenomenon of acetylene-binding polypeptides was also observed for strain CF8. These results suggest that butane monooxygenase in strain CF8 is a third example of the copper-containing monooxygenases previously described in ammonia oxidizers and methanotrophs. PMID:10779707

  3. Di(2-ethylhexyl) phthalate biodegradation and denitrification by a Pseudoxanthomonas sp. strain.

    PubMed

    Meng, Xuezheng; Niu, Guilong; Yang, Weiming; Cao, Xiangsheng

    2015-03-01

    A bacterial strain (designated as N4) of Pseudoxanthomonas was isolated from a denitrification biofilter reactor. This study examined its degradation capability of di(2-ethylhexyl) phthalate (DEHP) and its denitrification ability. All results showed that, strain N4 could use DEHP as a carbon and energy source. Strain N4 demonstrated good DEHP degradation ability over a broad pH and temperature range. The optimal temperature and pH for DEHP degradation were 32°C and 6.0, respectively. The kinetics of DEHP degradation by strain N4 were exponential in nature. Strain N4 showed denitrification ability and could reduce nitrate and nitrite but not with DEHP as its carbon source. PMID:25596917

  4. Comparative amperometric study of uptake hydrogenase and hydrogen photoproduction activities between heterocystous cyanobacterium Anabaena cylindrica B629 and nonheterocystous cyanobacterium Oscillatoria sp. strain Miami BG7

    SciTech Connect

    Kumazawa, S.; Mitsui, A.

    1985-08-01

    Heterocystous filamentous cyanobacterium Anabaena cylindrica B629 and nonheterocystous filamentous cyanobacterium Oscillatoria sp. strain Miami BG7 were cultured in media with N/sub 2/ as the sole nitrogen source; and activities of oxygen-dependent hydrogen uptake, photohydrogen production photooxygen evolution, and respiration were compared amperometrically under the same or similar experimental conditions for both strains. Distinct differences in these activities were observed in both strains. The rates of hydrogen photoproduction and hydrogen accumulation were significantly higher in Oscillatoria sp. strain BG7 than in A. cylindrica B629 at every light intensity tested. The major reason for the difference was attributable to the fact that the heterocystous cyanobacterium had a high rate of oxygen-dependent hydrogen consumption activity and the nonheterocystous cyanobacterium did not. The activity of oxygen photoevolution and respiration also contributed to the difference. Oscillatoria sp. strain BG7 had lower O/sub 2/ evolution and higher respiration than did A. cylindrica B629. Thus, the effect of O/sub 2/ on hydrogen photoproduction was minimized in Oscillatoria sp. strain BG7. 32 references, 5 figures.

  5. Characterization of biphenyl catabolic genes of gram-positive polychlorinated biphenyl degrader rhodococcus sp. strain RHA1

    SciTech Connect

    Masai, Eiji; Hatta, Takashi; Kimbara, Kazuhide [Research Development Corporation of Japan, Shinsan (Japan)] [and others

    1995-06-01

    Rhodococcus sp. strain RHA1 is a gram-positive polychlorinated biphenyl (PCB) degrader which can degrade 10 ppm of PCB-48 (equivalent to Aroclor 1248), including tri-, tetra-, and pentachlorobiphenyls, in a few days. We isolated the 7.6-kb EcoRI-BamHI fragment carrying the biphenyl catabolic genes of RHA1 and determined their nucleotide sequence. On the basis of deduced amino acid sequence homology, we identified six bph genes, bphA1A2A3A4, bphB, and bphC, that are responsible for the initial three steps of biphenyl degradation. The order of bph genes in RHA1 is bphA1A2A3A4-bphC-bphB. This gene order differs from that of other PCB degraders reported previously. The amino acid sequences deduced from the RHA1 bph genes have a higher degree of homology with the tod genes from Pseudomonas putida F1 (49 to 79%) than with the bph genes of Pseudomonas sp. strains KF707 and KKS102 (30-65%). FIn Escherichia coli, bphA gene activity was not observed even when expression vectors were used. The activities of bphB and bphC, however, were confirmed by observing the transformation of biphenyl to a meta-cleavage compound with the aid of benzene dioxygenase activity that complemented the bphA gene activity (S. Irie, S. Djoi, T. Yorifuji, M. Takagi, and K. Yano, J. Bacteriol. 169:5174-5179, 1987). The expected products of the cloned bph genes, except bphA3, were observed in E. coli in an in vitro transcription-translation system. Insertion mutations of bphA1 and bphC of Rhodococcus sp. strain RHA1 were constructed by gene replacement with cloned gene fragments. The bphA1 and bphC insertion mutants lost the ability to grow on biphenyl, demonstrating that the cloned bph genes are essential for biphenyl catabolism in this strain. 31 refs., 5 figs., 2 tabs.

  6. TRANSFORMATION OF SUBSTITUTED FLUORENES AND FLUORENE ANALOGUES BY PSEUDOMONAS SP. STRAINS F274

    EPA Science Inventory

    Pseudomonas sp. F274, previously shown to catabolize fluorene via fluorenone and its angular deoxygenation, 2',3'-dihydroxy-2-carboxybiphenol, phthalate protocatechuate, was examined for its ability to transform substituted fluorenes and S- and N-heterocyclic analogues. alogen- a...

  7. Identification of Sesquiterpene Synthases from Nostoc punctiforme PCC 73102 and Nostoc sp. Strain PCC 7120

    Microsoft Academic Search

    Sean A. Agger; Fernando Lopez-Gallego; Thomas R. Hoye; Claudia Schmidt-Dannert

    2008-01-01

    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.

  8. Upregulation of Plasmid Genes during Stationary Phase in Synechocystis sp. Strain PCC 6803, a Cyanobacterium

    PubMed Central

    Berla, Bertram M.

    2012-01-01

    We analyzed DNA microarrays to identify highly expressed genes during stationary-phase growth of Synechocystis sp. PCC 6803. Many identified genes are on endogenous plasmids, with copy numbers between 0.4 and 7 per chromosome. The promoters of such genes will be useful for synthetic biology applications with this phototrophic host. PMID:22636001

  9. Induction of toluene oxidation activity in pseudomonas mendocina KR1 and pseudomonas sp. strain ENVPC5 by chlorinated solvents and alkanes

    SciTech Connect

    McClay, K.; Streger, S.H.; Steffan, R.J. [Envirogen Inc., Lawrenceville, NJ (United States)

    1995-09-01

    Toluene oxidation activity in Pseudomonas mendocina KR1 and Pseudomonas sp. strain ENVPC5 was induced by trichloroethylene (TCE), and induction was followed by the degradation of TCE. Higher levels of toluene oxidation activity were achieved in the presence of a supplemental growth substrate such as glutamate, with levels of activity of up to 86% of that observed with toluene-induced cells. Activity in P. mendocina KR1 was also induced by cis-1,2-dichloroethylene, perchloroethylene, chloroethane, hexane, pentane, and octane, but not by trans-1,2-dichloroethylene. Toluene oxidation was not induced by TCE in Burkholderia (Pseudomonas) cepacia G4, P. putida F1, Pseudomonas sp. strain ENV110, or Pseudomonas sp. strain ENV113. 22 refs., 4 tabs.

  10. Cloning, Expression, and Cell Surface Localization of Paenibacillus sp. Strain W-61 Xylanase 5, a Multidomain Xylanase

    PubMed Central

    Ito, Yasuko; Tomita, Toshio; Roy, Narayan; Nakano, Akito; Sugawara-Tomita, Noriko; Watanabe, Seiji; Okai, Naoko; Abe, Naoki; Kamio, Yoshiyuki

    2003-01-01

    We have shown that a xylan-degrading bacterium, W-61, excretes multiple xylanases, including xylanase 5 with a molecular mass of 140 kDa. Here, we emend the previously used classification of the bacterium (i.e., Aeromonas caviae W-61) to Paenibacillus sp. strain W-61 on the basis of the nucleotide sequence of the 16S rRNA gene, and we clone and express the xyn5 gene encoding xylanase 5 (Xyn5) in Escherichia coli and study the subcellular localization of Xyn5. xyn5 encodes 1,326 amino acid residues, including a 27-amino-acid signal sequence. Sequence analysis indicated that Xyn5 comprises two family 22 carbohydrate-binding modules (CBM), a family 10 catalytic domain of glycosyl hydrolases, a family 9 CBM, a domain similar to the lysine-rich region of Clostridium thermocellum SdbA, and three S-layer-homologous (SLH) domains. Recombinant Xyn5 bound to a crystalline cellulose, Avicel PH-101, while an N-terminal 90-kDa fragment of Xyn5, which lacks the C-terminal half of the family 9 CBM, did not bind to Avicel PH-101. Xyn5 was cell bound, and the cell-bound protein was digested by exogenous trypsin to produce immunoreactive and xylanolytic fragments with molecular masses of 80 and 60 kDa. Xyn5 was exclusively distributed in the cell envelope fraction consisting of a peptidoglycan-containing layer and an associated S layer. Thus, Paenibacillus sp. strain W-61 Xyn5 is a cell surface-anchored modular xylanase possessing a functional cellulose-binding module and SLH domains. Possible cooperative action of multiple xylanases produced by strain W-61 is discussed on the basis of the modular structure of Xyn5. PMID:14660338

  11. Metabolic profiling and biological activities of bioactive compounds produced by Pseudomonas sp. strain ICTB-745 isolated from Ladakh, India.

    PubMed

    Kamal, Ahmed; Shaik, Anver Basha; Kumar, C Ganesh; Mongolla, Poornima; Rani, P Usha; Krishna, K V S Rama; Mamidyala, Suman Kumar; Joseph, Joveeta

    2012-01-01

    In an ongoing survey of the bioactive potential of microorganisms from Ladakh, India, the culture medium of a bacterial strain of a new Pseudomonas sp., strain ICTB-745, isolated from an alkaline soil sample collected from Leh, Ladakh, India, was found to contain metabolites that exhibited broad-spectrum antimicrobial and biosurfactant activities. Bioactivity-guided purification resulted in the isolation of four bioactive compounds. Their chemical structures were elucidated by (1)H and (13)C NMR, 2D-NMR (HMBC, HSQC, (1)H,(1)H-COSY, and DEPT- 135), FT-IR, and mass spectroscopic methods, and were identified as 1-hydroxyphenazine, phenazine-1-carboxylic acid (PCA), rhamnolipid-1 (RL-1), and rhamnolipid-2 (RL-2). These metabolites exhibited various biological activities like antimicrobial and efficient cytotoxic potencies against different human tumor cell lines such as HeLa, HepG2, A549, and MDA MB 231. RL-1 and RL-2 exhibited a dose-dependent antifeedant activity against Spodoptera litura, producing about 82.06% and 73.66% antifeedant activity, whereas PCA showed a moderate antifeedant activity (63.67%) at 60 microgram/cm2 area of castor leaf. Furthermore, PCA, RL-1, and RL-2 exhibited about 65%, 52%, and 47% mortality, respectively, against Rhyzopertha dominica at 20 microgram/ml. This is the first report of rhamnolipids as antifeedant metabolites against Spodoptera litura and as insecticidal metabolites against Rhyzopertha dominica. The metabolites from Pseudomonas sp. strain ICTB-745 have interesting potential for use as a biopesticide in pest control programs. PMID:22297221

  12. Reduction of Fe(II)EDTA-NO by a newly isolated Pseudomonas sp. strain DN-2 in NOx scrubber solution.

    PubMed

    Zhang, Shi-Han; Li, Wei; Wu, Cheng-Zhi; Chen, Han; Shi, Yao

    2007-10-01

    Biological reduction of nitric oxide (NO) chelated by ferrous ethylenediaminetetraacetate (Fe(II)EDTA) to N2 is one of the core processes in a chemical absorption-biological reduction integrated technique for nitrogen oxide (NOx) removal from flue gases. A new isolate, identified as Pseudomonas sp. DN-2 by 16S rRNA sequence analysis, was able to reduce Fe(II)EDTA-NO. The specific reduction capacity as measured by NO was up to 4.17 mmol g DCW(-1) h(-1). Strain DN-2 can simultaneously use glucose and Fe(II)EDTA as electron donors for Fe(II)EDTA-NO reduction. Fe(III)EDTA, the oxidation of Fe(II)EDTA by oxygen, can also serve as electron acceptor by strain DN-2. The interdependency between various chemical species, e.g., Fe(II)EDTA-NO, Fe(II)EDTA, or Fe (III)EDTA, was investigated. Though each complex, e.g., Fe(II)EDTA-NO or Fe(III)EDTA, can be reduced by its own dedicated bacterial strain, strain DN-2 capable of reducing Fe(III)EDTA can enhance the regeneration of Fe(II)EDTA, hence can enlarge NO elimination capacity. Additionally, the inhibition of Fe(II)EDTA-NO on the Fe(III)EDTA reduction has been explored previously. Strain DN-2 is probably one of the major contributors for the continual removal of NOx due to the high Fe(II)EDTA-NO reduction rate and the ability of Fe(III)EDTA reduction. PMID:17598105

  13. Purification and Characterization of Phosphonoglycans from Glycomyces sp. Strain NRRL B-16210 and Stackebrandtia nassauensis NRRL B-16338

    PubMed Central

    Yu, Xiaomin; Price, Neil P. J.; Evans, Bradley S.

