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Sample records for bacterium desulfovibrio vulgaris

  1. Reclassification of the sulfate- and nitrate-reducing bacterium Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov.

    PubMed

    López-Cortés, Alejandro; Fardeau, Marie-Laure; Fauque, Guy; Joulian, Catherine; Ollivier, Bernard

    2006-07-01

    Desulfovibrio vulgaris subsp. oxamicus (type strain, DSM 1925(T)) was found to use nitrate as a terminal electron acceptor, the latter being reduced to ammonium. Phylogenetic studies indicated that strain DSM 1925(T) was distantly related to the type strain of Desulfovibrio vulgaris (95.4 % similarity of the small-subunit rRNA gene) and had as its closest phylogenetic relatives two other nitrate- and sulfate-reducing bacteria, namely Desulfovibrio termitidis (99.4 % similarity) and Desulfovibrio longreachensis (98.4 % similarity). Additional experiments were conducted to characterize better strain DSM 1925(T). This strain incompletely oxidized lactate and ethanol to acetate. It also oxidized butanol, pyruvate and citrate, but not glucose, fructose, acetate, propionate, butyrate, methanol, glycerol or peptone. The optimum temperature for growth was 37 degrees C (range 16-50 degrees C) and the optimum NaCl concentration for growth was 0.1 % (range 0-5 %). Because of significant genotypic and phenotypic differences from Desulfovibrio termitidis and Desulfovibrio longreachensis, reclassification of Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov., is proposed. The type strain is strain Monticello 2(T) (=DSM 1925(T)=NCIMB 9442(T)=ATCC 33405(T)).

  2. Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

    PubMed

    Caffrey, Sean M; Park, Hyung-Soo; Voordouw, Johanna K; He, Zhili; Zhou, Jizhong; Voordouw, Gerrit

    2007-09-01

    The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe] hydrogenase, an [NiFeSe] hydrogenase, and two [NiFe] hydrogenases encoded by the hyd, hys, hyn1, and hyn2 genes, respectively. In order to understand their cellular functions, we have compared the growth rates of existing (hyd and hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those of the wild type in defined media in which lactate or hydrogen at either 5 or 50% (vol/vol) was used as the sole electron donor for sulfate reduction. Only strains missing the [Fe] hydrogenase were significantly affected during growth with lactate or with 50% (vol/vol) hydrogen as the sole electron donor. When the cells were grown at low (5% [vol/vol]) hydrogen concentrations, those missing the [NiFeSe] hydrogenase suffered the greatest impairment. The growth rate data correlated strongly with gene expression results obtained from microarray hybridizations and real-time PCR using mRNA extracted from cells grown under the three conditions. Expression of the hys genes followed the order 5% hydrogen>50% hydrogen>lactate, whereas expression of the hyd genes followed the reverse order. These results suggest that growth with lactate and 50% hydrogen is associated with high intracellular hydrogen concentrations, which are best captured by the higher activity, lower affinity [Fe] hydrogenase. In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase.

  3. Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough▿ †

    PubMed Central

    Caffrey, Sean M.; Park, Hyung-Soo; Voordouw, Johanna K.; He, Zhili; Zhou, Jizhong; Voordouw, Gerrit

    2007-01-01

    The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe] hydrogenase, an [NiFeSe] hydrogenase, and two [NiFe] hydrogenases encoded by the hyd, hys, hyn1, and hyn2 genes, respectively. In order to understand their cellular functions, we have compared the growth rates of existing (hyd and hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those of the wild type in defined media in which lactate or hydrogen at either 5 or 50% (vol/vol) was used as the sole electron donor for sulfate reduction. Only strains missing the [Fe] hydrogenase were significantly affected during growth with lactate or with 50% (vol/vol) hydrogen as the sole electron donor. When the cells were grown at low (5% [vol/vol]) hydrogen concentrations, those missing the [NiFeSe] hydrogenase suffered the greatest impairment. The growth rate data correlated strongly with gene expression results obtained from microarray hybridizations and real-time PCR using mRNA extracted from cells grown under the three conditions. Expression of the hys genes followed the order 5% hydrogen > 50% hydrogen > lactate, whereas expression of the hyd genes followed the reverse order. These results suggest that growth with lactate and 50% hydrogen is associated with high intracellular hydrogen concentrations, which are best captured by the higher activity, lower affinity [Fe] hydrogenase. In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase. PMID:17601789

  4. Function of Periplasmic Hydrogenases in the Sulfate-ReducingBacterium Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Caffrey, Sean M.; Park, Hyung-Soo; Voordouw, Johanna K.; He,Zhili; Zhou, Jizhong; Voordouw, Gerrit

    2007-09-24

    The sulfate-reducing bacterium Desulfovibrio vulgarisHildenborough possesses four periplasmic hydrogenases to facilitate theoxidation of molecular hydrogen. These include an [Fe]hydrogenase, an[NiFeSe]hydrogenase, and two [NiFe]hydrogenases encoded by the hyd,hys, hyn1, and hyn2 genes, respectively. In order to understand theircellular functions, we have compared the growth rates of existing (hydand hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those ofthe wild type in defined media in which lactate or hydrogen at either 5or 50 percent (vol/vol) was used as the sole electron donor for sulfatereduction. Only strains missing the [Fe]hydrogenase were significantlyaffected during growth with lactate or with 50 percent (vol/vol) hydrogenas the sole electron donor. When the cells were grown at low (5 percent[vol/vol]) hydrogen concentrations, those missing the [NiFeSe]hydrogenase suffered the greatest impairment. The growth rate datacorrelated strongly with gene expression results obtained from microarrayhybridizations and real-time PCR using mRNA extracted from cells grownunder the three conditions. Expression of the hys genes followed theorder 5 percent hydrogen>50 percent hydrogen>lactate, whereasexpression of the hyd genes followed the reverse order. These resultssuggest that growth with lactate and 50 percent hydrogen is associatedwith high intracellular hydrogen concentrations, which are best capturedby the higher activity, lower affinity [Fe]hydrogenase. In contrast,growth with 5 percent hydrogen is associated with a low intracellularhydrogen concentration, requiring the lower activity, higher affinity[NiFeSe]hydrogenase.

  5. Purification and characterization of homo- and hetero-dimeric acetate kinases from the sulfate-reducing bacterium Desulfovibrio vulgaris.

    PubMed

    Yu, L; Ishida, T; Ozawa, K; Akutsu, H; Horiike, K

    2001-03-01

    Two distinct forms of acetate kinase were purified to homogeneity from a sulfate-reducing bacterium Desulfovibrio vulgaris Miyazaki F. The enzymes were separated from the soluble fraction of the cells on anion exchange columns. One acetate kinase (AK-I) was a homodimer (alpha(S)(2)) and the other (AK-II) was a heterodimer (alpha(S)alpha(L)). On SDS-PAGE, alpha(L) and alpha(S) subunits migrated as bands of 49.3 and 47.8 kDa, respectively, but they had an identical N-terminal amino acid sequence. A rapid HPLC method was developed to directly measure ADP and ATP in assay mixtures. Initial velocity data for AK-I and AK-II were collected by this method and analyzed based on a random sequential mechanism, assuming rapid equilibrium for the substrate binding steps. All kinetic parameters for both the forward acetyl phosphate formation and the reverse ATP formation catalyzed by AK-I and AK-II were successfully determined. The two enzymes showed similar kinetic properties in Mg(2+) requirement, pH-dependence and magnitude of kinetic parameters. These results suggest that two forms of acetate kinase are produced to finely regulate the enzyme function by post-translational modifications of a primary gene product in Desulfovibrio vulgaris.

  6. Effects of biocides on gene expression in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

    PubMed

    Lee, Meng-Hsin Phoebe; Caffrey, Sean M; Voordouw, Johanna K; Voordouw, Gerrit

    2010-07-01

    Although sulfate-reducing bacteria (SRB), such as Desulfovibrio vulgaris Hildenborough (DvH) are often eradicated in oil and gas operations with biocides, such as glutaraldehyde (Glut), tetrakis (hydroxymethyl) phosphonium sulfate (THPS), and benzalkonium chloride (BAC), their response to these agents is not well known. Whole genome microarrays of D. vulgaris treated with biocides well below the minimum inhibitory concentration showed that 256, 96, and 198 genes were responsive to Glut, THPS, and BAC, respectively, and that these three commonly used biocides affect the physiology of the cell quite differently. Glut induces expression of genes required to degrade or refold proteins inactivated by either chemical modification or heat shock, whereas BAC appears to target ribosomal structure. THPS appears to primarily affect energy metabolism of SRB. Mutants constructed for genes strongly up-regulated by Glut, were killed by Glut to a similar degree as the wild type. Hence, it is difficult to achieve increased sensitivity to this biocide by single gene mutations, because Glut affects so many targets. Our results increase understanding of the biocide's mode of action, allowing a more intelligent combination of mechanistically different agents. This can reduce stress on budgets for chemicals and on the environment.

  7. Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

    PubMed

    Price, Morgan N; Deutschbauer, Adam M; Kuehl, Jennifer V; Liu, Haichuan; Witkowska, H Ewa; Arkin, Adam P

    2011-10-01

    We used high-resolution tiling microarrays and 5' RNA sequencing to identify transcripts in Desulfovibrio vulgaris Hildenborough, a model sulfate-reducing bacterium. We identified the first nucleotide position for 1,124 transcripts, including 54 proteins with leaderless transcripts and another 72 genes for which a major transcript initiates within the upstream protein-coding gene, which confounds measurements of the upstream gene's expression. Sequence analysis of these promoters showed that D. vulgaris prefers -10 and -35 boxes different from those preferred by Escherichia coli. A total of 549 transcripts ended at intrinsic (rho-independent) terminators, but most of the other transcripts seemed to have variable ends. We found low-level antisense expression of most genes, and the 5' ends of these transcripts mapped to promoter-like sequences. Because antisense expression was reduced for highly expressed genes, we suspect that elongation of nonspecific antisense transcripts is suppressed by transcription of the sense strand. Finally, we combined the transcript results with comparative analysis and proteomics data to make 505 revisions to the original annotation of 3,531 proteins: we removed 255 (7.5%) proteins, changed 123 (3.6%) start codons, and added 127 (3.7%) proteins that had been missed. Tiling data had higher coverage than shotgun proteomics and hence led to most of the corrections, but many errors probably remain. Our data are available at http://genomics.lbl.gov/supplemental/DvHtranscripts2011/.

  8. Gene expression by the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough grown on an iron electrode under cathodic protection conditions.

    PubMed

    Caffrey, Sean M; Park, Hyung Soo; Been, Jenny; Gordon, Paul; Sensen, Christoph W; Voordouw, Gerrit

    2008-04-01

    The genome sequence of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough was reanalyzed to design unique 70-mer oligonucleotide probes against 2,824 probable protein-coding regions. These included three genes not previously annotated, including one that encodes a c-type cytochrome. Using microarrays printed with these 70-mer probes, we analyzed the gene expression profile of wild-type D. vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed negative potential of -1.1 V (cathodic protection conditions). The gene expression profile of cells grown on cathodic hydrogen was compared to that of cells grown with gaseous hydrogen bubbling through the culture. Relative to the latter, the electrode-grown cells overexpressed two hydrogenases, the hyn-1 genes for [NiFe] hydrogenase 1 and the hyd genes, encoding [Fe] hydrogenase. The hmc genes for the high-molecular-weight cytochrome complex, which allows electron flow from the hydrogenases across the cytoplasmic membrane, were also overexpressed. In contrast, cells grown on gaseous hydrogen overexpressed the hys genes for [NiFeSe] hydrogenase. Cells growing on the electrode also overexpressed genes encoding proteins which promote biofilm formation. Although the gene expression profiles for these two modes of growth were distinct, they were more closely related to each other than to that for cells grown in a lactate- and sulfate-containing medium. Electrochemically measured corrosion rates were lower for iron electrodes covered with hyn-1, hyd, and hmc mutant biofilms than for wild-type biofilms. This confirms the importance, suggested by the gene expression studies, of the corresponding gene products in D. vulgaris-mediated iron corrosion.

  9. Cloning and expression of the MutM gene from obligate anaerobic bacterium Desulfovibrio vulgaris (Miyazaki F).

    PubMed

    Sanada, Hideaki; Nakanishi, Takeshi; Inoue, Hideo; Kitamura, Masaya

    2009-04-01

    The gene encoding a MutM from Desulfovibrio vulgaris (Miyazaki F) was cloned and expressed in Escherichia coli. A 5.9-kb DNA fragment, isolated from D. vulgaris (Miyazaki F) by XhoI and PvuII, contained a MutM gene and other open reading frames. The nucleotide sequence of the MutM gene indicated that the protein was composed of 336 amino acids. The amino-acid sequence deduced from the MutM gene was highly homologous with the MutM of other bacteria; however an additional insert consisted of 64 amino acids. An expression system for the MutM gene under the control of the T7 promoter was constructed in E. coli. From the kinetic analysis results, the purified His-tagged MutM showed 8-oxoguanine-DNA glycosylase activity comparable with that of MutM from E. coli. In this study, the amounts of mRNA and protein for MutM were scant in the D. vulgaris (Miyazaki F). MutM activity may be induced by oxidative stress. However, its induction may not be frequently generated because sulfate-reducing bacteria generally grow in anaerobic conditions. MutM might play a role in the protection against the mutagenicity of oxygen when oxygen stress exceeded the capacity of the defense systems against oxygen toxicity.

  10. σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough

    DOE PAGES

    Kazakov, Alexey E.; Rajeev, Lara; Chen, Amy; ...

    2015-11-10

    The σ54 subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequenced bacteria. Finally, the cellular processes regulated by many of these EBPs remain unknown.

  11. Gene Expression by the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough Grown on an Iron Electrode under Cathodic Protection Conditions▿ †

    PubMed Central

    Caffrey, Sean M.; Park, Hyung Soo; Been, Jenny; Gordon, Paul; Sensen, Christoph W.; Voordouw, Gerrit

    2008-01-01

    The genome sequence of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough was reanalyzed to design unique 70-mer oligonucleotide probes against 2,824 probable protein-coding regions. These included three genes not previously annotated, including one that encodes a c-type cytochrome. Using microarrays printed with these 70-mer probes, we analyzed the gene expression profile of wild-type D. vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed negative potential of −1.1 V (cathodic protection conditions). The gene expression profile of cells grown on cathodic hydrogen was compared to that of cells grown with gaseous hydrogen bubbling through the culture. Relative to the latter, the electrode-grown cells overexpressed two hydrogenases, the hyn-1 genes for [NiFe] hydrogenase 1 and the hyd genes, encoding [Fe] hydrogenase. The hmc genes for the high-molecular-weight cytochrome complex, which allows electron flow from the hydrogenases across the cytoplasmic membrane, were also overexpressed. In contrast, cells grown on gaseous hydrogen overexpressed the hys genes for [NiFeSe] hydrogenase. Cells growing on the electrode also overexpressed genes encoding proteins which promote biofilm formation. Although the gene expression profiles for these two modes of growth were distinct, they were more closely related to each other than to that for cells grown in a lactate- and sulfate-containing medium. Electrochemically measured corrosion rates were lower for iron electrodes covered with hyn-1, hyd, and hmc mutant biofilms than for wild-type biofilms. This confirms the importance, suggested by the gene expression studies, of the corresponding gene products in D. vulgaris-mediated iron corrosion. PMID:18310429

  12. Recovery of temperate Desulfovibrio vulgaris bacteriophage on anovel host strain

    SciTech Connect

    Walker, C.B.; Stolyar, S.S.; Pinel, N.; Yen, H.C.; He, Z.; Zhou,J.; Wall, J.D.; Stahl, D.A.

    2007-04-02

    A novel sulfate-reducing bacterium (strain DePue) closelyrelated to Desulfovibrio vulgaris ssp. vulgaris strain Hildenborough wasisolated from the sediment of a heavy-metal impacted lake usingestablished techniques. Although few physiological differences betweenstrains DePue and Hildenborough were observed, pulsed-field gelelectrophoresis (PFGE) revealed a significant genome reduction in strainDePue. Comparative whole-genome microarray and PCR analyses demonstratedthat the absence of genes annotated in the Hildenborough genome as phageor phage-related contributed to the significant genome reduction instrain DePue. Two morphotypically distinct temperate bacteriophage fromstrain Hildenborough were recovered using strain DePue as a host forplaque isolation.

  13. Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Burns, Andrew; Joachimiak, Marcin; Deutschbauer, Adam; Arkin, Adam; Bender, Kelly

    2010-05-17

    Desulfovibrio vulgaris is an anaerobic sulfate-reducing bacterium capable of facilitating the removal of toxic metals such as uranium from contaminated sites via reduction. As such, it is essential to understand the intricate regulatory cascades involved in how D. vulgaris and its relatives respond to stressors in such sites. One approach is the identification and analysis of small non-coding RNAs (sRNAs); molecules ranging in size from 20-200 nucleotides that predominantly affect gene regulation by binding to complementary mRNA in an anti-sense fashion and therefore provide an immediate regulatory response. To identify sRNAs in D. vulgaris, a bacterium that does not possess an annotated hfq gene, RNA was pooled from stationary and exponential phases, nitrate exposure, and biofilm conditions. The subsequent RNA was size fractionated, modified, and converted to cDNA for high throughput transcriptomic deep sequencing. A computational approach to identify sRNAs via the alignment of seven separate Desulfovibrio genomes was also performed. From the deep sequencing analysis, 2,296 reads between 20 and 250 nt were identified with expression above genome background. Analysis of those reads limited the number of candidates to ~;;87 intergenic, while ~;;140 appeared to be antisense to annotated open reading frames (ORFs). Further BLAST analysis of the intergenic candidates and other Desulfovibrio genomes indicated that eight candidates were likely portions of ORFs not previously annotated in the D. vulgaris genome. Comparison of the intergenic and antisense data sets to the bioinformatical predicted candidates, resulted in ~;;54 common candidates. Current approaches using Northern analysis and qRT-PCR are being used toverify expression of the candidates and to further develop the role these sRNAs play in D. vulgaris regulation.

  14. Extracellular Electron Transfer Is a Bottleneck in the Microbiologically Influenced Corrosion of C1018 Carbon Steel by the Biofilm of Sulfate-Reducing Bacterium Desulfovibrio vulgaris.

    PubMed

    Li, Huabing; Xu, Dake; Li, Yingchao; Feng, Hao; Liu, Zhiyong; Li, Xiaogang; Gu, Tingyue; Yang, Ke

    2015-01-01

    Carbon steels are widely used in the oil and gas industry from downhole tubing to transport trunk lines. Microbes form biofilms, some of which cause the so-called microbiologically influenced corrosion (MIC) of carbon steels. MIC by sulfate reducing bacteria (SRB) is often a leading cause in MIC failures. Electrogenic SRB sessile cells harvest extracellular electrons from elemental iron oxidation for energy production in their metabolism. A previous study suggested that electron mediators riboflavin and flavin adenine dinucleotide (FAD) both accelerated the MIC of 304 stainless steel by the Desulfovibrio vulgaris biofilm that is a corrosive SRB biofilm. Compared with stainless steels, carbon steels are usually far more prone to SRB attacks because SRB biofilms form much denser biofilms on carbon steel surfaces with a sessile cell density that is two orders of magnitude higher. In this work, C1018 carbon steel coupons were used in tests of MIC by D. vulgaris with and without an electron mediator. Experimental weight loss and pit depth data conclusively confirmed that both riboflavin and FAD were able to accelerate D. vulgaris attack against the carbon steel considerably. It has important implications in MIC failure analysis and MIC mitigation in the oil and gas industry.

  15. Extracellular Electron Transfer Is a Bottleneck in the Microbiologically Influenced Corrosion of C1018 Carbon Steel by the Biofilm of Sulfate-Reducing Bacterium Desulfovibrio vulgaris

    PubMed Central

    Li, Yingchao; Feng, Hao; Liu, Zhiyong; Li, Xiaogang; Gu, Tingyue; Yang, Ke

    2015-01-01

    Carbon steels are widely used in the oil and gas industry from downhole tubing to transport trunk lines. Microbes form biofilms, some of which cause the so-called microbiologically influenced corrosion (MIC) of carbon steels. MIC by sulfate reducing bacteria (SRB) is often a leading cause in MIC failures. Electrogenic SRB sessile cells harvest extracellular electrons from elemental iron oxidation for energy production in their metabolism. A previous study suggested that electron mediators riboflavin and flavin adenine dinucleotide (FAD) both accelerated the MIC of 304 stainless steel by the Desulfovibrio vulgaris biofilm that is a corrosive SRB biofilm. Compared with stainless steels, carbon steels are usually far more prone to SRB attacks because SRB biofilms form much denser biofilms on carbon steel surfaces with a sessile cell density that is two orders of magnitude higher. In this work, C1018 carbon steel coupons were used in tests of MIC by D. vulgaris with and without an electron mediator. Experimental weight loss and pit depth data conclusively confirmed that both riboflavin and FAD were able to accelerate D. vulgaris attack against the carbon steel considerably. It has important implications in MIC failure analysis and MIC mitigation in the oil and gas industry. PMID:26308855

  16. Response of Desulfovibrio vulgaris to alkaline stress.

    PubMed

    Stolyar, Sergey; He, Qiang; Joachimiak, Marcin P; He, Zhili; Yang, Zamin Koo; Borglin, Sharon E; Joyner, Dominique C; Huang, Katherine; Alm, Eric; Hazen, Terry C; Zhou, Jizhong; Wall, Judy D; Arkin, Adam P; Stahl, David A

    2007-12-01

    The response of exponentially growing Desulfovibrio vulgaris Hildenborough to pH 10 stress was studied using oligonucleotide microarrays and a study set of mutants with genes suggested by microarray data to be involved in the alkaline stress response deleted. The data showed that the response of D. vulgaris to increased pH is generally similar to that of Escherichia coli but is apparently controlled by unique regulatory circuits since the alternative sigma factors (sigma S and sigma E) contributing to this stress response in E. coli appear to be absent in D. vulgaris. Genes previously reported to be up-regulated in E. coli were up-regulated in D. vulgaris; these genes included three ATPase genes and a tryptophan synthase gene. Transcription of chaperone and protease genes (encoding ATP-dependent Clp and La proteases and DnaK) was also elevated in D. vulgaris. As in E. coli, genes involved in flagellum synthesis were down-regulated. The transcriptional data also identified regulators, distinct from sigma S and sigma E, that are likely part of a D. vulgaris Hildenborough-specific stress response system. Characterization of a study set of mutants with genes implicated in alkaline stress response deleted confirmed that there was protective involvement of the sodium/proton antiporter NhaC-2, tryptophanase A, and two putative regulators/histidine kinases (DVU0331 and DVU2580).

  17. Response of Desulfovibrio vulgaris to Alkaline Stress

    SciTech Connect

    Stolyar, S.; He, Q.; He, Z.; Yang, Z.; Borglin, S.E.; Joyner, D.; Huang, K.; Alm, E.; Hazen, T.C.; Zhou, J.; Wall, J.D.; Arkin, A.P.; Stahl, D.A.

    2007-11-30

    The response of exponentially growing Desulfovibrio vulgarisHildenborough to pH 10 stress was studied using oligonucleotidemicroarrays and a study set of mutants with genes suggested by microarraydata to be involved in the alkaline stress response deleted. The datashowed that the response of D. vulgaris to increased pH is generallysimilar to that of Escherichia coli but is apparently controlled byunique regulatory circuits since the alternative sigma factors (sigma Sand sigma E) contributing to this stress response in E. coli appear to beabsent in D. vulgaris. Genes previously reported to be up-regulated in E.coli were up-regulated in D. vulgaris; these genes included three ATPasegenes and a tryptophan synthase gene. Transcription of chaperone andprotease genes (encoding ATP-dependent Clp and La proteases and DnaK) wasalso elevated in D. vulgaris. As in E. coli, genes involved in flagellumsynthesis were down-regulated. The transcriptional data also identifiedregulators, distinct from sigma S and sigma E, that are likely part of aD. vulgaris Hildenborough-specific stress response system.Characterization of a study set of mutants with genes implicated inalkaline stress response deleted confirmed that there was protectiveinvolvement of the sodium/proton antiporter NhaC-2, tryptophanase A, andtwo putative regulators/histidine kinases (DVU0331 andDVU2580).

  18. σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Kazakov, Alexey E.; Rajeev, Lara; Chen, Amy; Luning, Eric G.; Dubchak, Inna; Mukhopadhyay, Aindrila; Novichkov, Pavel S.

    2015-11-10

    The σ54 subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequenced bacteria. Finally, the cellular processes regulated by many of these EBPs remain unknown.

  19. A genomic island of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough promotes survival under stress conditions while decreasing the efficiency of anaerobic growth.

    PubMed

    Johnston, Shawna; Lin, Shiping; Lee, Phoebe; Caffrey, Sean M; Wildschut, Janine; Voordouw, Johanna K; da Silva, Sofia M; Pereira, Ines A C; Voordouw, Gerrit

    2009-04-01

    A 47 kb genomic island (GEI) bracketed by 50 bp direct repeats, containing 52 annotated genes, was found to delete spontaneously from the genome of Desulfovibrio vulgaris Hildenborough. The island contains genes for site-specific recombinases and transposases, rubredoxin:oxygen oxidoreductase-1 (Roo1) and hybrid cluster protein-1 (Hcp1), which promote survival in air and nitrite stress. The numbering distinguishes these from the Roo2 and Hcp2 homologues for which the genes are located elsewhere in the genome. Cells with and without the island (GEI(+) and GEI(-) cells respectively) were obtained by colony purification. GEI(-) cells arise in anaerobic cultures of colony-purified GEI(+) cells, indicating that the site-specific recombinases encoded by the island actively delete this region. GEI(+) cells survive better in microaerophilic conditions due to the presence of Roo1, whereas the Hcps appear to prevent inhibition by sulfur and polysulfide, which are formed by chemical reaction of sulfide and nitrite. Hence, the island confers resistance to oxygen and nitrite stress. However, GEI(-) cells have a higher growth rate in anaerobic media. Microarrays and enzyme activity stains indicated that the GEI(-) cells have increased expression of genes, which promote anaerobic energy conservation, explaining the higher growth rate. Hence, while lowering the efficiency of anaerobic metabolism, the GEI increases the fitness of D. vulgaris under stress conditions, a feature reminiscent of pathogenicity islands which allow more effective colonization of environments provided by the targeted hosts.

  20. Oxidation of benzaldehydes to benzoic acid derivatives by three Desulfovibrio strains. [Desulfovibrio vulgaris; Desulfovibrio simplex; Desulfovibrio sp

    SciTech Connect

    Zellner, G.; Winter, J. ); Kneifel, H. )

    1990-07-01

    Desulfovibrio vulgaris Marburg, Desulfovibrio simplex XVI, and Desulfovibrio sp. strain MP47 used benzaldehydes such as vanillin, 3,4,5-trimethoxybenzaldehyde, protocatechualdehyde, syringaldehyde, p-anisaldehyde, p-hydroxybenzaldehyde, and 2-methoxybenzaldehyde as electron donors for sulfate reduction and carbon dioxide and/or components of yeast extract as carbon sources for cell synthesis. The aldehydes were oxidized to their corresponding benzoic acids. The three sulfate reducers oxidized up to 7 mM vanillin and up to 4 mM p-anisaldehyde. Higher concentrations of vanillin or p-anisaldehyde were toxic. In addition, pyridoxal hydrochloride and o-vanillin served as electron donors for sulfate reduction. Salicylaldehyde, pyridine-2-aldehyde, pyridine-4-aldehyde, and 4-hydroxy-3-methoxybenzylalcohol were not oxidized. No molecular hydrogen was detected in the gas phase. The oxidized aldehydes were not further degraded.

  1. CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough.

    PubMed

    Wilkins, Michael J; Hoyt, David W; Marshall, Matthew J; Alderson, Paul A; Plymale, Andrew E; Markillie, L Meng; Tucker, Abby E; Walter, Eric D; Linggi, Bryan E; Dohnalkova, Alice C; Taylor, Ron C

    2014-01-01

    Geologic carbon dioxide (CO2) sequestration drives physical and geochemical changes in deep subsurface environments that impact indigenous microbial activities. The combined effects of pressurized CO2 on a model sulfate-reducing microorganism, Desulfovibrio vulgaris, have been assessed using a suite of genomic and kinetic measurements. Novel high-pressure NMR time-series measurements using (13)C-lactate were used to track D. vulgaris metabolism. We identified cessation of respiration at CO2 pressures of 10 bar, 25 bar, 50 bar, and 80 bar. Concurrent experiments using N2 as the pressurizing phase had no negative effect on microbial respiration, as inferred from reduction of sulfate to sulfide. Complementary pressurized batch incubations and fluorescence microscopy measurements supported NMR observations, and indicated that non-respiring cells were mostly viable at 50 bar CO2 for at least 4 h, and at 80 bar CO2 for 2 h. The fraction of dead cells increased rapidly after 4 h at 80 bar CO2. Transcriptomic (RNA-Seq) measurements on mRNA transcripts from CO2-incubated biomass indicated that cells up-regulated the production of certain amino acids (leucine, isoleucine) following CO2 exposure at elevated pressures, likely as part of a general stress response. Evidence for other poorly understood stress responses were also identified within RNA-Seq data, suggesting that while pressurized CO2 severely limits the growth and respiration of D. vulgaris cells, biomass retains intact cell membranes at pressures up to 80 bar CO2. Together, these data show that geologic sequestration of CO2 may have significant impacts on rates of sulfate reduction in many deep subsurface environments where this metabolism is a key respiratory process.

  2. CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough

    PubMed Central

    Wilkins, Michael J.; Hoyt, David W.; Marshall, Matthew J.; Alderson, Paul A.; Plymale, Andrew E.; Markillie, L. Meng; Tucker, Abby E.; Walter, Eric D.; Linggi, Bryan E.; Dohnalkova, Alice C.; Taylor, Ron C.