    2014-01-01

    Two related actinomycetes, Glycomyces sp. strain NRRL B-16210 and Stackebrandtia nassauensis NRRL B-16338, were identified as potential phosphonic acid producers by screening for the gene encoding phosphoenolpyruvate (PEP) mutase, which is required for the biosynthesis of most phosphonates. Using a variety of analytical techniques, both strains were subsequently shown to produce phosphonate-containing exopolysaccharides (EPS), also known as phosphonoglycans. The phosphonoglycans were purified by sequential organic solvent extractions, methanol precipitation, and ultrafiltration. The EPS from the Glycomyces strain has a mass of 40 to 50 kDa and is composed of galactose, xylose, and five distinct partially O-methylated galactose residues. Per-deutero-methylation analysis indicated that galactosyl residues in the polysaccharide backbone are 3,4-linked Gal, 2,4-linked 3-MeGal, 2,3-linked Gal, 3,6-linked 2-MeGal, and 4,6-linked 2,3-diMeGal. The EPS from the Stackebrandtia strain is comprised of glucose, galactose, xylose, and four partially O-methylated galactose residues. Isotopic labeling indicated that the O-methyl groups in the Stackebrandtia phosphonoglycan arise from S-adenosylmethionine. The phosphonate moiety in both phosphonoglycans was shown to be 2-hydroxyethylphosphonate (2-HEP) by 31P nuclear magnetic resonance (NMR) and mass spectrometry following strong acid hydrolysis of the purified molecules. Partial acid hydrolysis of the purified EPS from Glycomyces yielded 2-HEP in ester linkage to the O-5 or O-6 position of a hexose and a 2-HEP mono(2,3-dihydroxypropyl)ester. Partial acid hydrolysis of Stackebrandtia EPS also revealed the presence of 2-HEP mono(2,3-dihydroxypropyl)ester. Examination of the genome sequences of the two strains revealed similar pepM-containing gene clusters that are likely to be required for phosphonoglycan synthesis. PMID:24584498

  14. Isolation and characterization of an isoproturon mineralizing Sphingomonas sp. strain SH from a French agricultural soil

    Microsoft Academic Search

    Sabir Hussain; Marion Devers-Lamrani; Najoi El Azhari; Fabrice Martin-Laurent

    2011-01-01

    The phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was found to be rapidly mineralized in\\u000a an agricultural soil in France that had been periodically exposed to IPU. Enrichment cultures from samples of this soil isolated\\u000a a bacterial strain able to mineralize IPU. 16S rRNA sequence analysis showed that this strain belonged to the phylogeny of\\u000a the genus Sphingomonas (96% similarity with Sphingomonas

  15. Biodegradation of bisphenol A by cells and cell lysate from Sphingomonas sp. strain AO1

    Microsoft Academic Search

    Miho Sasaki; Jun-ichi Maki; Ko-ichi Oshiman; Yoshinobu Matsumura; Tetsuaki Tsuchido

    2005-01-01

    The capacity and pathway of bisphenol A [BPA; 2,2-bis(4-hydroxyphenyl)propane] degradation in Sphingomonassp. strain AO1, which was isolated from the soil of a vegetable-growing field in Japan, were investigated. The bacterial strain was able to grow in a basal mineral salt medium containing BPA as the sole carbon source (BSMB medium), and was able to degrade 115 µ g?ml-1 BPA in

  16. Isolation and partial characterization of antimicrobial compounds from a new strain Nonomuraea sp. NM94

    Microsoft Academic Search

    Boubekeur Badji; Abdellah Mostefaoui; Nasserdine Sabaou; Ahmed Lebrihi; Florence Mathieu; Elisabeth Seguin; François Tillequin

    2007-01-01

    An actinomycete strain NM94 was isolated from a Saharan soil sample by a dilution agar plating method using chitin-vitamins\\u000a B medium supplemented with penicillin. The strain presented the morphological and chemical characteristics of the genus Nonomuraea. On the basis of 16S rDNA analysis and physiological tests, this isolate was found to be quite different from the known species\\u000a of Nonomuraea

  17. Oxidation of Elemental Sulfur by Fusarium solani Strain THIF01 Harboring Endobacterium Bradyrhizobium sp

    Microsoft Academic Search

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

    2010-01-01

    Nineteen fungal strains having an ability to oxidize elemental sulfur in mineral salts medium were isolated from deteriorated\\u000a sandstones of Angkor monuments. These fungi formed clearing zone on agar medium supplemented with powder sulfur due to the\\u000a dissolution of sulfur. Representative of the isolates, strain THIF01, was identified as Fusarium solani on the basis of morphological characteristics and phylogenetic analyses.

  18. Identification of two genes, sll0804 and slr1306, as putative components of the CO2-concentrating mechanism in the cyanobacterium Synechocystis sp. strain PCC 6803.

    PubMed

    Zhang, Shulu; Spann, Kevin W; Frankel, Laurie K; Moroney, James V; Bricker, Terry M

    2008-12-01

    Insertional transposon mutations in the sll0804 and slr1306 genes were found to lead to a loss of optimal photoautotrophy in the cyanobacterium Synechocystis sp. strain PCC 6803 grown under ambient CO(2) concentrations (350 ppm). Mutants containing these insertions (4BA2 and 3ZA12, respectively) could grow photoheterotrophically on glucose or photoautotrophically at elevated CO(2) concentrations (50,000 ppm). Both of these mutants exhibited an impaired affinity for inorganic carbon. Consequently, the Sll0804 and Slr1306 proteins appear to be putative components of the carbon-concentrating mechanism in Synechocystis sp. strain PCC 6803. PMID:18931125

  19. Denitrification by a soil bacterium with phthalate and other aromatic compounds as substrates. [Pseudomonas sp. strain P136

    SciTech Connect

    Nozawa, T.; Maruyama, Y.

    1988-06-01

    A soil bacterium, Pseudomonas sp. strain P136, was isolated by selective enrichment for anaerobic utilization of o-phthalate through nitrate respiration. o-Phthalate, m-phthalate, p-phthalate, benzoate, cyclohex-1-ene-carboxylate, and cyclohex-3-ene-carboxylate were utilized by this strain under both aerobic and anaerobic conditions. m-Hydroxybenzoate and p-hydroxybenzoate were utilized only under anaerobic conditions. Cells grown anaerobically on one of these aromatic compounds also utilized all other aromatic compounds as substrates for denitrification without a lag period. On the other hand, cells grown on succinate utilized aromatic compounds after a lag period. Anaerobic growth on these substrates was dependent on the presence of nitrate and accompanied by the production of molecular nitrogen. The reduction of nitrite to nitrous oxide and the reduction of nitrous oxide to molecular nitrogen were also supported by anaerobic utilization of these aromatic compounds in this strain. Aerobically grown cells showed a lag period in denitrification with all substrates tested. Cells grown anaerobically on aromatic compounds also consumed oxygen. No lag period was observed for oxygen consumption during the transition period from anaerobic to aerobic conditions. Cells grown aerobically on one of these aromatic compounds were also adapted to utilize other aromatic compounds as substrates for respiration. However, cells grown on succinate showed a lag period during respiration with aromatic compounds.

  20. Characterization of insertion sequence IS892 and related elements from the cyanobacterium Anabaena sp. strain PCC 7120

    SciTech Connect

    Yuping Cai (Michigan State Univ. Plant Research Lab., East Lansing (United States))

    1991-09-01

    IS892, one of the several insertion sequence (IS) elements discovered in Anabaena sp. strain PCC 7120, is 1,675 bp with 24-bp near-perfect inverted terminal repeats and has two open reading frames (ORFs) that could code for proteins of 233 and 137 amino acids. Upon insertion into target sites, this IS generated an 8-bp directly repeated target duplication. A 32-bp sequence in the region between ORF1 and ORF2 is similar to the sequence of the inverted termini. Similar inverted repeats are found within each of those three segments, and the sequences of these repeats bear some similarity to the 11-bp direct repeats flanking the 11-kb insertion interrupting the nifD gene of this strain. A sequence similar to that of a binding site for the Escherichia coli integration host factor is found about 120 bp from the left end of IS892. Partial nucleotide sequences of active IS elements IS 892N and IS892T, members of the IS892 family from the same Anabaena strain, were shown to be very similar to the sequence of IS892.

  1. Isolation, characterization and antioxidative activity of C-phycocyanin from Limnothrix sp. strain 37-2-1

    PubMed Central

    Gantar, Miroslav; Simovi?, Dragan; Djilas, Sonja; Gonzalez, Walter W.; Miksovska, Jaroslava

    2012-01-01

    C-phycocyanin (C-PC) is a blue colored accessory photosynthetic pigment found in cyanobacteria. Some of the medicinal properties of Spirulina have been attributed to this pigment, which includes anticancer, antioxidant, and anti-inflammatory activity. We have screened cyanobacteria isolated from freshwater habitats in Florida for their high content of C-PC. Of 125 strains tested, one filamentous strain identified as Limnothrix sp. was selected for further research. This strain produced 18% C-PC of total dry biomass. Here we describe a simple method for obtaining C-PC of high purity without the use of ion exchange chromatography. The procedure is based on pigment precipitation from the cell lysate with an appropriate concentration of ammonium sulfate, then purification with activated carbon and chitosan, followed by a sample concentration using tangential flow filtration. We have shown that when the lower concentration of ammonium sulfate was used, C-PC with higher purity index was recovered. Characterization of C-PC from Limnothrix showed that it had an absorbance maximum at 620 nm and fluorescence at 639 nm. The molecular mass of intact C-PC was estimated to be ~50 kDa with ? and ? subunits forming dimmers. When C-PC content per unit biomass was compared to that of marketed Spirulina powder, we found that Limnothrix was superior. C-phycocyanin from Limnothrix had an antioxidative activity on DPPH free radicals similar to that found in a natural antioxidant – rutin. PMID:22353597

  2. [Extraction of surface active substance and analysis of demulsifying characteristics for the demulsifying strain Alcaligenes sp. S-XJ-1].

    PubMed

    Huang, Xiang-Feng; Zhang, Shu-Cong; Peng, Kai-Ming; Lu, Li-Jun; Liu, Jia

    2013-07-01

    Extraction and identification of surface active substance of Alcaligenes sp. S-XJ-1, as well as description of its emulsion breaking process were conducted to reveal the demulsifying characteristics of this demulsifying strain. Alkali solvent was adopted in the extraction process with conditions optimized as 35 degrees C, 0.08 mol x L(-1) of alkali concentration, 12 g x L(-1) of sample to solution ratio, and 4 h of extraction time by launching both single-factor and orthogonal tests. Under this optimal condition, the extracted surface active substance (the extraction ratio was 36.1%) achieved 77% emulsion breaking ratio for 500 mg x L(-1) within 48 h. FT-IR showed the existence of glycolipids, lipids and proteins in the surface active substance, the molecular weight of which mainly scattered between 55 and 61 256. Saccharides, lipids and proteins were identified as the three chief components in surface active substance with the content of 22.2%, 7.5% and 13.4%, respectively. The proteins were further proved to take the most responsibility for the emulsion breaking ability. Moreover, obvious difference in the emulsion breaking process was demonstrated between the original demulsifying strain S-XJ-1 and the extracted surface active substance by real time observation of Turbiscan Lab Expert. The results suggested that the demulsifying efficiency of the strain was jointly contributed by its surface active substance and demulsifying cell morphology, and the former possessed higher functional priority than the latter. PMID:24028031

  3. Biodegradation of endosulfan by Mortieralla sp. strain W8 in soil: Influence of different substrates on biodegradation.

    PubMed

    Kataoka, Ryota; Takagi, Kazuhiro; Sakakibara, Futa

    2011-10-01

    To examine the bioremediation potential of Mortierella sp. strain W8 in endosulfan contaminated soil, the fungus was inoculated into sterilized and unsterilized soil spiked with endosulfan. Wheat bran and cane molasses were used as substrates to understand the influence of different organic materials on the degradation of endosulfan in soil. Strain W8 degraded ?- and ?-endosulfan in both sterilized and unsterilized soil. In unsterilized soil with wheat bran+W8, ?- and ?- endosulfan were degraded by approximately 80% and 50%, respectively after 28 d incubation against the initial endosulfan concentration (3 mg kg(-1) dw). The corresponding values for ?- and ?-endosulfan degradation with wheat bran only were 50% and 3%. Endosulfan diol metabolite was detected after 14 d incubation in wheat bran+W8 whereas it was not found with wheat bran only. Production of endosulfan sulfate, the main metabolite of endosulfan, was suppressed with wheat bran+W8 treatment compared with wheat bran only. It was demonstrated that wheat bran is a more suitable substrate for strain W8 than cane molasses. Wheat bran+W8 is a superior fungus and substrate mix for bioremediation in soil contaminated with endosulfan. PMID:21893334

  4. Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1

    PubMed Central

    Han, Ruyang; Karaoz, Ulas; Lim, HsiaoChien; Brodie, Eoin L.

    2013-01-01

    Pelosinus spp. are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with aquifer sediment. Strain HCF1 ferments lactate to propionate and acetate (the methylmalonyl-coenzyme A [CoA] pathway was identified in the genome), and its genome encodes two [NiFe]- and four [FeFe]-hydrogenases for H2 cycling. The reduction of Cr(VI) and Fe(III) may be catalyzed by a flavoprotein with 42 to 51% sequence identity to both ChrR and FerB. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides, including dissimilatory reduction of nitrate to ammonium (two copies of NrfH and NrfA were identified along with NarGHI) and a nitric oxide reductase (NorCB). In this strain, either H2 or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of hydrogenases and nitrate and nitrite reductases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments. PMID:23064329

  5. Novel desosaminyl derivatives of dihydrochalcomycin from a genetically engineered strain of Streptomyces sp.

    PubMed

    Pageni, Binod Babu; Oh, Tae-Jin; Sohng, Jae Kyung

    2009-11-01

    Dihydrochalcomycin from Streptomyces sp. KCTC 0041BP is a 16-membered macrolide antibiotic containing two deoxysugars (D-chalcose and D-mycinose) that are O-glycosylated at the C-5 and C-20 positions, respectively. The desosamine sugar cassette was constructed from pikromycin-deoxysugar biosynthetic genes and transformed into Streptomyces sp. GerSM1, which was engineered for deletion of the genes related to TDP-D-chalcose biosynthesis (gerB, gerN and gerMI). Novel 16-membered macrolides (5-O-desosaminyl derivatives of dihydrochalcomycin) were detected by ESI-MS, LC/MS, and MS/MS thereby demonstrating combinatorial biosynthesis of the deoxysugar in 16-membered macrolide antibiotics. PMID:19590827

  6. Draft Genome Sequence of Thermoanaerobacter sp. Strain YS13, a Novel Thermophilic Bacterium

    PubMed Central

    Peng, Tingting; Pan, Siyi; Christopher, Lew; Sparling, Richard

    2015-01-01

    Here, we report the draft genome sequence of Thermoanerobacter sp. YS13, isolated from a geothermal hot spring in Yellowstone National Park, which consists of 2,713,030 bp with a mean G+C content of 34.05%. A total of 2,779 genes, including 2,707 protein-coding genes, 12 rRNAs, and 59 tRNAs were identified. PMID:26044430

  7. Draft Genome Sequence of Thermoanaerobacter sp. Strain YS13, a Novel Thermophilic Bacterium.

    PubMed

    Peng, Tingting; Pan, Siyi; Christopher, Lew; Sparling, Richard; Levin, David B

    2015-01-01

    Here, we report the draft genome sequence of Thermoanerobacter sp. YS13, isolated from a geothermal hot spring in Yellowstone National Park, which consists of 2,713,030 bp with a mean G+C content of 34.05%. A total of 2,779 genes, including 2,707 protein-coding genes, 12 rRNAs, and 59 tRNAs were identified. PMID:26044430

  8. Isolation and characterization of aniline-degrading Rhodococcus sp. strain AN5.

    PubMed

    Zhuang, Rensheng; Zhong, Wenhui; Yao, Jun; Chen, Huilun; Tian, Lin; Zhou, Yong; Wang, Fei; Bramanti, Emilia; Zaray, Gyula

    2007-11-01

    A pure culture using aniline as a sole source of carbon and energy was isolated by selective enrichment culturing on a minimum salt medium (MSM) from the Nanjing Chemical Plant, Nanjing, Jiangsu Province, China. An analysis of the 16S rRNA gene sequence and morphological and physiological characteristics showed that this strain was a member of the genus Rhodococcus, and it was designated as strain AN5. Its optimal conditions for aniline biodegradation were 30 degrees C (pH 7.0). Due to the water insolubility of aniline, growth of strain AN5 at various aniline concentrations was studied via spectrophotometry and microcalorimetry in different culture mediums. Strain AN5 not only utilized aniline as its sole carbon and energy resources, but also degraded phenol, benzoic acid and naphthalin. Glucose, peptone and ammonium sulfate, when utilized as its secondary carbon and nitrogen sources, had no active effect on the aniline biodegradation. Such findings would be valuable in the application of strain AN5 to depurate industrial waste water. PMID:17990163

  9. Isolation of an extremely acidophilic and highly efficient strain Acidithiobacillus sp. for chalcopyrite bioleaching.

    PubMed

    Feng, Shoushuai; Yang, Hailin; Xin, Yu; Zhang, Ling; Kang, Wenliang; Wang, Wu

    2012-11-01

    An extremely acidophilic sulfur-oxidizing bacterium was isolated from an industrial-scale bioheap of the Zijinshan copper mine and was named ZJJN. A tuft of flagella and a layer of thick capsule outside the cell envelope were clearly observed under transmission electron microscopy (TEM), which might be closely related to the extremely acid-proof capacity of ZJJN cells in the bioleaching system; 16S ribosomal RNA (rRNA) phylogeny showed that the isolated strain was highly homologous to the genera of Acidithiobacillus. The optimum temperature of ZJJN was determined at 30 °C and pH at 1.0. It was capable of growth at even pH 0. Strain ZJJN can utilize reduced sulfur as an energy source but not with organics or ferrous ion. Strain ZJJN was sensitive to all antibiotics with different concentrations; when it showed a certain resistance to different concentrations of Cu(2+). In the mixed strains of ZJJN and A. ferrooxidans system (initial pH 1.0), the copper-leaching efficiency was up to 60.1 %, which was far higher than other systems. Scanning electron microscopy (SEM) analysis showed that less jarosite precipitation was produced in the most efficient system. The extremely acidophilic strain ZJJN would be of great potential in the application of chalcopyrite bioleaching. PMID:22872498

  10. Role of Sigma Factors in Controlling Global Gene Expression in Light\\/Dark Transitions in the Cyanobacterium Synechocystis sp. Strain PCC 6803

    Microsoft Academic Search

    Tina C. Summerfield; Louis A. Sherman

    2007-01-01

    We report on differential gene expression in the cyanobacterium Synechocystis sp. strain PCC 6803 after light-dark transitions in wild-type, sigB, and sigD strains. We also studied the effect of day length in the presence of glucose on a sigB sigE mutant. Our results indicated that the absence of SigB or SigD predominately altered gene expression in the dark or in

  11. A Serine Protease-Encoding Gene (aprII) of Alteromonas sp. Strain O-7 Is Regulated by the Iron Uptake Regulator (Fur) Protein

    Microsoft Academic Search

    HIROSHI TSUJIBO; KATSUSHIRO MIYAMOTO; TAKASHI OKAMOTO; HIDEYUKI ORIKOSHI; YOSHIHIKO INAMORI

    2000-01-01

    The ferric uptake regulator (Fur) box-like sequence was located upstream of the serine protease-encoding gene (aprII) from a marine bacterium, Alteromonas sp. strain O-7. To clarify whether the production of AprII (the gene product of aprII) is regulated by the environmental iron concentrations, this strain was cultured under iron-depleted or iron-rich conditions and the level of AprII in the culture

  12. Nucleotide sequences of two cellulase genes from alkalophilic Bacillus sp. strain N-4 and their strong homology.

    PubMed Central

    Fukumori, F; Sashihara, N; Kudo, T; Horikoshi, K

    1986-01-01

    Two genes for cellulases of alkalophilic Bacillus sp. strain N-4 (ATCC 21833) have been sequenced. From the DNA sequences the cellulases encoded in the plasmids pNK1 and pNK2 consist of 488 and 409 amino acids, respectively. The DNA and protein sequences of the pNK1-encoded cellulase are related to those of the pNK2-encoded cellulase. The pNK2-encoded cellulase lacks the direct repeat sequence of a stretch of 60 amino acids near the C-terminal end of the pNK1-encoded cellulase. The duplication of the cellulase genes and the formation of the direct repeat in the pNK1-encoded cellulase occurred at almost the same time. PMID:3782013

  13. Factors affecting the photoproduction of ammonia from dinitrogen and water by the cyanobacterium Anabaena sp. strain ATCC 33047

    SciTech Connect

    Ramos, J.L.; Guerrero, M.G.; Losada, M.

    1987-04-01

    Synthesis of ammonia from dinitrogen and water by suspensions of Anabaena sp. strain ATCC 33047 treated with the glutamine synthetase inhibitor L-methionine-D,L-sulfoximine is strictly dependent on light. Under otherwise optimal conditions, the yield of ammonia production is influenced by irradiance, as well as by the density, depth, and turbulence of the cell suspension. The interaction among these factors seems to determine the actual amount of light available to each single cell or filament in the suspension for the photoproduction process. Under convenient illumination, the limiting factor in the synthesis of ammonia seems to be the cellular nitrogenase activity level, but under limiting light conditions the limiting factor could, however, be the assimilatory power required for nitrogen fixation. Photosynthetic ammonia production from atmospheric nitrogen and water can operate with an efficiency of ca. 10% of its theoretical maximum, representing a remarkable process for the conversion of light energy into chemical energy.

  14. Control of nitrogenase recovery from oxygen inactivation by ammonia in the cyanobacterium anabaena sp. strain CA (ATCC 33047)

    SciTech Connect

    Smith, R.L.; Van Baalen, C. (Univ. of Texas Marine Science Institute, Port Aransas (USA)); Tabita, F.R. (Univ. of Texas, Austin (USA) Ohio State Univ., Columbus (USA))

    1990-05-01

    The control of nitrogenase recovery from inactivation by oxygen was studied in Anabaena sp. strain CA (ATCC 33047). Nitrogenase activity (acetylene reduction) in cultures grown in 1% CO{sub 2} in air was inhibited by exposure to 1% CO{sub 2}-99% O{sub 2} and allowed to recover in the presence of high oxygen tensions. Cultures exposed to hyperbaric levels of oxygen in the presence of 10 mM NH{sub 4}NO{sub 3} were incapable of regaining nitrogenase activity, whereas control cultures returned to 65 to 80% of their original activity within about 3 h after exposure to high oxygen tension. In contrast to the regulation of heterocyst differentiation and nitrogenase synthesis, recovery from oxygen inactivation in this organism was shown to be under the control of NH{sub 4}{sup +} rather than NO{sub 3}{sup {minus}}.

  15. Purification and structure elucidation of three naturally bioactive molecules from the new terrestrial Streptomyces sp. TN17 strain.

    PubMed

    Smaoui, Slim; Mellouli, Lotfi; Lebrihi, Ahmed; Coppel, Yannick; Fguira, Lilia Fourati Ben; Mathieu, Florence

    2011-04-01

    Thirty litres of fermentation broth was extracted from the newly isolated Streptomyces sp. strain TN17 and various separation and purification steps led to the isolation of three pure bioactive compounds (1-3). Compound 1: cyclo (L-Leu-L-Arg), a diketopiperazine 'DKP' derivative; 2: di-(2-ethylhexyl) phthalate, a phthalate derivative; and 3: cyclo 1-[2-(cyclopentanecarbonyl-3-phenyl-propionyl]-pyrrolidine-2-carboxylic acid (1-carbamoyl-propyl)-amide, a cyclic tetrapeptide derivative. The chemical structure of these three active compounds was established on the basis of spectroscopic studies (MS and NMR) and by comparison with data from the literature. According to our biological studies, the pure compounds (1-3) possess antibacterial and antifungal activities. PMID:21331973

  16. Partial Chemical and Physical Characterization of Two Extracellular Polysaccharides Produced by Marine, Periphytic Pseudomonas sp. Strain NCMB 2021

    PubMed Central

    Christensen, Bjørn E.; Kjosbakken, Johs; Smidsrød, Olav

    1985-01-01

    The marine bacterium Pseudomonas sp. strain NCMB 2021, which can attach to solid, and especially hydrophobic, surfaces, elaborates two different extracellular polysaccharides in batch cultures. One (polysaccharide A) was produced only during exponential growth and contained glucose, galactose, glucuronic acid, and galacturonic acid in a molar ratio of 1.00:0.81:0.42:0.32. It produced viscous solutions, formed gels at high concentrations, and precipitated with several multivalent cations. The other (polysaccharide B) was released at the end of the exponential phase and in the stationary phase. It contained equimolar amounts of N-acetylglucosamine, 2-keto-3-deoxyoctulosonic acid, an unidentified 6-deoxyhexose, and also O-acetyl groups. Despite its high molecular weight (105 to 106 as judged by gel filtration), the polysaccharide produced aqueous solutions with very low viscosities and was also soluble in 90% aqueous phenol, 80% methanol, and 80% ethanol. PMID:16346916

  17. A Desaturase Gene Involved in the Formation of 1,14-Nonadecadiene in Synechococcus sp. Strain PCC 7002

    PubMed Central

    Mendez-Perez, Daniel; Herman, Nicolaus A.

    2014-01-01

    The marine cyanobacterium Synechococcus sp. strain PCC 7002 synthesizes two alkenes, 1-nonadecene and 1,14-nonadecadiene. Whereas the genetic basis for the biosynthesis of the terminal double bond in both alkenes has been characterized, the origin of the internal double bond in 1,14-nonadecadiene has not. In this study, we demonstrate that a gene encoding an uncharacterized desaturase is involved in the formation of the internal double bond of 1,14-nonadecadiene. Further, at low temperatures, the desaturase gene is essential for growth, and in wild-type cells the levels of 1,14-nonadecadiene increase relative to that of cells grown at 38°C. These data suggest that 1,14-nonadecadiene plays a role in responding to cold stress. PMID:25063658

  18. Degradation of Microcystin-LR and RR by a Stenotrophomonas sp. Strain EMS Isolated from Lake Taihu, China

    PubMed Central

    Chen, Jian; Hu, Liang Bin; Zhou, Wei; Yan, Shao Hua; Yang, Jing Dong; Xue, Yan Feng; Shi, Zhi Qi

    2010-01-01

    A bacterial strain EMS with the capability of degrading microcystins (MCs) was isolated from Lake Taihu, China. The bacterium was tentatively identified as a Stenotrophomonas sp. The bacterium could completely consume MC-LR and MC-RR within 24 hours at a concentration of 0.7 ?g/mL and 1.7 ?g/mL, respectively. The degradation of MC-LR and MC-RR by EMS occurred preferentially in an alkaline environment. In addition, mlrA gene involved in the degradation of MC-LR and MC-RR was detected in EMS. Due to the limited literature this gene has rare homologues. Sequencing analysis of the translated protein from mlrA suggested that MlrA might be a transmembrane protein, which suggests a possible new protease family having unique function. PMID:20479990

  19. Nucleotide sequence analysis of genes encoding a toluene/benzene-2-monooxygenase from pseudomonas sp. strain JS150

    SciTech Connect

    Johnson, G.R.; Olsen, R.H. [Univ. of Michigan Medical School, Ann Arbor, MI (United States)

    1995-09-01

    Pseudomonas sp. strain JS150 metabolizes benzene and alkyl- and chloro-substituted benzenes by using dioxygenase-initiated pathways coupled with multiple downstream metabolic pathways to accommodate catechol metabolism. By cloning genes encoding benzene-degradative enzymes, strain JS150 was also found to carry genes for a toluene/benzene-2-monooxygenase. The gene cluster encoding a 2-monooxygenase and its cognate regulator was cloned from a plasmid carried by strain JS150. Oxygen ({sup 18}O{sub 2}) incorporation experiments using Pseudomonas aeruginosa strains carrying the cloned genes confirmed toluene hydroxylation was catalyzed through an authentic monooxygenase reaction to yield ortho-cresol. Encoding the toluene-2-monooxygenase and regulatory gene product was localized in two regions of the cloned fragment. The nucleotide sequence of the toluene/benzene-2-monooxygenase locus was determined, revealing six open reading frames that were then designated tbmA, tbmB, tbmC, tbmD, tbmE, and tbmF. The deduced amino acid sequences for these genes showed the presence of motifs similar to well-conserved functional domains of multicomponent oxygenases. This analysis allowed the tentative identification of two terminal oxygenase subunits (TbmB and TbmD) and an electron transport protein (TbmF) for the monooxygenase enzyme. All the tbm polypeptides shared significant homology with protein components from other bacterial multicomponent monooxygenases. Overall, the tbm gene products shared greater similarity with polypeptides from the phenol hydroxylases of Pseudomo-KR1 and Burkholderia (Pseudomonas) picketti PKO1. The relationship found between the phenol hydroxlases and a toluene-2-monooxygenase, characterized in this study for the first time at the nucleotide sequence level, suggested DNA probes used for surveys of environmental populations should be carefully selected to reflect DNA sequences corresponding to the metabolic pathway of interest. 58 refs., 8 figs., 1 tab.