    2014-01-01

    Geologic carbon dioxide (CO2) sequestration drives physical and geochemical changes in deep subsurface environments that impact indigenous microbial activities. The combined effects of pressurized CO2 on a model sulfate-reducing microorganism, Desulfovibrio vulgaris, have been assessed using a suite of genomic and kinetic measurements. Novel high-pressure NMR time-series measurements using 13C-lactate were used to track D. vulgaris metabolism. We identified cessation of respiration at CO2 pressures of 10 bar, 25 bar, 50 bar, and 80 bar. Concurrent experiments using N2 as the pressurizing phase had no negative effect on microbial respiration, as inferred from reduction of sulfate to sulfide. Complementary pressurized batch incubations and fluorescence microscopy measurements supported NMR observations, and indicated that non-respiring cells were mostly viable at 50 bar CO2 for at least 4 h, and at 80 bar CO2 for 2 h. The fraction of dead cells increased rapidly after 4 h at 80 bar CO2. Transcriptomic (RNA-Seq) measurements on mRNA transcripts from CO2-incubated biomass indicated that cells up-regulated the production of certain amino acids (leucine, isoleucine) following CO2 exposure at elevated pressures, likely as part of a general stress response. Evidence for other poorly understood stress responses were also identified within RNA-Seq data, suggesting that while pressurized CO2 severely limits the growth and respiration of D. vulgaris cells, biomass retains intact cell membranes at pressures up to 80 bar CO2. Together, these data show that geologic sequestration of CO2 may have significant impacts on rates of sulfate reduction in many deep subsurface environments where this metabolism is a key respiratory process. PMID:25309528

  3. CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough

    SciTech Connect

    Wilkins, Michael J.; Hoyt, David W.; Marshall, Matthew J.; Alderson, Paul A.; Plymale, Andrew E.; Markillie, Lye Meng; Tucker, Abigail E.; Walter, Eric D.; Linggi, Bryan E.; Dohnalkova, Alice; Taylor, Ronald C.

    2014-09-01

    Geologic carbon dioxide (CO2) sequestration drives physical and geochemical changes in deep subsurface environments that impact indigenous microbial activities. The combined effects of pressurized CO2 on a model sulfate-reducing microorganism, Desulfovibrio vulgaris, have been assessed using a suite of genomic and kinetic measurements. Novel high-pressure NMR time-series measurements using 13C-lactate were used to track D. vulgaris metabolism. We identified cessation of respiration at CO2 pressures of 10 bar, 25 bar, 50 bar, and 80 bar. Concurrent experiments using N2 as the pressurizing phase had no negative effect on microbial respiration, as inferred from reduction of sulfate to sulfide. Complementary pressurized batch incubations and fluorescence microscopy measurements supported NMR observations, and indicated that non-respiring cells were mostly viable at 50 bar CO2 for at least four hours, and at 80 bar CO2 for two hours. The fraction of dead cells increased rapidly after four hours at 80 bar CO2. Transcriptomic (RNA-Seq) measurements on mRNA transcripts from CO2-incubated biomass indicated that cells up-regulated the production of certain amino acids (leucine, isoleucine) following CO2 exposure at elevated pressures, likely as part of a general stress response. Evidence for other poorly understood stress responses were also identified within RNA-Seq data, suggesting that while pressurized CO2 severely limits the growth and respiration of D. vulgaris cells, biomass retains intact cell membranes at pressures up to 80 bar CO2. Together, these data show that geologic sequestration of CO2 may have significant impacts on rates of sulfate reduction in many deep subsurface environments where this metabolism is a key respiratory process.

  4. Mutualistic growth of the sulfate-reducer Desulfovibrio vulgaris Hildenborough with different carbohydrates.

    PubMed

    Santana, M M; Portillo, M C; Gonzalez, J M

    2012-01-01

    Desulfovibrio vulgaris Hildenborough genome presents a phosphotransferase system putatively involved in the transport of carbohydrates. However, utilization of sugars by this sulfate-reducing bacterium has never been reported. Herein, we have observed proliferation of D. vulgaris Hildenborough with some carbohydrates, in mutualism with Stenotrophomonas maltophilia, a non-fermentative, gram-negative gammaproteobacterium, or Microbacterium, a gram-positive actinobacterium. These results suggest the importance of feedback interactions between different heterotrophic bacterial species including the alternative for D. vulgaris of exploiting additional organic resources and novel habitats. Thus, D. vulgaris strongly participates in the mineralization of carbohydrates both in complex natural and artificial systems.

  5. Bacterioferritin protects the anaerobe Desulfovibrio vulgaris Hildenborough against oxygen.

    PubMed

    Figueiredo, Mafalda C O; Lobo, Susana A L; Carita, João N; Nobre, Lígia S; Saraiva, Lígia M

    2012-08-01

    Intracellular free iron, is under aerobic conditions and via the Fenton reaction a catalyst for the formation of harmful reactive oxygen species. In this article, we analyzed the relation between intracellular iron storage and oxidative stress response in the sulfate reducing bacterium Desulfovibrio vulgaris Hildenborough, an anaerobe that is often found in oxygenated niches. To this end, we investigated the role of the iron storage protein bacterioferritin using transcriptomic and physiological approaches. We observed that transcription of bacterioferritin is strongly induced upon exposure of cells to an oxygenated atmosphere. When grown in the presence of high concentrations of oxygen the D. vulgaris bacterioferritin mutant exhibited, in comparison with the wild type strain, lower viability and a higher content of intracellular reactive oxygen species. Furthermore, the bacterioferritin gene is under the control of the oxidative stress response regulator D. vulgaris PerR. Altogether the data revealed a previously unrecognized ability for the iron storage bacterioferritin to contribute to the oxygen tolerance exhibited by D. vulgaris.

  6. The Carbon Monoxide Dehydrogenase from Desulfovibrio vulgaris.

    PubMed

    Hadj-Saïd, Jessica; Pandelia, Maria-Eirini; Léger, Christophe; Fourmond, Vincent; Dementin, Sébastien

    2015-12-01

    Ni-containing Carbon Monoxide Dehydrogenases (CODHs) catalyze the reversible conversion between CO and CO₂and are involved in energy conservation and carbon fixation. These homodimeric enzymes house two NiFeS active sites (C-clusters) and three accessory [4Fe-4S] clusters. The Desulfovibrio vulgaris (Dv) genome contains a two-gene CODH operon coding for a CODH (cooS) and a maturation protein (cooC) involved in nickel insertion in the active site. According to the literature, the question of the precise function of CooC as a chaperone folding the C-cluster in a form which accommodates free nickel or as a mere nickel donor is not resolved. Here, we report the biochemical and spectroscopic characterization of two recombinant forms of the CODH, produced in the absence and in the presence of CooC, designated CooS and CooS(C), respectively. CooS contains no nickel and cannot be activated, supporting the idea that the role of CooC is to fold the C-cluster so that it can bind nickel. As expected, CooS(C) is Ni-loaded, reversibly converts CO and CO₂, displays the typical Cred1 and Cred2 EPR signatures of the C-cluster and activates in the presence of methyl viologen and CO in an autocatalytic process. However, Ni-loaded CooS(C) reaches maximum activity only upon reductive treatment in the presence of exogenous nickel, a phenomenon that had not been observed before. Surprisingly, the enzyme displays the Cred1 and Cred2 signatures whether it has been activated or not, showing that this activation process of the Ni-loaded Dv CODH is not associated with structural changes at the active site.

  7. Membrane protein complex of APS reductase and Qmo is present in Desulfovibrio vulgaris and Desulfovibrio alaskensis.

    PubMed

    Krumholz, Lee R; Wang, Luyao; Beck, David A C; Wang, Tiansong; Hackett, Murray; Mooney, Brian; Juba, Thomas R; McInerney, Michael J; Meyer, Birte; Wall, Judy D; Stahl, David A

    2013-10-01

    Due to their adjacent location in the genomes of Desulfovibrio species and their potential for formation of an electron transfer pathway in sulfate-reducing prokaryotes, adenosyl phosphosulfate (APS) reductase (Apr) and quinone-interacting membrane-bound oxidoreductase (Qmo) have been thought to interact together during the reduction of APS. This interaction was recently verified in Desulfovibrio desulfuricans. Membrane proteins of Desulfovibrio vulgaris Hildenborough ΔqmoABCD JW9021, a deletion mutant, were compared to the parent strain using blue-native PAGE to determine whether Qmo formed a complex with Apr or other proteins. In the parent strain of D. vulgaris, a unique band was observed that contained all four Qmo subunits, and another band contained three subunits of Qmo, as well as subunits of AprA and AprB. Similar results were observed with bands excised from membrane preparations of Desulfovibrio alaskensis strain G20. These results are in support of the formation of a physical complex between the two proteins; a result that was further confirmed by the co-purification of QmoA/B and AprA/B from affinity-tagged D. vulgaris Hildenborough strains (AprA, QmoA and QmoB) regardless of which subunit had been tagged. This provides clear evidence for the presence of a Qmo-Apr complex that is at least partially stable in protein extracts of D. vulgaris and D. alaskensis.

  8. Biofilm formation in Desulfovibrio vulgaris Hildenborough is dependent upon protein filaments.

    PubMed

    Clark, Melinda E; Edelmann, Richard E; Duley, Matt L; Wall, Judy D; Fields, Matthew W

    2007-11-01

    Desulfovibrio vulgaris Hildenborough is a Gram-negative sulfate-reducing bacterium (SRB), and the physiology of SRBs can impact many anaerobic environments including radionuclide waste sites, oil reservoirs and metal pipelines. In an attempt to understand D. vulgaris as a population that can adhere to surfaces, D. vulgaris cultures were grown in a defined medium and analysed for carbohydrate production, motility and biofilm formation. Desulfovibrio vulgaris wild-type cells had increasing amounts of carbohydrate into stationary phase and approximately half of the carbohydrate remained internal. In comparison, a mutant that lacked the 200 kb megaplasmid, strain DeltaMP, produced less carbohydrate and the majority of carbohydrate remained internal of the cell proper. To assess the possibility of carbohydrate re-allocation, biofilm formation was investigated. Wild-type cells produced approximately threefold more biofilm on glass slides compared with DeltaMP; however, wild-type biofilm did not contain significant levels of exopolysaccharide. In addition, stains specific for extracellular carbohydrate did not reveal polysaccharide material within the biofilm. Desulfovibrio vulgaris wild-type biofilms contained long filaments as observed with scanning electron microscopy (SEM), and the biofilm-deficient DeltaMP strain was also deficient in motility. Biofilms grown directly on silica oxide transmission electron microscopy (TEM) grids did not contain significant levels of an exopolysaccharide matrix when viewed with TEM and SEM, and samples stained with ammonium molybdate also showed long filaments that resembled flagella. Biofilms subjected to protease treatments were degraded, and different proteases that were added at the time of inoculation inhibited biofilm formation. The data indicated that D. vulgaris did not produce an extensive exopolysaccharide matrix, used protein filaments to form biofilm between cells and silica oxide surfaces, and the filaments appeared to be

  9. Function of formate dehydrogenases in Desulfovibrio vulgaris Hildenborough energy metabolism.

    PubMed

    da Silva, Sofia M; Voordouw, Johanna; Leitão, Cristina; Martins, Mónica; Voordouw, Gerrit; Pereira, Inês A C

    2013-08-01

    The genome of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough encodes three formate dehydrogenases (FDHs), two of which are soluble periplasmic enzymes (FdhAB and FdhABC3) and one that is periplasmic but membrane-associated (FdhM). FdhAB and FdhABC3 were recently shown to be the main enzymes present during growth with lactate, formate or hydrogen. To address the role of these two enzymes, ΔfdhAB and ΔfdhABC3, mutants were generated and studied. Different phenotypes were observed in the presence of either molybdenum or tungsten, since both enzymes were important for growth on formate in the presence of Mo, whereas in the presence of W only FdhAB played a role. Both ΔfdhAB and ΔfdhABC3 mutants displayed defects in growth with lactate and sulfate providing the first direct evidence for the involvement of formate cycling under these conditions. In support of this mechanism, incubation of concentrated cell suspensions of the mutant strains with lactate and limiting sulfate also gave elevated formate concentrations, as compared to the wild-type strain. In contrast, both mutants grew similarly to the wild-type with H2 and sulfate. In the absence of sulfate, the wild-type D. vulgaris cells produced formate when supplied with H2 and CO2, which resulted from CO2 reduction by the periplasmic FDHs. The conversion of H2 and CO2 to formate allows the reversible storage of reducing power in a much more soluble molecule. Furthermore, we propose this may be an expression of the ability of some sulfate-reducing bacteria to grow by hydrogen oxidation, in syntrophy with organisms that consume formate, but are less efficient in H2 utilization.

  10. Toxic effects of dissolved heavy metals on Desulfovibrio vulgaris and Desulfovibrio sp. strains.

    PubMed

    Cabrera, G; Pérez, R; Gómez, J M; Abalos, A; Cantero, D

    2006-07-31

    Biological treatment of metal-containing wastewaters with sulphate-reducing bacteria (SRB) is an attractive technique for the bioremediation of this kind of medium. In order to design a suitable engineering process to address this environmental problem, it is crucial to understand the inhibitory effect of dissolved heavy metals on these bacteria. Batch studies were carried out to evaluate the toxic effects of several heavy metal ions [Cr(III), Cu(II), Mn(II), Ni(II) and Zn(II)] on two cultures of SRB (Desulfovibrio vulgaris and Desulfovibrio sp.). The experimental data indicate that SRB show different responses to each metal. At the highest metal concentration tolerated for each metal, the precipitation levels for D. vulgaris were as follows: 24.7%-15 ppm Cr(III), 45%-4 ppm Cu(II), 60%-10 ppm Mn(II), 96%-8.5 ppm Ni(II) and 9%-20 ppm Zn(II). The corresponding values for Desulfovibrio sp. were: 25.5%-15 ppm Cr(III), 71%-4 ppm Cu(II), 66.2%-10 ppm Mn(II), 96.1%-8.5 ppm Ni(II) and 93%-20 ppm Zn(II). Results obtained in batch studies will be taken into account for the subsequent design of a sulphate-reducing bioreactor to reduce levels of heavy metals present in different types of contaminated media.

  11. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity

    SciTech Connect

    Walker, Christopher; Stolyar, Sergey; Chivian, Dylan; Pinel, Nicolas; Gabster, Jeffrey; Dehal, Paramvir; He, Zhili; Yang, Zamin Koo; Yen, Huei-Che; Zhou, Jizhong; Hazen, Terry; Arkin, Adam; Stahl, David

    2009-01-01

    The genome of Desulfovibrio vulgaris strain DePue, a sulfate-reducing Deltaproteobacterium isolated from heavy metal-impacted lake sediment, was completely sequenced and compared with the type strain D. vulgaris Hildenborough. The two genomes share a high degree of relatedness and synteny, but harbour distinct prophage and signatures of past phage encounters. In addition to a highly variable phage contribution, the genome of strain DePue contains a cluster of open-reading frames not found in strain Hildenborough coding for the production and export of a capsule exopolysaccharide, possibly of relevance to heavy metal resistance. Comparative whole-genome microarray analysis on four additional D. vulgaris strains established greater interstrain variation within regions associated with phage insertion and exopolysaccharide biosynthesis.

  12. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity.

    PubMed

    Walker, Christopher B; Stolyar, Sergey; Chivian, Dylan; Pinel, Nicolas; Gabster, Jeffrey A; Dehal, Paramvir S; He, Zhili; Yang, Zamin Koo; Yen, Huei-Che B; Zhou, Jizhong; Wall, Judy D; Hazen, Terry C; Arkin, Adam P; Stahl, David A

    2009-09-01

    The genome of Desulfovibrio vulgaris strain DePue, a sulfate-reducing Deltaproteobacterium isolated from heavy metal-impacted lake sediment, was completely sequenced and compared with the type strain D. vulgaris Hildenborough. The two genomes share a high degree of relatedness and synteny, but harbour distinct prophage and signatures of past phage encounters. In addition to a highly variable phage contribution, the genome of strain DePue contains a cluster of open-reading frames not found in strain Hildenborough coding for the production and export of a capsule exopolysaccharide, possibly of relevance to heavy metal resistance. Comparative whole-genome microarray analysis on four additional D. vulgaris strains established greater interstrain variation within regions associated with phage insertion and exopolysaccharide biosynthesis.

  13. Use of immunomagnetic separation for the detection of Desulfovibrio vulgaris from environmental samples

    SciTech Connect

    Chakraborty, R.; Hazen, T.C.; Joyner, D.C.; Kusel, K.; Singer, M.E.; Sitte, J.; Torok, T.

    2011-04-15

    Immunomagnetic separation (IMS) has proved highly efficient for recovering microorganisms from heterogeneous samples. Current investigation targeted the separation of viable cells of the sulfate-reducing bacterium, Desulfovibrio vulgaris. Streptavidin-coupled paramagnetic beads and biotin labeled antibodies raised against surface antigens of this microorganism were used to capture D. vulgaris cells in both bioreactor grown laboratory samples and from extremely low-biomass environmental soil and subsurface drilling samples. Initial studies on detection, recovery efficiency and viability for IMS were performed with laboratory grown D. vulgaris cells using various cell densities. Efficiency of cell isolation and recovery (i.e., release of the microbial cells from the beads following separation) was followed by microscopic imaging and acridine orange direct counts (AODC). Excellent recovery efficiency encouraged the use of IMS to capture Desulfovibrio spp. cells from low-biomass environmental samples. The environmental samples were obtained from a radionuclide-contaminated site in Germany and the chromium (VI)-contaminated Hanford site, an ongoing bioremediation project of the U.S. Department of Energy. Field deployable IMS technology may greatly facilitate environmental sampling and bioremediation process monitoring and enable transcriptomics and proteomics/metabolomics-based studies directly on cells collected from the field.

  14. Use of immunomagnetic separation for the detection of Desulfovibrio vulgaris from environmental samples.

    PubMed

    Chakraborty, Romy; Hazen, Terry C; Joyner, Dominique C; Küsel, Kirsten; Singer, Mary E; Sitte, Jana; Torok, Tamas

    2011-08-01

    Immunomagnetic separation (IMS) has proved highly efficient for recovering microorganisms from heterogeneous samples. Current investigation targeted the separation of viable cells of the sulfate-reducing bacterium, Desulfovibrio vulgaris. Streptavidin-coupled paramagnetic beads and biotin labeled antibodies raised against surface antigens of this microorganism were used to capture D. vulgaris cells in both bioreactor grown laboratory samples and from extremely low-biomass environmental soil and subsurface drilling samples. Initial studies on detection, recovery efficiency and viability for IMS were performed with laboratory grown D. vulgaris cells using various cell densities. Efficiency of cell isolation and recovery (i.e., release of the microbial cells from the beads following separation) was followed by microscopic imaging and acridine orange direct counts (AODC). Excellent recovery efficiency encouraged the use of IMS to capture Desulfovibrio spp. cells from low-biomass environmental samples. The environmental samples were obtained from a radionuclide-contaminated site in Germany and the chromium (VI)-contaminated Hanford site, an ongoing bioremediation project of the U.S. Department of Energy. Field deployable IMS technology may greatly facilitate environmental sampling and bioremediation process monitoring and enable transcriptomics and proteomics/metabolomics-based studies directly on cells collected from the field.

  15. Recovery of temperate Desulfovibrio vulgaris bacteriophage using a novel host strain.

    PubMed

    Walker, Christopher B; Stolyar, Sergey S; Pinel, Nic; Yen, Huei-Che B; He, Zhili; Zhou, Jizhong; Wall, Judy D; Stahl, David A

    2006-11-01

    A novel sulfate-reducing bacterium (strain DePue) closely related to Desulfovibrio vulgaris ssp. vulgaris strain Hildenborough was isolated from the sediment of a heavy-metal impacted lake using established techniques. Although few physiological differences between strains DePue and Hildenborough were observed, pulse-field gel electrophoresis (PFGE) revealed a significant genome reduction in strain DePue. Comparative whole-genome microarray and polymerase chain reaction analyses demonstrated that the absence of genes annotated in the Hildenborough genome as phage or phage-related contributed to the significant genome reduction in strain DePue. Two morphotypically distinct temperate bacteriophage from strain Hildenborough were recovered using strain DePue as a host for plaque isolation.

  16. Post-translational modifications of Desulfovibrio vulgaris Hildenborough sulfate reduction pathway proteins.

    PubMed

    Gaucher, Sara P; Redding, Alyssa M; Mukhopadhyay, Aindrila; Keasling, Jay D; Singh, Anup K

    2008-06-01

    Recent developments in shotgun proteomics have enabled high-throughput studies of a variety of microorganisms at a proteome level and provide experimental validation for predicted open reading frames in the corresponding genome. More importantly, advances in mass spectrometric data analysis now allow mining of large proteomics data sets for the presence of post-translational modifications (PTMs). Although PTMs are a critical aspect of cellular activity, such information eludes cell-wide studies conducted at the transcript level. Here, we analyze several mass spectrometric data sets acquired using two-dimensional liquid chromatography tandem mass spectrometry, 2D-LC/MS/MS, for the sulfate reducing bacterium, Desulfovibrio vulgaris Hildenborough. Our searches of the raw spectra led us to discover several post-translationally modified peptides in D. vulgaris. Of these, several peptides containing a lysine with a +42 Da modification were found reproducibly across all data sets. Both acetylation and trimethylation have the same nominal +42 Da mass, and are therefore candidates for this modification. Several spectra were identified having markers for trimethylation, while one is consistent with an acetylation. Surprisingly, these modified peptides predominantly mapped to proteins involved in sulfate respiration. Other highly expressed proteins in D. vulgaris, such as enzymes involved in electron transport and other central metabolic processes, did not contain this modification. Decoy database searches were used to control for random spectrum/sequence matches. Additional validation for these modifications was provided by alternate workflows, for example, two-dimensional gel electrophoresis followed by mass spectrometry analysis of the dissimilatory sulfite reductase gamma-subunit (DsrC) protein. MS data for DsrC in this alternate workflow also contained the +42 Da modification at the same loci. Furthermore, the DsrC homologue in another sulfate reducing bacterium

  17. Post-Translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins

    SciTech Connect

    Gaucher, S.P.; Redding, A.M.; Mukhopadhyay, A.; Keasling, J.D.; Singh, A.K.

    2008-03-01

    Recent developments in shotgun proteomics have enabled high-throughput studies of a variety of microorganisms at a proteome level and provide experimental validation for predicted open reading frames in the corresponding genome. More importantly, advances in mass spectrometric data analysis now allow mining of large proteomics data sets for the presence of post-translational modifications(PTMs). Although PTMs are a critical aspectof cellular activity, such information eludes cell-wide studies conducted at the transcript level. Here, we analyze several mass spectrometric data sets acquired using two-dimensional liquid chromatography tandem mass spectrometry, 2D-LC/MS/MS, for the sulfate reducing bacterium, Desulfovibrio vulgaris Hildenborough. Our searches of the raw spectra led us to discover several post-translationally modified peptides in D. vulgaris. Of these, several peptides containing a lysine with a +42 Da modification were found reproducibly across all data sets. Both acetylation and trimethylation have the same nominal +42 Da mass, and are therefore candidates for this modification. Several spectra were identified having markers for trimethylation, while one is consistent with an acetylation. Surprisingly, these modified peptides predominantly mapped to proteins involved in sulfate respiration. Other highly expressed proteins in D. vulgaris, such as enzymes involved in electron transport and other central metabolic processes, did not contain this modification. Decoy database searches were used to control for random spectrum/sequence matches. Additional validation for these modifications was provided by alternate workflows, for example, two-dimensional gel electrophoresis followed by mass spectrometry analysis of the dissimilatory sulfite reductase gamma-subunit(DsrC) protein. MS data for DsrC in this alternate workflow also contained the +42 Da modification at the same loci. Furthermore, the DsrC homologue in another sulfate reducing bacterium

  18. Salt Stress in Desulfovibrio vulgaris Hildenborough: An integratedgenomics approach

    SciTech Connect

    Mukhopadhyay, Aindrila; He, Zhili; Alm, Eric J.; Arkin, Adam P.; Baidoo, Edward E.; Borglin, Sharon C.; Chen, Wenqiong; Hazen, Terry C.; He, Qiang; Holman, Hoi-Ying; Huang, Katherine; Huang, Rick; Hoyner,Dominique C.; Katz, Natalie; Keller, Martin; Oeller, Paul; Redding,Alyssa; Sun, Jun; Wall, Judy; Wei, Jing; Yang, Zamin; Yen, Huei-Che; Zhou, Jizhong; Keasling Jay D.

    2005-12-08

    The ability of Desulfovibrio vulgaris Hildenborough to reduce, and therefore contain, toxic and radioactive metal waste has made all factors that affect the physiology of this organism of great interest. Increased salinity is an important and frequent fluctuation faced by D. vulgaris in its natural habitat. In liquid culture, exposure to excess salt resulted in striking elongation of D. vulgaris cells. Using data from transcriptomics, proteomics, metabolite assays, phospholipid fatty acid profiling, and electron microscopy, we used a systems approach to explore the effects of excess NaCl on D. vulgaris. In this study we demonstrated that import of osmoprotectants, such as glycine betaine and ectoine, is the primary mechanism used by D. vulgaris to counter hyperionic stress. Several efflux systems were also highly up-regulated, as was the ATP synthesis pathway. Increases in the levels of both RNA and DNA helicases suggested that salt stress affected the stability of nucleic acid base pairing. An overall increase in the level of branched fatty acids indicated that there were changes in cell wall fluidity. The immediate response to salt stress included up-regulation of chemotaxis genes, although flagellar biosynthesis was down-regulated. Other down-regulated systems included lactate uptake permeases and ABC transport systems. The results of an extensive NaCl stress analysis were compared with microarray data from a KCl stress analysis, and unlike many other bacteria, D. vulgaris responded similarly to the two stresses. Integration of data from multiple methods allowed us to develop a conceptual model for the salt stress response in D. vulgaris that can be compared to those in other microorganisms.

  19. Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach.

    PubMed

    Mukhopadhyay, Aindrila; He, Zhili; Alm, Eric J; Arkin, Adam P; Baidoo, Edward E; Borglin, Sharon C; Chen, Wenqiong; Hazen, Terry C; He, Qiang; Holman, Hoi-Ying; Huang, Katherine; Huang, Rick; Joyner, Dominique C; Katz, Natalie; Keller, Martin; Oeller, Paul; Redding, Alyssa; Sun, Jun; Wall, Judy; Wei, Jing; Yang, Zamin; Yen, Huei-Che; Zhou, Jizhong; Keasling, Jay D

    2006-06-01

    The ability of Desulfovibrio vulgaris Hildenborough to reduce, and therefore contain, toxic and radioactive metal waste has made all factors that affect the physiology of this organism of great interest. Increased salinity is an important and frequent fluctuation faced by D. vulgaris in its natural habitat. In liquid culture, exposure to excess salt resulted in striking elongation of D. vulgaris cells. Using data from transcriptomics, proteomics, metabolite assays, phospholipid fatty acid profiling, and electron microscopy, we used a systems approach to explore the effects of excess NaCl on D. vulgaris. In this study we demonstrated that import of osmoprotectants, such as glycine betaine and ectoine, is the primary mechanism used by D. vulgaris to counter hyperionic stress. Several efflux systems were also highly up-regulated, as was the ATP synthesis pathway. Increases in the levels of both RNA and DNA helicases suggested that salt stress affected the stability of nucleic acid base pairing. An overall increase in the level of branched fatty acids indicated that there were changes in cell wall fluidity. The immediate response to salt stress included up-regulation of chemotaxis genes, although flagellar biosynthesis was down-regulated. Other down-regulated systems included lactate uptake permeases and ABC transport systems. The results of an extensive NaCl stress analysis were compared with microarray data from a KCl stress analysis, and unlike many other bacteria, D. vulgaris responded similarly to the two stresses. Integration of data from multiple methods allowed us to develop a conceptual model for the salt stress response in D. vulgaris that can be compared to those in other microorganisms.

  20. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough.

    PubMed

    Bender, Kelly S; Yen, Huei-Che Bill; Hemme, Christopher L; Yang, Zamin; He, Zhili; He, Qiang; Zhou, Jizhong; Huang, Katherine H; Alm, Eric J; Hazen, Terry C; Arkin, Adam P; Wall, Judy D

    2007-09-01

    Previous experiments examining the transcriptional profile of the anaerobe Desulfovibrio vulgaris demonstrated up-regulation of the Fur regulon in response to various environmental stressors. To test the involvement of Fur in the growth response and transcriptional regulation of D. vulgaris, a targeted mutagenesis procedure was used for deleting the fur gene. Growth of the resulting Deltafur mutant (JW707) was not affected by iron availability, but the mutant did exhibit increased sensitivity to nitrite and osmotic stresses compared to the wild type. Transcriptional profiling of JW707 indicated that iron-bound Fur acts as a traditional repressor for ferrous iron uptake genes (feoAB) and other genes containing a predicted Fur binding site within their promoter. Despite the apparent lack of siderophore biosynthesis genes within the D. vulgaris genome, a large 12-gene operon encoding orthologs to TonB and TolQR also appeared to be repressed by iron-bound Fur. While other genes predicted to be involved in iron homeostasis were unaffected by the presence or absence of Fur, alternative expression patterns that could be interpreted as repression or activation by iron-free Fur were observed. Both the physiological and transcriptional data implicate a global regulatory role for Fur in the sulfate-reducing bacterium D. vulgaris.

  1. Analysis of a Ferric Uptake Regulator (Fur) Mutant ofDesulfovibrio vulgaris Hildenborough

    SciTech Connect

    Bender, Kelly S.; Yen, Huei-Che Bill; Hemme, Christopher L.; Yang, Zamin K.; He, Zhili; He, Qiang; Zhou, Jizhong; Huang, Katherine H.; Alm, Eric J.; Hazen, Terry C.; Arkin, Adam P.; Wall, Judy D.

    2007-09-21

    Previous experiments examining the transcriptional profileof the anaerobe Desulfovibrio vulgaris demonstrated up-regulation of theFur regulon in response to various environmental stressors. To test theinvolvement of Fur in the growth response and transcriptional regulationof D. vulgaris, a targeted mutagenesis procedure was used for deletingthe fur gene. Growth of the resulting ?fur mutant (JW707) was notaffected by iron availability, but the mutant did exhibit increasedsensitivity to nitrite and osmotic stresses compared to the wild type.Transcriptional profiling of JW707 indicated that iron-bound Fur acts asa traditional repressor for ferrous iron uptake genes (feoAB) and othergenes containing a predicted Fur binding site within their promoter.Despite the apparent lack of siderophore biosynthesis genes within the D.vulgaris genome, a large 12-gene operon encoding orthologs to TonB andTolQR also appeared to be repressed by iron-bound Fur. While other genespredicted to be involved in iron homeostasis were unaffected by thepresence or absence of Fur, alternative expression patterns that could beinterpreted as repression or activation by iron-free Fur were observed.Both the physiological and transcriptional data implicate a globalregulatory role for Fur in the sulfate-reducing bacterium D.vulgaris.