  20. Cloning of a Novel Nicotine Oxidase Gene from Pseudomonas sp. Strain HZN6 Whose Product Nonenantioselectively Degrades Nicotine to Pseudooxynicotine

    PubMed Central

    Qiu, Jiguo; Ma, Yun; Zhang, Jing; Wen, Yuezhong

    2013-01-01

    Pseudomonas sp. strain HZN6 utilizes nicotine as its sole source of carbon, nitrogen, and energy. However, its catabolic mechanism has not been elucidated. In this study, self-formed adaptor PCR was performed to amplify the upstream sequence of the pseudooxynicotine amine oxidase gene. A 1,437-bp open reading frame (designated nox) was found to encode a nicotine oxidase (NOX) that shows 30% amino acid sequence identity with 6-hydroxy-l-nicotine oxidase from Arthrobacter nicotinovorans. The nox gene was cloned into a broad-host-range cloning vector and transferred into the non-nicotine-degrading bacteria Escherichia coli DH5? (DH-nox) and Pseudomonas putida KT2440 (KT-nox). The transconjugant KT-nox obtained nicotine degradation ability and yielded an equimolar amount of pseudooxynicotine, while DH-nox did not. Reverse transcription-PCR showed that the nox gene is expressed in both DH5? and KT2440, suggesting that additional factors required for nicotine degradation are present in a Pseudomonas strain(s), but not in E. coli. The mutant of strain HZN6 with nox disrupted lost the ability to degrade nicotine, but not pseudooxynicotine. These results suggested that the nox gene is responsible for the first step of nicotine degradation. The (RS)-nicotine degradation results showed that the two enantiomers were degraded at approximately the same rate, indicating that NOX does not show chiral selectivity. Site-directed mutagenesis revealed that both the conserved flavin adenine dinucleotide (FAD)-binding GXGXXG motif and His456 are essential for nicotine degradation activity. PMID:23335761

  1. Three Types of Taxis Used in the Response of Acidovorax sp. Strain JS42 to 2-Nitrotoluene

    PubMed Central

    Rabinovitch-Deere, Christine A.

    2012-01-01

    Acidovorax sp. strain JS42 is able to utilize 2-nitrotoluene (2NT) as its sole carbon, nitrogen, and energy source. We report here that strain JS42 is chemotactic to 2NT and that the response is increased when cells are grown on compounds such as 2NT that are known to induce the first step of 2NT degradation. Assays with JS42 mutants unable to oxidize 2NT showed that the first step of 2NT metabolism was required for the induced response, but not for a portion of the constitutive response, indicating that 2NT itself is an attractant. The 2NT metabolite nitrite was shown to be a strong attractant for strain JS42, and sufficient nitrite was produced during the taxis assay to account for a large part of the induced response. A mutant with an inactivated ntdY gene, which is located adjacent to the 2NT degradation genes and codes for a putative methyl-accepting chemotaxis protein, showed a defect in taxis toward 2NT that may involve a reduced response to nitrite. Responses of a mutant defective for the energy-taxis receptor, Aer, indicated that a functional aer gene is required for a substantial part of the wild-type induced response to 2NT. In summary, strain JS42 utilizes three types of taxis to sense and respond to 2NT: constitutive 2NT-specific chemotaxis to directly sense 2NT, metabolism-dependent nitrite-specific chemotaxis that may be mediated by NtdY, and energy taxis mediated by Aer. PMID:22286989

  2. Biodegradation of methyl red by Bacillus sp. strain UN2: decolorization capacity, metabolites characterization, and enzyme analysis.

    PubMed

    Zhao, Ming; Sun, Peng-Fei; Du, Lin-Na; Wang, Guan; Jia, Xiao-Ming; Zhao, Yu-Hua

    2014-05-01

    Azo dyes are recalcitrant and refractory pollutants that constitute a significant menace to the environment. The present study is focused on exploring the capability of Bacillus sp. strain UN2 for application in methyl red (MR) degradation. Effects of physicochemical parameters (pH of medium, temperature, initial concentration of dye, and composition of the medium) were studied in detail. The suitable pH and temperature range for MR degradation by strain UN2 were respectively 7.0-9.0 and 30-40 °C, and the optimal pH value and temperature were respectively 8.0 and 35 °C. Mg(2+) and Mn(2+) (1 mM) were found to significantly accelerate the MR removal rate, while the enhancement by either Fe(3+) or Fe(2+) was slight. Under the optimal degradation conditions, strain UN2 exhibited greater than 98 % degradation of the toxic azo dye MR (100 ppm) within 30 min. Analysis of samples from decolorized culture flasks confirmed biodegradation of MR into two prime metabolites: N,N'dimethyl-p-phenyle-nediamine and 2-aminobenzoic acid. A study of the enzymes responsible for the biodegradation of MR, in the control and cells obtained during (10 min) and after (30 min) degradation, showed a significant increase in the activities of azoreductase, laccase, and NADH-DCIP reductase. Furthermore, a phytotoxicity analysis demonstrated that the germination inhibition was almost eliminated for both the plants Triticum aestivum and Sorghum bicolor by MR metabolites at 100 mg/L concentration, yet the germination inhibition of parent dye was significant. Consequently, the high efficiency of MR degradation enables this strain to be a potential candidate for bioremediation of wastewater containing MR. PMID:24474566

  3. The Insertion Sequences of Anabaena sp. Strain PCC 7120 and Their Effects on Its Open Reading Frames ? †

    PubMed Central

    Wolk, C. Peter; Lechno-Yossef, Sigal; Jäger, Karin M.

    2010-01-01

    Anabaena sp. strain PCC 7120, widely studied, has 145 annotated transposase genes that are part of transposable elements called insertion sequences (ISs). To determine the entirety of the ISs, we aligned transposase genes and their flanking regions; identified the ISs' possible terminal inverted repeats, usually flanked by direct repeats; and compared IS-interrupted sequences with homologous sequences. We thereby determined both ends of 87 ISs bearing 110 transposase genes in eight IS families (http://www-is.biotoul.fr/) and in a cluster of unclassified ISs, and of hitherto unknown miniature inverted-repeat transposable elements. Open reading frames were then identified to which ISs contributed and others—some encoding proteins of predictable function, including protein kinases, and restriction endonucleases—that were interrupted by ISs. Anabaena sp. ISs were often more closely related to exogenous than to other endogenous ISs, suggesting that numerous variant ISs were not degraded within PCC 7120 but transferred from without. This observation leads to the expectation that further sequencing projects will extend this and similar analyses. We also propose an adaptive role for poly(A) sequences in ISs. PMID:20656907

  4. Photophosphorylation and oxidative phosphorylation in intact cells and chromatophores of an aerobic photosynthetic bacterium, Erythrobacter sp. strain OCh114.

    PubMed Central

    Okamura, K; Mitsumori, F; Ito, O; Takamiya, K; Nishimura, M

    1986-01-01

    Light-induced ATP synthesis was studied in intact cells and chromatophores of Erythrobacter sp. strain OCh114. ATP synthesis was measured by both the pH method and the luciferin-luciferase luminescence method. The rate of ATP synthesis was moderate (a typical value of 0.65 mol of ATP per mol of bacteriochlorophyll per min), and synthesis was inhibited by antimycin A. ATP was synthesized under illumination only under aerobic conditions and not under anaerobic conditions. This characteristic was similar to that of other light-induced energy transduction processes in this bacterial species, such as oxidation of reaction center, oxidation of cytochrome c551, and translocation of H+, which were not observed under anaerobic conditions. This phenomenon was reconciled with the fact that the Erythrobacter sp. could not grow anaerobically even in the light. The characteristics of oxidative phosphorylation and ATP hydrolysis were also investigated. The respiratory ratio of chromatophores was 2.3. Typical rates of oxidative phosphorylation by NADH and by succinate were 2.9 mol of ATP per mol of bacteriochlorophyll per min (P/O = 0.22) and 1.1 mol of ATP per mol of bacteriochlorophyll per min (P/O = 0.19), respectively. A typical rate of ATP hydrolysis was 0.25 mol of ATP per mol of bacteriochlorophyll per min in chromatophores. ATPase and adenylate kinase are also involved in the metabolism of adenine nucleotides in this bacterium. PMID:3782035

  5. Purification and biochemical characterization of a highly thermostable xylanase from Actinomadura sp. strain Cpt20 isolated from poultry compost.

    PubMed

    Taibi, Zina; Saoudi, Boudjemaa; Boudelaa, Mokhtar; Trigui, Héla; Belghith, Hafedh; Gargouri, Ali; Ladjama, Ali

    2012-02-01

    An extracellular thermostable xylanase from a newly isolated thermophilic Actinomadura sp. strain Cpt20 was purified and characterized. Based on matrix-assisted laser desorption-ionization time-of-flight mass spectrometry analysis, the purified enzyme is a monomer with a molecular mass of 20,110.13 Da. The 19 residue N-terminal sequence of the enzyme showed 84% homology with those of actinomycete endoxylanases. The optimum pH and temperature values for xylanase activity were pH 10 and 80 °C, respectively. This xylanase was stable within a pH range of 5-10 and up to a temperature of 90 °C. It showed high thermostability at 60 °C for 5 days and half-life times at 90 °C and 100 °C were 2 and 1 h, respectively. The xylanase was specific for xylans, showing higher specific activity on soluble oat-spelt xylan followed by beechwood xylan. This enzyme obeyed the Michaelis-Menten kinetics, with the K (m) and k (cat) values being 1.55 mg soluble oat-spelt xylan/ml and 388 min(-1), respectively. While the xylanase from Actinomadura sp. Cpt20 was activated by Mn(2+), Ca(2+), and Cu(2+), it was, strongly inhibited by Hg(2+), Zn(2+), and Ba(2+). These properties make this enzyme a potential candidate for future use in biotechnological applications particularly in the pulp and paper industry. PMID:22161140

  6. Identification and Characterization of the Rhizobium sp. Strain GIN611 Glycoside Oxidoreductase Resulting in the Deglycosylation of Ginsenosides

    PubMed Central

    Kim, Eun-Mi; Kim, Juhan; Seo, Joo-Hyun; Park, Jun-Seong; Kim, Duck-Hee

    2012-01-01

    Using enrichment culture, Rhizobium sp. strain GIN611 was isolated as having activity for deglycosylation of a ginsenoside, compound K (CK). The purified heterodimeric protein complex from Rhizobium sp. GIN611 consisted of two subunits with molecular masses of 63.5 kDa and 17.5 kDa. In the genome, the coding sequence for the small subunit was located right after the sequence for the large subunit, with one nucleotide overlapping. The large subunit showed CK oxidation activity, and the deglycosylation of compound K was performed via oxidation of ginsenoside glucose by glycoside oxidoreductase. Coexpression of the small subunit helped soluble expression of the large subunit in recombinant Escherichia coli. The purified large subunit also showed oxidation activity against other ginsenoside compounds, such as Rb1, Rb2, Rb3, Rc, F2, CK, Rh2, Re, F1, and the isoflavone daidzin, but at a much lower rate. When oxidized CK was extracted and incubated in phosphate buffer with or without enzyme, (S)-protopanaxadiol [PPD(S)] was detected in both cases, which suggests that deglycosylation of oxidized glucose is spontaneous. PMID:22020506

  7. Identification and characterization of the Rhizobium sp. strain GIN611 glycoside oxidoreductase resulting in the deglycosylation of ginsenosides.

    PubMed

    Kim, Eun-Mi; Kim, Juhan; Seo, Joo-Hyun; Park, Jun-Seong; Kim, Duck-Hee; Kim, Byung-Gee

    2012-01-01

    Using enrichment culture, Rhizobium sp. strain GIN611 was isolated as having activity for deglycosylation of a ginsenoside, compound K (CK). The purified heterodimeric protein complex from Rhizobium sp. GIN611 consisted of two subunits with molecular masses of 63.5 kDa and 17.5 kDa. In the genome, the coding sequence for the small subunit was located right after the sequence for the large subunit, with one nucleotide overlapping. The large subunit showed CK oxidation activity, and the deglycosylation of compound K was performed via oxidation of ginsenoside glucose by glycoside oxidoreductase. Coexpression of the small subunit helped soluble expression of the large subunit in recombinant Escherichia coli. The purified large subunit also showed oxidation activity against other ginsenoside compounds, such as Rb1, Rb2, Rb3, Rc, F2, CK, Rh2, Re, F1, and the isoflavone daidzin, but at a much lower rate. When oxidized CK was extracted and incubated in phosphate buffer with or without enzyme, (S)-protopanaxadiol [PPD(S)] was detected in both cases, which suggests that deglycosylation of oxidized glucose is spontaneous. PMID:22020506

  8. Physicochemical effects on sulfite transformation in a lipid-rich Chlorella sp. strain

    NASA Astrophysics Data System (ADS)

    Liang, Fang; Wen, Xiaobin; Luo, Liming; Geng, Yahong; Li, Yeguang

    2014-11-01

    SO2 is very rapidly hydrated to sulfurous acid in water solution at pH value above 6.0, whereby sulfite is yielded from the disassociation of protons. We aimed to improve the sulfite transformation efficiency and provide a basis for the direct utilization of SO2 from flue gas by a microalgal suspension. Chlorella sp. XQ-20044 was cultured in a medium with 20 mmol/L sodium sulfite under different physicochemical conditions. Under light conditions, sulfite concentration in the algal suspension reduced linearly over time, and was completely converted into sulfate within 8 h. The highest sulfite transformation rate (3.25 mmol/(L·h)) was obtained under the following conditions: 35°C, light intensity of 300 ?mol/(m2·s), NaHCO3 concentration of 6 g/L, initial cell density (OD540) of 0.8 and pH of 9-10. There was a positive correlation between sulfite transformation rate and the growth of Chlorella, with the conditions favorable to algal growth giving better sulfite transformation. Although oxygen in the air plays a role in the transformation of SO2- 3 to SO2- 4, the transformation is mainly dependent on the metabolic activity of algal cells. Chlorella sp. XQ-20044 is capable of tolerating high sulfite concentration, and can utilize sulfite as the sole sulfur source for maintaining healthy growth. We found that sulfite ?20 mmol/L had no obvious effect on the total lipid content and fatty acid profiles of the algae. Thus, the results suggest it is feasible to use flue gas for the mass production of feedstock for biodiesel using Chlorella sp. XQ-20044, without preliminary removal of SO2, assuming there is adequate control of the pH.

  9. Molecular nature of spontaneous modifications in gacS which cause colony phase variation in Pseudomonas sp. strain PCL1171.

    PubMed

    van den Broek, Daan; Chin-A-Woeng, Thomas F C; Bloemberg, Guido V; Lugtenberg, Ben J J

    2005-01-01

    Pseudomonas sp. strain PCL1171 displays colony phase variation between opaque phase I and translucent phase II colonies, thereby regulating the production of secondary metabolites and exoenzymes. Complementation and sequence analysis of 26 phase II mutants and of 13 wild-type phase II sectors growing out of phase I colonies showed that in all these cases the phase II phenotype is caused by spontaneous mutations in gacA or/and gacS. Mutation of gac reduced both the length of the lag phase and the generation time. Isolation and sequencing of the gacS genes from the phase II bacteria revealed one insertion as well as several random point mutations, deletions, and DNA rearrangements. Most phase II colonies reverted with a high frequency, resulting in wild-type gacA and gacS genes and a phase I phenotype. Some phase II bacteria retained the phase II phenotype but changed genotypically as a result of (re)introduction of mutations in either gacA or gacS. The reversion of gacA or gacS to the wild type was not affected by mutation of recA and recB. We conclude that in Pseudomonas sp. strain PCL1171, mutations in gacA and gacS are the basis for phase variation from phase I to phase II colonies and that, since these mutations are efficiently removed, mutations in gac result in dynamic switches between the "wild-type" population and the subpopulations harboring spontaneous mutations in gacA and or gacS, thereby enabling both populations to be maintained. PMID:15629930

  10. Role of Rhodobacter sp. Strain PS9, a Purple Non-Sulfur Photosynthetic Bacterium Isolated from an Anaerobic Swine Waste Lagoon, in Odor Remediation

    PubMed Central

    Do, Young S.; Schmidt, Thomas M.; Zahn, James A.; Boyd, Eric S.; de la Mora, Arlene; DiSpirito, Alan A.

    2003-01-01

    Temporal pigmentation changes resulting from the development of a purple color in anaerobic swine waste lagoons were investigated during a 4-year period. The major purple photosynthetic bacterium responsible for these color changes and the corresponding reductions in odor was isolated from nine photosynthetic lagoons. By using morphological, physiological, and phylogenetic characterization methods we identified the predominant photosynthetic bacterium as a new strain of Rhodobacter, designated Rhodobacter sp. strain PS9. Rhodobacter sp. strain PS9 is capable of photoorganotrophic growth on a variety of organic compounds, including all of the characteristic volatile organic compounds (VOC) responsible for the odor associated with swine production facilities (J. A. Zahn, A. A. DiSpirito, Y. S. Do, B. E. Brooks, E. E. Copper, and J. L. Hatfield, J. Environ. Qual. 30:624-634, 2001). The seasonal variations in airborne VOC emitted from waste lagoons showed that there was a 80 to 93% decrease in the concentration of VOC during a photosynthetic bloom. During the height of a bloom, the Rhodobacter sp. strain PS9 population accounted for 10% of the total community and up to 27% of the eubacterial community based on 16S ribosomal DNA signals. Additional observations based on seasonal variations in meteorological, biological, and chemical parameters suggested that the photosynthetic blooms of Rhodobacter sp. strain PS9 were correlated with lagoon water temperature and with the concentrations of sulfate and phosphate. In addition, the photosynthetic blooms of Rhodobacter sp. strain PS9 were inversely correlated with the concentrations of protein and fluoride. PMID:12620863

  11. The chlorobenzoate dioxygenase genes of Burkholderia sp. strain NK8 involved in the catabolism of chlorobenzoates

    Microsoft Academic Search

    Perigio B. Francisco Jr; Naoto Ogawa; Katsuhisa Suzuki; Kiyotaka Miyashita

    Burkholderia sp. NK8 grows abundantly on 3-chlorobenzoate (3CB), 4-chlorobenzoate (4CB) and benzoate. The genes encoding the oxidation of (chloro)benzoates (cbeABCD) and catechol (catA, catBC), the LysR-type regulatory gene cbeR and the gene cbeE with unknown function, all of which form a single cluster in NK8, were cloned and analysed. The protein sequence of chlorobenzoate 1,2-dioxygenase (CbeABC) is 50-65% identical to

  12. A halotolerant Alcanivorax sp. strain with potential application in saline soil remediation.

    PubMed

    Dastgheib, Seyed Mohammad Mehdi; Amoozegar, Mohamad Ali; Khajeh, Khosro; Ventosa, Antonio

    2011-04-01

    Biodegradation of petroleum compounds in saline environments seems intricate and needs more attention. In this study, tetracosane was used to enrich alkane-degrading bacteria from oil-contaminated saline soils. Among the isolates, strain Qtet3, with the highest 16s rRNA gene sequence similarity to Alcanivorax dieselolei B-5(T), was able to grow at a wide range of NaCl concentrations and was shown by GC analysis to degrade more than 90% of tetracosane in 10 days. This strain has at least two alkB genes and could grow on crude oil and diesel fuel, and utilize various pure aliphatic hydrocarbon substrates (from C(12) to C(34)). Highly hydrophobic cell surfaces and lack of significant surface tension reduction in the media suggest that the main mechanism of the cells for accessing substrate is to attach directly to hydrocarbon particles. Application of this strain for remediating crude oil-contaminated soils irrigated with defined saline water demonstrated that this halotolerant bacterium could survive and grow in saline soils irrigated with NaCl solutions up to 5% w/v, with the highest hydrocarbon degradation of 26.1% observed at 2.5% NaCl. This strain is promising for future industrial applications especially in bioremediation of saline soils and wastes. PMID:21153810

  13. Phenotypic and genotypic characterization of some Moorella sp. strains isolated from canned foods.

    PubMed

    Carlier, Jean-Philippe; Bedora-Faure, Marie

    2006-11-01

    Six anaerobic thermophilic strains isolated from various spoiled cans including fish soups and cooked meats were characterized using a polyphasic approach. These strains were closely related to Moorella thermoacetica or Moorella thermoautotrophica species. Except the spacer region between the 16S and the 23S rRNA genes, which exhibited two PCR profiles distinguishing both species, the genotypic and phylogenetic analyses grouped these isolates, the type strains, and all sequences of Moorella thermoacetica and Moorella thermoautotrophica species contained in the GenBank database within a unique cluster. Moreover, all 16S rDNA sequences shared two characteristic DNA fragments, which were highly specific of Moorella thermoacetica/Moorella thermoautotrophica strains. However, taken together, the phenotypic, physiological and genotypic methods were conflicting, and did not enable affiliation of the isolates with one or the other species. To our knowledge, this study represents the first report of characterization of Moorella species isolated from spoiled cans. These results and previous work, very strongly argue in favor of questioning the taxonomic status of the two species. PMID:16458469

  14. Draft Genome Sequence of a Metabolically Diverse Antarctic Supraglacial Stream Organism, Polaromonas sp. Strain CG9_12, Determined Using Pacific Biosciences Single-Molecule Real-Time Sequencing Technology

    PubMed Central

    Smith, Heidi J.; Ramaraj, Thiruvarangan

    2014-01-01

    Polaromonas species are found in a diversity of environments and are particularly common in icy ecosystems. Polaromonas sp. strain CG9_12 is an aerobic, Gram-negative, catalase-positive, white-pigmented bacterium of the Proteobacteria phylum. Here, we present the draft genome sequence of Polaromonas sp. strain CG9_12, isolated from an Antarctic supraglacial stream. PMID:25477404

  15. Draft Genome Sequence of a Metabolically Diverse Antarctic Supraglacial Stream Organism, Polaromonas sp. Strain CG9_12, Determined Using Pacific Biosciences Single-Molecule Real-Time Sequencing Technology.

    PubMed

    Smith, Heidi J; Foreman, Christine M; Ramaraj, Thiruvarangan

    2014-01-01

    Polaromonas species are found in a diversity of environments and are particularly common in icy ecosystems. Polaromonas sp. strain CG9_12 is an aerobic, Gram-negative, catalase-positive, white-pigmented bacterium of the Proteobacteria phylum. Here, we present the draft genome sequence of Polaromonas sp. strain CG9_12, isolated from an Antarctic supraglacial stream. PMID:25477404

  16. Characterization of the wzc gene from Pantoea sp. strain PPE7 and its influence on extracellular polysaccharide production and virulence on Pleurotus eryngii.

    PubMed

    Kim, Min Keun; Lee, Young Han; Kim, Hyeran; Lee, Jeongyeo; Ryu, Jae San

    2015-01-01

    To characterize of the pathogenicity gene from the soft rot pathogen Pantoea sp. PPE7 in Pleurotus eryngii, we constructed over 10,000 kanamycin-resistant transposon mutants of Pantoea sp. strain PPE7 by transposon mutagenesis. One mutant, Pantoea sp. NPPE9535, did not cause a soft rot disease on Pleurotus eryngii was confirmed by the pathogenicity test. The transposon was inserted into the wzc gene and the disruption of the wzc gene resulted in the reduction of polysaccharide production and abolished the virulence of Pantoea sp. strain PPE7 in P. eryngii. Analysis of the hydropathic profile of this protein indicated that it is composed of two main domains: an N-terminal domain including two transmembrane ?-helices and a C-terminal cytoplasmic domain consisting of a tyrosine-rich region. Comparative analysis indicated that the amino acid sequence of Wzc is similar to that of a number of proteins involved in the synthesis or export of polysaccharides in other bacterial species. Purified GST-Wzc was found to affect the phosphorylation of tyrosine residue in vivo. These results showed that the wzc gene might play an important role in the virulence of Pantoea sp. strain PPE7 in P. eryngii. PMID:25183654

  17. Comprehensive Analysis of a Vibrio parahaemolyticus Strain Extracellular Serine Protease VpSP37

    PubMed Central

    Bennici, Carmelo; Quatrini, Paola; Catania, Valentina; Mazzola, Salvatore; Ghersi, Giulio; Cuttitta, Angela

    2015-01-01

    Proteases play an important role in the field of tissue dissociation combined with regenerative medicine. During the years new sources of proteolytic enzymes have been studied including proteases from different marine organisms both eukaryotic and prokaryotic. Herein we have purified a secreted component of an isolate of Vibrio parahaemolyticus, with electrophoretic mobilities corresponding to 36 kDa, belonging to the serine proteases family. Sequencing of the N-terminus enabled the in silico identification of the whole primary structure consisting of 345 amino acid residues with a calculated molecular mass of 37.4 KDa. The purified enzyme, named VpSP37, contains a Serine protease domain between residues 35 and 276 and a canonical Trypsin/Chimotrypsin 3D structure. Functional assays were performed to evaluate protease activity of purified enzyme. Additionally the performance of VpSP37 was evaluated in tissue dissociations experiments and the use of such enzyme as a component of enzyme blend for tissue dissociation procedures is strongly recommended. PMID:26162075

  18. The bile acid-inducible baiF gene from Eubacterium sp. strain VPI 12708 encodes a bile acid-coenzyme

    Microsoft Academic Search

    Darrell H. Mallonee; James E. Wells; Ingemar Björkhem; Phillip B. Hylemon

    The human intestinal Eubacterium sp. strain VPI 12708 has been shown to have a multistep biochemical path- way for bile acid 7 a -dehydroxylation. A bile acid-inducible operon encoding 9 open reading frames has been cloned and sequenced from this organism. Several of the genes in this operon have been shown to catalyze specific reactions in the 7 a -dehydroxylation

  19. Draft Genome Sequence of Nitrincola sp. Strain A-D6, an Arsenic-Resistant Gammaproteobacterium Isolated from a Salt Flat

    PubMed Central

    Valdés, Natalia; Rivera-Araya, Javier; Bijman, Jonathan; Escudero, Lorena; Fernández, Sebastián; Ferrer, Alonso; Chávez, Renato

    2014-01-01

    We report Nitrincola sp. strain A-D6, which was characterized as an arsenic-resistant bacterium isolated from the Ascotán Salt Flat in northern Chile. The size of the genome is 3,795,776 bp, with a G+C content of 49.96%. Genes for the arsenic-resistant Ars system and arsenic oxidation have been encoded. PMID:25414492

  20. Draft Genome Sequence of Paenibacillus sp. Strain DMB20, Isolated from Alang Ship-Breaking Yard, Which Harbors Genes for Xenobiotic Degradation

    PubMed Central

    Shah, Binal; Jain, Kunal; Patel, Namrata; Pandit, Ramesh; Patel, Anand; Joshi, Chaitanya G.

    2015-01-01

    Paenibacillus sp. strain DMB20, in cometabolism with other Proteobacteria and Firmicutes, exhibits azoreduction of textile dyes. Here, we report the draft genome sequence of this bacterium, consisting of 6,647,181 bp with 7,668 coding sequences (CDSs). The data presented highlight multiple sets of functional genes associated with xenobiotic compound degradation. PMID:26067950

  1. Convergent synthesis of a tetrasaccharide repeating unit of the O-specific polysaccharide from the cell wall lipopolysaccharide of Azospirillum brasilense strain Sp7

    PubMed Central

    Dhara, Debashis; Misra, Anup Kumar

    2014-01-01

    Summary A straightforward convergent synthesis has been carried out for the tetrasaccharide repeating unit of the O-specific cell wall lipopolysaccharide of the strain Sp7 of Azospirillum brasilense. The target tetrasaccharide has been synthesized from suitably protected monosaccharide intermediates in 42% overall yield in seven steps by using a [2 + 2] block glycosylation approach. PMID:24605150

  2. Draft Genome Sequence of Micrococcus sp. Strain MS-AsIII-49, an Arsenate-Reducing Isolate from Tropical Metal-Rich Sediment

    PubMed Central

    Costa, Patrícia S.; Tschoeke, Diogo A.; Silva, Bruno S. O.; Thompson, Fabiano; Reis, Mariana P.; Chartone-Souza, Edmar

    2015-01-01

    Micrococcus sp. strain MS-AsIII-49, which was isolated from a tropical metal-polluted stream sediment in Brazil, has the ability to reduce AsV to AsIII. Analysis of its draft genome revealed 186 contigs with a total size of 2,440,924 bp encoding several metal resistance genes. PMID:25883272

  3. Draft Genome Sequence of Paenibacillus sp. Strain DMB20, Isolated from Alang Ship-Breaking Yard, Which Harbors Genes for Xenobiotic Degradation.