  2. Mapping the Two-component Regulatory Networks in Desulfovibrio vulgaris

    SciTech Connect

    Rajeev, Lara; Luning, Eric; Dehal, Paramvir; Joachimiak, Marcin; Mukhopadhyay, Aindrila

    2010-05-17

    D. vulgaris Hildenborough has 72 response regulators. The Desulfovibrio are sulfate reducing bacteria that are important in the sulfur and carbon cycles in anoxic habitats. Its large number of two componenent systems are probably critical to its ability to sense and respond to its environment. Our goal is to map these RRs to the genes they regulate using a DNA-affinity-purification-chip (DAP-chip) protocol. First target determined usuing EMSA. A positive target was determined for as many RRs as possible using EMSA. Targets were selected based on gene proximity, regulon predictions and/or predicted sigma54 dependent promoters. qPCR was used to ensure that the target was enriched from sheared genomic DNA before proceeding to the DAP-chip.

  3. Response of Desulfovibrio vulgaris Hildenborough to hydrogen peroxide: enzymatic and transcriptional analyses.

    PubMed

    Brioukhanov, Andrei L; Durand, Marie-Claire; Dolla, Alain; Aubert, Corinne

    2010-09-01

    We studied the effect of hydrogen peroxide (H(2)O(2)) stress on the anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. In a lactate/sulfate medium, growth was affected from 0.1 mM H(2)O(2) and totally inhibited at 0.7 mM. Surprisingly, transcript analyses revealed that the PerR regulon exhibited opposite regulation in the presence of 0.1 and 0.3 mM H(2)O(2). The variations in peroxidase- and superoxide dismutase-specific activities in the cell-free extracts of H(2)O(2)-stressed cultures were related to changes in the corresponding transcript abundance. Our data suggest that sod, sor, ngr and tpx genes, in addition to the PerR regulon, belong to the H(2)O(2) stimulon.

  4. Cell-Wide Responses to Low-Oxygen Exposure in Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Mukhopadhyay, Aindrila; Redding, Alyssa; Joachimiak, Marcin; Arkin, Adam; Borglin, sharon; Dehal, Paramvir; Chakraborty, Romy; Geller, Jil; Hazen, Terry; HE, Qiang; Joyner, Dominique C.; Martin, Vincent; Wall, Judy; Yang, Zamin Koo; Zhou, Jizhong; Keasling, Jay

    2007-08-01

    The responses of the anaerobic, sulfate-reducing organism Desulfovibrio vulgaris Hildenborough to low-oxygen exposure (0.1% O2) were monitored via transcriptomics and proteomics. Exposure to 0.1% O2 caused a decrease in the growth rate without affecting viability. Concerted upregulation of the predicted peroxide stress response regulon (PerR) genes was observed in response to the 0.1% O2 exposure. Several of the candidates also showed increases in protein abundance. Among the remaining small number of transcript changes was the upregulation of the predicted transmembrane tetraheme cytochrome c3 complex. Other known oxidative stress response candidates remained unchanged during the low-O2 exposure. To fully understand the results of the 0.1% O2 exposure, transcriptomics and proteomics data were collected for exposure to air using a similar experimental protocol. In contrast to the 0.1% O2 exposure, air exposure was detrimental to both the growth rate and viability and caused dramatic changes at both the transcriptome and proteome levels. Interestingly, the transcripts of the predicted PerR regulon genes were downregulated during air exposure. Our results highlight the differences in the cell-wide responses to low and high O2 levels in D. vulgaris and suggest that while exposure to air is highly detrimental to D. vulgaris, this bacterium can successfully cope with periodic exposure to low O2 levels in its environment.

  5. Desulfovibrio vulgaris Growth Coupled to Formate-Driven H2 Production.

    PubMed

    Martins, Mónica; Mourato, Cláudia; Pereira, Inês A C

    2015-12-15

    Formate is recognized as a superior substrate for biological H2 production by several bacteria. However, the growth of a single organism coupled to this energetic pathway has not been shown in mesophilic conditions. In the present study, a bioreactor with gas sparging was used, where we observed for the first time that H2 production from formate can be coupled with growth of the model sulfate-reducing bacterium Desulfovibrio vulgaris in the absence of sulfate or a syntrophic partner. In these conditions, D. vulgaris had a maximum growth rate of 0.078 h(-1) and a doubling time of 9 h, and the ΔG of the reaction ranged between -21 and -18 kJ mol(-1). This is the first report of a single mesophilic organism that can grow while catalyzing the oxidation of formate to H2 and bicarbonate. Furthermore, high volumetric and specific H2 production rates (125 mL L(-1) h(-1) and 2500 mL gdcw(-1) h(-1)) were achieved in a new bioreactor designed and optimized for H2 production. This high H2 production demonstrates that the nonconventional H2-producing organism D. vulgaris is a good biocatalyst for converting formate to H2.

  6. CoIIIEDTA- reduction by Desulfovibrio vulgaris and propagation of reactions involving dissolved sulfide and polysulfides.

    PubMed

    Blessing, T C; Wielinga, B W; Morra, M J; Fendorf, S

    2001-04-15

    The migration of 60Co, dominantly via transport of Co-EDTA complexes, into surface water and groundwater is a recognized concern at many nuclear production and storage sites. Reduction of CoIIIEDTA- to CoIIEDTA2- should decrease the mobility of 60Co in natural environments by stimulating ligand displacement with Fe(III) or Al(III) or by precipitation of CoSx in sulfidic environments. In this study, we examine direct (enzymatic) and indirect (metabolite) reduction processes of CoIIIEDTA- by the sulfate-reducing bacterium Desulfovibrio vulgaris. D. vulgaris reduces CoIIIEDTA- to CoIIEDTA2-, but growth using it as a terminal electron acceptor was not demonstrated. Rather than acting as a competing electron acceptor and limiting cobalt reduction, introducing sulfate with D. vulgaris enhances the reduction of CoIIIEDTA- as a result of sulfide production. Sulfide reduces CoIIIEDTA- in a pathway involving polysulfide formation and leads to a CoS precipitate. Thus, both direct and indirect (i.e., through the production of sulfide) microbial reduction pathways of CoIIIEDTA- may help to retard its migration within soils and waters.

  7. The electron transfer system of syntrophically grown Desulfovibrio vulgaris.

    PubMed

    Walker, Christopher B; He, Zhili; Yang, Zamin K; Ringbauer, Joseph A; He, Qiang; Zhou, Jizhong; Voordouw, Gerrit; Wall, Judy D; Arkin, Adam P; Hazen, Terry C; Stolyar, Sergey; Stahl, David A

    2009-09-01

    Interspecies hydrogen transfer between organisms producing and consuming hydrogen promotes the decomposition of organic matter in most anoxic environments. Although syntrophic coupling between hydrogen producers and consumers is a major feature of the carbon cycle, mechanisms for energy recovery at the extremely low free energies of reactions typical of these anaerobic communities have not been established. In this study, comparative transcriptional analysis of a model sulfate-reducing microbe, Desulfovibrio vulgaris Hildenborough, suggested the use of alternative electron transfer systems dependent on growth modality. During syntrophic growth on lactate with a hydrogenotrophic methanogen, numerous genes involved in electron transfer and energy generation were upregulated in D. vulgaris compared with their expression in sulfate-limited monocultures. In particular, genes coding for the putative membrane-bound Coo hydrogenase, two periplasmic hydrogenases (Hyd and Hyn), and the well-characterized high-molecular-weight cytochrome (Hmc) were among the most highly expressed and upregulated genes. Additionally, a predicted operon containing genes involved in lactate transport and oxidation exhibited upregulation, further suggesting an alternative pathway for electrons derived from lactate oxidation during syntrophic growth. Mutations in a subset of genes coding for Coo, Hmc, Hyd, and Hyn impaired or severely limited syntrophic growth but had little effect on growth via sulfate respiration. These results demonstrate that syntrophic growth and sulfate respiration use largely independent energy generation pathways and imply that to understand microbial processes that sustain nutrient cycling, lifestyles not captured in pure culture must be considered.

  8. The Electron Transfer System of Syntrophically Grown Desulfovibrio vulgaris

    SciTech Connect

    PBD; ENIGMA; GTL; VIMSS; Walker, Christopher B.; He, Zhili; Yang, Zamin K.; Ringbauer Jr., Joseph A.; He, Qiang; Zhou, Jizhong; Voordouw, Gerrit; Wall, Judy D.; Arkin, Adam P.; Hazen, Terry C.; Stolyar, Sergey; Stahl, David A.

    2009-06-22

    Interspecies hydrogen transfer between organisms producing and consuming hydrogen promotes the decomposition of organic matter in most anoxic environments. Although syntrophic couplings between hydrogen producers and consumers are a major feature of the carbon cycle, mechanisms for energy recovery at the extremely low free energies of reactions typical of these anaerobic communities have not been established. In this study, comparative transcriptional analysis of a model sulfate-reducing microbe, Desulfovibrio vulgaris Hildenborough, suggested the use of alternative electron transfer systems dependent upon growth modality. During syntrophic growth on lactate with a hydrogenotrophic methanogen, D. vulgaris up-regulated numerous genes involved in electron transfer and energy generation when compared with sulfate-limited monocultures. In particular, genes coding for the putative membrane-bound Coo hydrogenase, two periplasmic hydrogenases (Hyd and Hyn) and the well-characterized high-molecular weight cytochrome (Hmc) were among the most highly expressed and up-regulated. Additionally, a predicted operon coding for genes involved in lactate transport and oxidation exhibited up-regulation, further suggesting an alternative pathway for electrons derived from lactate oxidation during syntrophic growth. Mutations in a subset of genes coding for Coo, Hmc, Hyd and Hyn impaired or severely limited syntrophic growth but had little affect on growth via sulfate-respiration. These results demonstrate that syntrophic growth and sulfate-respiration use largely independent energy generation pathways and imply that understanding of microbial processes sustaining nutrient cycling must consider lifestyles not captured in pure culture.

  9. The electron transfer system of synthrophically grown desulfovibrio vulgaris

    SciTech Connect

    Walker, Christopher; He, Zhili; Yang, Zamin Koo; Ringbauer, Joseph; HE, Qiang; Zhou, Jizhong; Voordouw, Gerrit; Wall, Judy; Arkin, Adam; Hazen, Terry; Stolyar, Sergey; Stahl, David

    2009-01-01

    Interspecies hydrogen transfer between organisms producing and consuming hydrogen promotes the decomposition of organic matter in most anoxic environments. Although syntrophic coupling between hydrogen producers and consumers is a major feature of the carbon cycle, mechanisms for energy recovery at the extremely low free energies of reactions typical of these anaerobic communities have not been established. In this study, comparative transcriptional analysis of a model sulfate-reducing microbe, Desulfovibrio vulgaris Hildenborough, suggested the use of alternative electron transfer systems dependent on growth modality. During syntrophic growth on lactate with a hydrogenotrophic methanogen, numerous genes involved in electron transfer and energy generation were upregulated in D. vulgaris compared with their expression in sulfate-limited monocultures. In particular, genes coding for the putative membrane-bound Coo hydrogenase, two periplasmic hydrogenases (Hyd and Hyn), and the well-characterized high-molecular-weight cytochrome (Hmc) were among the most highly expressed and upregulated genes. Additionally, a predicted operon containing genes involved in lactate transport and oxidation exhibited upregulation, further suggesting an alternative pathway for electrons derived from lactate oxidation during syntrophic growth. Mutations in a subset of genes coding for Coo, Hmc, Hyd, and Hyn impaired or severely limited syntrophic growth but had little effect on growth via sulfate respiration. These results demonstrate that syntrophic growth and sulfate respiration use largely independent energy generation pathways and imply that to understand microbial processes that sustain nutrient cycling, lifestyles not captured in pure culture must be considered.

  10. The electron transfer system of syntrophically grown Desulfovibrio vulgaris

    SciTech Connect

    Walker, C.B.; He, Z.; Yang, Z.K.; Ringbauer, Jr., J.A.; He, Q.; Zhou, J.; Voordouw, G.; Wall, J.D.; Arkin, A.P.; Hazen, T.C.; Stolyar, S.; Stahl, D.A.

    2009-05-01

    Interspecies hydrogen transfer between organisms producing and consuming hydrogen promotes the decomposition of organic matter in most anoxic environments. Although syntrophic couplings between hydrogen producers and consumers are a major feature of the carbon cycle, mechanisms for energy recovery at the extremely low free energies of reactions typical of these anaerobic communities have not been established. In this study, comparative transcriptional analysis of a model sulfate-reducing microbe, Desulfovibrio vulgaris Hildenborough, suggested the use of alternative electron transfer systems dependent upon growth modality. During syntrophic growth on lactate with a hydrogenotrophic methanogen, D. vulgaris up-regulated numerous genes involved in electron transfer and energy generation when compared with sulfate-limited monocultures. In particular, genes coding for the putative membrane-bound Coo hydrogenase, two periplasmic hydrogenases (Hyd and Hyn) and the well-characterized high-molecular weight cytochrome (Hmc) were among the most highly expressed and up-regulated. Additionally, a predicted operon coding for genes involved in lactate transport and oxidation exhibited up-regulation, further suggesting an alternative pathway for electrons derived from lactate oxidation during syntrophic growth. Mutations in a subset of genes coding for Coo, Hmc, Hyd and Hyn impaired or severely limited syntrophic growth but had little affect on growth via sulfate-respiration. These results demonstrate that syntrophic growth and sulfate-respiration use largely independent energy generation pathways and imply that understanding of microbial processes sustaining nutrient cycling must consider lifestyles not captured in pure culture.

  11. Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough.

    SciTech Connect

    Chhabra, S.R.; He, Q.; Huang, K.H.; Gaucher, S.P.; Alm, E.J.; He,Z.; Hadi, M.Z.; Hazen, T.C.; Wall, J.D.; Zhou, J.; Arkin, A.P.; Singh, A.K.

    2005-09-16

    Desulfovibrio vulgaris Hildenborough belongs to a class ofsulfate-reducing bacteria (SRB) and is found ubiquitously in nature.Given the importance of SRB-mediated reduction for bioremediation ofmetal ion contaminants, ongoing research on D. vulgaris has been in thedirection of elucidating regulatory mechanisms for this organism under avariety of stress conditions. This work presents a global view of thisorganism's response to elevated growth temperature using whole-celltranscriptomics and proteomics tools. Transcriptional response (1.7-foldchange or greater; Z>1.5) ranged from 1,135 genes at 15 min to 1,463genes at 120 min for a temperature up-shift of 13oC from a growthtemperature of 37oC for this organism and suggested both direct andindirect modes of heat sensing. Clusters of orthologous group categoriesthat were significantly affected included posttranslationalmodifications; protein turnover and chaperones (up-regulated); energyproduction and conversion (down-regulated), nucleotide transport,metabolism (down-regulated), and translation; ribosomal structure; andbiogenesis (down-regulated). Analysis of the genome sequence revealed thepresence of features of both negative and positive regulation whichincluded the CIRCE element and promoter sequences corresponding to thealternate sigma factors ?32 and ?54. While mechanisms of heat shockcontrol for some genes appeared to coincide with those established forEscherichia coli and Bacillus subtilis, the presence of unique controlschemes for several other genes was also evident. Analysis of proteinexpression levels using differential in-gel electrophoresis suggestedgood agreement with transcriptional profiles of several heat shockproteins, including DnaK (DVU0811), HtpG (DVU2643), HtrA (DVU1468), andAhpC (DVU2247). The proteomics study also suggested the possibility ofposttranslational modifications in the chaperones DnaK, AhpC, GroES(DVU1977), and GroEL (DVU1976) and also several periplasmic ABCtransporters.

  12. Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis.

    PubMed

    Pereira, Patrícia M; He, Qiang; Valente, Filipa M A; Xavier, António V; Zhou, Jizhong; Pereira, Inês A C; Louro, Ricardo O

    2008-05-01

    Sulphate-reducing bacteria are important players in the global sulphur and carbon cycles, with considerable economical and ecological impact. However, the process of sulphate respiration is still incompletely understood. Several mechanisms of energy conservation have been proposed, but it is unclear how the different strategies contribute to the overall process. In order to obtain a deeper insight into the energy metabolism of sulphate-reducers whole-genome microarrays were used to compare the transcriptional response of Desulfovibrio vulgaris Hildenborough grown with hydrogen/sulphate, pyruvate/sulphate, pyruvate with limiting sulphate, and lactate/thiosulphate, relative to growth in lactate/sulphate. Growth with hydrogen/sulphate showed the largest number of differentially expressed genes and the largest changes in transcript levels. In this condition the most up-regulated energy metabolism genes were those coding for the periplasmic [NiFeSe] hydrogenase, followed by the Ech hydrogenase. The results also provide evidence for the involvement of formate cycling and the recently proposed ethanol pathway during growth in hydrogen. The pathway involving CO cycling is relevant during growth on lactate and pyruvate, but not during growth in hydrogen as the most down-regulated genes were those coding for the CO-induced hydrogenase. Growth on lactate/thiosulphate reveals a down-regulation of several energy metabolism genes similar to what was observed in the presence of nitrite. This study identifies the role of several proteins involved in the energy metabolism of D. vulgaris and highlights several novel genes related to this process, revealing a more complex bioenergetic metabolism than previously considered.

  13. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough.

    SciTech Connect

    Arkin, A. P.; Wall, J. D.; Hazen, T. C.; He, Z.; Zhou, J.; Huang, K. H.; Gaucher, Sara P.; He, Q.; Hadi, Masood Z.; Chhabra, Swapnil R.; Alm, Eric J.; Singh, A. K.

    2005-08-01

    Desulfovibrio vulgaris Hildenborough belongs to a class of sulfate-reducing bacteria (SRB) and is found ubiquitously in nature. Given the importance of SRB-mediated reduction for bioremediation of metal ion contaminants, ongoing research on D. vulgaris has been in the direction of elucidating regulatory mechanisms for this organism under a variety of stress conditions. This work presents a global view of this organism's response to elevated growth temperature using whole-cell transcriptomics and proteomics tools. Transcriptional response (1.7-fold change or greater; Z {ge} 1.5) ranged from 1,135 genes at 15 min to 1,463 genes at 120 min for a temperature up-shift of 13 C from a growth temperature of 37 C for this organism and suggested both direct and indirect modes of heat sensing. Clusters of orthologous group categories that were significantly affected included posttranslational modifications; protein turnover and chaperones (up-regulated); energy production and conversion (down-regulated), nucleotide transport, metabolism (down-regulated), and translation; ribosomal structure; and biogenesis (down-regulated). Analysis of the genome sequence revealed the presence of features of both negative and positive regulation which included the CIRCE element and promoter sequences corresponding to the alternate sigma factors {sigma}{sup 32} and {sigma}{sup 54}. While mechanisms of heat shock control for some genes appeared to coincide with those established for Escherichia coli and Bacillus subtilis, the presence of unique control schemes for several other genes was also evident. Analysis of protein expression levels using differential in-gel electrophoresis suggested good agreement with transcriptional profiles of several heat shock proteins, including DnaK (DVU0811), HtpG (DVU2643), HtrA (DVU1468), and AhpC (DVU2247). The proteomics study also suggested the possibility of posttranslational modifications in the chaperones DnaK, AhpC, GroES (DVU1977), and GroEL (DVU1976

  14. Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis

    SciTech Connect

    Pereira, Patricia M.; He, Qiang; Valente, Filipa M.A.; Xavier, Antonio V.; Zhou, Jizhong; Pereira, Ines A.C.; Louro, Ricardo O.

    2007-11-01

    Sulphate-reducing bacteria are important players in the global sulphur and carbon cycles, with considerable economical and ecological impact. However, the process of sulphate respiration is still incompletely understood. Several mechanisms of energy conservation have been proposed, but it is unclear how the different strategies contribute to the overall process. In order to obtain a deeper insight into the energy metabolism of sulphate-reducers whole-genome microarrays were used to compare the transcriptional response of Desulfovibrio vulgaris Hildenborough grown with hydrogen/sulphate, pyruvate/sulphate, pyruvate with limiting sulphate, and lactate/thiosulphate, relative to growth in lactate/sulphate. Growth with hydrogen/sulphate showed the largest number of differentially expressed genes and the largest changes in transcript levels. In this condition the most up-regulated energy metabolism genes were those coding for the periplasmic [NiFeSe]hydrogenase, followed by the Ech hydrogenase. The results also provide evidence for the involvement of formate cycling and the recently proposed ethanol pathway during growth in hydrogen. The pathway involving CO cycling is relevant during growth on lactate and pyruvate, but not during growth in hydrogen as the most down-regulated genes were those coding for the CO-induced hydrogenase. Growth on lactate/thiosulphate reveals a down-regulation of several energymetabolism genes similar to what was observed in the presence of nitrite. This study identifies the role of several proteins involved in the energy metabolism of D. vulgaris and highlights several novel genes related to this process, revealing a more complex bioenergetic metabolism than previously considered.

  15. Reduction of uranium by cytochrome c3 of Desulfovibrio vulgaris

    USGS Publications Warehouse

    Lovley, D.R.; Widman, P.K.; Woodward, J.C.; Phillips, E.J.P.

    1993-01-01

    The mechanism for U(VI) reduction by Desulfovibrio vulgaris (Hildenborough) was investigated. The H2-dependent U(VI) reductase activity in the soluble fraction of the cells was lost when the soluble fraction was passed over a cationic exchange column which extracted cytochrome c3. Addition of cytochrome c3 back to the soluble fraction that had been passed over the cationic exchange column restored the U(VI)-reducing capacity. Reduced cytochrome c3 was oxidized by U(VI), as was a c-type cytochrome(s) in whole-cell suspensions. When cytochrome c3 was combined with hydrogenase, its physiological electron donor, U(VI) was reduced in the presence of H2. Hydrogenase alone could not reduce U(VI). Rapid U(VI) reduction was followed by a subsequent slow precipitation of the U(IV) mineral uraninite. Cytochrome c3 reduced U(VI) in a uranium-contaminated surface water and groundwater. Cytochrome c3 provides the first enzyme model for the reduction and biomineralization of uranium in sedimentary environments. Furthermore, the finding that cytochrome c3 can catalyze the reductive precipitation of uranium may aid in the development of fixed-enzyme reactors and/or organisms with enhanced U(VI)-reducing capacity for the bioremediation of uranium- contaminated waters and waste streams.

  16. Reduction of uranium by cytochrome c3 of Desulfovibrio vulgaris.

    PubMed Central

    Lovley, D R; Widman, P K; Woodward, J C; Phillips, E J

    1993-01-01

    The mechanism for U(VI) reduction by Desulfovibrio vulgaris (Hildenborough) was investigated. The H2-dependent U(VI) reductase activity in the soluble fraction of the cells was lost when the soluble fraction was passed over a cationic exchange column which extracted cytochrome c3. Addition of cytochrome c3 back to the soluble fraction that had been passed over the cationic exchange column restored the U(VI)-reducing capacity. Reduced cytochrome c3 was oxidized by U(VI), as was a c-type cytochrome(s) in whole-cell suspensions. When cytochrome c3 was combined with hydrogenase, its physiological electron donor, U(VI) was reduced in the presence of H2. Hydrogenase alone could not reduce U(VI). Rapid U(VI) reduction was followed by a subsequent slow precipitation of the U(IV) mineral uraninite. Cytochrome c3 reduced U(VI) in a uranium-contaminated surface water and groundwater. Cytochrome c3 provides the first enzyme model for the reduction and biomineralization of uranium in sedimentary environments. Furthermore, the finding that cytochrome c3 can catalyze the reductive precipitation of uranium may aid in the development of fixed-enzyme reactors and/or organisms with enhanced U(VI)-reducing capacity for the bioremediation of uranium-contaminated waters and waste streams. PMID:8285665

  17. Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription.

    PubMed

    Rajeev, Lara; Hillesland, Kristina L; Zane, Grant M; Zhou, Aifen; Joachimiak, Marcin P; He, Zhili; Zhou, Jizhong; Arkin, Adam P; Wall, Judy D; Stahl, David A

    2012-11-01

    The carbon monoxide-sensing transcriptional factor CooA has been studied only in hydrogenogenic organisms that can grow using CO as the sole source of energy. Homologs for the canonical CO oxidation system, including CooA, CO dehydrogenase (CODH), and a CO-dependent Coo hydrogenase, are present in the sulfate-reducing bacterium Desulfovibrio vulgaris, although it grows only poorly on CO. We show that D. vulgaris Hildenborough has an active CO dehydrogenase capable of consuming exogenous CO and that the expression of the CO dehydrogenase, but not that of a gene annotated as encoding a Coo hydrogenase, is dependent on both CO and CooA. Carbon monoxide did not act as a general metabolic inhibitor, since growth of a strain deleted for cooA was inhibited by CO on lactate-sulfate but not pyruvate-sulfate. While the deletion strain did not accumulate CO in excess, as would have been expected if CooA were important in the cycling of CO as a metabolic intermediate, global transcriptional analyses suggested that CooA and CODH are used during normal metabolism.

  18. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough.

    PubMed

    Zhou, Aifen; He, Zhili; Redding-Johanson, Alyssa M; Mukhopadhyay, Aindrila; Hemme, Christopher L; Joachimiak, Marcin P; Luo, Feng; Deng, Ye; Bender, Kelly S; He, Qiang; Keasling, Jay D; Stahl, David A; Fields, Matthew W; Hazen, Terry C; Arkin, Adam P; Wall, Judy D; Zhou, Jizhong

    2010-10-01

    To understand how sulphate-reducing bacteria respond to oxidative stresses, the responses of Desulfovibrio vulgaris Hildenborough to H(2)O(2)-induced stresses were investigated with transcriptomic, proteomic and genetic approaches. H(2)O(2) and induced chemical species (e.g. polysulfide, ROS) and redox potential shift increased the expressions of the genes involved in detoxification, thioredoxin-dependent reduction system, protein and DNA repair, and decreased those involved in sulfate reduction, lactate oxidation and protein synthesis. A gene coexpression network analysis revealed complicated network interactions among differentially expressed genes, and suggested possible importance of several hypothetical genes in H(2)O(2) stress. Also, most of the genes in PerR and Fur regulons were highly induced, and the abundance of a Fur regulon protein increased. Mutant analysis suggested that PerR and Fur are functionally overlapped in response to stresses induced by H(2)O(2) and reaction products, and the upregulation of thioredoxin-dependent reduction genes was independent of PerR or Fur. It appears that induction of those stress response genes could contribute to the increased resistance of deletion mutants to H(2)O(2)-induced stresses. In addition, a conceptual cellular model of D. vulgaris responses to H(2)O(2) stress was constructed to illustrate that this bacterium may employ a complicated molecular mechanism to defend against the H(2)O(2)-induced stresses.

  19. Functional characterization of the early steps of tetrapyrrole biosynthesis and modification in Desulfovibrio vulgaris Hildenborough.

    PubMed

    Lobo, Susana A L; Brindley, Amanda; Warren, Martin J; Saraiva, Lígia M

    2009-05-13

    The biosynthesis of the tetrapyrrole framework has been investigated in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough by characterization of the enzymes required for the transformation of aminolaevulinic acid into sirohydrochlorin. PBG (porphobilinogen) synthase (HemB) was found to be a zinc-dependent enzyme that exists in its native state as a homohexamer. PBG deaminase (HemC) was shown to contain the dipyrromethane cofactor. Uroporphyrinogen III synthase is found fused with a uroporphyrinogen III methyltransferase (HemD-CobA). Both activities could be demonstrated in this amalgamated protein and the individual enzyme activities were separated by dissecting the relevant gene to allow the production of two distinct proteins. A gene annotated in the genome as a bifunctional precorrin-2 dehydrogenase/sirohydrochlorin ferrochelatase was in fact shown to act only as a dehydrogenase and is simply capable of synthesizing sirohydrochlorin rather than sirohaem. Genome analysis also reveals a lack of any uroporphyrinogen III decarboxylase, an enzyme necessary for the classical route to haem synthesis. However, the genome does encode some predicted haem d1 biosynthetic enzymes even though the bacterium does not contain the cd1 nitrite reductase. We suggest that sirohydrochlorin acts as a substrate for haem synthesis using a novel pathway that involves homologues of the d1 biogenesis system. This explains why the uroporphyrinogen III synthase is found fused with the methyltransferase, bypassing the need for uroporphyrinogen III decarboxylase activity.

  20. Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism.

    PubMed

    Plugge, Caroline M; Scholten, Johannes C M; Culley, David E; Nie, Lei; Brockman, Fred J; Zhang, Weiwen

    2010-09-01

    Desulfovibrio vulgaris is a metabolically flexible micro-organism. It can use sulfate as an electron acceptor to catabolize a variety of substrates, or in the absence of sulfate can utilize organic acids and alcohols by forming a syntrophic association with a hydrogen-scavenging partner to relieve inhibition by hydrogen. These alternative metabolic types increase the chance of survival for D. vulgaris in environments where one of the potential external electron acceptors becomes depleted. In this work, whole-genome D. vulgaris microarrays were used to determine relative transcript levels as D. vulgaris shifted its metabolism from syntrophic in a lactate-oxidizing dual-culture with Methanosarcina barkeri to a sulfidogenic metabolism. Syntrophic dual-cultures were grown in two independent chemostats and perturbation was introduced after six volume changes with the addition of sulfate. The results showed that 132 genes were differentially expressed in D. vulgaris 2 h after addition of sulfate. Functional analyses suggested that genes involved in cell envelope and energy metabolism were the most regulated when comparing syntrophic and sulfidogenic metabolism. Upregulation was observed for genes encoding ATPase and the membrane-integrated energy-conserving hydrogenase (Ech) when cells shifted to a sulfidogenic metabolism. A five-gene cluster encoding several lipoproteins and membrane-bound proteins was downregulated when cells were shifted to a sulfidogenic metabolism. Interestingly, this gene cluster has orthologues found only in another syntrophic bacterium, Syntrophobacter fumaroxidans, and four recently sequenced Desulfovibrio strains. This study also identified several novel c-type cytochrome-encoding genes, which may be involved in the sulfidogenic metabolism.