    PubMed

    Shah, Binal; Jain, Kunal; Patel, Namrata; Pandit, Ramesh; Patel, Anand; Joshi, Chaitanya G; Madamwar, Datta

    2015-01-01

    Paenibacillus sp. strain DMB20, in cometabolism with other Proteobacteria and Firmicutes, exhibits azoreduction of textile dyes. Here, we report the draft genome sequence of this bacterium, consisting of 6,647,181 bp with 7,668 coding sequences (CDSs). The data presented highlight multiple sets of functional genes associated with xenobiotic compound degradation. PMID:26067950

  4. Genome Sequence of "Candidatus Arthromitus" sp. Strain SFB-Mouse-NL, a Commensal Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions.

    PubMed

    Bolotin, Alexander; de Wouters, Tomas; Schnupf, Pamela; Bouchier, Christiane; Loux, Valentin; Rhimi, Moez; Jamet, Alexandre; Dervyn, Rozenn; Boudebbouze, Samira; Blottière, Hervé M; Sorokin, Alexei; Snel, Johannes; Cerf-Bensussan, Nadine; Gaboriau-Routhiau, Valérie; van de Guchte, Maarten; Maguin, Emmanuelle

    2014-01-01

    "Candidatus Arthromitus" sp. strain SFB-mouse-NL (SFB, segmented filamentous bacteria) is a commensal bacterium necessary for inducing the postnatal maturation of homeostatic innate and adaptive immune responses in the mouse gut. Here, we report the genome sequence of this bacterium, which sets it apart from earlier sequenced mouse SFB isolates. PMID:25035333

  5. Genome Sequence of “Candidatus Arthromitus” sp. Strain SFB-Mouse-NL, a Commensal Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions

    PubMed Central

    Bolotin, Alexander; de Wouters, Tomas; Schnupf, Pamela; Bouchier, Christiane; Loux, Valentin; Rhimi, Moez; Jamet, Alexandre; Dervyn, Rozenn; Boudebbouze, Samira; Blottière, Hervé M.; Sorokin, Alexei; Snel, Johannes; Cerf-Bensussan, Nadine; Gaboriau-Routhiau, Valérie; van de Guchte, Maarten

    2014-01-01

    “Candidatus Arthromitus” sp. strain SFB-mouse-NL (SFB, segmented filamentous bacteria) is a commensal bacterium necessary for inducing the postnatal maturation of homeostatic innate and adaptive immune responses in the mouse gut. Here, we report the genome sequence of this bacterium, which sets it apart from earlier sequenced mouse SFB isolates. PMID:25035333

  6. Draft Genome Sequence of Frankia sp. Strain QA3, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodule of Alnus nitida

    PubMed Central

    Sen, Arnab; Beauchemin, Nicholas; Bruce, David; Chain, Patrick; Chen, Amy; Walston Davenport, Karen; Deshpande, Shweta; Detter, Chris; Furnholm, Teal; Ghodbhane-Gtari, Faten; Goodwin, Lynne; Gtari, Maher; Han, Cliff; Han, James; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos; Land, Miriam L.; Markowitz, Victor; Mavrommatis, Kostas; Nolan, Matt; Nouioui, Imen; Pagani, Ioanna; Pati, Amrita; Pitluck, Sam; Santos, Catarina L.; Sur, Saubashya; Szeto, Ernest; Tavares, Fernando; Teshima, Hazuki; Thakur, Subarna; Wall, Luis; Woyke, Tanja; Wishart, Jessie

    2013-01-01

    Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different families of actinorhizal plants. We report a high-quality draft genome sequence for Frankia sp. strain QA3, a nitrogen-fixing actinobacterium isolated from root nodules of Alnus nitida. PMID:23516220

  7. Draft Genome sequence of Frankia sp. strains CN3 , an atypical, non-infective (Nod-) ineffective (Fix-) isolate from Coriaria nepalensis

    SciTech Connect

    Ghodhbane-Gtari, Faten [University of New Hampshire; Beauchemin, Nicholas [University of New Hampshire; Bruce, David [Los Alamos National Laboratory (LANL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Davenport, Karen W. [Los Alamos National Laboratory (LANL); Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Furnholm, Teal [University of New Hampshire; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Gtari, Maher [University of New Hampshire; Han, Cliff [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Nouioui, Imen [University of Tunis-El Manar, Tunisia; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Santos, Catarina [Instiuto Celular e Aplicada, Portugal; Sen, Arnab [University of North Bengal, Siliguri, India; Sur, Saubashya [University of North Bengal, Siliguri, India; Szeto, Ernest [U.S. Department of Energy, Joint Genome Institute; Tavares, Fernando [Instiuto Celular e Aplicada, Portugal; Hazuki, Teshima [Los Alamos National Laboratory (LANL); Thakur, Subarna [University of North Bengal, Siliguri, India; Wall, Luis [University of Quilmes, Argentina; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Tisa, Louis S. [University of New Hampshire

    2013-01-01

    We report here the genome sequence of Frankia sp. strain CN3, which was isolated from Coriaria nepalensis. This genome sequence is the first from the fourth lineage of Frankia, that are unable to re-infect actinorhizal plants. At 10 Mb, it represents the largest Frankia genome sequenced to date.

  8. Changes in the antenna size of Photosystem I and Photosystem II in Synechococcus sp. strain PCC 7942 grown in the presence of SANDOZ 9785 — a Photosystem II inhibitor

    Microsoft Academic Search

    Madhulika Srivastava; Devaki Bhaya; Salil Bose

    1994-01-01

    SANDOZ 9785, also known as BASF 13.338, is a pyridazinone derivative that inhibits Photosystem II (PS II) activity leading to an imbalance in the rate of electron transport through the photosystems. Synechococcus sp. strain PCC 7942 cells grown in the presence of sublethal concentration of SANDOZ 9785 (SAN 9785) for 48 hours exhibited a 20% decrease in Chl a per

  9. Draft Genome Sequence of Comamonas sp. Strain E6 (NBRC 107749), a Degrader of Phthalate Isomers through the Protocatechuate 4,5-Cleavage Pathway.

    PubMed

    Shimodaira, Jun; Kamimura, Naofumi; Hosoyama, Akira; Yamazoe, Atsushi; Fujita, Nobuyuki; Masai, Eiji

    2015-01-01

    Comamonas sp. strain E6 can degrade o-phthalate, terephthalate, and isophthalate via the protocatechuate 4,5-cleavage pathway. Here, we report the draft genome sequence of E6 in order to provide insights into its mechanisms in o-phthalate catabolism and its potential use for biotechnological applications. PMID:26089421

  10. Draft Genome Sequence of Calcium-Dependent Paenibacillus sp. Strain TCA20, Isolated from a Hot Spring Containing a High Concentration of Calcium Ions.

    PubMed

    Fujinami, Shun; Takeda-Yano, Kiyoko; Onodera, Takefumi; Satoh, Katsuya; Sano, Motohiko; Takahashi, Yuka; Narumi, Issay; Ito, Masahiro

    2014-01-01

    Calcium-dependent Paenibacillus sp. strain TCA20 was isolated from a water sample of a hot spring containing a high concentration of calcium ions. Here, we report the draft genome sequence of this bacterium, which may be the basis for the research of calcium ion homeostasis. PMID:25189580

  11. Draft Genome Sequence of Sphingobacterium sp. Strain PM2-P1-29, a Tetracycline-Degrading TetX-Expressing Aerobic Bacterium Isolated from Agricultural Soil

    PubMed Central

    Ghosh, Sudeshna; LaPara, Timothy M.

    2014-01-01

    The genome of Sphingobacterium sp. strain PM2-P1-29 was sequenced. The bacterium contains a physiologically active tet(X) gene, encoding a tetracycline-degrading monooxygenase. To our knowledge, this is the only bacterium naturally harboring tet(X) for which tetracycline degradation has been demonstrated. PMID:25301646

  12. Temporal Orchestration of Glycogen Synthase (GlgA) Gene Expression and Glycogen Accumulation in the Oceanic Picoplanktonic Cyanobacterium Synechococcus sp. Strain WH8103

    PubMed Central

    Thom, Claire

    2012-01-01

    Glycogen is accumulated during the latter half of the diel cycle in Synechococcus sp. strain WH8103 following a midday maximum in glgA (encoding glycogen synthase) mRNA abundance. This temporal pattern is quite distinct from that of Prochlorococcus and may highlight divergent regulatory control of carbon/nitrogen metabolism in these closely related picocyanobacteria. PMID:22522678

  13. Similarities between the antABC-Encoded Anthranilate Dioxygenase and the benABC-Encoded Benzoate Dioxygenase of Acinetobacter sp. Strain ADP1

    Microsoft Academic Search

    BECKY M. BUNDY; ALAN L. CAMPBELL; ELLEN L. NEIDLE

    1998-01-01

    Acinetobacter sp. strain ADP1 can use benzoate or anthranilate as a sole carbon source. These structurally similar compounds are independently converted to catechol, allowing further degradation to proceed via the b- ketoadipate pathway. In this study, the first step in anthranilate catabolism was characterized. A mutant un- able to grow on anthranilate, ACN26, was selected. The sequence of a wild-type

  14. Complete Genome Sequence of Paenibacillus sp. Strain IHBB 10380 Using PacBio Single-Molecule Real-Time Sequencing Technology.

    PubMed

    Pal, Mohinder; Swarnkar, Mohit K; Thakur, Rishu; Kiran, Shashi; Chhibber, Sanjay; Singh, Anil K; Gulati, Arvind

    2015-01-01

    The complete genome sequence of 5.77 Mb is reported for Paenibacillus sp. strain IHBB 10380, isolated from the cold desert area of the northwestern Himalayas and exhibiting amylase and cellulase activities. The gene-coding clusters predicted the presence of genes for hydrolytic enzymes in the genome. PMID:25908145

  15. Directed introduction of DNA cleavage sites to produce a high-resolution genetic and physical map of the Acinetobacter sp. strain ADP1 (BD413UE) chromosome

    Microsoft Academic Search

    Elizabeth M. Gralton; Alan L. Campbell; Ellen L. Neidle

    1997-01-01

    The natural transformability of the soil bacterium Acinetobacter sp. ADPl (BD413UE), formerly classified as A. calcoaceticus, has facilitated previous physiological and biochemical investigations. In the present studies, the natural transformation system was exploited to generate a physical and genetic map of this strain's 378021 91 kbp circular chromosome. Previously isolated Acinetobacter genes were modified in vitro to incorporate a recognition

  16. Draft Genome Sequence of Comamonas sp. Strain E6 (NBRC 107749), a Degrader of Phthalate Isomers through the Protocatechuate 4,5-Cleavage Pathway

    PubMed Central

    Shimodaira, Jun; Kamimura, Naofumi; Hosoyama, Akira; Yamazoe, Atsushi; Fujita, Nobuyuki

    2015-01-01

    Comamonas sp. strain E6 can degrade o-phthalate, terephthalate, and isophthalate via the protocatechuate 4,5-cleavage pathway. Here, we report the draft genome sequence of E6 in order to provide insights into its mechanisms in o-phthalate catabolism and its potential use for biotechnological applications.

  17. A novel cellulolytic, anaerobic, and thermophilic bacterium, Moorella sp. strain F21.

    PubMed

    Karita, Shuichi; Nakayama, Kengo; Goto, Masakazu; Sakka, Kazuo; Kim, Wan-Jae; Ogawa, Satoru

    2003-01-01

    A cellulolytic and thermophilic anaerobe was isolated from soil. This bacterium made a halo on a roll-tube culture containing Avicel. Analysis of the PCR-based 16S rRNA gene sequence showed that the bacterium was closely related to Moorella thermoacetica. Scanning electron microscopy showed the bacterium is a rod and has no protuberant structure on the surface of cells growing on cellulose, suggesting that this strain is a non-cellulosomal cellulolytic bacterium. Carboxymethyl cellulase and xylanase activities were detected in the culture broth. A major fermentation product from ball-milled cellulose was acetate. This strain has a potential to convert cellulosic biomass to acetate, directly. PMID:12619693

  18. Ecological Physiology of Synechococcus sp. Strain SH-94-5, a Naturally Occurring Cyanobacterium Deficient in Nitrate Assimilation

    PubMed Central

    Miller, Scott R.; Castenholz, Richard W.

    2001-01-01

    Synechococcus sp. strain SH-94-5 is a nitrate assimilation-deficient cyanobacterium which was isolated from an ammonium-replete hot spring in central Oregon. While this clone could grow on ammonium and some forms of organic nitrogen as sole nitrogen sources, it could not grow on either nitrate or nitrite, even under conditions favoring passive diffusion. It was determined that this clone does not express functional nitrate reductase or nitrite reductase and that the lack of activity of either enzyme is not due to inactivation of the cyanobacterial nitrogen control protein NtcA. A few other naturally occurring cyanobacterial strains are also nitrate assimilation deficient, and phylogenetic analyses indicated that the ability to utilize nitrate has been independently lost at least four times during the evolutionary history of the cyanobacteria. This phenotype is associated with the presence of environmental ammonium, a negative regulator of nitrate assimilation gene expression, which may indicate that natural selection to maintain functional copies of nitrate assimilation genes has been relaxed in these habitats. These results suggest how the evolutionary fates of conditionally expressed genes might differ between environments and thereby effect ecological divergence and biogeographical structure in the microbial world. PMID:11425713

  19. Identification of novel regulatory mechanisms controlling heterocyst development in Anabaena Sp. strain PCC 7120 

    E-print Network

    Aldea, Maria Ramona

    2009-05-15

    on medium without a source of combined nitrogen showing a pattern of single heterocysts spaced along filaments. (C) A patS deletion mutant (strain AMC451) grown on medium without a source of combined nitrogen displaying multiple...-to-cell signals (enclosed in boxes). Fixed nitrogen originating from the differentiating cells and mature heterocysts in the form of amino acids presumably inhibit differentiation of neighboring cells and establish the ultimate spacing between heterocysts...

  20. Nodulation of Lupinus albus by Strains of Ochrobactrum lupini sp. nov

    Microsoft Academic Search

    Martha E. Trujillo; Anne Willems; Adriana Abril; A.-M. Planchuelo; R. Rivas; D. Ludena; P. F. Mateos; E. Martinez-Molina; E. Velazquez

    2005-01-01

    The nodulation of legumes has for more than a century been considered an exclusive capacity of a group of microorganisms commonly known as rhizobia and belonging to the -Proteobacteria. However, in the last 3 years four nonrhizobial species, belonging to and subclasses of the Proteobacteria, have been described as legume-nodulating bacteria. In the present study, two fast-growing strains, LUP21 and

  1. Family 10 and 11 xylanase genes from Caldicellulosiruptor sp. strain Rt69B.1

    Microsoft Academic Search

    Daniel D. Morris; Moreland D. Gibbs; Michelle Ford; Justin Thomas; Peter L. Bergquist

    1999-01-01

    Three family 10 xylanase genes (xynA, xynB, and xynC) and a single family 11 xylanase gene (xynD) were identified from the extreme thermophile Caldicellulosiruptor strain Rt69B.1 through the use of consensus PCR in conjunction with sequencing and polyacrylamide gel electrophoresis. These\\u000a genes appear to comprise the complete endoxylanase system of Rt69B.1. The xynA gene was found to be homologous to

  2. Housekeeping recA gene interrupted by group II intron in the thermophilic Geobacillus kaustophilus

    Microsoft Academic Search

    Gab-Joo Chee; Hideto Takami

    2005-01-01

    Most of group II introns are found in intergenes and CDSs with unknown functions, but not in housekeeping genes. In particular, no group II intron within the housekeeping recA gene has been reported either in eukaryotic genomes or in prokaryotic genomes. In this study, we found that the recA gene of the thermophilic Geobacillus kaustophilus genome is interrupted by a

  3. Isolation and partial characterization of antimicrobial compounds from a new strain Nonomuraea sp. NM94.

    PubMed

    Badji, Boubekeur; Mostefaoui, Abdellah; Sabaou, Nasserdine; Lebrihi, Ahmed; Mathieu, Florence; Seguin, Elisabeth; Tillequin, François

    2007-06-01

    An actinomycete strain NM94 was isolated from a Saharan soil sample by a dilution agar plating method using chitin-vitamins B medium supplemented with penicillin. The strain presented the morphological and chemical characteristics of the genus Nonomuraea. On the basis of 16S rDNA analysis and physiological tests, this isolate was found to be quite different from the known species of Nonomuraea and might be new. The strain NM94 secreted several antibiotics on yeast extract malt extract glucose medium that were active against some Gram-positive bacteria, yeast, and fungi. The antibiotics were extracted with dichloromethane and detected by bioautography on silica gel plates using Mucor ramannianus and Bacillus subtilis as the test organisms. Among these antibiotics, a complex called 94A showed interesting antifungal activity. It was selected and purified by reverse-phase HPLC. This complex was composed of five compounds. Spectroscopic studies by infrared, mass, and (1)H NMR of the compounds were carried out. Initial results showed that these molecules differed from the known antibiotics produced by other Nonomuraea species. PMID:17318487

  4. Biological Efficacy of Streptomyces sp. Strain BN1 against the Cereal Head Blight Pathogen Fusarium graminearum

    PubMed Central

    Jung, Boknam; Park, Sook-Young; Lee, Yin-Won; Lee, Jungkwan

    2013-01-01

    Fusarium head blight (FHB) caused by the filamentous fungus Fusarium graminearum is one of the most severe diseases threatening the production of small grains. Infected grains are often contaminated with mycotoxins such as zearalenone and trichothecences. During survey of contamination by FHB in rice grains, we found a bacterial isolate, designated as BN1, antagonistic to F. graminearum. The strain BN1 had branching vegetative hyphae and spores, and its aerial hyphae often had long, straight filaments bearing spores. The 16S rRNA gene of BN1 had 100% sequence identity with those found in several Streptomyces species. Phylogenetic analysis of ITS regions showed that BN1 grouped with S. sampsonii with 77% bootstrap value, suggesting that BN1 was not a known Streptomyces species. In addition, the efficacy of the BN1 strain against F. graminearum strains was tested both in vitro and in vivo. Wheat seedling length was significantly decreased by F. graminearum infection. However, this effect was mitigated when wheat seeds were treated with BN1 spore suspension prior to F. graminearum infection. BN1 also significantly decreased FHB severity when it was sprayed onto wheat heads, whereas BN1 was not effective when wheat heads were point inoculated. These results suggest that spraying of BN1 spores onto wheat heads during the wheat flowering season can be efficient for plant protection. Mechanistic studies on the antagonistic effect of BN1 against F. graminearum remain to be analyzed. PMID:25288928

  5. Draft Genome Sequence of Serratia sp. Strain ATCC 39006, a Model Bacterium for Analysis of the Biosynthesis and Regulation of Prodigiosin, a Carbapenem, and Gas Vesicles

    PubMed Central

    Iglesias Cans, Marina C.; Ramsay, Joshua P.; Wilf, Nabil M.; Cossyleon, Desiree; McNeil, Matthew B.; Williamson, Neil R.; Monson, Rita E.; Becher, S. Anette; Stanton, Jo-Ann L.; Brügger, Kim; Brown, Steven D.

    2013-01-01

    Serratia sp. strain ATCC 39006 is a Gram-negative bacterium and a member of the Enterobacteriaceae that produces various bioactive secondary metabolites, including the tripyrrole red pigment prodigiosin and the ?-lactam antibiotic 1-carbapenen-2-em-3-carboxylic acid (a carbapenem). This strain is the only member of the Enterobacteriaceae known to naturally produce gas vesicles, as flotation organelles. Here we present the genome sequence of this strain, which has served as a model for analysis of the biosynthesis and regulation of antibiotic production. PMID:24336377

  6. Arsenic-resistant Pseudomonas spp. and Bacillus sp. bacterial strains reducing As(V) to As(III), isolated from Alps soils, Italy

    Microsoft Academic Search

    M. Pepi; G. Protano; M. Ruta; V. Nicolardi; E. Bernardini; S. E. Focardi; C. Gaggi

    2011-01-01

    Five arsenic-resistant bacterial strains (designated MP1400, MP1400a, MP1400d, APSLA3, and BPSLA3) were isolated from soils\\u000a collected at the Alps region (Italy), which showed no contamination by arsenic. Phylogenetic analysis of the 16S rRNA gene\\u000a sequences assigned them to the genera Pseudomonas and Bacillus. Bacillus sp. strain 1400d and Pseudomonas spp. strains APSLA3 and MP1400 showed higher tolerance to As(III), as

  7. Cell Envelope Components Influencing Filament Length in the Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120

    PubMed Central

    Burnat, Mireia; Schleiff, Enrico

    2014-01-01

    Heterocyst-forming cyanobacteria grow as chains of cells (known as trichomes or filaments) that can be hundreds of cells long. The filament consists of individual cells surrounded by a cytoplasmic membrane and peptidoglycan layers. The cells, however, share a continuous outer membrane, and septal proteins, such as SepJ, are important for cell-cell contact and filament formation. Here, we addressed a possible role of cell envelope components in filamentation, the process of producing and maintaining filaments, in the model cyanobacterium Anabaena sp. strain PCC 7120. We studied filament length and the response of the filaments to mechanical fragmentation in a number of strains with mutations in genes encoding cell envelope components. Previously published peptidoglycan- and outer membrane-related gene mutants and strains with mutations in two genes (all5045 and alr0718) encoding class B penicillin-binding proteins isolated in this work were used. Our results show that filament length is affected in most cell envelope mutants, but the filaments of alr5045 and alr2270 gene mutants were particularly fragmented. All5045 is a dd-transpeptidase involved in peptidoglycan elongation during cell growth, and Alr2270 is an enzyme involved in the biosynthesis of lipid A, a key component of lipopolysaccharide. These results indicate that both components of the cell envelope, the murein sacculus and the outer membrane, influence filamentation. As deduced from the filament fragmentation phenotypes of their mutants, however, none of these elements is as important for filamentation as the septal protein SepJ. PMID:25201945

  8. Influence of Carbon Sources and Electron Shuttles on Ferric Iron Reduction by Cellulomonas sp. Strain ES6

    SciTech Connect

    Erin K. Field; Robin Gerlach; Sridhar Viamajala; Laura K. Jennings; Alfred B. Cunningham; Brent M. Peyton; William A. Apel

    2011-09-01

    The reduction of hexavalent chromium, Cr(VI), to trivalent chromium, Cr(III), can be an important aspect of remediation processes at Department of Energy (DOE) and other contaminated sites. Cellulomonas species are found at several Cr(VI) contaminated and uncontaminated locations at the DOE site in Hanford, Washington. Members of this genus have demonstrated the ability to effectively reduce Cr(VI) to Cr(III) fermentatively and therefore play a potential role in hexavalent chromium remediation at this site. Batch studies were conducted with Cellulomonas sp. strain ES6 to assess the influence of various carbon sources, iron minerals, and electron shuttling compounds on Cr(VI) reduction. These chemical species are likely to be present in these terrestrial environments during in situ bioremediation. Results indicated that there were a number of interactions between these compounds that influenced Cr(VI) reduction rates. The type of carbon source as well as the type of electron shuttle present influenced Cr(VI) reduction rates. When an electron shuttle, such as anthraquinone-2,6-disulfonate (AQDS), was present in the system, reduction rates increased significantly. Biologically reduced AQDS (AHDS) reduced Cr(VI) almost instantaneously. The presence of iron minerals and their concentrations did not significantly influence Cr(VI) reduction rates. However, strain ES6 or AQDS could directly reduce surface-associated Fe(III) to Fe(II) which was capable of reducing Cr(VI) at a near instantaneous rate. These results suggest the rate limiting step in these systems is the transfer of electrons from strain ES6 to the intermediate or terminal electron acceptor whether that is Cr(VI), Fe(III), or AQDS.

  9. Family 10 and 11 xylanase genes from Caldicellulosiruptor sp. strain Rt69B.1.

    PubMed

    Morris, D D; Gibbs, M D; Ford, M; Thomas, J; Bergquist, P L

    1999-05-01

    Three family 10 xylanase genes (xynA, xynB, and xynC) and a single family 11 xylanase gene (xynD) were identified from the extreme thermophile Caldicellulosiruptor strain Rt69B.1 through the use of consensus PCR in conjunction with sequencing and polyacrylamide gel electrophoresis. These genes appear to comprise the complete endoxylanase system of Rt69B.1. The xynA gene was found to be homologous to the xynA gene of the closely related Caldicellulosiruptor strain Rt8B.4, and primers designed previously to amplify the Rt8B.4 xynA gene could amplify homologous full-length xynA gene fragments from Rt69B.1. The complete nucleotide sequences of the Rt69B.1 xynB, xynC, and xynD genes were obtained using genomic walking PCR. The full-length xynB and xynC genes are more than 5 kb in length and encode highly modular enzymes that are the largest xylanases reported to date. XynB has an architecture similar to the family 10 xylanases from Thermoanaerobacterium saccharolyticum (XynA) and Clostridium thermocellum (XynX) and may be cell wall associated, while XynC is a bifunctional enzyme with an architecture similar to the bifunctional beta-glycanases from Caldicellulosiroptor saccharolyticus. The xynD gene encodes a two-domain family 11 xylanase that is identical in architecture to the XynB family 11 xylanase from the unrelated extreme thermophile Dictyoglomus thermophilum strain Rt46B.1. The sequence similarities between the Rt69B.1 xylanases with respect to their evolution are discussed. PMID:10356996

  10. Effect of Glucose Utilization on Nitrite Excretion by the Unicellular Cyanobacterium Synechocystis sp. Strain PCC 6803

    PubMed Central

    Reyes, J. C.; Chávez, S.; Muro-Pastor, M. I.; Candau, P.; Florencio, F. J.