  1. Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism

    SciTech Connect

    Plugge, Caroline M.; Scholten, Johannes C.; Culley, David E.; Nie, Lei; Brockman, Fred J.; Zhang, Weiwen

    2010-09-01

    Abstract Desulfovibrio vulgaris is a metabolically flexible microorganism. It can use sulfate as electron acceptor to catabolize a variety of substrates, or in the absence of sulfate can utilize organic acids and alcohols by forming a syntrophic association with hydrogen scavenging partner to relieve inhibition by hydrogen. These alternativemetabolic types increase the chance of survival for D. vulgaris in environments where one of the potential external electron acceptors becomes depleted. In this work, whole-genome D. vulgaris microarrays were used to determine relative transcript levels as D. vulgaris shifted its metabolism from syntroph in a lactate-oxidizing dual-culture with Methanosarcina barkeri to a sulfidogenic metabolism. Syntrophic dual-cultures were grown in two independent chemostats and perturbation was introduced after six volume changes with the addition of sulfate. The results showed that 132 genes were differentially expressed in D. vulgaris 2 hours after addition of sulfate. Functional analyses suggested that genes involved in cell envelope and energy metabolism were the most regulated when comparing syntrophic and sulfidogenic metabolism. Up-regulation was observed for genes encoding ATPase and the membrane-integrated energy conserving hydrogenase (Ech) when cells shifted to a sulfidogenic metabolism. A five-gene cluster encoding several lipo- and membrane-bound proteins was down-regulated when cells were shifted to a sulfidogenic metabolism. Interestingly, this gene cluster has orthologs found only in another syntrophic bacterium Syntrophobacter fumaroxidans and four recently sequenced Desulfovibrio strains. This study also identified several novel c-type cytochrome encoding genes which may be involved in the sulfidogenic metabolism.

  2. The haem-copper oxygen reductase of Desulfovibrio vulgaris contains a dihaem cytochrome c in subunit II.

    PubMed

    Lobo, Susana A L; Almeida, Claúdia C; Carita, João N; Teixeira, Miguel; Saraiva, Lígia M

    2008-12-01

    The genome of the sulphate reducing bacterium Desulfovibrio vulgaris Hildenborough, still considered a strict anaerobe, encodes two oxygen reductases of the bd and haem-copper types. The haem-copper oxygen reductase deduced amino acid sequence reveals that it is a Type A2 enzyme, which in its subunit II contains two c-type haem binding motifs. We have characterized the cytochrome c domain of subunit II and confirmed the binding of two haem groups, both with Met-His iron coordination. Hence, this enzyme constitutes the first example of a ccaa3 haem-copper oxygen reductase. The expression of D. vulgaris haem-copper oxygen reductase was found to be independent of the electron donor and acceptor source and is not altered by stress factors such as oxygen exposure, nitrite, nitrate, and iron; therefore the haem-copper oxygen reductase seems to be constitutive. The KCN sensitive oxygen reduction by D. vulgaris membranes demonstrated in this work indicates the presence of an active haem-copper oxygen reductase. D. vulgaris membranes perform oxygen reduction when accepting electrons from the monohaem cytochrome c553, thus revealing the first possible electron donor to the terminal oxygen reductase of D. vulgaris. The physiological implication of the presence of the oxygen reductase in this organism is discussed.

  3. Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome.

    PubMed

    Chhabra, S R; Butland, G; Elias, D A; Chandonia, J-M; Fok, O-Y; Juba, T R; Gorur, A; Allen, S; Leung, C M; Keller, K L; Reveco, S; Zane, G M; Semkiw, E; Prathapam, R; Gold, B; Singer, M; Ouellet, M; Szakal, E D; Jorgens, D; Price, M N; Witkowska, H E; Beller, H R; Arkin, A P; Hazen, T C; Biggin, M D; Auer, M; Wall, J D; Keasling, J D

    2011-11-01

    The ability to conduct advanced functional genomic studies of the thousands of sequenced bacteria has been hampered by the lack of available tools for making high-throughput chromosomal manipulations in a systematic manner that can be applied across diverse species. In this work, we highlight the use of synthetic biological tools to assemble custom suicide vectors with reusable and interchangeable DNA "parts" to facilitate chromosomal modification at designated loci. These constructs enable an array of downstream applications, including gene replacement and the creation of gene fusions with affinity purification or localization tags. We employed this approach to engineer chromosomal modifications in a bacterium that has previously proven difficult to manipulate genetically, Desulfovibrio vulgaris Hildenborough, to generate a library of over 700 strains. Furthermore, we demonstrate how these modifications can be used for examining metabolic pathways, protein-protein interactions, and protein localization. The ubiquity of suicide constructs in gene replacement throughout biology suggests that this approach can be applied to engineer a broad range of species for a diverse array of systems biological applications and is amenable to high-throughput implementation.

  4. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

    PubMed Central

    Elias, Dwayne A.; Mukhopadhyay, Aindrila; Joachimiak, Marcin P.; Drury, Elliott C.; Redding, Alyssa M.; Yen, Huei-Che B.; Fields, Matthew W.; Hazen, Terry C.; Arkin, Adam P.; Keasling, Jay D.; Wall, Judy D.

    2009-01-01

    Hypothetical (HyP) and conserved HyP genes account for >30% of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved HyP (9.5%) along with 887 HyP genes (24.4%). Given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. The study goals were to determine which genes were expressed and provide a more functionally based annotation. To accomplish this, expression profiles of 1234 HyP and conserved genes were used from transcriptomic datasets of 11 environmental stresses, complemented with shotgun LC–MS/MS and AMT tag proteomic data. Genes were divided into putatively polycistronic operons and those predicted to be monocistronic, then classified by basal expression levels and grouped according to changes in expression for one or multiple stresses. One thousand two hundred and twelve of these genes were transcribed with 786 producing detectable proteins. There was no evidence for expression of 17 predicted genes. Except for the latter, monocistronic gene annotation was expanded using the above criteria along with matching Clusters of Orthologous Groups. Polycistronic genes were annotated in the same manner with inferences from their proximity to more confidently annotated genes. Two targeted deletion mutants were used as test cases to determine the relevance of the inferred functional annotations. PMID:19293273

  5. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

    SciTech Connect

    Elias, Dwayne A.; Mukhopadhyay, Aindrila; Joachimiak, Marcine P.; Drury, Elliott C.; Redding, Alyssa M.; Yen, Huei-Che B.; Fields, Matthew; Hazen, Terry C.; Arkin, Adam P.; Keasling, Jay D.; Wall, Judy D.

    2009-03-17

    Hypothetical (HyP) and conserved HyP genes account for >30% of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved HyP (9.5%) along with 887 HyP genes (24.4%). Given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. The study goals were to determine which genes were expressed and provide a more functionally based annotation. To accomplish this, expression profiles of 1234 HyP and conserved genes were used from transcriptomic datasets of 11 environmental stresses, complemented with shotgun LC–MS/MS and AMT tag proteomic data. Genes were divided into putatively polycistronic operons and those predicted to be monocistronic, then classified by basal expression levels and grouped according to changes in expression for one or multiple stresses. One thousand two hundred and twelve of these genes were transcribed with 786 producing detectable proteins. There was no evidence for expression of 17 predicted genes.

  6. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

    SciTech Connect

    Elias, Dwayne A.; Mukhopadhyay, Aindrila; Joachimiak, Marcin P.; Drury, Elliott C.; Redding, Alyssa M.; Yen, Huei-Che B.; Fields, Matthew W.; Hazen, Terry C.; Arkin, Adam P.; Keasling, Jay D.; Wall, Judy D.

    2008-10-27

    Hypothetical and conserved hypothetical genes account for>30percent of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved hypothetical (9.5percent) along with 887 hypothetical genes (24.4percent). Given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. The study goals were to determine which genes were expressed and provide a more functionally based annotation. To accomplish this, expression profiles of 1234 hypothetical and conserved genes were used from transcriptomic datasets of 11 environmental stresses, complemented with shotgun LC-MS/MS and AMT tag proteomic data. Genes were divided into putatively polycistronic operons and those predicted to be monocistronic, then classified by basal expression levels and grouped according to changes in expression for one or multiple stresses. 1212 of these genes were transcribed with 786 producing detectable proteins. There was no evidence for expression of 17 predicted genes. Except for the latter, monocistronic gene annotation was expanded using the above criteria along with matching Clusters of Orthologous Groups. Polycistronic genes were annotated in the same manner with inferences from their proximity to more confidently annotated genes. Two targeted deletion mutants were used as test cases to determine the relevance of the inferred functional annotations.

  7. Study of Nitrate Stress in Desulfovibrio vulgaris Hildenborough Using iTRAQ Proteomics

    SciTech Connect

    Redding, A.M.; Mukhopadhyay, A.; Joyner, D.; Hazen, T.C.; Keasling, J.D.

    2006-10-12

    The response of Desulfovibrio vulgaris Hildenborough (DvH),a sulphate-reducing bacterium, to nitrate stress was examined usingquantitative proteomic analysis. DvH was stressed with 105 m M sodiumnitrate(NaNO3), a level that caused a 50 percent inhibition in growth.The protein profile of stressed cells was compared with that of cellsgrown in the absence of nitrate using the iTRAQ peptide labellingstrategy and tandem liquid chromatography separation coupled with massspectrometry (quadrupoletime-of-flight) detection. A total of 737 uniqueproteins were identified by two or more peptides, representing 22 percentof the total DvH proteome and spanning every functional category. Theresults indicate that this was a mild stress, as proteins involved incentral metabolism and the sulphate reduction pathway were unperturbed.Proteins involved in the nitrate reduction pathway increased. Increasesseen in transport systems for proline, glycine^ betaineandglutamateindicate that the NaNO3 exposure led to both salt stress and nitratestress.Up-regulation observed in oxidative stress response proteins (Rbr,RbO, etc.) and a large number of ABC transport systems as well as in iron^ sulphur -cluster-containing proteins, however, appear to be specific tonitrate exposure. Finally, a number of hypothetical proteins were amongthe most significant changers, indicating that there may be unknownmechanisms initiated upon nitrate stress in DvH.

  8. Generalized Schemes for High Throughput Manipulation of the Desulfovibrio vulgaris Hildenborough Genome.

    SciTech Connect

    Chhabra, Swapnil; Butland, Gareth; Elias, Dwayne A; Chandonia, John-Marc; Fok, Olivia; Juba, tom; Gorur, A.; Allen, S.; Leung, C. M.; Keller, Kim; Reveco, S.; Zane, Mr. Grant M.; Semkiw, Elizabeth M.; Prathapam, R.; Gold, B.; Singer, Mary; Ouellet, M.; Sazakal, E. D.; Jorgens, Dominique; Price, Morgan N.; Witkowska, Ewa; Beller, Harry R.; Hazen, Terry; Biggin, Mark D.; Auer, Dr. Manfred; Wall, Judy D.; Keasling, Jay

    2011-01-01

    The ability to conduct advanced functional genomic studies of the thousands of 38 sequenced bacteria has been hampered by the lack of available tools for making high39 throughput chromosomal manipulations in a systematic manner that can be applied across 40 diverse species. In this work, we highlight the use of synthetic biological tools to 41 assemble custom suicide vectors with reusable and interchangeable DNA parts to 42 facilitate chromosomal modification at designated loci. These constructs enable an array 43 of downstream applications including gene replacement and creation of gene fusions with 44 affinity purification or localization tags. We employed this approach to engineer 45 chromosomal modifications in a bacterium that has previously proven difficult to 46 manipulate genetically, Desulfovibrio vulgaris Hildenborough, to generate a library of 47 662 strains. Furthermore, we demonstrate how these modifications can be used for 48 examining metabolic pathways, protein-protein interactions, and protein localization. The 49 ubiquity of suicide constructs in gene replacement throughout biology suggests that this 50 approach can be applied to engineer a broad range of species for a diverse array of 51 systems biological applications and is amenable to high-throughput implementation.

  9. Generalized schemes for high throughput manipulation of the Desulfovibrio vulgaris Hildenborough genome

    SciTech Connect

    Chhabra, S.R.; Butland, G.; Elias, D.; Chandonia, J.-M.; Fok, V.; Juba, T.; Gorur, A.; Allen, S.; Leung, C.-M.; Keller, K.; Reveco, S.; Zane, G.; Semkiw, E.; Prathapam, R.; Gold, B.; Singer, M.; Ouellet, M.; Sazakal, E.; Jorgens, D.; Price, M.; Witkowska, E.; Beller, H.; Hazen, T.C.; Biggin, M.; Auer, M.; Wall, J.; Keasling, J.

    2011-07-15

    The ability to conduct advanced functional genomic studies of the thousands of sequenced bacteria has been hampered by the lack of available tools for making high- throughput chromosomal manipulations in a systematic manner that can be applied across diverse species. In this work, we highlight the use of synthetic biological tools to assemble custom suicide vectors with reusable and interchangeable DNA “parts” to facilitate chromosomal modification at designated loci. These constructs enable an array of downstream applications including gene replacement and creation of gene fusions with affinity purification or localization tags. We employed this approach to engineer chromosomal modifications in a bacterium that has previously proven difficult to manipulate genetically, Desulfovibrio vulgaris Hildenborough, to generate a library of over 700 strains. Furthermore, we demonstrate how these modifications can be used for examining metabolic pathways, protein-protein interactions, and protein localization. The ubiquity of suicide constructs in gene replacement throughout biology suggests that this approach can be applied to engineer a broad range of species for a diverse array of systems biological applications and is amenable to high-throughput implementation.

  10. Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris.

    PubMed

    He, Qiang; He, Zhili; Joyner, Dominique C; Joachimiak, Marcin; Price, Morgan N; Yang, Zamin K; Yen, Huei-Che Bill; Hemme, Christopher L; Chen, Wenqiong; Fields, Matthew M; Stahl, David A; Keasling, Jay D; Keller, Martin; Arkin, Adam P; Hazen, Terry C; Wall, Judy D; Zhou, Jizhong

    2010-11-01

    Sulfate-reducing bacteria have been extensively studied for their potential in heavy-metal bioremediation. However, the occurrence of elevated nitrate in contaminated environments has been shown to inhibit sulfate reduction activity. Although the inhibition has been suggested to result from the competition with nitrate-reducing bacteria, the possibility of direct inhibition of sulfate reducers by elevated nitrate needs to be explored. Using Desulfovibrio vulgaris as a model sulfate-reducing bacterium, functional genomics analysis reveals that osmotic stress contributed to growth inhibition by nitrate as shown by the upregulation of the glycine/betaine transporter genes and the relief of nitrate inhibition by osmoprotectants. The observation that significant growth inhibition was effected by 70 mM NaNO(3) but not by 70 mM NaCl suggests the presence of inhibitory mechanisms in addition to osmotic stress. The differential expression of genes characteristic of nitrite stress responses, such as the hybrid cluster protein gene, under nitrate stress condition further indicates that nitrate stress response by D. vulgaris was linked to components of both osmotic and nitrite stress responses. The involvement of the oxidative stress response pathway, however, might be the result of a more general stress response. Given the low similarities between the response profiles to nitrate and other stresses, less-defined stress response pathways could also be important in nitrate stress, which might involve the shift in energy metabolism. The involvement of nitrite stress response upon exposure to nitrate may provide detoxification mechanisms for nitrite, which is inhibitory to sulfate-reducing bacteria, produced by microbial nitrate reduction as a metabolic intermediate and may enhance the survival of sulfate-reducing bacteria in environments with elevated nitrate level.

  11. Hydrogen-peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Zhou, A.; He, Z.; Redding-Johanson, A.M.; Mukhopadhyay, A.; Hemme, C.L.; Joachimiak, M.P.; Bender, K.S.; Keasling, J.D.; Stahl, D.A.; Fields, M.W.; Hazen, T.C.; Arkin, A.P.; Wall, J.D.; Zhou, J.; Luo, F.; Deng, Y.; He, Q.

    2010-07-01

    To understand how sulphate-reducing bacteria respond to oxidative stresses, the responses of Desulfovibrio vulgaris Hildenborough to H{sub 2}O{sub 2}-induced stresses were investigated with transcriptomic, proteomic and genetic approaches. H{sub 2}O{sub 2} and induced chemical species (e.g. polysulfide, ROS) and redox potential shift increased the expressions of the genes involved in detoxification, thioredoxin-dependent reduction system, protein and DNA repair, and decreased those involved in sulfate reduction, lactate oxidation and protein synthesis. A gene coexpression network analysis revealed complicated network interactions among differentially expressed genes, and suggested possible importance of several hypothetical genes in H{sub 2}O{sub 2} stress. Also, most of the genes in PerR and Fur regulons were highly induced, and the abundance of a Fur regulon protein increased. Mutant analysis suggested that PerR and Fur are functionally overlapped in response to stresses induced by H{sub 2}O{sub 2} and reaction products, and the upregulation of thioredoxin-dependent reduction genes was independent of PerR or Fur. It appears that induction of those stress response genes could contribute to the increased resistance of deletion mutants to H{sub 2}O{sub 2}-induced stresses. In addition, a conceptual cellular model of D. vulgaris responses to H{sub 2}O{sub 2} stress was constructed to illustrate that this bacterium may employ a complicated molecular mechanism to defend against the H{sub 2}O{sub 2}-induced stresses.

  12. Impact of elevated nitrate on sulfate-reducing bacteria: A comparative study of Desulfovibrio vulgaris

    SciTech Connect

    He, Q.; He, Z.; Joyner, D.C.; Joachimiak, M.; Price, M.N.; Yang, Z.K.; Yen, H.-C. B.; Hemme, C. L.; Chen, W.; Fields, M.; Stahl, D. A.; Keasling, J. D.; Keller, M.; Arkin, A. P.; Hazen, T. C.; Wall, J. D.; Zhou, J.

    2010-07-15

    Sulfate-reducing bacteria have been extensively studied for their potential in heavy-metal bioremediation. However, the occurrence of elevated nitrate in contaminated environments has been shown to inhibit sulfate reduction activity. Although the inhibition has been suggested to result from the competition with nitrate-reducing bacteria, the possibility of direct inhibition of sulfate reducers by elevated nitrate needs to be explored. Using Desulfovibrio vulgaris as a model sulfate-reducing bacterium, functional genomics analysis reveals that osmotic stress contributed to growth inhibition by nitrate as shown by the upregulation of the glycine/betaine transporter genes and the relief of nitrate inhibition by osmoprotectants. The observation that significant growth inhibition was effected by 70 mM NaNO{sub 3} but not by 70 mM NaCl suggests the presence of inhibitory mechanisms in addition to osmotic stress. The differential expression of genes characteristic of nitrite stress responses, such as the hybrid cluster protein gene, under nitrate stress condition further indicates that nitrate stress response by D. vulgaris was linked to components of both osmotic and nitrite stress responses. The involvement of the oxidative stress response pathway, however, might be the result of a more general stress response. Given the low similarities between the response profiles to nitrate and other stresses, less-defined stress response pathways could also be important in nitrate stress, which might involve the shift in energy metabolism. The involvement of nitrite stress response upon exposure to nitrate may provide detoxification mechanisms for nitrite, which is inhibitory to sulfate-reducing bacteria, produced by microbial nitrate reduction as a metabolic intermediate and may enhance the survival of sulfate-reducing bacteria in environments with elevated nitrate level.

  13. Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: A multiple regression to identify sources of variations

    SciTech Connect

    Nie, Lei; Wu, G; Zhang, Weiwen

    2006-01-13

    Using whole-genome microarray and LC-MC/MS proteomic data collected from Desulfovibrio vulgaris grown under three different conditions, we systematically investigate the relationship between mRNA and protein abundunce by a multiple regression approach.

  14. Hybrid cluster proteins and flavodiiron proteins afford protection to Desulfovibrio vulgaris upon macrophage infection.

    PubMed

    Figueiredo, Mafalda C O; Lobo, Susana A L; Sousa, Sara H; Pereira, Fábio P; Wall, Judy D; Nobre, Lígia S; Saraiva, Lígia M

    2013-06-01

    Desulfovibrio species are Gram-negative anaerobic sulfate-reducing bacteria that colonize the human gut. Recently, Desulfovibrio spp. have been implicated in gastrointestinal diseases and shown to stimulate the epithelial immune response, leading to increased production of inflammatory cytokines by macrophages. Activated macrophages are key cells of the immune system that impose nitrosative stress during phagocytosis. Hence, we have analyzed the in vitro and in vivo responses of Desulfovibrio vulgaris Hildenborough to nitric oxide (NO) and the role of the hybrid cluster proteins (HCP1 and HCP2) and rubredoxin oxygen oxidoreductases (ROO1 and ROO2) in NO protection. Among the four genes, hcp2 was the gene most highly induced by NO, and the hcp2 transposon mutant exhibited the lowest viability under conditions of NO stress. Studies in murine macrophages revealed that D. vulgaris survives incubation with these phagocytes and triggers NO production at levels similar to those stimulated by the cytokine gamma interferon (IFN-γ). Furthermore, D. vulgaris hcp and roo mutants exhibited reduced viability when incubated with macrophages, revealing that these gene products contribute to the survival of D. vulgaris during macrophage infection.

  15. Cloning and sequencing of the gene encoding cytochrome c sub 553 from Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    van Rooijen, G.J.H.; Voordouw, G. ); Bruschi, M. )

    1989-06-01

    The gene encoding cytochrome c{sub 553} from Desulfovibrio vulgaris Hildenborough was cloned by using two synthetic deoxyoligonucleotide probes. The amino acid sequence derived from the sequence of the gene differs from that reported by Bruschi and LeGall. Renewed protein sequencing confirmed the correctness of the DNA-derived sequence. The gene sequence indicates cytochrome c{sub 553} to be synthesized as a precursor protein with an NH{sub 2}-terminal signal sequence of 24 residues.

  16. Metabolic dynamics of Desulfovibrio vulgaris biofilm grown on a steel surface.

    PubMed

    Zhang, Yang; Pei, Guangsheng; Chen, Lei; Zhang, Weiwen

    2016-08-01

    In this study, a comparative metabolomics approach combining gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) was applied first between planktonic cells and biofilms and then between pure cultures and biofilms of Desulfovibrio vulgaris. The results revealed that the overall metabolic level of the biofilm cells was down-regulated, especially for metabolites related to the central carbon metabolism, compared to the planktonic cells and the pure culture of D. vulgaris. In addition, pathway enrichment analysis of the 58 metabolites identified by GC-MS showed that fatty acid biosynthesis in the biofilm cells was up-regulated, suggesting that fatty acids may be important for the formation, maintenance and function of D. vulgaris biofilm. This study offers a valuable perspective on the metabolic dynamics of the D. vulgaris biofilm.

  17. Complementation of an Escherichia coli pyrF mutant with DNA from Desulfovibrio vulgaris

    SciTech Connect

    Li, C.; Peck, H.D. Jr.; Przybyla, A.E.

    1986-02-01

    A PyrF/sup -/ mutant of Escherichia coli (SK1108, pyrF::Tn5 Kan/sup r/) was complemented with the Desulfovibrio vulgaris (Hildenborough) structural gene for orotidine-5'-phosphate decarboxylase. Either orientation of a 1.6-kilobase-pair D. vulgaris DNA fragment (pLP3B or pLP3A) complemented the PyrF/sup -/ strain suggesting that the D. vulgaris pyrF promoter was functional. The apparent product of the D. vulgaris pyrF gene was a single 26-kilodalton polypeptide. These results demonstrate the utility of E. coli cloning systems in studying metabolic and energetic pathways in sulfate-reducing bacteria.

  18. Efficacy of natural biocide on control of microbial induced corrosion in oil pipelines mediated by Desulfovibrio vulgaris and Desulfovibrio gigas.

    PubMed

    Lavania, Meeta; Sarma, Priyangshu M; Mandal, Ajoy K; Cheema, Simrita; Lal, Banwari

    2011-01-01

    We compared the efficacy of a natural biocide with four chemical tetrakishydroxymethyl phosphonium sulfonate, benzyl trimethyl ammonium chloride, and formaldehyde, glutaraldehyde, to control microbial induced corrosion in oil pipelines. The efficacy of biocides were monitored against Desulfovibrio vulgaris and Desulfovibrio gigas in experimental pipes by measuring cell counts, H2S production, Fe(II) production, production of extracellular polymeric substances and structure of biofilm. The treatment with cow urine had minimum planktonic cell counts of 3 x 10(2) CFU/mL as well as biofilm cell counts of 9 x 10(1) CFU/mL as compared with tetrakishydroxyl methyl phosphonium sulfonate, benzyl trimethyl ammonium chloride, formaldehyde and glutaraldehyde. Sulfide production was the lowest with cow urine (0.08 mmol/L), followed by tetrakishydroxymethyl phosphonium sulfonate 0.72 mmol/L. On day 90 of treatment, Fe(II) production was also found to be the lowest with cow urine. The scanning electron microscopic studies indicated that the biofilm bacteria were killed by cow urine. These results demonstrate the cow urine mediated control of microbially induced corrosion, and this is indicative of its potential as a viable substitute of toxic biocides. To the best of our knowledge, this seems to be the first report which screens possible biocidal activity by cow urine as compared to the most common biocides which oil industry is currently using.

  19. The Role of the Tetraheme Cytochrome c3 in Desulfovibrio vulgaris Hildenborough Metabolism

    SciTech Connect

    Semkiw, Elizabeth; Zane, Grant; Wall, Judy

    2010-05-17

    The role of tetraheme cytochrome c3 (CycA) in the metabolism of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) was investigated by deletion of the cycA gene using a marker-exchange deletion strategy. A highly abundant periplasmic cytochrome, CycA has the important function of transferring electrons from periplasmic hydrogenases (Hyd, Hyn, Hys) to transmembrane complexes which transport the electrons to the cytoplasm where sulfate is reduced. Previous studies have indicated that during its interaction with periplasmic hydrogenases, CycA is also involved in the reduction of toxic metals. Growth of the cycA mutant strain on lactate as the electron donor and sulfate as the terminal electron acceptor showed that, despite its abundance, CycA is not essential for DvH growth. However, the rate of growth of the mutant strain was significantly lower, and the extent of growth less, than rates and extents of growth of the wild type and complement strains on lactate/sulfate medium. This indicates that a portion of the electrons generated from cytoplasmic lactate oxidation are transported by CycA for energy production, possibly in a hydrogen cycling mechanism employed to generate ATP. Failure of the mutant strain to grow on either formate or H2, with sulfate or sulfite as electron acceptors, further indicated that CycA may be the only redox partner of periplasmic hydrogenases. The cycA mutant strain also did not grow as well as either the wild type or complement strains on medium supplemented with pyruvate/sulfate. Final growth on pyruvate/sulfate was comparable, but the mutant grew more slowly than the wild type and complement strains. Interestingly, the mutant grew better than the wild type or complement strains on pyruvate alone, possibly due to the release of H2 and/or CO2 in concentrations which may be somewhat inhibitory to wild type growth.

  20. Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete.

    PubMed

    Gao, Shu-Hong; Ho, Jun Yuan; Fan, Lu; Richardson, David J; Yuan, Zhiguo; Bond, Philip L

    2016-09-15

    antimicrobial mechanisms of FNA are largely unknown. In this study, we identified the key responses (decreased anaerobic respiration, reducing FNA, combating oxidative stress, and shutting down protein synthesis) of Desulfovibrio vulgaris Hildenborough, a model sewer corrosion bacterium, to FNA exposure by examining the growth, physiological, and gene expression changes. These findings provide new insight and underpinning knowledge for understanding the responses of D. vulgaris to FNA exposure, thereby benefiting the practical application of FNA for improved control of sewer corrosion and odor.

  1. Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete

    PubMed Central

    Gao, Shu-Hong; Ho, Jun Yuan; Fan, Lu; Richardson, David J.; Yuan, Zhiguo

    2016-01-01

    details of the antimicrobial mechanisms of FNA are largely unknown. In this study, we identified the key responses (decreased anaerobic respiration, reducing FNA, combating oxidative stress, and shutting down protein synthesis) of Desulfovibrio vulgaris Hildenborough, a model sewer corrosion bacterium, to FNA exposure by examining the growth, physiological, and gene expression changes. These findings provide new insight and underpinning knowledge for understanding the responses of D. vulgaris to FNA exposure, thereby benefiting the practical application of FNA for improved control of sewer corrosion and odor. PMID:27371588

  2. Identification of Molecular and Cellular Responses of Desulfovibrio vulgaris Biofilms under Culture Conditions Relevant to Field Conditions for Bioreduction

    SciTech Connect

    Fields, Matthew W.

    2006-06-01

    Desulfovibrio vulgaris ATCC29579 is a sulfate- reducing bacterium (SRB) that is commonly used as a model for direct and indirect heavy metal reduction, and can also be a causitative agent of metal corrosion. During growth with lactate and sulfate, internal carbohydrate levels increased throughout exponential-phase, and peaked as the cells transitioned to stationary-phase. The carbohydrate to protein ratio (C:P) peaked at 0.05 ug/ug as the cells transitioned to stationary-phase, and then declined to 0.02 ug/ug during extended stationary-phase. In contrast, a strain of D. vulgaris that does not contain the megaplasmid, maintained higher internal carbohydrate levels and the C:P ratio peaked at 0.1 ug/ug (2-fold increase compared to wild-type). Under the tested growth conditions, we observed biofilm formation in wild-type cells, but the plasmid-less strain formed less biofilm (2-fold decrease). We hypothesized that carbohydrate was re-allocated to the external cell proper for biofilm formation. However, biofilm contained relatively little carbohydrate (0.6 to 1.0 ug/ml) and had a similar C:P ratio compared to wild-type early stationary-phase cells. Staining with calcafluor white also indicated the presence of little external carbohydrate in D. vulgaris biofilms. Less biofilm was formed in the presence of protinease K, trypsin, and chymotrypsin, however, the growth of planktonic cells was not affected. In addition, when D. vulgaris biofilm was treated with a protease, less biofilm was observed. Electron micrographs suggested the presence of filaments between the biofilm cells, and filaments appeared to be susceptible to protease treatment. Biofilm filtrates contained soluble protein, and SDS-PAGE analysis suggested different polypeptide profiles between a filtrate, a planktonic, and a biofilm sample.

  3. Toward a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Chhabra, S.R.; Joachimiak, M.P.; Petzold, C.J.; Zane, G.M.; Price, M.N.; Gaucher, S.; Reveco, S.A.; Fok, V.; Johanson, A.R.; Batth, T.S.; Singer, M.; Chandonia, J.M.; Joyner, D.; Hazen, T.C.; Arkin, A.P.; Wall, J.D.; Singh, A.K.; Keasling, J.D.

    2011-05-01

    Protein–protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study E. coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio 5 vulgaris Hildenborough, a model anaerobe and sulfate reducer. In this paper we present the first attempt to identify protein-protein interactions in an obligate anaerobic bacterium. We used suicide vector-assisted chromosomal modification of 12 open reading frames encoded by this sulfate reducer to append an eight amino acid affinity tag to the carboxy-terminus of the chosen proteins. Three biological replicates of the 10 ‘pulled-down’ proteins were separated and analyzed using liquid chromatography-mass spectrometry. Replicate agreement ranged between 35% and 69%. An interaction network among 12 bait and 90 prey proteins was reconstructed based on 134 bait-prey interactions computationally identified to be of high confidence. We discuss the biological significance of several unique metabolic features of D. vulgaris revealed by this protein-protein interaction data 15 and protein modifications that were observed. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.

  4. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris.

    PubMed

    Walian, Peter J; Allen, Simon; Shatsky, Maxim; Zeng, Lucy; Szakal, Evelin D; Liu, Haichuan; Hall, Steven C; Fisher, Susan J; Lam, Bonita R; Singer, Mary E; Geller, Jil T; Brenner, Steven E; Chandonia, John-Marc; Hazen, Terry C; Witkowska, H Ewa; Biggin, Mark D; Jap, Bing K

    2012-12-07

    Cell membranes represent the "front line" of cellular defense and the interface between a cell and its environment. To determine the range of proteins and protein complexes that are present in the cell membranes of a target organism, we have utilized a "tagless" process for the system-wide isolation and identification of native membrane protein complexes. As an initial subject for study, we have chosen the Gram-negative sulfate-reducing bacterium Desulfovibrio vulgaris. With this tagless methodology, we have identified about two-thirds of the outer membrane- associated proteins anticipated. Approximately three-fourths of these appear to form homomeric complexes. Statistical and machine-learning methods used to analyze data compiled over multiple experiments revealed networks of additional protein-protein interactions providing insight into heteromeric contacts made between proteins across this region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be essential for the detection and characterization of environment-driven changes in the outer membrane proteome and in the modeling of stress response pathways. The workflow utilized here should be effective for the global characterization of membrane protein complexes in a wide range of organisms.

  5. High-throughput Isolation and Characterization of Untagged Membrane Protein Complexes: Outer Membrane Complexes of Desulfovibrio vulgaris

    PubMed Central

    2012-01-01

    Cell membranes represent the “front line” of cellular defense and the interface between a cell and its environment. To determine the range of proteins and protein complexes that are present in the cell membranes of a target organism, we have utilized a “tagless” process for the system-wide isolation and identification of native membrane protein complexes. As an initial subject for study, we have chosen the Gram-negative sulfate-reducing bacterium Desulfovibrio vulgaris. With this tagless methodology, we have identified about two-thirds of the outer membrane- associated proteins anticipated. Approximately three-fourths of these appear to form homomeric complexes. Statistical and machine-learning methods used to analyze data compiled over multiple experiments revealed networks of additional protein–protein interactions providing insight into heteromeric contacts made between proteins across this region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be essential for the detection and characterization of environment-driven changes in the outer membrane proteome and in the modeling of stress response pathways. The workflow utilized here should be effective for the global characterization of membrane protein complexes in a wide range of organisms. PMID:23098413

  6. The primary pathway for lactate oxidation in Desulfovibrio vulgaris.

    PubMed

    Vita, Nicolas; Valette, Odile; Brasseur, Gaël; Lignon, Sabrina; Denis, Yann; Ansaldi, Mireille; Dolla, Alain; Pieulle, Laetitia

    2015-01-01

    The ability to respire sulfate linked to lactate oxidation is a key metabolic signature of the Desulfovibrio genus. Lactate oxidation by these incomplete oxidizers generates reductants through lactate dehydrogenase (LDH) and pyruvate-ferredoxin oxidoreductase (PFOR), with the latter catalyzing pyruvate conversion into acetyl-CoA. Acetyl-CoA is the source of substrate-level phosphorylation through the production of ATP. Here, we show that these crucial steps are performed by enzymes encoded by a nonacistronic transcriptional unit named now as operon luo (for lactate utilization operon). Using a combination of genetic and biochemical techniques, we assigned a physiological role to the operon genes DVU3027-28 and DVU3032-33. The growth of mutant Δ26-28 was highly disrupted on D-lactate, whereas the growth of mutant Δ32-33 was slower on L-lactate, which could be related to a decrease in the activity of D-lactate or L-lactate oxidase in the corresponding mutants. The DVU3027-28 and DVU3032-33 genes thus encode functional D-LDH and L-LDH enzymes, respectively. Scanning of the genome for lactate utilization revealed several lactate permease and dehydrogenase homologs. However, transcriptional compensation was not observed in any of the mutants except for lactate permease. Although there is a high degree of redundancy for lactate oxidase, it is not functionally efficient in LDH mutants. This result could be related to the identification of several operon enzymes, including LDHs, in the PFOR activity bands, suggesting the occurrence of a lactate-oxidizing supermolecular structure that can optimize the performance of lactate utilization in Desulfovibrio species.

  7. The primary pathway for lactate oxidation in Desulfovibrio vulgaris

    PubMed Central

    Vita, Nicolas; Valette, Odile; Brasseur, Gaël; Lignon, Sabrina; Denis, Yann; Ansaldi, Mireille; Dolla, Alain; Pieulle, Laetitia

    2015-01-01

    The ability to respire sulfate linked to lactate oxidation is a key metabolic signature of the Desulfovibrio genus. Lactate oxidation by these incomplete oxidizers generates reductants through lactate dehydrogenase (LDH) and pyruvate-ferredoxin oxidoreductase (PFOR), with the latter catalyzing pyruvate conversion into acetyl-CoA. Acetyl-CoA is the source of substrate-level phosphorylation through the production of ATP. Here, we show that these crucial steps are performed by enzymes encoded by a nonacistronic transcriptional unit named now as operon luo (for lactate utilization operon). Using a combination of genetic and biochemical techniques, we assigned a physiological role to the operon genes DVU3027-28 and DVU3032-33. The growth of mutant Δ26-28 was highly disrupted on D-lactate, whereas the growth of mutant Δ32-33 was slower on L-lactate, which could be related to a decrease in the activity of D-lactate or L-lactate oxidase in the corresponding mutants. The DVU3027-28 and DVU3032-33 genes thus encode functional D-LDH and L-LDH enzymes, respectively. Scanning of the genome for lactate utilization revealed several lactate permease and dehydrogenase homologs. However, transcriptional compensation was not observed in any of the mutants except for lactate permease. Although there is a high degree of redundancy for lactate oxidase, it is not functionally efficient in LDH mutants. This result could be related to the identification of several operon enzymes, including LDHs, in the PFOR activity bands, suggesting the occurrence of a lactate-oxidizing supermolecular structure that can optimize the performance of lactate utilization in Desulfovibrio species. PMID:26167158

  8. Characterisation of Desulfovibrio vulgaris haem b synthase, a radical SAM family member.

    PubMed

    Lobo, Susana A L; Lawrence, Andrew D; Romão, Célia V; Warren, Martin J; Teixeira, Miguel; Saraiva, Lígia M

    2014-07-01

    An alternative route for haem b biosynthesis is operative in sulfate-reducing bacteria of the Desulfovibrio genus and in methanogenic Archaea. This pathway diverges from the canonical one at the level of uroporphyrinogen III and progresses via a distinct branch, where sirohaem acts as an intermediate precursor being converted into haem b by a set of novel enzymes, named the alternative haem biosynthetic proteins (Ahb). In this work, we report the biochemical characterisation of the Desulfovibrio vulgaris AhbD enzyme that catalyses the last step of the pathway. Mass spectrometry analysis showed that AhbD promotes the cleavage of S-adenosylmethionine (SAM) and converts iron-coproporphyrin III via two oxidative decarboxylations to yield haem b, methionine and the 5'-deoxyadenosyl radical. Electron paramagnetic resonance spectroscopy studies demonstrated that AhbD contains two [4Fe-4S](2+/1+) centres and that binding of the substrates S-adenosylmethionine and iron-coproporphyrin III induces conformational modifications in both centres. Amino acid sequence comparisons indicated that D. vulgaris AhbD belongs to the radical SAM protein superfamily, with a GGE-like motif and two cysteine-rich sequences typical for ligation of SAM molecules and iron-sulfur clusters, respectively. A structural model of D. vulgaris AhbD with putative binding pockets for the iron-sulfur centres and the substrates SAM and iron-coproporphyrin III is discussed.

  9. Organization of the genes encoding [Fe] hydrogenase in Desulfovibrio vulgaris subsp. oxamicus Monticello.

    PubMed Central

    Voordouw, G; Strang, J D; Wilson, F R

    1989-01-01

    The genes encoding the periplasmic [Fe] hydrogenase from Desulfovibrio vulgaris subsp. oxamicus Monticello were cloned by exploiting their homology with the hydAB genes from D. vulgaris subsp. vulgaris Hildenborough, in which this enzyme is present as a heterologous dimer of alpha and beta subunits. Nucleotide sequencing showed that the enzyme is encoded by an operon in which the gene for the 46-kilodalton (kDa) alpha subunit precedes that of the 13.5-kDa beta subunit, exactly as in the Hildenborough strain. The pairs of hydA and hydB genes are highly homologous; both alpha subunits (420 amino acid residues) share 79% sequence identity, while the unprocessed beta subunits (124 and 123 amino acid residues, respectively) share 71% sequence identity. In contrast, there appears to be no sequence homology outside these coding regions, with the exception of a possible promoter element, which was found approximately 90 base pairs upstream from the translational start of the hydA gene. The recently discovered hydC gene, which may code for a 65.8-kDa fusion protein (gamma) of the alpha and beta subunits and is present immediately downstream from the hydAB genes in the Hildenborough strain, was found to be absent from the Monticello strain. The implication of this result for the possible function of the hydC gene product in Desulfovibrio species is discussed. Images PMID:2661538

  10. Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation.

    PubMed

    He, Zhili; Zhou, Aifen; Baidoo, Edward; He, Qiang; Joachimiak, Marcin P; Benke, Peter; Phan, Richard; Mukhopadhyay, Aindrila; Hemme, Christopher L; Huang, Katherine; Alm, Eric J; Fields, Matthew W; Wall, Judy; Stahl, David; Hazen, Terry C; Keasling, Jay D; Arkin, Adam P; Zhou, Jizhong

    2010-03-01

    The response of Desulfovibrio vulgaris Hildenborough to salt adaptation (long-term NaCl exposure) was examined by performing physiological, global transcriptional, and metabolite analyses. Salt adaptation was reflected by increased expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). The expression of genes involved in carbon metabolism, cell growth, and phage structures was decreased. Transcriptome profiles of D. vulgaris responses to salt adaptation were compared with transcriptome profiles of D. vulgaris responses to salt shock (short-term NaCl exposure). Metabolite assays showed that glutamate and alanine accumulated under salt adaptation conditions, suggesting that these amino acids may be used as osmoprotectants in D. vulgaris. Addition of amino acids (glutamate, alanine, and tryptophan) or yeast extract to the growth medium relieved salt-related growth inhibition. A conceptual model that links the observed results to currently available knowledge is proposed to increase our understanding of the mechanisms of D. vulgaris adaptation to elevated NaCl levels.

  11. Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation

    SciTech Connect

    He, Z.; Zhou, A.; Baidoo, E.; He, Q.; Joachimiak, M. P.; Benke, P.; Phan, R.; Mukhopadhyay, A.; Hemme, C.L.; Huang, K.; Alm, E.J.; Fields, M.W.; Wall, J.; Stahl, D.; Hazen, T.C.; Keasling, J.D.; Arkin, A.P.; Zhou, J.

    2009-12-01

    The response of Desulfovibrio vulgaris Hildenborough to salt adaptation (long-term NaCl exposure) was examined by physiological, global transcriptional, and metabolite analyses. The growth of D. vulgaris was inhibited by high levels of NaCl, and the growth inhibition could be relieved by the addition of exogenous amino acids (e.g., glutamate, alanine, tryptophan) or yeast extract. Salt adaptation induced the expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). Genes involved in carbon metabolism, cell motility, and phage structures were repressed. Comparison of transcriptomic profiles of D. vulgaris responses to salt adaptation with those of salt shock (short-term NaCl exposure) showed some similarity as well as a significant difference. Metabolite assays showed that glutamate and alanine were accumulated under salt adaptation, suggesting that they may be used as osmoprotectants in D. vulgaris. A conceptual model is proposed to link the observed results to currently available knowledge for further understanding the mechanisms of D. vulgaris adaptation to elevated NaCl.

  12. Desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir.

    PubMed

    Feio, Maria J; Zinkevich, Vitaly; Beech, Iwona B; Llobet-Brossa, Enric; Eaton, Peter; Schmitt, Jürgen; Guezennec, Jean

    2004-09-01

    A novel sulphate-reducing bacterium (Al1T) was recovered from a soured oil well in Purdu Bay, Alaska. Light and atomic force microscopy observations revealed that cells were Gram-negative, vibrio-shaped and motile by means of a single polar flagellum. The carbon and energy sources used by the isolate and the salinity, temperature and pH ranges facilitating its growth proved to be typical of a partial lactate-oxidizing, moderately halophilic, mesophilic, sulphate-reducing bacterium. Analysis of the fatty acid profile revealed that C(18 : 0), isoC(15 : 0) and isoC(17 : 1)omega7c were the predominant species. Fatty acid profile and complete 16S rRNA gene sequencing demonstrated the similarity between strain Al1T and members of the genus Desulfovibrio. The position of strain Al1T within the phylogenetic tree indicated that it clustered closely with Desulfovibrio vietnamensis DSM 10520T (98.9 % sequence similarity), a strain recovered from a similar habitat. However, whole-cell protein profiles, Fourier-transform infrared studies and DNA-DNA hybridization demonstrated that, in spite of the high level of 16S rRNA gene sequence similarity, there is sufficient dissimilarity at the DNA sequence level between D. vietnamensis DSM 10520T and strain Al1T (10.2 % similarity) to propose that strain Al1T belongs to a separate species within the genus Desulfovibrio. Based on the results obtained, the name Desulfovibrio alaskensis sp. nov. is therefore proposed, with Al1T (= NCIMB 13491T = DSM 16109T) as the type strain.

  13. Hexavalent chromium reduction in Desulfovibrio vulgaris Hildenborough causes transitory inhibition of sulfate reduction and cell growth.

    PubMed

    Klonowska, A; Clark, M E; Thieman, S B; Giles, B J; Wall, J D; Fields, M W

    2008-04-01

    Desulfovibrio vulgaris Hildenborough is a well-studied sulfate reducer that can reduce heavy metals and radionuclides [e.g., Cr(VI) and U(VI)]. Cultures grown in a defined medium had a lag period of approximately 30 h when exposed to 0.05 mM Cr(VI). Substrate analyses revealed that although Cr(VI) was reduced within the first 5 h, growth was not observed for an additional 20 h. The growth lag could be explained by a decline in cell viability; however, during this time small amounts of lactate were still utilized without sulfate reduction or acetate formation. Approximately 40 h after Cr exposure (0.05 mM), sulfate reduction occurred concurrently with the accumulation of acetate. Similar amounts of hydrogen were produced by Cr-exposed cells compared to control cells, and lactate was not converted to glycogen during non-growth conditions. D. vulgaris cells treated with a reducing agent and then exposed to Cr(VI) still experienced a growth lag, but the addition of ascorbate at the time of Cr(VI) addition prevented the lag period. In addition, cells grown on pyruvate displayed more tolerance to Cr(VI) compared to lactate-grown cells. These results indicated that D. vulgaris utilized lactate during Cr(VI) exposure without the reduction of sulfate or production of acetate, and that ascorbate and pyruvate could protect D. vulgaris cells from Cr(VI)/Cr(III) toxicity.

  14. IHF is required for the transcriptional regulation of the Desulfovibrio vulgaris Hildenborough orp operons.

    PubMed

    Fiévet, Anouchka; Cascales, Eric; Valette, Odile; Dolla, Alain; Aubert, Corinne

    2014-01-01

    Transcriptional activation of σ(54)-dependent promoters is usually tightly regulated in response to environmental cues. The high abundance of potential σ(54)-dependent promoters in the anaerobe bacteria, Desulfovibrio vulgaris Hildenborough, reflects the high versatility of this bacteria suggesting that σ(54) factor is the nexus of a large regulatory network. Understanding the key players of σ(54)-regulation in this organism is therefore essential to gain insights into the adaptation to anaerobiosis. Recently, the D. vulgaris orp genes, specifically found in anaerobe bacteria, have been shown to be transcribed by the RNA polymerase coupled to the σ(54) alternative sigma factor. In this study, using in vitro binding experiments and in vivo reporter fusion assays in the Escherichia coli heterologous host, we showed that the expression of the divergent orp promoters is strongly dependent on the integration host factor IHF. Bioinformatic and mutational analysis coupled to reporter fusion activities and mobility shift assays identified two functional IHF binding site sequences located between the orp1 and orp2 promoters. We further determined that the D. vulgaris DVU0396 (IHFα) and DVU1864 (IHFβ) subunits are required to control the expression of the orp operons suggesting that they form a functionally active IHF heterodimer. Interestingly results obtained from the in vivo inactivation of DVU0396, which is required for orp operons transcription, suggest that several functionally IHF active homodimer or heterodimer are present in D. vulgaris.

  15. Hexavalent chromium reduction in Desulfovibrio vulgarisHildenborough causes transitory inhibition of sulfate reduction and cellgrowth

    SciTech Connect

    Klonowska, A.; Clark, M.E.; Thieman, S.B.; Giles, B.J.; Wall,J.D.; Fields, M.W.

    2008-01-07

    Desulfovibrio vulgaris Hildenborough is a well-studiedsulfate reducer that can reduce heavy metals and radionuclides [e.g.,Cr(VI) and U(VI)]. Cultures grown in a defined medium had a lag period ofapproximately 30 h when exposed to 0.05 mM Cr(VI). Substrate analysesrevealed that although Cr(VI) was reduced within the first 5 h, growthwas not observed for an additional 20 h. The growth lag could beexplained by a decline in cell viability; however, during this time smallamounts of lactate were still utilized without sulfate reduction oracetate formation. Approximately 40 h after Cr exposure (0.05 mM),sulfate reduction occurred concurrently with the accumulation of acetate.Similar amounts of hydrogen were produced by Cr-exposed cells compared tocontrol cells, and lactate was not converted to glycogen duringnon-growth conditions. D. vulgaris cells treated with a reducing agentand then exposed to Cr(VI) still experienced a growth lag, but theaddition of ascorbate at the time of Cr(VI) addition prevented the lagperiod. In addition, cells grown on pyruvate displayed more tolerance toCr(VI) compared to lactate-grown cells. These results indicated that D.vulgaris utilized lactate during Cr(VI) exposure without the reduction ofsulfate or production of acetate, and that ascorbate and pyruvate couldprotect D. vulgaris cells from Cr(VI)/Cr(III) toxicity.

  16. Desulfovibrio marrakechensis sp. nov., a 1,4-tyrosol-oxidizing, sulfate-reducing bacterium isolated from olive mill wastewater.

    PubMed

    Chamkh, Fatima; Spröer, Cathrin; Lemos, Paulo Costa; Besson, Stephane; El Asli, Abdel-Ghani; Bennisse, Rhizlane; Labat, Marc; Reis, Maria; Qatibi, Abdel-Illah

    2009-05-01

    A novel mesophilic sulfate-reducing bacterium, EMSSDQ(4)(T), was isolated from olive mill wastewater in the semi-arid region of Morocco (Marrakech). Cells were Gram-negative, catalase-positive, straight rods that were non-motile and non-spore-forming and contained cytochrome c(3) and desulfoviridin. The DNA G+C content was 65.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the genus Desulfovibrio with Desulfovibrio carbinoliphilus D41(T), Desulfovibrio alcoholivorans SPSN(T), Desulfovibrio fructosivorans JJ(T) and Desulfovibrio carbinolicus EDK82(T) as the most closely related strains with validly published names. In addition to the classical substrates used by Desulfovibrio species, the isolate oxidized 1,4-tyrosol, one of the most abundant phenolic compounds occurring in olive mill wastewater, to 4-hydroxyphenylacetate without ring cleavage. D. alcoholivorans SPSN(T) was also found to carry out this reaction. Under air, strain EMSSDQ(4)(T) exhibited limited growth on lactate and yeast extract in the absence of sulfate. On the basis of genotypic and phenotypic characteristics, it is proposed that the isolate represents a novel species, Desulfovibrio marrakechensis sp. nov. The type strain is EMSSDQ(4)(T) (=DSM 19337(T) =ATCC BAA-1562(T)).

  17. Two-Component Signal Transduction Systems of Desulfovibrio Vulgaris: Structural and Phylogenetic Analysis and Deduction of Putative Cognate Pairs

    SciTech Connect

    Zhang, Weiwen; Culley, David E.; Wu, Gang; Brockman, Fred J.

    2006-01-20

    ABSTRACT-Two-component signal transduction systems (TCSTS) composed of sensory histidine kinases (HK) and response regulators (RR), constitute a key element of the mechanism by which bacteria sense and respond to changes in environments. A large number of TCSTSs including 59 putative HKs and 55 RRs were identified from the Desulfovibrio vulgaris genome, indicating their important roles in regulation of cellular metabolism. In this study, the structural and phylogenetic analysis of all putative TCSTSs in D. vulgaris was performed. The results showed D. vulgaris contained an unexpectedly large number of hybrid-type HKs, implying that multiple-step phosphorelay may be a common signal transduction mechanism in D. vulgaris. Most TCSTS components of D. vulgaris were found clustered into several subfamilies previously recognized in other bacteria and extensive co-evolution between D. vulgaris HKs and RRs was observed, suggesting that the concordance of HKs and RRs in cognate phylogenetic groups could be indicative of cognate TCSTSs...

  18. Effect of sulfide on growth physiology and gene expression of Desulfovibrio vulgaris Hildenborough.

    PubMed

    Caffrey, Sean M; Voordouw, Gerrit

    2010-01-01

    Hydrogen sulfide, the metabolic end product of sulfate-reducing bacteria (SRB), is toxic to most life forms. This includes the SRB themselves. Although many of these are probably among the most sulfide resistant life forms, the presence of sulfide nevertheless presents a stress, which SRB must overcome. Although the response of SRB, especially the genus Desulfovibrio, to numerous stressors has been studied, their response to sulfide stress is unknown. We determined the effect of sulfide stress by comparing cells of Desulfovibrio vulgaris Hildenborough grown under conditions in which sulfide accumulated (high sulfide, 10 mM) with cells grown under conditions in which sulfide was removed by continuous gassing (low sulfide, 1 mM). High sulfide decreased the instantaneous growth rate constant and the final cell density of the culture by 52 and 33%, respectively, indicating a decreased bioenergetic fitness. Changes in gene expression caused by exposure to high sulfide were determined using full-genome D. vulgaris microarrays. The transcription of ribosomal protein-encoding genes was decreased, in agreement with the lower growth rate of D. vulgaris under high sulfide conditions. Interestingly, expression of the gene for DsrD, located downstream of the genes for dissimilatory sulfite reductase was also strongly down-regulated. In contrast, the expression of many genes involved in iron accumulation, stress response and proteolysis were increased. This indicates that high sulfide represents a significant stress condition, in which the bioavailability of metals like iron may be lowered. Overall this leads to a reduced growth rate and less efficient biomass production.

  19. Expression of a tetraheme protein, Desulfovibrio vulgaris Miyazaki F cytochrome c(3), in Shewanella oneidensis MR-1

    NASA Technical Reports Server (NTRS)

    Ozawa, K.; Tsapin, A. I.; Nealson, K. H.; Cusanovich, M. A.; Akutsu, H.

    2000-01-01

    Cytochrome c(3) from Desulfovibrio vulgaris Miyazaki F was successfully expressed in the facultative aerobe Shewanella oneidensis MR-1 under anaerobic, microaerophilic, and aerobic conditions, with yields of 0.3 to 0.5 mg of cytochrome/g of cells. A derivative of the broad-host-range plasmid pRK415 containing the cytochrome c(3) gene from D. vulgaris Miyazaki F was used for transformation of S. oneidensis MR-1, resulting in the production of protein product that was indistinguishable from that produced by D. vulgaris Miyazaki F, except for the presence of one extra alanine residue at the N terminus.

  20. Expression of a tetraheme protein, Desulfovibrio vulgaris Miyazaki F cytochrome c(3), in Shewanella oneidensis MR-1.

    PubMed

    Ozawa, K; Tsapin, A I; Nealson, K H; Cusanovich, M A; Akutsu, H

    2000-09-01

    Cytochrome c(3) from Desulfovibrio vulgaris Miyazaki F was successfully expressed in the facultative aerobe Shewanella oneidensis MR-1 under anaerobic, microaerophilic, and aerobic conditions, with yields of 0.3 to 0.5 mg of cytochrome/g of cells. A derivative of the broad-host-range plasmid pRK415 containing the cytochrome c(3) gene from D. vulgaris Miyazaki F was used for transformation of S. oneidensis MR-1, resulting in the production of protein product that was indistinguishable from that produced by D. vulgaris Miyazaki F, except for the presence of one extra alanine residue at the N terminus.

  1. Oxidative Stress and Heat-Shock Responses in Desulfovibrio vulgaris by Genome-Wide Transcriptomic Analysis

    SciTech Connect

    Zhang, Weiwen; Culley, David E.; Hogan, Mike; Vitiritti, Luigi; Brockman, Fred J.

    2006-05-30

    Abstract Sulfate-reducing bacteria, like Desulfovibrio vulgaris have developed a set of reactions allowing them to survive in environments. To obtain further knowledge of the protecting mechanisms employed in D. vulgaris against the oxidative stress and heat shock, we performed a genome-wide transcriptomic analysis to determine the cellular responses to both stimuli. The results showed that 130 genes were responsive to oxidative stress, while 427 genes responsive to heat-shock, respectively. Functional analyses suggested that the genes regulated were involved in a variety of cellular functions. Metabolic analysis showed that amino acid biosynthetic pathways were induced by both oxidative stress and heat shock treatments, while fatty acid metabolism, purine and cofactor biosynthesis were induced by heat shock only. Rubrerythrin gene (rbR) were upregulated by the oxidative stress, suggesting its important role in the oxidative resistance, whereas the expression of rubredoxin oxidoreductase (rbO), superoxide ismutase (sodB) and catalase (katA) genes were not subjected to regulation by oxidative stress in D. vulgaris. In addition, the results showed that thioredoxin reductase (trxB) was responsive to oxidative stress, suggesting the thiol-specific redox system might be involved in oxidative protection in D. vulgaris. Comparison of cellular responses to oxidative stress and heat-shock allowed the identification of 66 genes that showed a similar drastic response to both environmental stimuli, implying that they might be part of the general stress response (GSR) network in D. vulgaris, which was further supported by the finding of a conserved motif upstream these common-responsive genes.

  2. Effect of growth conditions on microbial activity and iron-sulfide production by Desulfovibrio vulgaris.

    PubMed

    Zhou, Chen; Vannela, Raveender; Hayes, Kim F; Rittmann, Bruce E

    2014-05-15

    Sulfate-reducing bacteria (SRB) can produce iron sulfide (FeS) solids with mineralogical characteristics that may be beneficial for a variety of biogeochemical applications, such as long-term immobilization of uranium. In this study, the growth and metabolism of Desulfovibrio vulgaris, one of the best-studied SRB species, were comprehensively monitored in batch studies, and the biogenic FeS solids were characterized by X-ray diffraction. Controlling the pH by varying the initial pH, the iron-to-sulfate ratio, or the electron donor - affected the growth of D. vulgaris and strongly influenced the formation and growth of FeS solids. In particular, lower pH (from initial conditions or a decrease caused by less sulfate reduction, FeS precipitation, or using pyruvate as the electron donor) produced larger-sized mackinawite (Fe1+xS). Greater accumulation of free sulfide, from more sulfate reduction by D. vulgaris, also led to larger-sized mackinawite and particularly stimulated mackinawite transformation to greigite (Fe3S4) when the free sulfide concentration was 29.3mM. Furthermore, sufficient free Fe(2+) led to the additional formation of vivianite [Fe3(PO4)2·8(H2O)]. Thus, microbially relevant conditions (initial pH, choice of electron donor, and excess or deficiency of sulfide) are tools to generate biogenic FeS solids of different characteristics.

  3. Transcriptional response of Desulfovibrio vulgaris Hildenborough to oxidative stress mimicking environmental conditions.

    PubMed

    Pereira, Patrícia M; He, Qiang; Xavier, António V; Zhou, Jizhong; Pereira, Inês A C; Louro, Ricardo O

    2008-05-01

    Sulfate-reducing bacteria (SRB) are anaerobes readily found in oxic-anoxic interfaces. Multiple defense pathways against oxidative conditions were identified in these organisms and proposed to be differentially expressed under different concentrations of oxygen, contributing to their ability to survive oxic conditions. In this study, Desulfovibrio vulgaris Hildenborough cells were exposed to the highest concentration of oxygen that SRB are likely to encounter in natural habitats, and the global transcriptomic response was determined. Three hundred and seven genes were responsive, with cellular roles in energy metabolism, protein fate, cell envelope and regulatory functions, including multiple genes encoding heat shock proteins, peptidases and proteins with heat shock promoters. Of the oxygen reducing mechanisms of D. vulgaris only the periplasmic hydrogen-dependent mechanism was up-regulated, involving the [NiFeSe] hydrogenase, formate dehydrogenase(s) and the Hmc membrane complex. The oxidative defense response concentrated on damage repair by metal-free enzymes. These data, together with the down-regulation of the ferric uptake regulator operon, which restricts the availability of iron, and the lack of response of the peroxide-sensing regulator operon, suggest that a major effect of this oxygen stress is the inactivation and/or degradation of multiple metalloproteins present in D. vulgaris as a consequence of oxidative damage to their metal clusters.

  4. Transcriptional Response of Desulfovibrio vulgaris Hildenborough to Oxidative Stress Mimicking Environmental Conditions

    SciTech Connect

    Pereira, Patricia M.; He, Qiang; Xavier, Antonio V.; Zhou, Jizhong; Pereira, Ines A.C.; Louro, Ricardo O.