    1993-01-01

    Up to 1 mM nitrite was excreted by Synechocystis strain 6803 cells growing under mixotrophic or photoheterotrophic conditions. This excretion is not due to a lower ratio of nitrite and nitrate reductase activities in the presence of glucose but seems to be related to a shortage of reduced ferredoxin, their electron donor, as a result of a decrease in noncyclic photosynthetic flow observed under these circumstances. Because about 60% of the reduced nitrate is excreted, the potential utilization of cyanobacteria for removal of nitrate from contaminated waters containing high concentrations of organic compounds is questioned. PMID:16349056

  11. A gene cluster encoding steps in conversion of naphthalene to gentisate in Pseudomonas sp. strain U2.

    PubMed

    Fuenmayor, S L; Wild, M; Boyes, A L; Williams, P A

    1998-05-01

    Pseudomonas sp. strain U2 was isolated from oil-contaminated soil in Venezuela by selective enrichment on naphthalene as the sole carbon source. The genes for naphthalene dioxygenase were cloned from the plasmid DNA of strain U2 on an 8.3-kb BamHI fragment. The genes for the naphthalene dioxygenase genes nagAa (for ferredoxin reductase), nagAb (for ferredoxin), and nagAc and nagAd (for the large and small subunits of dioxygenase, respectively) were located by Southern hybridizations and by nucleotide sequencing. The genes for nagB (for naphthalene cis-dihydrodiol dehydrogenase) and nagF (for salicylaldehyde dehydrogenase) were inferred from subclones by their biochemical activities. Between nagAa and nagAb were two open reading frames, homologs of which have also been identified in similar locations in two nitrotoluene-using strains (J. V. Parales, A. Kumar, R. E. Parales, and D. T. Gibson, Gene 181:57-61, 1996; W.-C. Suen, B. Haigler, and J. C. Spain, J. Bacteriol. 178:4926-4934, 1996) and a naphthalene-using strain (G. J. Zylstra, E. Kim, and A. K. Goyal, Genet. Eng. 19:257-269, 1997). Recombinant Escherichia coli strains with plasmids carrying this region were able to convert salicylate to gentisate, which was identified by a combination of gas chromatography-mass spectrometry and nuclear magnetic resonance. The first open reading frame, designated nagG, encodes a protein with characteristics of a Rieske-type iron-sulfur center homologous to the large subunits of dihydroxylating dioxygenases, and the second open reading frame, designated nagH, encodes a protein with limited homology to the small subunits of the same dioxygenases. Cloned together in E. coli, nagG, nagH, and nagAb, were able to convert salicylate (2-hydroxybenzoate) into gentisate (2,5-dihydroxybenzoate) and therefore encode a salicylate 5-hydroxylase activity. Single-gene knockouts of nagG, nagH, and nagAb demonstrated their functional roles in the formation of gentisate. It is proposed that NagG and NagH are structural subunits of salicylate 5-hydroxylase linked to an electron transport chain consisting of NagAb and NagAa, although E. coli appears to be able to partially substitute for the latter. This constitutes a novel mechanism for monohydroxylation of the aromatic ring. Salicylate hydroxylase and catechol 2,3-dioxygenase in strain U2 could not be detected either by enzyme assay or by Southern hybridization. However growth on both naphthalene and salicylate caused induction of gentisate 1,2-dioxygenase, confirming this route for salicylate catabolism in strain U2. Sequence comparisons suggest that the novel gene order nagAa-nagG-nagH-nagAb-nagAc-nagAd-++ +nagB-nagF represents the archetype for naphthalene strains which use the gentisate pathway rather than the meta cleavage pathway of catechol. PMID:9573207

  12. Molecular Characterization of the Genes pcaG and pcaH, Encoding Protocatechuate 3,4Dioxygenase, Which Are Essential for Vanillin Catabolism in Pseudomonas sp. Strain HR199

    Microsoft Academic Search

    JORG OVERHAGE; ANDREAS U. KRESSE; HORST PRIEFERT; HORST SOMMER; GERHARD KRAMMER; JURGEN RABENHORST; ALEXANDER STEINBUCHEL

    1999-01-01

    Pseudomonas sp. strain HR199 is able to utilize eugenol (4-allyl-2-methoxyphenol), vanillin (4-hydroxy-3- methoxybenzaldehyde), or protocatechuate as the sole carbon source for growth. Mutants of this strain which were impaired in the catabolism of vanillin but retained the ability to utilize eugenol or protocatechuate were obtained after nitrosoguanidine mutagenesis. One mutant (SK6169) was used as recipient of a Pseudomonas sp. strain

  13. Survival and retention of the probiotic properties of Bacillus sp. strains under marine stress starvation conditions and their potential use as a probiotic in Artemia culture.

    PubMed

    Mahdhi, Abdelkarim; Esteban, Maria Ángeles; Hmila, Zeineb; Bekir, Karima; Kamoun, Fathi; Bakhrouf, Amina; Krifi, Boubaker

    2012-12-01

    The probiotic properties of Bacillus strains isolated from Artemia culture and the effect of marine stress on viability and survival were investigated, as well as the changes occurring in their properties. Analyses showed that these bacteria corresponded to the genus Bacillus sp. Antagonism and adherence assays revealed that Bacillus strains have an inhibitory effect against tested pathogenic bacteria and are fairly adherent. Normal and starved cells showed different enzymatic profiles. Challenge tests performed with Artemia larvae provided evidence that the tested Bacillus strains were neither pathogenic nor toxic to the host and conferred protection for Artemia culture against pathogens. The tested strains maintained their viability and their probiotic properties during the period of study. The results suggest that the tested strains have suffered changes allowing them to survive in seawater in the absence of nutrients and outside their natural host, identifying them as potential probiotic candidates for Artemia culture. PMID:22673028

  14. Structural properties of the tubular appendage spinae from marine bacterium Roseobacter sp. strain YSCB

    PubMed Central

    Bernadac, A.; Wu, L.-F.; Santini, C.-L.; Vidaud, C.; Sturgis, J. N.; Menguy, N.; Bergam, P.; Nicoletti, C.; Xiao, T.

    2012-01-01

    Spinae are tubular surface appendages broadly found in Gram-negative bacteria. Little is known about their architecture, function or origin. Here, we report structural characterization of the spinae from marine bacteria Roseobacter sp. YSCB. Electron cryo-tomography revealed that a single filament winds into a hollow flared base with progressive change to a cylinder. Proteinase K unwound the spinae into proteolysis-resistant filaments. Thermal treatment ripped the spinae into ribbons that were melted with prolonged heating. Circular dichroism spectroscopy revealed a dominant beta-structure of the spinae. Differential scanning calorimetry analyses showed three endothermic transformations at 50–85°C, 98°C and 123°C, respectively. The heating almost completely disintegrated the spinae, abolished the 98°C transition and destroyed the beta-structure. Infrared spectroscopy identified the amide I spectrum maximum at a position similar to that of amyloid fibrils. Therefore, the spinae distinguish from other bacterial appendages, e.g. flagella and stalks, in both the structure and mechanism of assembly. PMID:23230515

  15. Characterization of three bioenergetically active respiratory terminal oxidases in the cyanobacterium Synechocystis sp. strain PCC 6803.

    PubMed

    Pils, D; Schmetterer, G

    2001-09-25

    Synechocystis sp. PCC 6803 contains three respiratory terminal oxidases (RTOs): cytochrome c oxidase (Cox), quinol oxidase (Cyd), and alternate RTO (ARTO). Mutants lacking combinations of the RTOs were used to characterize these key enzymes of respiration. Pentachlorophenol and 2-heptyl-4-hydroxy-quinoline-N-oxide inhibited Cyd completely, but had little effect on electron transport to the other RTOs. KCN inhibited all three RTOs but the in vivo K(I) for Cox and Cyd was quite different (7 vs. 27 microM), as was their affinity for oxygen (K(M) 1.0 vs. 0.35 microM). ARTO has a very low respiratory activity. However, when uptake of 3-O-methylglucose, an active H+ co-transport, was used to monitor energization of the cytoplasmic membrane, ARTO was similarly effective as the other RTOs. As removal of the gene for cytochrome c(553) had the same effects as removal of ARTO genes, we propose that the ARTO might be a second Cox. The possible functions, localization and regulation of the RTOs are discussed. PMID:11583851

  16. DECONTAMINATION ASSESSMENT OF BACILLUS ANTHRACIS, BACILLUS SUBTILIS, AND GEOBACILLUS STEAROTHERMOPHILUS SPORES ON INDOOR SURFACTS USING A HYDROGEN PERIOXIDE GAS GENERATOR

    EPA Science Inventory

    Aims: To evaluate the decontamination of Bacillus anthracis, Bacillus subtilis, and Geobacillus stearothermophilus spores on indoor surface materials using hydrogen peroxide gas. Methods and Results: B. anthracis, B. subtilis, and G. Stearothermophilus spores were dried on seven...

  17. A new lipopeptide biosurfactant produced by Arthrobacter sp. strain MIS38.

    PubMed Central

    Morikawa, M; Daido, H; Takao, T; Murata, S; Shimonishi, Y; Imanaka, T

    1993-01-01

    A biosurfactant termed arthrofactin produced by Arthrobacter species strain MIS38 was purified and chemically characterized as 3-hydroxydecanoyl-D-leucyl-D-asparagyl-D-threonyl-D- leucyl-D-leucyl-D-seryl-L-leucyl-D-seryl-L-isoleucyl-L-isoleucyl-L-as paragyl lactone. Surface activity of arthrofactin was examined, with surfactin as a control. Critical micelle concentration values of arthrofactin and surfactin were around 1.0 x 10(-5) M and 7.0 x 10(-5) M at 25 degrees C, respectively. Arthrofactin was found to be five to seven times more effective than surfactin. The minimum surface tension value of arthrofactin was 24 mN/m at a concentration higher than the critical micelle concentration. According to the oil displacement assay, arthrofactin was a better oil remover than synthetic surfactants, such as Triton X-100 and sodium dodecyl sulfate. Arthrofactin is one of the most effective lipopeptide biosurfactants. Images PMID:8407822

  18. Characterization of Klebsiella sp. strain 10982, a colonizer of humans that contains novel antibiotic resistance alleles and exhibits genetic similarities to plant and clinical Klebsiella isolates.

    PubMed

    Hazen, Tracy H; Zhao, LiCheng; Sahl, Jason W; Robinson, Gwen; Harris, Anthony D; Rasko, David A; Johnson, J Kristie

    2014-01-01

    A unique Klebsiella species strain, 10982, was cultured from a perianal swab specimen obtained from a patient in the University of Maryland Medical Center intensive care unit. Klebsiella sp. 10982 possesses a large IncA/C multidrug resistance plasmid encoding a novel FOX AmpC ?-lactamase designated FOX-10. A novel variant of the LEN ?-lactamase was also identified. Genome sequencing and bioinformatic analysis demonstrated that this isolate contains genes associated with nitrogen fixation, allantoin metabolism, and citrate fermentation. These three gene regions are typically present in either Klebsiella pneumoniae clinical isolates or Klebsiella nitrogen-fixing endophytes but usually not in the same organism. Phylogenomic analysis of Klebsiella sp. 10982 and sequenced Klebsiella genomes demonstrated that Klebsiella sp. 10982 is present on a branch that is located intermediate between the genomes of nitrogen-fixing endophytes and K. pneumoniae clinical isolates. Metabolic features identified in the genome of Klebsiella sp. 10982 distinguish this isolate from other Klebsiella clinical isolates. These features include the nitrogen fixation (nif) gene cluster, which is typically present in endophytic Klebsiella isolates and is absent from Klebsiella clinical isolates. Additionally, the Klebsiella sp. 10982 genome contains genes associated with allantoin metabolism, which have been detected primarily in K. pneumoniae isolates from liver abscesses. Comparative genomic analysis of Klebsiella sp. 10982 demonstrated that this organism has acquired genes conferring new metabolic strategies and novel antibiotic resistance alleles, both of which may enhance its ability to colonize the human body. PMID:24395222

  19. Methanobactin from Methylocystis sp. strain SB2 affects gene expression and methane monooxygenase activity in Methylosinus trichosporium OB3b.

    PubMed

    Farhan Ul-Haque, Muhammad; Kalidass, Bhagyalakshmi; Vorobev, Alexey; Baral, Bipin S; DiSpirito, Alan A; Semrau, Jeremy D

    2015-04-01

    Methanotrophs can express a cytoplasmic (soluble) methane monooxygenase (sMMO) or membrane-bound (particulate) methane monooxygenase (pMMO). Expression of these MMOs is strongly regulated by the availability of copper. Many methanotrophs have been found to synthesize a novel compound, methanobactin (Mb), that is responsible for the uptake of copper, and methanobactin produced by Methylosinus trichosporium OB3b plays a key role in controlling expression of MMO genes in this strain. As all known forms of methanobactin are structurally similar, it was hypothesized that methanobactin from one methanotroph may alter gene expression in another. When Methylosinus trichosporium OB3b was grown in the presence of 1 ?M CuCl2, expression of mmoX, encoding a subunit of the hydroxylase component of sMMO, was very low. mmoX expression increased, however, when methanobactin from Methylocystis sp. strain SB2 (SB2-Mb) was added, as did whole-cell sMMO activity, but there was no significant change in the amount of copper associated with M. trichosporium OB3b. If M. trichosporium OB3b was grown in the absence of CuCl2, the mmoX expression level was high but decreased by several orders of magnitude if copper prebound to SB2-Mb (Cu-SB2-Mb) was added, and biomass-associated copper was increased. Exposure of Methylosinus trichosporium OB3b to SB2-Mb had no effect on expression of mbnA, encoding the polypeptide precursor of methanobactin in either the presence or absence of CuCl2. mbnA expression, however, was reduced when Cu-SB2-Mb was added in both the absence and presence of CuCl2. These data suggest that methanobactin acts as a general signaling molecule in methanotrophs and that methanobactin "piracy" may be commonplace. PMID:25616801

  20. Cooperative degradation of chitin by extracellular and cell surface-expressed chitinases from Paenibacillus sp. strain FPU-7.

    PubMed

    Itoh, Takafumi; Hibi, Takao; Fujii, Yutaka; Sugimoto, Ikumi; Fujiwara, Akihiro; Suzuki, Fumiko; Iwasaki, Yukimoto; Kim, Jin-Kyung; Taketo, Akira; Kimoto, Hisashi

    2013-12-01

    Chitin, a major component of fungal cell walls and invertebrate cuticles, is an exceedingly abundant polysaccharide, ranking next to cellulose. Industrial demand for chitin and its degradation products as raw materials for fine chemical products is increasing. A bacterium with high chitin-decomposing activity, Paenibacillus sp. strain FPU-7, was isolated from soil by using a screening medium containing ?-chitin powder. Although FPU-7 secreted several extracellular chitinases and thoroughly digested the powder, the extracellular fluid alone broke them down incompletely. Based on expression cloning and phylogenetic analysis, at least seven family 18 chitinase genes were found in the FPU-7 genome. Interestingly, the product of only one gene (chiW) was identified as possessing three S-layer homology (SLH) domains and two glycosyl hydrolase family 18 catalytic domains. Since SLH domains are known to function as anchors to the Gram-positive bacterial cell surface, ChiW was suggested to be a novel multimodular surface-expressed enzyme and to play an important role in the complete degradation of chitin. Indeed, the ChiW protein was localized on the cell surface. Each of the seven chitinase genes (chiA to chiF and chiW) was cloned and expressed in Escherichia coli cells for biochemical characterization of their products. In particular, ChiE and ChiW showed high activity for insoluble chitin. The high chitinolytic activity of strain FPU-7 and the chitinases may be useful for environmentally friendly processing of chitin in the manufacture of food and/or medicine. PMID:24077704