    2008-03-12

    Sulphate-reducing bacteria are anaerobes readily found in oxic-anoxic interfaces. Multiple defence pathways against oxidative conditions were identified in these organisms and proposed to be differentially expressed under different concentrations of oxygen, contributing to their ability to survive oxic conditions. In this study, Desulfovibrio vulgaris Hildenborough cells were exposed to the highest concentration of oxygen that sulphate-reducing bacteria are likely to encounter in natural habitats, and the global transcriptomic response was determined. 307 genes were responsive, with cellular roles in energy metabolism, protein fate, cell envelope and regulatory functions, including multiple genes encoding heat shock proteins, peptidases and proteins with heat shock promoters. Of the oxygen reducing mechanisms of D. vulgaris only the periplasmic hydrogen-dependent mechanism is up-regulated, involving the [NiFeSe]hydrogenase, formate dehydrogenase(s) and the Hmc membrane complex. The oxidative defence response concentrates on damage repair by metal-free enzymes. These data, together with the down regulation of the Fur operon, which restricts the availability of iron, and the lack of response of the PerR operon, suggest that a major effect of this oxygen stress is the inactivation and/or degradation of multiple metalloproteins present in D. vulgaris as a consequence of oxidative damage to their metal clusters.

  5. Growth of Desulfovibrio vulgaris when respiring U(VI) and characterization of biogenic uraninite.

    PubMed

    Zhou, Chen; Vannela, Raveender; Hyun, Sung Pil; Hayes, Kim F; Rittmann, Bruce E

    2014-06-17

    The capacity of Desulfovibrio vulgaris to reduce U(VI) was studied previously with nongrowth conditions involving a high biomass concentration; thus, bacterial growth through respiration of U(VI) was not proven. In this study, we conducted a series of batch tests on U(VI) reduction by D. vulgaris at a low initial biomass (10 to 20 mg/L of protein) that could reveal biomass growth. D. vulgaris grew with U(VI) respiration alone, as well as with simultaneous sulfate reduction. Patterns of growth kinetics and solids production were affected by sulfate and Fe(2+). Biogenic sulfide nonenzymatically reduced 76% of the U(VI) and greatly enhanced the overall reduction rate in the absence of Fe(2+) but was rapidly scavenged by Fe(2+) to form FeS in the presence of Fe(2+). Biogenic U solids were uraninite (UO2) nanocrystallites associated with 20 mg/g biomass as protein. The crystallite thickness of UO2 was 4 to 5 nm without Fe(2+) but was <1.4 nm in the presence of Fe(2+), indicating poor crystallization inhibited by adsorbed Fe(2+) and other amorphous Fe solids, such as FeS or FeCO3. This work fills critical gaps in understanding the metabolic utilization of U by microorganisms and formation of UO2 solids in bioremediation sites.

  6. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis.

    PubMed

    He, Qiang; Huang, Katherine H; He, Zhili; Alm, Eric J; Fields, Matthew W; Hazen, Terry C; Arkin, Adam P; Wall, Judy D; Zhou, Jizhong

    2006-06-01

    Many of the proteins that are candidates for bioenergetic pathways involved with sulfate respiration in Desulfovibrio spp. have been studied, but complete pathways and overall cell physiology remain to be resolved for many environmentally relevant conditions. In order to understand the metabolism of these microorganisms under adverse environmental conditions for improved bioremediation efforts, Desulfovibrio vulgaris Hildenborough was used as a model organism to study stress response to nitrite, an important intermediate in the nitrogen cycle. Previous physiological studies demonstrated that growth was inhibited by nitrite and that nitrite reduction was observed to be the primary mechanism of detoxification. Global transcriptional profiling with whole-genome microarrays revealed coordinated cascades of responses to nitrite in pathways of energy metabolism, nitrogen metabolism, oxidative stress response, and iron homeostasis. In agreement with previous observations, nitrite-stressed cells showed a decrease in the expression of genes encoding sulfate reduction functions in addition to respiratory oxidative phosphorylation and ATP synthase activity. Consequently, the stressed cells had decreased expression of the genes encoding ATP-dependent amino acid transporters and proteins involved in translation. Other genes up-regulated in response to nitrite include the genes in the Fur regulon, which is suggested to be involved in iron homeostasis, and genes in the Per regulon, which is predicted to be responsible for oxidative stress response.

  7. Energetic Consequences of nitrite stress in Desulfovibrio vulgarisHildenborough, inferred from global transcriptional analysis

    SciTech Connect

    He, Qiang; Huang, Katherine H.; He, Zhili; Alm, Eric J.; Fields,Matthew W.; Hazen, Terry C.; Arkin, Adam P.; Wall, Judy D.; Zhou, Jizhong

    2005-11-03

    Many of the proteins that are candidates for bioenergetic pathways involved with sulfate respiration in Desulfovibrio spp. have been studied, but complete pathways and overall cell physiology remain to be resolved for many environmentally relevant conditions. In order to understand the metabolism of these microorganisms under adverse environmental conditions for improved bioremediation efforts, Desulfovibrio vulgaris Hildenborough was used as a model organism to study stress response to nitrite, an important intermediate in the nitrogen cycle. Previous physiological studies demonstrated that growth was inhibited by nitrite and that nitrite reduction was observed to be the primary mechanism of detoxification. Global transcriptional profiling with whole-genome microarrays revealed coordinated cascades of responses to nitrite in pathways of energy metabolism, nitrogen metabolism, oxidative stress response, and iron homeostasis. In agreement with previous observations, nitrite-stressed cells showed a decrease in the expression of genes encoding sulfate reduction functions in addition to respiratory oxidative phosphorylation and ATP synthase activity. Consequently, the stressed cells had decreased expression of the genes encoding ATP-dependent amino acid transporters and proteins involved in translation. Other genes up-regulated in response to nitrite include the genes in the Fur regulon, which is suggested to be involved in iron homeostasis, and genes in the Per regulon, which is predicted to be responsible for oxidative stress response.

  8. Redox states of Desulfovibrio vulgaris DsrC, a key protein in dissimilatory sulfite reduction.

    PubMed

    Venceslau, Sofia S; Cort, John R; Baker, Erin S; Chu, Rosalie K; Robinson, Errol W; Dahl, Christiane; Saraiva, Lígia M; Pereira, Inês A C

    2013-11-29

    Dissimilatory reduction of sulfite is carried out by the siroheme enzyme DsrAB, with the involvement of the protein DsrC, which has two conserved redox-active cysteines. DsrC was initially believed to be a third subunit of DsrAB. Here, we report a study of the distribution of DsrC in cell extracts to show that, in the model sulfate reducer Desulfovibrio vulgaris, the majority of DsrC is not associated with DsrAB and is thus free to interact with other proteins. In addition, we developed a cysteine-labelling gel-shift assay to monitor the DsrC redox state and behaviour, and procedures to produce the different redox forms. The oxidized state of DsrC with an intramolecular disulfide bond, which is proposed to be a key metabolic intermediate, could be successfully produced for the first time by treatment with arginine.

  9. Redox states of Desulfovibrio vulgaris DsrC, a key protein in dissimilatory sulfite reduction

    SciTech Connect

    Venceslau, Sofia S.; Cort, John R.; Baker, Erin Shammel; Chu, Rosalie K.; Robinson, Errol W.; Dahl, Christiane; Saraiva, Ligia M.; Pereira, Ines Ac

    2013-11-29

    Dissimilatory reduction of sulfite is carried out by the siroheme enzyme DsrAB, with the involvement of the protein DsrC having two conserved cysteine residues. Here, we report a study of the distribution of DsrC in cell extracts, a cysteine-labelling gel-shift assay to monitor its redox state and behaviour, and procedures to produce the different redox forms. We show that, in the model sulfate reducer Desulfovibrio vulgaris, the majority of DsrC is not associated with DsrAB and is thus free to interact with other proteins. In addition, we successfully produced DsrC with an intramolecular disulfide bond (oxidized state) by treatment with arginine.

  10. Desulfovibrio brasiliensis sp. nov., a moderate halophilic sulfate-reducing bacterium from Lagoa Vermelha (Brazil) mediating dolomite formation.

    PubMed

    Warthmann, Rolf; Vasconcelos, Crisogono; Sass, Henrik; McKenzie, Judith A

    2005-06-01

    A novel halotolerant sulfate-reducing bacterium, Desulfovibrio brasiliensis strain LVform1, was isolated from sediments of a dolomite-forming hypersaline coastal lagoon, Lagoa Vermelha, in the state of Rio de Janeiro, Brazil. The cells are vibrio-shaped and 0.30 to 0.45 microm by 1.0 to 3.5 microm in size. These bacteria mediate the precipitation of dolomite [CaMg(CO3)2] in culture experiments. The strain was identified as a member of the genus Desulfovibrio in the delta-subclass of the Proteobacteria on the basis of its 16S rRNA gene sequence, its physiological and morphological properties. Strain LVform1 is obligate sodium-dependent and grows at NaCl concentrations of up to 15%. The 16S rRNA sequence revealed that this strain is closely related to Desulfovibrio halophilus (96.2% similarity) and to Desulfovibrio oxyclinae (96.8% similarity), which were both isolated from Solar Lake, a hypersaline coastal lake in the Sinai, Egypt. Strain LVform1 is barotolerant, growing under pressures of up to 370 bar (37 MPa). We propose strain LVform1 to be the type strain of a novel species of the genus Desulfovibrio, Desulfovibrio brasiliensis (type strain LVform1 = DSMZ No. 15816 and JCM No. 12178). The GenBank/EMBL accession number for the 16S rDNA sequence of strain LVform1 is AJ544687.

  11. Construction and Evaluation of Desulfovibrio vulgaris Whole-Genome Oligonucleotide Microarrays

    SciTech Connect

    Z. He; Q. He; L. Wu; M.E. Clark; J.D. Wall; Jizhong Zhou; Matthew W. Fields

    2004-03-17

    Desulfovibrio vulgaris Hildenborough has been the focus of biochemical and physiological studies in the laboratory, and the metabolic versatility of this organism has been largely recognized, particularly the reduction of sulfate, fumarate, iron, uranium and chromium. In addition, a Desulfovibrio sp. has been shown to utilize uranium as the sole electron acceptor. D. vulgaris is a d-Proteobacterium with a genome size of 3.6 Mb and 3584 ORFs. The whole-genome microarrays of D. vulgaris have been constructed using 70mer oligonucleotides. All ORFs in the genome were represented with 3471 (97.1%) unique probes and 103 (2.9%) non-specific probes that may have cross-hybridization with other ORFs. In preparation for use of the experimental microarrays, artificial probes and targets were designed to assess specificity and sensitivity and identify optimal hybridization conditions for oligonucleotide microarrays. The results indicated that for 50mer and 70mer oligonucleotide arrays, hybridization at 45 C to 50 C, washing at 37 C and a wash time of 2.5 to 5 minutes obtained specific and strong hybridization signals. In order to evaluate the performance of the experimental microarrays, growth conditions were selected that were expected to give significant hybridization differences for different sets of genes. The initial evaluations were performed using D. vulgaris cells grown at logarithmic and stationary phases. Transcriptional analysis of D. vulgaris cells sampled during logarithmic phase growth indicated that 25% of annotated ORFs were up-regulated and 3% of annotated ORFs were downregulated compared to stationary phase cells. The up-regulated genes included ORFs predicted to be involved with acyl chain biosynthesis, amino acid ABC transporter, translational initiation factors, and ribosomal proteins. In the stationary phase growth cells, the two most up-regulated ORFs (70-fold) were annotated as a carboxynorspermidine decarboxylase and a 2C-methyl-D-erythritol-2

  12. LC-MS/MS Based Proteomic Analysis and Functional Inference of Hypothetical Proteins in Desulfovibrio Vulgaris

    SciTech Connect

    Zhang, Weiwen; Culley, David E.; Gritsenko, Marina A.; Moore, Ronald J.; Nie, Lei; Scholten, Johannes C.; Petritis, Konstantinos; Strittmatter, Eric F.; Camp, David G.; Smith, Richard D.; Brockman, Fred J.

    2006-11-03

    Direct liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to examine the proteins extracted from Desulfovibrio vulgaris cells. While our previous study provided a proteomic overview of the cellular metabolism based on proteins with known functions (Zhang et al., 2006a, Proteomics, 6: 4286-4299), this study describes the global detection and functional inference for hypothetical D. vulgaris proteins. Across six growth conditions, 15,841 tryptic peptides were identified with high confidence. Using a criterion of peptide identification from at least two out of three independent LC-MS/MS analyses per protein, 176 open reading frames (ORFs) originally annotated as hypothetical proteins were found to encode expressed proteins. These proteins ranged from 6.0 to 153 kDa, and had calculated pI values ranging from 3.7 to 11.5. Based on homology search results (with E value <= 0.01 as a cutoff), 159 proteins were defined as conserved hypothetical proteins, and 17 proteins were unique to the D. vulgaris genome. Functional inference of the conserved hypothetical proteins was performed by a combination of several non-homology based methods: genomic context analysis, phylogenomic profiling, and analysis of a combination of experimental information including peptide detection in cells grown under specific culture conditions and cellular location of the proteins. Using this approach we were able to assign possible functions to 27 conserved hypothetical proteins. This study demonstrated that a combination of proteomics and bioinformatics methodologies can provide verification for the authenticity of hypothetical proteins and improve annotation for the D. vulgaris genome.

  13. Genome sequence of Desulfovibrio sp. A2, a highly copper resistant, sulfate-reducing bacterium isolated from effluents of a zinc smelter at the Urals.

    PubMed

    Mancini, Stefano; Abicht, Helge K; Karnachuk, Olga V; Solioz, Marc

    2011-12-01

    Desulfovibrio sp. A2 is an anaerobic gram-negative sulfate-reducing bacterium with remarkable tolerance to copper. It was isolated from wastewater effluents of a zinc smelter at the Urals. Here, we report the 4.2-Mb draft genome sequence of Desulfovibrio sp. A2 and identify potential copper resistance mechanisms.

  14. Effects of Chromium(VI) and Chromium(III) on Desulfovibrio vulgaris Cells

    SciTech Connect

    M.E. Clark; A. Klonowska; S.B. Thieman; B. Giles; J.D. Wall; and M.W. Fields

    2007-04-19

    Desulfovibrio vulgaris ATCC 29579 is a well studied sulfate reducer that has known capabilities of reducing heavy metals and radionuclides, like chromium and uranium. Cultures grown in a defined medium (i.e. LS4D) had a lag period of approximately 40 h when exposed to 50 μMof Cr(VI). Substrate analysis revealed that although chromium is reduced within the first 5 h, growth does not resume for another 35 h. During this time, small amounts of lactate are still utilized but the reduction of sulfate does not occur. Sulfate reduction occurs concurrently with the accumulation of acetate approximately 40 h after inoculation, when growth resumes. Similar amounts of hydrogen are produced during this time compared to hydrogen production by cells not exposed to Cr(VI); therefore an accumulation of hydrogen cannot account for the utilization of lactate. There is a significant decrease in the carbohydrate to protein ratio at approximately 25 h, and this result indicated that lactate is not converted to glycogen. Most probable number analysis indicated that cell viability decreased steadily after inoculation and reached approximately 6 x 104 cells/ml 20 h post-chromium exposure. Regeneration of reducing conditions during chromium exposure does not induce growth and in fact may make the growth conditions even more unfavorable. This result suggested that an increase in Eh was not solely responsible for the decline in viability. Cell pellets collected 10 h after chromium-exposure were unable to resume growth when suspended into fresh medium. Supernatants from these pellets were able to support cell growth upon re- inoculation. D. vulgaris cells treated with a non-dose dependent addition of ascorbate at the same time of Cr(VI) addition did not enter a lag period. Ascorbate added 3 h post-Cr(VI) exposure did not prevent the growth lag. These results indicated that Desulfovibrio utilized lactate to reduce Cr(VI) without the reduction of sulfate, that the decline in cell viability and

  15. Identification of Molecular and Cellular Responses of Desulfovibrio vulgaris Biofilms under Culture Conditions Relevant to Field Conditions for Bioreduction of

    SciTech Connect

    Wall, Judy D.

    2006-06-01

    Desulfovibrio vulgaris Hildenborough forms biofilms under stress and nutrient limitation conditions. Analysis of the transcriptional responses to acid exposure suggested that genes encoding arginine and polyamine biosynthesis were increased in expression. A literature search showed that polyamines had been suggested to stimulate biofilm formation in some bacteria. Therefore, biofilm formation by D. vulgaris was then examined. Two different assay methods were used to estimate the biofilm formation. First, the classical crystal violet stainable material attached to glass test tubes was measured. Second protein attached to the test tube sides and especially precipitated at the bottom was measured.

  16. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough.

    PubMed

    Zhou, Aifen; Chen, Yunyu I; Zane, Grant M; He, Zhili; Hemme, Christopher L; Joachimiak, Marcin P; Baumohl, Jason K; He, Qiang; Fields, Matthew W; Arkin, Adam P; Wall, Judy D; Hazen, Terry C; Zhou, Jizhong

    2012-02-01

    Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. However, little is known about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was conducted to characterize their roles in stress responses. Similar growth phenotypes were observed for the crp/fnr deletion mutants under multiple stress conditions. Nevertheless, the idea of distinct functions of Crp/Fnr-type regulators in stress responses was supported by phylogeny, gene transcription changes, fitness changes, and physiological differences. The four D. vulgaris Crp/Fnr homologs are localized in three subfamilies (HcpR, CooA, and cc). The crp/fnr knockout mutants were well separated by transcriptional profiling using detrended correspondence analysis (DCA), and more genes significantly changed in expression in a ΔDVU3111 mutant (JW9013) than in the other three paralogs. In fitness studies, strain JW9013 showed the lowest fitness under standard growth conditions (i.e., sulfate reduction) and the highest fitness under NaCl or chromate stress conditions; better fitness was observed for a ΔDVU2547 mutant (JW9011) under nitrite stress conditions and a ΔDVU2097 mutant (JW9009) under air stress conditions. A higher Cr(VI) reduction rate was observed for strain JW9013 in experiments with washed cells. These results suggested that the four Crp/Fnr-type global regulators play distinct roles in stress responses of D. vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses.

  17. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution.

    PubMed

    Zhou, Aifen; Baidoo, Edward; He, Zhili; Mukhopadhyay, Aindrila; Baumohl, Jason K; Benke, Peter; Joachimiak, Marcin P; Xie, Ming; Song, Rong; Arkin, Adam P; Hazen, Terry C; Keasling, Jay D; Wall, Judy D; Stahl, David A; Zhou, Jizhong

    2013-09-01

    Desulfovibrio vulgaris Hildenborough strains with significantly increased tolerance to NaCl were obtained via experimental evolution. A NaCl-evolved strain, ES9-11, isolated from a population cultured for 1200 generations in medium amended with 100 mM NaCl, showed better tolerance to NaCl than a control strain, EC3-10, cultured for 1200 generations in parallel but without NaCl amendment in medium. To understand the NaCl adaptation mechanism in ES9-11, we analyzed the transcriptional, metabolite and phospholipid fatty acid (PLFA) profiles of strain ES9-11 with 0, 100- or 250 mM-added NaCl in medium compared with the ancestral strain and EC3-10 as controls. In all the culture conditions, increased expressions of genes involved in amino-acid synthesis and transport, energy production, cation efflux and decreased expression of flagellar assembly genes were detected in ES9-11. Consistently, increased abundances of organic solutes and decreased cell motility were observed in ES9-11. Glutamate appears to be the most important osmoprotectant in D. vulgaris under NaCl stress, whereas, other organic solutes such as glutamine, glycine and glycine betaine might contribute to NaCl tolerance under low NaCl concentration only. Unsaturation indices of PLFA significantly increased in ES9-11. Branched unsaturated PLFAs i17:1 ω9c, a17:1 ω9c and branched saturated i15:0 might have important roles in maintaining proper membrane fluidity under NaCl stress. Taken together, these data suggest that the accumulation of osmolytes, increased membrane fluidity, decreased cell motility and possibly an increased exclusion of Na(+) contribute to increased NaCl tolerance in NaCl-evolved D. vulgaris.

  18. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

    PubMed Central

    Zhou, Aifen; Baidoo, Edward; He, Zhili; Mukhopadhyay, Aindrila; Baumohl, Jason K; Benke, Peter; Joachimiak, Marcin P; Xie, Ming; Song, Rong; Arkin, Adam P; Hazen, Terry C; Keasling, Jay D; Wall, Judy D; Stahl, David A; Zhou, Jizhong

    2013-01-01

    Desulfovibrio vulgaris Hildenborough strains with significantly increased tolerance to NaCl were obtained via experimental evolution. A NaCl-evolved strain, ES9-11, isolated from a population cultured for 1200 generations in medium amended with 100 mM NaCl, showed better tolerance to NaCl than a control strain, EC3-10, cultured for 1200 generations in parallel but without NaCl amendment in medium. To understand the NaCl adaptation mechanism in ES9-11, we analyzed the transcriptional, metabolite and phospholipid fatty acid (PLFA) profiles of strain ES9-11 with 0, 100- or 250 mM-added NaCl in medium compared with the ancestral strain and EC3-10 as controls. In all the culture conditions, increased expressions of genes involved in amino-acid synthesis and transport, energy production, cation efflux and decreased expression of flagellar assembly genes were detected in ES9-11. Consistently, increased abundances of organic solutes and decreased cell motility were observed in ES9-11. Glutamate appears to be the most important osmoprotectant in D. vulgaris under NaCl stress, whereas, other organic solutes such as glutamine, glycine and glycine betaine might contribute to NaCl tolerance under low NaCl concentration only. Unsaturation indices of PLFA significantly increased in ES9-11. Branched unsaturated PLFAs i17:1 ω9c, a17:1 ω9c and branched saturated i15:0 might have important roles in maintaining proper membrane fluidity under NaCl stress. Taken together, these data suggest that the accumulation of osmolytes, increased membrane fluidity, decreased cell motility and possibly an increased exclusion of Na+ contribute to increased NaCl tolerance in NaCl-evolved D. vulgaris. PMID:23575373

  19. Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

    PubMed Central

    Zhou, Aifen; Chen, Yunyu I.; Zane, Grant M.; He, Zhili; Hemme, Christopher L.; Joachimiak, Marcin P.; Baumohl, Jason K.; He, Qiang; Fields, Matthew W.; Arkin, Adam P.; Wall, Judy D.; Hazen, Terry C.

    2012-01-01

    Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. However, little is known about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was conducted to characterize their roles in stress responses. Similar growth phenotypes were observed for the crp/fnr deletion mutants under multiple stress conditions. Nevertheless, the idea of distinct functions of Crp/Fnr-type regulators in stress responses was supported by phylogeny, gene transcription changes, fitness changes, and physiological differences. The four D. vulgaris Crp/Fnr homologs are localized in three subfamilies (HcpR, CooA, and cc). The crp/fnr knockout mutants were well separated by transcriptional profiling using detrended correspondence analysis (DCA), and more genes significantly changed in expression in a ΔDVU3111 mutant (JW9013) than in the other three paralogs. In fitness studies, strain JW9013 showed the lowest fitness under standard growth conditions (i.e., sulfate reduction) and the highest fitness under NaCl or chromate stress conditions; better fitness was observed for a ΔDVU2547 mutant (JW9011) under nitrite stress conditions and a ΔDVU2097 mutant (JW9009) under air stress conditions. A higher Cr(VI) reduction rate was observed for strain JW9013 in experiments with washed cells. These results suggested that the four Crp/Fnr-type global regulators play distinct roles in stress responses of D. vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses. PMID:22156435

  20. Temporal transcriptomic analyses of Desulfovibrio vulgarisHildenborough during electron donor depletion

    SciTech Connect

    Clark, M.E.; He, Q.; He, Z.; Alm, E.; Huang, K.; Hazen, T.C.; Arkin, A.P.; Wall, J.D.; Zhou, J.; Fields, M.W.

    2006-05-20

    Desulfovibrio vulgaris was cultivated in a defined mediumand biomass was sampled over time for approximately 70 h to characterizethe shifts in gene expression as cells transitioned from exponential tostationary phase during electron donor depletion. In addition to temporaltranscriptomics; total protein, carbohydrate, lactate, acetate, andsulfate levels were measured. The microarray data were analyzed forstatistically significant expression changes, hierarchical clusteranalysis, and promoter element prediction, and were validated viaquantitative PCR. As the cells transitioned from exponential tostationary-phase a majority of the down-expressed genes were involved intranslation and transcription, and this trend continued in the remainingtime points. Intracellular trafficking and secretion, ion transport, andcoenzyme metabolism showed a general increase in relative expression asthe cells entered stationary phase. As expected, DNA replicationmachinery was down expressed, and genes involved in DNA repair increasedin expression during stationary-phase. Genes involved in amino acidacquisition, carbohydrate metabolism, energy production, and cellenvelope biogenesis did not exhibit uniform transcriptional responses.Interestingly, most phage-related genes were up-expressed at the onset ofstationary-phase. This result suggested that nutrient depletion mayimpact community dynamics and DNA transfer mechanisms of sulfate-reducingbacteria via phage cycle. The putative feoAB system (in addition to otherpresumptive iron metabolism genes) was significantly up-expressed, andsuggested the possible importance of Fe2+ acquisition undermetal-reducing conditions. A large subset of carbohydrate-related geneshad altered gene expression, and the total cellular carbohydrate levelsdeclined during the growth phase transition. Interestingly, the D.vulgaris genome does not contain a putative rpoS gene, a common attributeof the d-Proteobacteria genomes sequenced to date, and other putative

  1. Global Transcriptomic Analysis of Desulfovibrio vulgaris Grown on Different Carbon Sources

    SciTech Connect

    Zhang, Weiwen; Culley, David E.; Scholten, Johannes C.; Hogan, Mike; Vitiritti, Luigi; Brockman, Fred J.

    2006-02-01

    Abstract Whole-genome microarrays of Desulfovibrio vulgaris were used to determine relative transcript levels in cells grown to exponential or stationary phase on a minimal medium containing either lactate or formate as electron donor. The results showed that 158 and 477 genes were differentially expressed when comparing exponential to stationary phase in lactate- or formate-based media, respectively; and 505 and 355 genes were responsive to the electron donor used at exponential or stationary phase, respectively. Functional analyses suggested that genes differentially regulated were involved in almost every aspect of cellular metabolism, with the genes involved in protein synthesis, carbon, and energy metabolism being the most regulated. The results suggested that hynAB-1 might function as a primary periplasmic hydrogenase responsible for oxidation of H2 inked to the proton gradient in lactate-based medium, while several periplasmic hydrogenases including hynAB-1 and hyd might carry out this role in formate-based medium. The results also indicated the proton gradient pathway catalyzed by alcohol dehydrogenase and heterodisulfide reductase might be actively functioning for ATP synthesis in D. vulgaris. The possible pathways for ethanol generation from lactate and formate metabolism were also discussed. In addition, hierarchical clustering analysis using expression data across carbon sources and growth phases allowed the identification of the common change specifically associated with the exponential to stationary phase transition, and that specifically associated with the carbon source change from lactate to formate. The study provides the first global description and a functional interpretation of transcriptomic response to growth phase and carbon source in D. vulgaris.

  2. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris.

    PubMed

    Zhou, Aifen; Hillesland, Kristina L; He, Zhili; Schackwitz, Wendy; Tu, Qichao; Zane, Grant M; Ma, Qiao; Qu, Yuanyuan; Stahl, David A; Wall, Judy D; Hazen, Terry C; Fields, Matthew W; Arkin, Adam P; Zhou, Jizhong

    2015-11-01

    To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.

  3. Oxygen reduction in the strict anaerobe Desulfovibrio vulgaris Hildenborough: characterization of two membrane-bound oxygen reductases.

    PubMed

    Lamrabet, O; Pieulle, L; Aubert, C; Mouhamar, F; Stocker, P; Dolla, A; Brasseur, G

    2011-09-01

    Although Desulfovibrio vulgaris Hildenborough (DvH) is a strictly anaerobic bacterium, it is able to consume oxygen in different cellular compartments, including extensive periplasmic O₂ reduction with hydrogen as electron donor. The genome of DvH revealed the presence of cydAB and cox genes, encoding a quinol oxidase bd and a cytochrome c oxidase, respectively. In the membranes of DvH, we detected both quinol oxygen reductase [inhibited by heptyl-hydroxyquinoline-N-oxide (HQNO)] and cytochrome c oxidase activities. Spectral and HPLC data for the membrane fraction revealed the presence of o-, b- and d-type haems, in addition to a majority of c-type haems, but no a-type haem, in agreement with carbon monoxide-binding analysis. The cytochrome c oxidase is thus of the cc(o/b)o₃ type, a type not previously described. The monohaem cytochrome c₅₅₃ is an electron donor to the cytochrome c oxidase; its encoding gene is located upstream of the cox operon and is 50-fold more transcribed than coxI encoding the cytochrome c oxidase subunit I. Even when DvH is grown under anaerobic conditions in lactate/sulfate medium, the two terminal oxidase-encoding genes are expressed. Furthermore, the quinol oxidase bd-encoding genes are more highly expressed than the cox genes. The cox operon exhibits an atypical genomic organization, with the gene coxII located downstream of coxIV. The occurrence of these membrane-bound oxygen reductases in other strictly anaerobic Deltaproteobacteria is discussed.

  4. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

    PubMed Central

    Zhou, Aifen; Hillesland, Kristina L; He, Zhili; Schackwitz, Wendy; Tu, Qichao; Zane, Grant M; Ma, Qiao; Qu, Yuanyuan; Stahl, David A; Wall, Judy D; Hazen, Terry C; Fields, Matthew W; Arkin, Adam P; Zhou, Jizhong

    2015-01-01

    To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance. PMID:25848870

  5. Oxygen exposure increases resistance of Desulfovibrio vulgaris Hildenborough to killing by hydrogen peroxide.

    PubMed

    Wildschut, Janine D; Caffrey, Sean M; Voordouw, Johanna K; Voordouw, Gerrit

    2012-02-01

    Inactivation of PerR by oxidative stress and a corresponding increase in expression of the perR regulon genes is part of the oxidative stress defense in a variety of anaerobic bacteria. Diluted anaerobic, nearly sulfide-free cultures of mutant and wild-type Desulfovibrio vulgaris (10(5)-10(6) colony-forming units/ml) were treated with 0 to 2,500 μM H(2)O(2) for only 5 min to prevent readjustment of gene expression. Survivors were then scored by plating. The wild type and perR mutant had 50% survival at 58 and 269 μM H(2)O(2), respectively, indicating the latter to be 4.6-fold more resistant to killing by H(2)O(2) under these conditions. Significantly increased resistance of the wild type (38-fold; 50% killing at 2188 μM H(2)O(2)) was observed if cells were pretreated with full air for 30 min, conditions that did not affect cell viability. The resistance of the perR mutant increased less (4.6-fold; 50% killing at 1230 μM H(2)O(2)), when similarly pretreated. Interestingly, no increased resistance of either was achieved by exposure with 10.6 μM H(2)O(2) for 30 min, the highest concentration that could be used without killing the cells. Hence, in environments with low D. vulgaris biomass only the presence of external O(2) effectively activates the perR regulon. As a result, mutant strains lacking one of the perR regulon genes ahpC, dvu0772, rbr1 or rbr2 displayed decreased resistance to H(2)O(2) stress only following pretreatment with air.

  6. Distinctive Oxidative Stress Responses to Hydrogen Peroxide in Sulfate Reducing Bacteria Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Zhou, Aifen; He, Zhili; Redding, A.M.; Mukhopadhyay, Aindrila; Hemme, Christopher L.; Joachimiak, Marcin P.; Bender, Kelly S.; Keasling, Jay D.; Stahl, David A.; Fields, Matthew W.; Hazen, Terry C.; Arkin, Adam P.; Wall, Judy D.; Zhou, Jizhong

    2009-01-01

    Response of Desulfovibrio vulgaris Hildenborough to hydrogen peroxide (H2O2, 1 mM) was investigated with transcriptomic, proteomic and genetic approaches. Microarray data demonstrated that gene expression was extensively affected by H2O2 with the response peaking at 120 min after H2O2 treatment. Genes affected include those involved with energy production, sulfate reduction, ribosomal structure and translation, H2O2 scavenging, posttranslational modification and DNA repair as evidenced by gene coexpression networks generated via a random matrix-theory based approach. Data from this study support the hypothesis that both PerR and Fur play important roles in H2O2-induced oxidative stress response. First, both PerR and Fur regulon genes were significantly up-regulated. Second, predicted PerR regulon genes ahpC and rbr2 were derepressedin Delta PerR and Delta Fur mutants and induction of neither gene was observed in both Delta PerR and Delta Fur when challenged with peroxide, suggesting possible overlap of these regulons. Third, both Delta PerR and Delta Fur appeared to be more tolerant of H2O2 as measured by optical density. Forth, proteomics data suggested de-repression of Fur during the oxidative stress response. In terms of the intracellular enzymatic H2O2 scavenging, gene expression data suggested that Rdl and Rbr2 may play major roles in the detoxification of H2O2. In addition, induction of thioredoxin reductase and thioredoxin appeared to be independent of PerR and Fur. Considering all data together, D. vulgaris employed a distinctive stress resistance mechanism to defend against increased cellular H2O2, and the temporal gene expression changes were consistent with the slowdown of cell growth at the onset of oxidative stress.

  7. Membrane-bound oxygen reductases of the anaerobic sulfate-reducing Desulfovibrio vulgaris Hildenborough: roles in oxygen defence and electron link with periplasmic hydrogen oxidation.

    PubMed

    Ramel, F; Amrani, A; Pieulle, L; Lamrabet, O; Voordouw, G; Seddiki, N; Brèthes, D; Company, M; Dolla, A; Brasseur, G

    2013-12-01

    Cytoplasmic membranes of the strictly anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough contain two terminal oxygen reductases, a bd quinol oxidase and a cc(b/o)o3 cytochrome oxidase (Cox). Viability assays pointed out that single Δbd, Δcox and double ΔbdΔcox deletion mutant strains were more sensitive to oxygen exposure than the WT strain, showing the involvement of these oxygen reductases in the detoxification of oxygen. The Δcox strain was slightly more sensitive than the Δbd strain, pointing to the importance of the cc(b/o)o3 cytochrome oxidase in oxygen protection. Decreased O2 reduction rates were measured in mutant cells and membranes using lactate, NADH, ubiquinol and menadiol as substrates. The affinity for oxygen measured with the bd quinol oxidase (Km, 300 nM) was higher than that of the cc(b/o)o3 cytochrome oxidase (Km, 620 nM). The total membrane activity of the bd quinol oxidase was higher than that of the cytochrome oxidase activity in line with the higher expression of the bd oxidase genes. In addition, analysis of the ΔbdΔcox mutant strain indicated the presence of at least one O2-scavenging membrane-bound system able to reduce O2 with menaquinol as electron donor with an O2 affinity that was two orders of magnitude lower than that of the bd quinol oxidase. The lower O2 reductase activity in mutant cells with hydrogen as electron donor and the use of specific inhibitors indicated an electron transfer link between periplasmic H2 oxidation and membrane-bound oxygen reduction via the menaquinol pool. This linkage is crucial in defence of the strictly anaerobic bacterium Desulfovibrio against oxygen stress.

  8. /sup 34/S//sup 32/S fractionation in sulfur cycles catalyzed by anaerobic bacteria. [Chlorobium vibrioforme; Desulfovibrio vulgaris

    SciTech Connect

    Fry, B.; Gest, H.; Hayes, J.M.

    1988-01-01

    Stable isotopic distributions in the sulfur cycle were studied with pure and mixed cultures of the anaerobic bacteria, Chlorobium vibrioforme and Desulfovibrio vulgaris. D. vulgaris and C. vibrioforme can catalyze three reactions constituting a complete anaerobic sulfur cycle: reduction of sulfate to sulfide (D. vulgaris), oxidation of sulfide to elemental sulfur (C. vibrioforme), and oxidation of sulfur to sulfate (C. vibrioforme). In all experiments, the first and last reactions favored concentration of the light /sup 32/S isotope in products (isotopic fractionation factor ..sigma.. = -7.2 and -1.7 per thousand, respectively), whereas oxidation of sulfide favored concentration of the heavy /sup 34/S isotope in products (..sigma.. = +1.7 per thousand). Experimental results and model calculations suggest that elemental sulfur enriched in /sup 34/S versus sulfide may be a biogeochemical marker for the presence of sulfide-oxidizing bacteria in modern and ancient environments.

  9. Single-Cell Analysis of Growth and Cell Division of the Anaerobe Desulfovibrio vulgaris Hildenborough.

    PubMed

    Fievet, Anouchka; Ducret, Adrien; Mignot, Tâm; Valette, Odile; Robert, Lydia; Pardoux, Romain; Dolla, Alain R; Aubert, Corinne

    2015-01-01

    Recent years have seen significant progress in understanding basic bacterial cell cycle properties such as cell growth and cell division. While characterization and regulation of bacterial cell cycle is quite well-documented in the case of fast growing aerobic model organisms, no data has been so far reported for anaerobic bacteria. This lack of information in anaerobic microorganisms can mainly be explained by the absence of molecular and cellular tools such as single cell microscopy and fluorescent probes usable for anaerobes and essential to study cellular events and/or subcellular localization of the actors involved in cell cycle. In this study, single-cell microscopy has been adapted to study for the first time, in real time, the cell cycle of a bacterial anaerobe, Desulfovibrio vulgaris Hildenborough (DvH). This single-cell analysis provides mechanistic insights into the cell division cycle of DvH, which seems to be governed by the recently discussed so-called incremental model that generates remarkably homogeneous cell sizes. Furthermore, cell division was reversibly blocked during oxygen exposure. This may constitute a strategy for anaerobic cells to cope with transient exposure to oxygen that they may encounter in their natural environment, thereby contributing to their aerotolerance. This study lays the foundation for the first molecular, single-cell assay that will address factors that cannot otherwise be resolved in bulk assays and that will allow visualization of a wide range of molecular mechanisms within living anaerobic cells.

  10. Electron mediators accelerate the microbiologically influenced corrosion of 304 stainless steel by the Desulfovibrio vulgaris biofilm.

    PubMed

    Zhang, Peiyu; Xu, Dake; Li, Yingchao; Yang, Ke; Gu, Tingyue

    2015-02-01

    In the microbiologically influenced corrosion (MIC) caused by sulfate reducing bacteria (SRB), iron oxidation happens outside sessile cells while the utilization of the electrons released by the oxidation process for sulfate reduction occurs in the SRB cytoplasm. Thus, cross-cell wall electron transfer is needed. It can only be achieved by electrogenic biofilms. This work hypothesized that the electron transfer is a bottleneck in MIC by SRB. To prove this, MIC tests were carried out using 304 stainless steel coupons covered with the Desulfovibrio vulgaris (ATCC 7757) biofilm in the ATCC 1249 medium. It was found that both riboflavin and flavin adenine dinucleotide (FAD), two common electron mediators that enhance electron transfer, accelerated pitting corrosion and weight loss on the coupons when 10ppm (w/w) of either of them was added to the culture medium in 7-day anaerobic lab tests. This finding has important implications in MIC forensics and biofilm synergy in MIC that causes billions of dollars of damages to the US industry each year.

  11. Tungsten and molybdenum regulation of formate dehydrogenase expression in Desulfovibrio vulgaris Hildenborough.

    PubMed

    da Silva, Sofia M; Pimentel, Catarina; Valente, Filipa M A; Rodrigues-Pousada, Claudina; Pereira, Inês A C

    2011-06-01

    Formate is an important energy substrate for sulfate-reducing bacteria in natural environments, and both molybdenum- and tungsten-containing formate dehydrogenases have been reported in these organisms. In this work, we studied the effect of both metals on the levels of the three formate dehydrogenases encoded in the genome of Desulfovibrio vulgaris Hildenborough, with lactate, formate, or hydrogen as electron donors. Using Western blot analysis, quantitative real-time PCR, activity-stained gels, and protein purification, we show that a metal-dependent regulatory mechanism is present, resulting in the dimeric FdhAB protein being the main enzyme present in cells grown in the presence of tungsten and the trimeric FdhABC₃ protein being the main enzyme in cells grown in the presence of molybdenum. The putatively membrane-associated formate dehydrogenase is detected only at low levels after growth with tungsten. Purification of the three enzymes and metal analysis shows that FdhABC₃ specifically incorporates Mo, whereas FdhAB can incorporate both metals. The FdhAB enzyme has a much higher catalytic efficiency than the other two. Since sulfate reducers are likely to experience high sulfide concentrations that may result in low Mo bioavailability, the ability to use W is likely to constitute a selective advantage.

  12. Genetic Adaptation to Salt Stress in Experimental Evolution of Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Zhou, Aifen; Hillesland, Kristina; He, Zhili; Joachimiak, Marcin; Zane, Grant; Dehal, Paramvir; Arkin, Adam; Stahl, David; Wall, Judy; Hazen, Terry; Zhou, Jizhong; Baidoo, Edward; Benke, Peter; Mukhopadhyay, Aindrila

    2010-05-17

    High salinity is one of the most common environmental stressors. In order to understand how environmental organisms adapt to salty environment, an experiment evolution with sulfate reducing bacteria Desulfovibrio vugaris Hildenborough was conducted. Control lines and salt-stressed lines (6 lines each) grown in minimal medium LS4D or LS4D + 100 mM NaCl were transferred for 1200 generations. The salt tolerance was tested with LS4D supplemented with 250 mM NaCl. Statistical analysis of the growth data suggested that all lines adapted to their evolutionary environment. In addition, the control lines performed better than the ancestor with faster growth rate, higher biomass yield and shorter lag phase under salty environment they did not evolve in. However, the salt-adapted lines performed better than the control lines on measures of growth rate and yield under salty environment, suggesting that the salt?evolved lines acquired mutations specific to having extra salt in LS4D. Growth data and gene transcription data suggested that populations tended to improve till 1000 generations and active mutations tended to be fixed at the stage of 1000 generations. Point mutations and insertion/deletions were identified in isolated colonies from salt-adapted and control lines via whole genome sequencing. Glu, Gln and Ala appears to be the major osmoprotectant in evolved salt-stressed line. Ongoing studies are now characterizing the contribution of specific mutations identified in the salt-evolved D. vulgaris.

  13. Redox states of Desulfovibrio vulgaris DsrC, a key protein in dissimilatory sulfite reduction

    SciTech Connect

    Venceslau, Sofia S.; Cort, John R.; Baker, Erin S.; Chu, Rosalie K.; Robinson, Errol W.; Dahl, Christiane; Saraiva, Lígia M.; Pereira, Inês A.C.

    2013-11-29

    Highlights: •DsrC is known to interact with the dissimilatory sulfite reductase enzyme (DsrAB). •We show that, however, most cellular DsrC is not associated with DsrAB. •A gel-shift assay was developed that allows monitoring of the DsrC redox state. •The DsrC intramolecularly oxidized state could only be produced by arginine treatment. -- Abstract: Dissimilatory reduction of sulfite is carried out by the siroheme enzyme DsrAB, with the involvement of the protein DsrC, which has two conserved redox-active cysteines. DsrC was initially believed to be a third subunit of DsrAB. Here, we report a study of the distribution of DsrC in cell extracts to show that, in the model sulfate reducer Desulfovibrio vulgaris, the majority of DsrC is not associated with DsrAB and is thus free to interact with other proteins. In addition, we developed a cysteine-labelling gel-shift assay to monitor the DsrC redox state and behaviour, and procedures to produce the different redox forms. The oxidized state of DsrC with an intramolecular disulfide bond, which is proposed to be a key metabolic intermediate, could be successfully produced for the first time by treatment with arginine.

  14. Single-Cell Analysis of Growth and Cell Division of the Anaerobe Desulfovibrio vulgaris Hildenborough

    PubMed Central

    Fievet, Anouchka; Ducret, Adrien; Mignot, Tâm; Valette, Odile; Robert, Lydia; Pardoux, Romain; Dolla, Alain R.; Aubert, Corinne

    2015-01-01

    Recent years have seen significant progress in understanding basic bacterial cell cycle properties such as cell growth and cell division. While characterization and regulation of bacterial cell cycle is quite well-documented in the case of fast growing aerobic model organisms, no data has been so far reported for anaerobic bacteria. This lack of information in anaerobic microorganisms can mainly be explained by the absence of molecular and cellular tools such as single cell microscopy and fluorescent probes usable for anaerobes and essential to study cellular events and/or subcellular localization of the actors involved in cell cycle. In this study, single-cell microscopy has been adapted to study for the first time, in real time, the cell cycle of a bacterial anaerobe, Desulfovibrio vulgaris Hildenborough (DvH). This single-cell analysis provides mechanistic insights into the cell division cycle of DvH, which seems to be governed by the recently discussed so-called incremental model that generates remarkably homogeneous cell sizes. Furthermore, cell division was reversibly blocked during oxygen exposure. This may constitute a strategy for anaerobic cells to cope with transient exposure to oxygen that they may encounter in their natural environment, thereby contributing to their aerotolerance. This study lays the foundation for the first molecular, single-cell assay that will address factors that cannot otherwise be resolved in bulk assays and that will allow visualization of a wide range of molecular mechanisms within living anaerobic cells. PMID:26696987

  15. Fractionation of sulfur and hydrogen isotopes in Desulfovibrio vulgaris with perturbed DsrC expression.

    PubMed

    Leavitt, William D; Venceslau, Sofia S; Pereira, Inês A C; Johnston, David T; Bradley, Alexander S

    2016-10-01

    Dissimilatory sulfate reduction is the central microbial metabolism in global sulfur cycling. Understanding the importance of sulfate reduction to Earth's biogeochemical S cycle requires aggregating single-cell processes with geochemical signals. For sulfate reduction, these signals include the ratio of stable sulfur isotopes preserved in minerals, as well as the hydrogen isotope ratios and structures of microbial membrane lipids preserved in organic matter. In this study, we cultivated the model sulfate reducer, Desulfovibrio vulgaris DSM 644(T), to investigate how these parameters were perturbed by changes in expression of the protein DsrC. DsrC is critical to the final metabolic step in sulfate reduction to sulfide. S and H isotopic fractionation imposed by the wild type was compared to three mutants. Discrimination against (34)S in sulfate, as calculated from the residual reactant, did not discernibly differ among all strains. However, a closed-system sulfur isotope distillation model, based on accumulated sulfide, produced inconsistent results in one mutant strain IPFG09. Lipids produced by IPFG09 were also slightly enriched in (2)H. These results suggest that DsrC alone does not have a major impact on sulfate-S, though may influence sulfide-S and lipid-H isotopic compositions. While intriguing, a mechanistic explanation requires further study under continuous culture conditions.

  16. Resonance assignment of DVU2108 that is part of the Orange Protein complex in Desulfovibrio vulgaris Hildenborough.

    PubMed

    Neca, António J; Soares, Rui; Carepo, Marta S P; Pauleta, Sofia R

    2016-04-01

    We report the 94 % assignment of DVU2108, a protein belonging to the Orange Protein family, that in Desulfovibrio vulgaris Hildenborough forms a protein complex named the Orange Protein complex. This complex has been shown to be implicated in the cell division of this organism. DVU2108 is a conserved protein in anaerobic microorganisms and in Desulfovibrio gigas the homologous protein was isolated with a novel Mo-Cu cluster non-covalently attached to the polypeptide chain. However, the heterologously produced DVU2108 did not contain any bound metal. These assignments provide the means to characterize the interaction of DVU2108 with the proteins that form the Orange Protein complex using NMR methods.

  17. Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion.

    PubMed

    Clark, M E; He, Q; He, Z; Huang, K H; Alm, E J; Wan, X-F; Hazen, T C; Arkin, A P; Wall, J D; Zhou, J-Z; Fields, M W

    2006-08-01

    Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the stationary phase during electron donor depletion. In addition to temporal transcriptomics, total protein, carbohydrate, lactate, acetate, and sulfate levels were measured. The microarray data were examined for statistically significant expression changes, hierarchical cluster analysis, and promoter element prediction and were validated by quantitative PCR. As the cells transitioned from the exponential phase to the stationary phase, a majority of the down-expressed genes were involved in translation and transcription, and this trend continued at the remaining times. There were general increases in relative expression for intracellular trafficking and secretion, ion transport, and coenzyme metabolism as the cells entered the stationary phase. As expected, the DNA replication machinery was down-expressed, and the expression of genes involved in DNA repair increased during the stationary phase. Genes involved in amino acid acquisition, carbohydrate metabolism, energy production, and cell envelope biogenesis did not exhibit uniform transcriptional responses. Interestingly, most phage-related genes were up-expressed at the onset of the stationary phase. This result suggested that nutrient depletion may affect community dynamics and DNA transfer mechanisms of sulfate-reducing bacteria via the phage cycle. The putative feoAB system (in addition to other presumptive iron metabolism genes) was significantly up-expressed, and this suggested the possible importance of Fe2+ acquisition under metal-reducing conditions. The expression of a large subset of carbohydrate-related genes was altered, and the total cellular carbohydrate levels declined during the growth phase transition. Interestingly, the D. vulgaris genome does not contain a putative rpoS gene, a common attribute of

  18. Temporal transcriptomic analysis of Desulfovibrio vulgaris Hildenborough transition into stationary phase growth during electrondonor depletion

    SciTech Connect

    Clark, M.E.; He, Q.; He, Z.; Huang, K.H.; Alm, E.J.; Wan, X.-F.; Hazen, T.C.; Arkin, A.P.; Wall, J.D.; Zhou, J.-Z.; Fields, M.W.

    2006-08-01

    Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the stationary phase during electron donor depletion. In addition to temporal transcriptomics, total protein, carbohydrate, lactate, acetate, and sulfate levels were measured. The microarray data were examined for statistically significant expression changes, hierarchical cluster analysis, and promoter element prediction and were validated by quantitative PCR. As the cells transitioned from the exponential phase to the stationary phase, a majority of the down-expressed genes were involved in translation and transcription, and this trend continued at the remaining times. There were general increases in relative expression for intracellular trafficking and secretion, ion transport, and coenzyme metabolism as the cells entered the stationary phase. As expected, the DNA replication machinery was down-expressed, and the expression of genes involved in DNA repair increased during the stationary phase. Genes involved in amino acid acquisition, carbohydrate metabolism, energy production, and cell envelope biogenesis did not exhibit uniform transcriptional responses. Interestingly, most phage-related genes were up-expressed at the onset of the stationary phase. This result suggested that nutrient depletion may affect community dynamics and DNA transfer mechanisms of sulfate-reducing bacteria via the phage cycle. The putative feoAB system (in addition to other presumptive iron metabolism genes) was significantly up-expressed, and this suggested the possible importance of Fe{sup 2+} acquisition under metal-reducing conditions. The expression of a large subset of carbohydrate-related genes was altered, and the total cellular carbohydrate levels declined during the growth phase transition. Interestingly, the D. vulgaris genome does not contain a putative rpoS gene, a common attribute

  19. Development of a markerless genetic exchange system for Desulfovibrio vulgaris Hildenborough and its use in generating a strain with increased transformation efficiency.

    PubMed

    Keller, Kimberly L; Bender, Kelly S; Wall, Judy D

    2009-12-01

    In recent years, the genetic manipulation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough has seen enormous progress. In spite of this progress, the current marker exchange deletion method does not allow for easy selection of multiple sequential gene deletions in a single strain because of the limited number of selectable markers available in D. vulgaris. To broaden the repertoire of genetic tools for manipulation, an in-frame, markerless deletion system has been developed. The counterselectable marker that makes this deletion system possible is the pyrimidine salvage enzyme, uracil phosphoribosyltransferase, encoded by upp. In wild-type D. vulgaris, growth was shown to be inhibited by the toxic pyrimidine analog 5-fluorouracil (5-FU), whereas a mutant bearing a deletion of the upp gene was resistant to 5-FU. When a plasmid containing the wild-type upp gene expressed constitutively from the aph(3')-II promoter (promoter for the kanamycin resistance gene in Tn5) was introduced into the upp deletion strain, sensitivity to 5-FU was restored. This observation allowed us to develop a two-step integration and excision strategy for the deletion of genes of interest. Since this in-frame deletion strategy does not retain an antibiotic cassette, multiple deletions can be generated in a single strain without the accumulation of genes conferring antibiotic resistances. We used this strategy to generate a deletion strain lacking the endonuclease (hsdR, DVU1703) of a type I restriction-modification system that we designated JW7035. The transformation efficiency of the JW7035 strain was found to be 100 to 1,000 times greater than that of the wild-type strain when stable plasmids were introduced via electroporation.

  20. Development of a Markerless Genetic Exchange System in Desulfovibrio vulgaris Hildenborough and Its Use in Generating a Strain with Increased Transformation Efficiency

    SciTech Connect

    Keller, Kimberly L.; Bender, Kelly S.; Wall, Judy D.

    2009-07-21

    In recent years, the genetic manipulation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough has seen enormous progress. In spite of this progress, the current marker exchange deletion method does not allow for easy selection of multiple sequential gene deletions in a single strain because of the limited number of selectable markers available in D. vulgaris. To broaden the repertoire of genetic tools for manipulation, an in-frame, markerless deletion system has been developed. The counterselectable marker that makes this deletion system possible is the pyrimidine salvage enzyme, uracil phosphoribosyltransferase, encoded by upp. In wild-type D. vulgaris, growth was shown to be inhibited by the toxic pyrimidine analog 5-fluorouracil (5-FU); whereas, a mutant bearing a deletion of the upp gene was resistant to 5-FU. When a plasmid containing the wild-type upp gene expressed constitutively from the aph(3')-II promoter (promoter for the kanamycin resistance gene in Tn5) was introduced into the upp deletion strain, sensitivity to 5-FU was restored. This observation allowed us to develop a two-step integration and excision strategy for the deletion of genes of interest. Since this inframe deletion strategy does not retain an antibiotic cassette, multiple deletions can be generated in a single strain without the accumulation of genes conferring antibiotic resistances. We used this strategy to generate a deletion strain lacking the endonuclease (hsdR, DVU1703) of a type I restriction-modification system, that we designated JW7035. The transformation efficiency of the JW7035 strain was found to be 100 to 1000 times greater than that of the wild-type strain when stable plasmids were introduced via electroporation.

  1. Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris Hildenborough and use of nitrite as a substrate for growth.

    PubMed

    Korte, Hannah L; Saini, Avneesh; Trotter, Valentine V; Butland, Gareth P; Arkin, Adam P; Wall, Judy D

    2015-01-20

    Sulfate-reducing microbes, such as Desulfovibrio vulgaris Hildenborough, cause “souring” of petroleum reservoirs through produced sulfide and precipitate heavy metals, either as sulfides or by alteration of the metal reduction state. Thus, inhibitors of these microbes, including nitrate and nitrite ions, are studied in order to limit their impact. Nitrite is a potent inhibitor of sulfate reducers, and it has been suggested that nitrate does not inhibit these microbes directly but by reduction to nitrite, which serves as the ultimate inhibitor. Here we provide evidence that nitrate inhibition of D. vulgaris can be independent of nitrite production. We also show that D. vulgaris can use nitrite as a nitrogen source or terminal electron acceptor for growth. Moreover, we report that use of nitrite as a terminal electron acceptor requires nitrite reductase (nrfA) as a D. vulgaris nrfA mutant cannot respire nitrite but remains capable of utilizing nitrite as a nitrogen source. These results illuminate previously uncharacterized metabolic abilities of D. vulgaris that may allow niche expansion in low-sulfate environments. Understanding these abilities may lead to better control of sulfate-reducing bacteria in industrial settings and more accurate prediction of their interactions in the environment.

  2. Single-cell analysis reveals gene-expression heterogeneity in syntrophic dual-culture of Desulfovibrio vulgaris with Methanosarcina barkeri

    NASA Astrophysics Data System (ADS)

    Qi, Zhenhua; Pei, Guangsheng; Chen, Lei; Zhang, Weiwen

    2014-12-01

    Microbial syntrophic metabolism has been well accepted as the heart of how methanogenic and other anaerobic microbial communities function. In this work, we applied a single-cell RT-qPCR approach to reveal gene-expression heterogeneity in a model syntrophic system of Desulfovibrio vulgaris and Methanosarcina barkeri, as compared with the D. vulgaris monoculture. Using the optimized primers and single-cell analytical protocol, we quantitatively determine gene-expression levels of 6 selected target genes in each of the 120 single cells of D. vulgaris isolated from its monoculture and dual-culture with M. barkeri. The results demonstrated very significant cell-to-cell gene-expression heterogeneity for the selected D. vulgaris genes in both the monoculture and the syntrophic dual-culture. Interestingly, no obvious increase in gene-expression heterogeneity for the selected genes was observed for the syntrophic dual-culture when compared with its monoculture, although the community structure and cell-cell interactions have become more complicated in the syntrophic dual-culture. In addition, the single-cell RT-qPCR analysis also provided further evidence that the gene cluster (DVU0148-DVU0150) may be involved syntrophic metabolism between D. vulgaris and M. barkeri. Finally, the study validated that single-cell RT-qPCR analysis could be a valuable tool in deciphering gene functions and metabolism in mixed-cultured microbial communities.

  3. Single-cell analysis reveals gene-expression heterogeneity in syntrophic dual-culture of Desulfovibrio vulgaris with Methanosarcina barkeri.

    PubMed

    Qi, Zhenhua; Pei, Guangsheng; Chen, Lei; Zhang, Weiwen

    2014-12-15

    Microbial syntrophic metabolism has been well accepted as the heart of how methanogenic and other anaerobic microbial communities function. In this work, we applied a single-cell RT-qPCR approach to reveal gene-expression heterogeneity in a model syntrophic system of Desulfovibrio vulgaris and Methanosarcina barkeri, as compared with the D. vulgaris monoculture. Using the optimized primers and single-cell analytical protocol, we quantitatively determine gene-expression levels of 6 selected target genes in each of the 120 single cells of D. vulgaris isolated from its monoculture and dual-culture with M. barkeri. The results demonstrated very significant cell-to-cell gene-expression heterogeneity for the selected D. vulgaris genes in both the monoculture and the syntrophic dual-culture. Interestingly, no obvious increase in gene-expression heterogeneity for the selected genes was observed for the syntrophic dual-culture when compared with its monoculture, although the community structure and cell-cell interactions have become more complicated in the syntrophic dual-culture. In addition, the single-cell RT-qPCR analysis also provided further evidence that the gene cluster (DVU0148-DVU0150) may be involved syntrophic metabolism between D. vulgaris and M. barkeri. Finally, the study validated that single-cell RT-qPCR analysis could be a valuable tool in deciphering gene functions and metabolism in mixed-cultured microbial communities.

  4. Global Transcriptional, Physiological, and Metabolite Analyses of the Responses of Desulfovibrio vulgaris Hildenborough to Salt Adaptation ▿ †

    PubMed Central

    He, Zhili; Zhou, Aifen; Baidoo, Edward; He, Qiang; Joachimiak, Marcin P.; Benke, Peter; Phan, Richard; Mukhopadhyay, Aindrila; Hemme, Christopher L.; Huang, Katherine; Alm, Eric J.; Fields, Matthew W.; Wall, Judy; Stahl, David; Hazen, Terry C.; Keasling, Jay D.; Arkin, Adam P.; Zhou, Jizhong

    2010-01-01

    The response of Desulfovibrio vulgaris Hildenborough to salt adaptation (long-term NaCl exposure) was examined by performing physiological, global transcriptional, and metabolite analyses. Salt adaptation was reflected by increased expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). The expression of genes involved in carbon metabolism, cell growth, and phage structures was decreased. Transcriptome profiles of D. vulgaris responses to salt adaptation were compared with transcriptome profiles of D. vulgaris responses to salt shock (short-term NaCl exposure). Metabolite assays showed that glutamate and alanine accumulated under salt adaptation conditions, suggesting that these amino acids may be used as osmoprotectants in D. vulgaris. Addition of amino acids (glutamate, alanine, and tryptophan) or yeast extract to the growth medium relieved salt-related growth inhibition. A conceptual model that links the observed results to currently available knowledge is proposed to increase our understanding of the mechanisms of D. vulgaris adaptation to elevated NaCl levels. PMID:20038696

  5. Novel H2-oxidizing [NiFeSe]hydrogenase from Desulfovibrio vulgaris Miyazaki F.

    PubMed

    Nonaka, Kyoshiro; Nguyen, Nga T; Yoon, Ki-Seok; Ogo, Seiji

    2013-04-01

    [NiFeSe]hydrogenases are promising biocatalysts in H2-based technology due to their high catalytic activity and O2-stability. Here, we report purification and characterization of a new membrane-associated [NiFeSe]hydrogenase from Desulfovibrio vulgaris Miyazaki F ([NiFeSe]DvMF). The [NiFeSe]DvMF was composed of two subunits, corresponding to a large subunit of 58.3 kDa and a small subunit of 29.3 kDa determined by SDS-PAGE. Unlike conventional [NiFeSe]hydrogenases having catalytic bias toward H2-production, the [NiFeSe]DvMF showed 11-fold higher specific activity of H2-oxidation (2444 U/mg) than that of H2-production (217 U/mg). At the optimal reaction temperature of the enzyme (65°C), the specific activity of H2-oxidation could reach up to 21,553 U/mg. Amperometric assays of the [NiFeSe]DvMF clearly indicated that the enzyme had a remarkable O2-stability. According to the amino acid sequence alignment, the conserved cysteine residue at position 281 in medial cluster of other [NiFeSe]hydrogenases was specifically replaced by a serine residue (Ser281) in the [NiFeSe]DvMF. These results indicate that the [NiFeSe]DvMF can play as a new H2-oxidizing and O2-stable biocatalyst, along with providing helpful insights into the structure-function relationship of [NiFeSe]hydrogenases.

  6. Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: Carbon and energy flow contribute to the distinct biofilm growth state

    PubMed Central

    2012-01-01

    Background Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations. Results The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from

  7. Spectroscopic and electrochemical characterization of the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Miyazaki F: reversible redox behavior and interactions between electron transfer centers.

    PubMed

    Riethausen, Jana; Rüdiger, Olaf; Gärtner, Wolfgang; Lubitz, Wolfgang; Shafaat, Hannah S

    2013-09-23

    Characterizing a new hydrogenase: The newly isolated [NiFeSe] hydrogenase from Desulfovibrio vulgaris Miyazaki F displays catalytic properties distinct from other hydrogenase proteins. Here we apply site-specific spectroscopic and electrochemical techniques to characterize these unique features at the molecular level.

  8. A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry.

    PubMed

    Zhang, Weiwen; Gritsenko, Marina A; Moore, Ronald J; Culley, David E; Nie, Lei; Petritis, Konstantinos; Strittmatter, Eric F; Camp, David G; Smith, Richard D; Brockman, Fred J

    2006-08-01

    Direct LC-MS/MS was used to examine the proteins extracted from exponential or stationary phase Desulfovibrio vulgaris cells that had been grown on a minimal medium containing either lactate or formate as the primary carbon source. Across all four growth conditions, 976 gene products were identified with high confidence, which is equal to approximately 28% of all predicted proteins in the D. vulgaris genome. Bioinformatic analysis showed that the proteins identified were distributed among almost all functional classes, with the energy metabolism category containing the greatest number of identified proteins. At least 154 ORFs originally annotated as hypothetical proteins were found to encode the expressed proteins, which provided verification for the authenticity of these hypothetical proteins. Proteomic analysis showed that proteins potentially involved in ATP biosynthesis using the proton gradient across membrane, such as ATPase, alcohol dehydrogenases, heterodisulfide reductases, and [NiFe] hydrogenase (HynAB-1) of the hydrogen cycling were highly expressed in all four growth conditions, suggesting they may be the primary pathways for ATP synthesis in D. vulgaris. Most of the enzymes involved in substrate-level phosphorylation were also detected in all tested conditions. However, no enzyme involved in CO cycling or formate cycling was detected, suggesting that they are not the primary ATP-biosynthesis pathways under the tested conditions. This study provides the first proteomic overview of the cellular metabolism of D. vulgaris. The complete list of proteins identified in this study and their abundances (peptide hits) is provided in Supplementary Table 1.

  9. Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: involvement of an ancient horizontal gene transfer

    SciTech Connect

    Scholten, Johannes C.; Culley, David E.; Brockman, Fred J.; Wu, Gang; Zhang, Weiwen

    2007-01-05

    The sulfate reducing bacteria Desulfovibrio vulgaris and the methanogenic archaea Methanosarcina barkeri can grow syntrophically on lactate. In this study, three functionally unknown genes of D. vulgaris, DVU2103, DVU2104 and DVU2108, were found to be up-regulated 2-4 fold following the lifestyle shift from syntroph to sulfatereducer; moreover, none of these genes were regulated when D. vulgaris was grown alone in various pure culture conditions. These results suggest that these genes may play roles related to the lifestyle change of D. vulgaris from syntroph to sulfate reducer. This hypothesis is further supported by phylogenomic analyses showing that homologies of these genes were only narrowly present in several groups of bacteria, most of which are restricted to a syntrophic life-style, such as Pelobacter carbinolicus, Syntrophobacter fumaroxidans, Syntrophomonas wolfei and Syntrophus aciditrophicus. Phylogenetic analysis showed that the genes tended to be clustered with archaeal genera, and they were rooted on archaeal species in the phylogenetic trees, suggesting that they originated from an archaeal methanogen and were horizontally transferred to a common ancestor of delta- Proteobacteria, Clostridia and Thermotogae. While lost in most species during evolution, these genes appear to have been retained in bacteria capable of syntrophic relationships, probably due to their providing a selective advantage. In addition, no significant bias in codon and amino acid usages was detected between these genes and the rest of the D. vulgaris genome, suggesting these gene transfers may have occurred early in the evolutionary history so that sufficient time has elapsed to allow an adaptation to the codon and amino acid usages of D. vulgaris. This report provides novel insights into the origin and evolution of bacterial genes involved in the syntrophic lifestyle.

  10. The sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 as a model for understanding bacterial mercury methylation

    SciTech Connect

    Gilmour, C C; Elias, Dwayne A; Kucken, A M; Brown, Steven D; Palumbo, Anthony Vito; Schadt, Christopher Warren; Wall, Judy D.

    2011-01-01

    We propose the use of Desulfovibrio desulfuricans ND132 as a model species for understanding the mechanism of microbial Hg methylation. Strain ND132 is an anaerobic dissimilatory sulfate-reducing bacterium (DSRB), isolated from estuarine mid-Chesapeake Bay sediments. It was chosen for study because of its exceptionally high rates of Hg methylation in culture and its metabolic similarity to the lost strain D. desulfuricans LS, the only organism for which methylation pathways have been partially defined. Strain ND132 is an incomplete oxidizer of short-chain fatty acids. It is capable of respiratory growth using fumarate as an electron acceptor, supporting growth without sulfide production. We used enriched stable Hg isotopes to show that ND132 simultaneously produces and degrades methylmercury (MeHg) during growth but does not produce elemental Hg. MeHg produced by cells is mainly excreted, and no MeHg is produced in spent medium. Mass balances for Hg and MeHg during the growth of cultures, including the distribution between filterable and particulate phases, illustrate how medium chemistry and growth phase dramatically affect Hg solubility and availability for methylation. The available information on Hg methylation among strains in the genus Desulfovibrio is summarized, and we present methylation rates for several previously untested species. About 50% of Desulfovibrio strains tested to date have the ability to produce MeHg. Importantly, the ability to produce MeHg is constitutive and does not confer Hg resistance. A 16S rRNA-based alignment of the genus Desulfovibrio allows the very preliminary assessment that there may be some evolutionary basis for the ability to produce MeHg within this genus.

  11. Structural and functional relationships in the hybrid cluster protein family: structure of the anaerobically purified hybrid cluster protein from Desulfovibrio vulgaris at 1.35 A resolution.

    PubMed

    Aragão, David; Mitchell, Edward P; Frazão, Carlos F; Carrondo, Maria Arménia; Lindley, Peter F

    2008-06-01

    The hybrid cluster protein (HCP) from the sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough has been isolated and crystallized anaerobically. The phase problem was solved for a P2(1)2(1)2(1) crystal form using multiple-wavelength anomalous diffraction data collected in the vicinity of the Fe K absorption edge. Although the overall protein structure is essentially the same as that previously obtained, it shows that the nature of the hybrid cluster has particular differences when isolated and crystallized in the absence of oxygen and this provides insight into the structural features associated with changes in the oxidation state. A comparison between HCPs and carbon monoxide dehydrogenases (CoDs) shows that they possess a similar fold and that the dehydrogenases have a related cluster at the equivalent HCP hybrid cluster position. This helps to understand the nature of the hybrid cluster and to predict a dimeric structure for class 3 HCPs, which lack the N-terminal region.

  12. Comparative Transcriptome Analysis of Desulfovibrio Vulgaris Grown in Planktonic Culture and Mature Biofilm on a Steel Surface

    SciTech Connect

    Zhang, Weiwen; Culley, David E.; Nie, Lei; Scholten, Johannes C.

    2007-08-01

    The build-up of biofilms of sulphate -reducing bacteria (SRB) on metals surfaces may lead to severe corrosion of iron. To understand the processes at molecular level, in this study, a whole-genome oligonucleotide microarray was used to examine differential expression patterns between planktonic populations and mature biofilm of model SRB species Desulfovibrio vulgaris. Statistical analysis revealed that 472 genes were differentially expressed (1.5 fold or more with a p value less than 0.025) when comparing biofilm to planktonic cells. Among the differentially expressed genes were several that corresponded to biofilm formation genes identified in many aerobic bacterial biofilms (i.e., Pseudomonas species and Escherichia coli), such as down-regulation of genes encoding flagellin, flagellar motor switch protein and chemotaxis proteins involved in cell motility and induction of genes encoding sugar transferase and glycogen synthase involved in exopolysaccharide biosynthesis. In addition, D. vulgaris biofilm-bound cells exhibited decreased transcription of genes involved in protein synthesis, energy metabolism and sulfate reduction, as well as genes involved in general stress responses. These findings were all consistent with early suggestion that the average physiology of biofilm cells were similar to planktonic cells of stationary phases. Most notably, up-regulation of large number of outer membrane proteins was observed in D. vulgaris biofilm. Although their function is still unknown, the higher expression of these genes in D. vulgaris biofilm could implicate important roles formation and maintenance of multi-cellular consortium on metal surface. The study provided insights into the metabolic networks associated with D. vulgaris biofilm formation and maintenance on an iron surface.

  13. Glyceryl trinitrate and caprylic acid for the mitigation of the Desulfovibrio vulgaris biofilm on C1018 carbon steel.

    PubMed

    Li, Y; Zhang, P; Cai, W; Rosenblatt, J S; Raad, I I; Xu, D; Gu, T

    2016-02-01

    Microbiologically influenced corrosion (MIC), also known as biocorrosion, is caused by corrosive biofilms. MIC is a growing problem, especially in the oil and gas industry. Among various corrosive microbes, sulfate reducing bacteria (SRB) are often the leading culprit. Biofilm mitigation is the key to MIC mitigation. Biocide applications against biofilms promote resistance over time. Thus, it is imperative to develop new biodegradable and cost-effective biocides for large-scale field applications. Using the corrosive Desulfovibrio vulgaris (an SRB) biofilm as a model biofilm, this work demonstrated that a cocktail of glyceryl trinitrate (GTN) and caprylic acid (CA) was very effective for biofilm prevention and mitigation of established biofilms on C1018 carbon steel coupons. The most probable number sessile cell count data and confocal laser scanning microscope biofilm images proved that the biocide cocktail of 25 ppm (w/w) GTN + 0.1% (w/w) CA successfully prevented the D. vulgaris biofilm establishment on C1018 carbon steel coupons while 100 ppm GTN + 0.1% CA effectively mitigated pre-established D. vulgaris biofilms on C1018 carbon steel coupons. In both cases, the cocktails were able to reduce the sessile cell count from 10(6) cells/cm(2) to an undetectable level.

  14. Crystallization and preliminary structure determination of the membrane-bound complex cytochrome c nitrite reductase from Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Rodrigues, M. L.; Oliveira, T.; Matias, P. M.; Martins, I. C.; Valente, F. M. A.; Pereira, I. A. C.; Archer, M.

    2006-06-01

    The cytochrome c nitrite reductase complex from D. vulgaris Hildenborough has been crystallized. The preliminary crystallographic structure reveals a 2:1 NrfA:NrfH complex stoichiometry. The cytochrome c nitrite reductase (cNiR) isolated from Desulfovibrio vulgaris Hildenborough is a membrane-bound complex formed of NrfA and NrfH subunits. The catalytic subunit NrfA is a soluble pentahaem cytochrome c that forms a physiological dimer of about 120 kDa. The electron-donor subunit NrfH is a membrane-anchored tetrahaem cytochrome c of about 18 kDa molecular weight and belongs to the NapC/NirT family of quinol dehydrogenases, for which no structures are known. Crystals of the native cNiR membrane complex, solubilized with dodecylmaltoside detergent (DDM), were obtained using PEG 4K as precipitant. Anomalous diffraction data were measured at the Swiss Light Source to 2.3 Å resolution. Crystals belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 79.5, b = 256.7, c = 578.2 Å. Molecular-replacement and MAD methods were combined to solve the structure. The data presented reveal that D. vulgaris cNiR contains one NrfH subunit per NrfA dimer.

  15. Quantification of Desulfovibrio vulgaris dissimilatory sulfite reductase gene expression during electron donor- and electron acceptor-limited growth.

    PubMed

    Villanueva, Laura; Haveman, Shelley A; Summers, Zara M; Lovley, Derek R

    2008-09-01

    Previous studies have suggested that levels of transcripts for dsrA, a gene encoding a subunit of the dissimilatory sulfite reductase, are not directly related to the rates of sulfate reduction in sediments under all conditions. This phenomenon was further investigated with chemostat-grown Desulfovibrio vulgaris. Under sulfate-limiting conditions, dsrA transcript levels increased as the bulk rates of sulfate reduction in the chemostat increased, but transcript levels were similar at all sulfate reduction rates under electron donor-limiting conditions. When both electron donor- and electron acceptor-limiting conditions were considered, there was a direct correspondence between dsrA transcript levels and the rates of sulfate reduction per cell. These results suggest that dsrA transcript levels may provide important information on the metabolic state of sulfate reducers.

  16. 1H, 13C and 15N chemical shift assignments of the thioredoxin from the obligate anaerobe Desulfovibrio vulgaris Hildenborough.

    PubMed

    Garcin, Edwige B; Bornet, Olivier; Pieulle, Laetitia; Guerlesquin, Françoise; Sebban-Kreuzer, Corinne

    2011-10-01

    Thioredoxins are ubiquitous key antioxidant enzymes which play an essential role in cell defense against oxidative stress. They maintain the redox homeostasis owing to the regulation of thiol-disulfide exchange. In the present paper, we report the full resonance assignments of (1)H, (13)C and (15)N atoms for the reduced and oxidized forms of Desulfovibrio vulgaris Hildenborough thioredoxin 1 (Trx1). 2D and 3D heteronuclear NMR experiments were performed using uniformly (15)N-, (13)C-labelled Trx1. Chemical shifts of 97% of the backbone and 90% of the side chain atoms were obtained for the oxidized and reduced form (BMRB deposits with accession number 17299 and 17300, respectively).

  17. Genome Sequence of the Piezophilic, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio indicus J2T

    PubMed Central

    Maignien, Lois; Shao, Zongze; Alain, Karine

    2016-01-01

    The complete genome sequence of Desulfovibrio indicus J2T, a member of the family Desulfovibrionaceae, consists of 3,966,573-bp in one contig and encodes 3,461 predicted genes, 5 noncoding RNAs, 3 rRNAs operons, and 52 tRNA-encoding genes. The genome is consistent with a heterotrophic, anaerobic lifestyle including the sulfate reduction pathway. PMID:27056223

  18. Electron microscopic characterization of the sulfate reducer Desulfovibrio vulgaris: biofilms and clumps

    NASA Astrophysics Data System (ADS)

    Auer, M.; Remis, J.; Jorgens, D.; Zemla, M.; Singer, M.; Schmitt, J.; Gorby, Y.; Hazen, T.; Wall, J.; Elias, D.; Torok, T.

    2008-12-01

    Numerous studies have helped characterize the stress response of the anaerobic sulfate reducer Desulfovibrio vulgaris Hildenborough (DvH). Yet all of these techniques represent bulk analyses of cells grown mostly under liquid culture conditions in large reactors. Such results represent an average over a large variety of individual cellular responses, hence assuming a homogeneous distribution of physiological traits. Moreover, only recently are those techniques applied to the environmentally more relevant condition of microbial communities (biofilms). What is missing is a detailed ultrastructural analysis of such biofilms in order to determine biofilm organization and its extracellular metal deposition distribution. Using sophisticated sample cryo-preparation approaches such as high-pressure freezing, freeze-substitution or microwave- assisted processing, followed serial section TEM imaging, we have found a large heterogeneity with respect to metal precipitation with some cells being surrounded by metal precipitates whereas neighboring cells, being genetically identical and seeing virtually the exact same microenvironment, completely lack extracellular metal deposits. Interestingly, apart from metal deposits near cell surfaces, we also found string- and sheet- like metal deposits in between neighboring cells that in mature biofilms can extend for hundreds of micrometers. In mature DvH biofilms such deposits were predominantly associated with areas of intact cells in biofilms, with areas devoid of such metal deposits displayed predominantly cell debris, suggesting a role of such deposits for cell survival, which may be of high significance to biofilms at DOE sites. Upon tomographic imaging we found that extracellular metal deposits were often associated with thin filaments and vesicle-like features. To complement our serial section 2D analysis of resin-embedded samples and the resulting limitation of sampling 3D biofilm as thin sections of arbitrary orientation, we

  19. Effects of Sulfate and Sulfide on Dehalococcoides Strain 195 and Desulfovibrio vulgaris Hildenborough Ability to Biodegrade Trichloroethene

    NASA Astrophysics Data System (ADS)

    Polasko, A. L.; Mao, X.; Alvarez-Cohen, L.

    2014-12-01

    Trichloroethene (TCE) is a prevalent groundwater contaminant across the USA. Dehalococcoides is the only known bacterium that can reductively dechlorinate TCE to the benign end product ethene. Sulfate is also a common ubiquitous compound in groundwater. Little research has been conducted on the toxicity of sulfate or sulfide on Dehalococcoides and its effect on dechlorination. This study evaluated the inhibitory effects of high sulfate/sulfide concentrations on pure cultures Dehalococcoides mccartyi 195 (strain 195), sulfate reducer Desulfovibrio vulgaris Hildenborough (DVH) and the syntrophic co-culture of strain 195 with DVH. Strain 195 was maintained in defined medium with H2 as electron donor, acetate as carbon source, and 78 μmol TCE as the electron acceptor. 2.5 mM sulfate showed no inhibitory effect on strain 195 dechlorination rates (5.3 μmol d-1); whereas, 2mM sulfide completely inhibited ethene production and only 14 μmol of cis-DCE was produced. DVH was maintained using lactate as the energy and carbon source and sulfate as the electron acceptor. High sulfate concentrations (30 mM) did not show an inhibitory effect on DVH growth and 90% of the amended sulfate was reduced within 24 hours. The cell yield of DVH was 1.3±0.1x108 mL-1, which was comparable to the control (1.5±0.2x108 mL-1). Similarly, 5mM sulfide did not show an inhibitory effect on the cell growth of DVH (1.8±0.3x108 mL-1). In the syntrophic co-culture containing strain 195 and DVH, DVH fermented lactate to H2 and acetate, and strain 195 used H2 as the electron donor for dechlorination. When 1 mM sulfate was amended to the consortia, the TCE dechlorination rate (13 μmol d-1) was similar to the control (no sulfate addition); whereas, the cell number of DVH increased from 8.7±0.4x107 (control) to 2.6±0.7x108 (1 mM sulfate). TCE dechlorination was completely inhibited when 5mM sulfate was amended, and only 10% of the total TCE added was dechlorinated to cis-DCE (8μmol). Accordingly

  20. A Proteomic View of Desulfovibrio Vulgaris Metabolim as Determined by Liquid Chromatography Coupled with Tandem Mass Spectrometry

    SciTech Connect

    Zhang, Weiwen; Gritsenko, Marina A.; Moore, Ronald J.; Culley, David E.; Nie, Lei; Petritis, Konstantinos; Strittmatter, Eric F.; Camp, David G.; Smith, Richard D.; Brockman, Fred J.

    2006-08-15

    Direct liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to examine the proteins from Desulfovibrio vulgaris grown at exponential or stationary phase on a minimal medium containing either lactate or formate as the primary carbon source, with the goal of an initial characterization of the diversity of proteins synthesized under these conditions. Across all four growth conditions, 976 gene products were identified with high confidence, which is equal to approximately 28% of all predicted proteins in the D. vulgaris genome. Among these, fifty-two out of 55 predicted ribosomal proteins (~95%) were identified with high confidence. Functional analysis showed that the proteins identified were distributed among almost all functional classes, with the energy metabolism category containing the greatest number of identified proteins. At least 154 open reading frames (ORFs) originally annotated as hypothetical proteins were found to encode expressed proteins, which provided verification for the authenticity of these hypothetical proteins. Proteomic analysis showed that members of the proton gradient pathway, catalyzed by alcohol dehydrogenases and heterodisulfide reductases, and [NiFe] hydrogenase (HynAB-1) of the hydrogen cycling pathway were highly expressed in all four growth conditions, suggesting they may be the primary pathways for ATP synthesis in D. vulgaris. Most of the enzymes involved in substrate-level phosphorylation were also detected in all tested conditions. However, no enzyme involved in CO cycling or formate cycling was detected, suggesting these are not the primary pathways for ATP biosynthesis under the tested conditions. This study provides the first proteomic overview of the cellular metabolism of D. vulgaris.

  1. Fractionation of sulfur isotopes by Desulfovibrio vulgaris mutants lacking hydrogenases or type I tetraheme cytochrome c 3.

    PubMed

    Sim, Min Sub; Wang, David T; Zane, Grant M; Wall, Judy D; Bosak, Tanja; Ono, Shuhei

    2013-01-01

    The sulfur isotope effect produced by sulfate reducing microbes is commonly used to trace biogeochemical cycles of sulfur and carbon in aquatic and sedimentary environments. To test the contribution of intracellular coupling between carbon and sulfur metabolisms to the overall magnitude of the sulfur isotope effect, this study compared sulfur isotope fractionations by mutants of Desulfovibrio vulgaris Hildenborough. We tested mutant strains lacking one or two periplasmic (Hyd, Hyn-1, Hyn-2, and Hys) or cytoplasmic hydrogenases (Ech and CooL), and a mutant lacking type I tetraheme cytochrome (TpI-c 3). In batch culture, wild-type D. vulgaris and its hydrogenase mutants had comparable growth kinetics and produced the same sulfur isotope effects. This is consistent with the reported redundancy of hydrogenases in D. vulgaris. However, the TpI-c 3 mutant (ΔcycA) exhibited slower growth and sulfate reduction rates in batch culture, and produced more H2 and an approximately 50% larger sulfur isotope effect, compared to the wild type. The magnitude of sulfur isotope fractionation in the CycA deletion strain, thus, increased due to the disrupted coupling of the carbon oxidation and sulfate reduction pathways. In continuous culture, wild-type D. vulgaris and the CycA mutant produced similar sulfur isotope effects, underscoring the influence of environmental conditions on the relative contribution of hydrogen cycling to the electron transport. The large sulfur isotope effects associated with the non-ideal stoichiometry of sulfate reduction in this study imply that simultaneous fermentation and sulfate reduction may be responsible for some of the large naturally-occurring sulfur isotope effects. Overall, mutant strains provide a powerful tool to test the effect of specific redox proteins and pathways on sulfur isotope fractionation.

  2. Overcoming the anaerobic hurdle in phenotypic microarrays: generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough.

    PubMed

    Borglin, Sharon; Joyner, Dominique; Jacobsen, Janet; Mukhopadhyay, Aindrila; Hazen, Terry C

    2009-02-01

    Growing anaerobic microorganisms in phenotypic microarrays (PM) and 96-well microtiter plates is an emerging technology that allows high throughput survey of the growth and physiology and/or phenotype of cultivable microorganisms. For non-model bacteria, a method for phenotypic analysis is invaluable, not only to serve as a starting point for further evaluation, but also to provide a broad understanding of the physiology of an uncharacterized wild-type organism or the physiology/phenotype of a newly created mutant of that organism. Given recent advances in genetic characterization and targeted mutations to elucidate genetic networks and metabolic pathways, high-throughput methods for determining phenotypic differences are essential. Here we outline challenges presented in studying the physiology and phenotype of a sulfate-reducing anaerobic delta proteobacterium, Desulfovibrio vulgaris Hildenborough. Modifications of the commercially available OmniLog system (Hayward, CA) for experimental setup, and configuration, as well as considerations in PM data analysis are presented. Also highlighted here is data viewing software that enables users to view and compare multiple PM data sets. The PM method promises to be a valuable strategy in our systems biology approach to D. vulgaris studies and is readily applicable to other anaerobic and aerobic bacteria.

  3. Purification, crystallization and preliminary X-ray analysis of the dissimilatory sulfite reductase from Desulfovibrio vulgaris Miyazaki F.

    PubMed

    Ogata, Hideaki; Shomura, Yasuhito; Goenka Agrawal, Aruna; Kaur, Amrit Pal; Gärtner, Wolfgang; Higuchi, Yoshiki; Lubitz, Wolfgang

    2010-11-01

    Dissimilatory sulfite reductase (Dsr) plays an important role in sulfate respiration in many sulfate-reducing bacteria. Dsr from Desulfovibrio vulgaris Miyazaki F has been purified and crystallized at 277 K using the sitting-drop vapour-diffusion method with PEG 3350 and potassium thiocyanate as precipitants. A data set was collected to 3.7 Å resolution from a single crystal at 100 K using synchrotron radiation. The Dsr crystal belonged to space group P4(1)2(1)2, with unit-cell parameters a = b = 163.26, c = 435.32 Å. The crystal structure of Dsr was determined by the molecular-replacement method based on the three-dimensional structure of Dsr from D. vulgaris Hildenborough. The crystal contained three α(2)β(2)γ(2) units per asymmetric unit, with a Matthews coefficient (V(M)) of 2.35 Å(3) Da(-1); the solvent content was estimated to be 47.7%.

  4. Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough.

    PubMed

    Chhabra, Swapnil R; Joachimiak, Marcin P; Petzold, Christopher J; Zane, Grant M; Price, Morgan N; Reveco, Sonia A; Fok, Veronica; Johanson, Alyssa R; Batth, Tanveer S; Singer, Mary; Chandonia, John-Marc; Joyner, Dominique; Hazen, Terry C; Arkin, Adam P; Wall, Judy D; Singh, Anup K; Keasling, Jay D

    2011-01-01

    Protein-protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study Escherichia coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio vulgaris Hildenborough, a model obligate anaerobe and sulfate reducer and the subject of this study. Here we carried out affinity purification followed by mass spectrometry to reconstruct an interaction network among 12 chromosomally encoded bait and 90 prey proteins based on 134 bait-prey interactions identified to be of high confidence. Protein-protein interaction data are often plagued by the lack of adequate controls and replication analyses necessary to assess confidence in the results, including identification of potential false positives. We addressed these issues through the use of biological replication, exponentially modified protein abundance indices, results from an experimental negative control, and a statistical test to assign confidence to each putative interacting pair applicable to small interaction data studies. We discuss the biological significance of metabolic features of D. vulgaris revealed by these protein-protein interaction data and the observed protein modifications. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.

  5. Overcoming the anaerobic hurdle in phenotypic microarrays: Generation andvisualization of growth curve data for Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Borglin, Sharon E; Joyner, Dominique; Jacobsen, Janet; Mukhopadhyay, Aindrila; Hazen, Terry C.

    2008-10-04

    Growing anaerobic microorganisms in phenotypic microarrays (PM) and 96-well microtiter plates is an emerging technology that allows high throughput survey of the growth and physiology and/or phenotype of cultivable microorganisms. For non-model bacteria, a method for phenotypic analysis is invaluable, not only to serve as a starting point for further evaluation, but also to provide a broad understanding of the physiology of an uncharacterized wild-type organism or the physiology/phenotype of a newly created mutant of that organism. Given recent advances in genetic characterization and targeted mutations to elucidate genetic networks and metabolic pathways, high-throughput methods for determining phenotypic differences are essential. Here we outline challenges presented in studying the physiology and phenotype of a sulfate reducing anaerobic delta proteobacterium, Desulfovibrio vulgaris Hildenborough. Modifications of the commercially available OmniLog(TM) system (Hayward, CA) for experimental setup, and configuration, as well as considerations in PM data analysis are presented. Also highlighted here is data viewing software that enables users to view and compare multiple PM data sets. The PM method promises to be a valuable strategy in our systems biology approach to D. vulgaris studies and is readily applicable to other anaerobic and aerobic bacteria.

  6. Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough

    PubMed Central

    Petzold, Christopher J.; Zane, Grant M.; Price, Morgan N.; Reveco, Sonia A.; Fok, Veronica; Johanson, Alyssa R.; Batth, Tanveer S.; Singer, Mary; Chandonia, John-Marc; Joyner, Dominique; Hazen, Terry C.; Arkin, Adam P.; Wall, Judy D.; Singh, Anup K.; Keasling, Jay D.

    2011-01-01

    Protein–protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study Escherichia coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio vulgaris Hildenborough, a model obligate anaerobe and sulfate reducer and the subject of this study. Here we carried out affinity purification followed by mass spectrometry to reconstruct an interaction network among 12 chromosomally encoded bait and 90 prey proteins based on 134 bait-prey interactions identified to be of high confidence. Protein-protein interaction data are often plagued by the lack of adequate controls and replication analyses necessary to assess confidence in the results, including identification of potential false positives. We addressed these issues through the use of biological replication, exponentially modified protein abundance indices, results from an experimental negative control, and a statistical test to assign confidence to each putative interacting pair applicable to small interaction data studies. We discuss the biological significance of metabolic features of D. vulgaris revealed by these protein-protein interaction data and the observed protein modifications. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction. PMID:21738675

  7. Improving interpretation of geoelectrical signatures arising from biomineralization process in porous media: Low-frequency dielectric spectroscopy measurements on Desulfovibrio vulgaris cell suspensions

    NASA Astrophysics Data System (ADS)

    Zhang, C.; Prodan, C.; Slater, L. D.; Bot, C.; Ntarlagiannis, D.

    2009-12-01

    Previous geophysical studies have demonstrated the sensitivity of complex conductivity measurements to microbial growth, biofilm formation, and microbial-mineral alternations, indicating that complex conductivity has the potential to serve as non-invasive tool for bioremediation monitoring. However, the inherent dielectric properties of microbes and how they might directly contribute to the geophysical responses observed during microbial-mineral transformations are not well understood. As a first step towards improving the understanding of electrical signals from microbial-mineral transformations in porous media, we studied the low frequency dielectric properties of sulfate-reducing bacteria (Desulfovibrio vulgaris) cell suspensions, a common soil borne microorganism involved in remediation of toxic metals in solution. We utilized a two-electrode dielectric spectroscopy measurement, common in biophysics applications,to acquire high quality dielectric dispersion curves of Desulfovibrio vulgaris cell suspensions over the frequency range 0.1 Hz to 1M Hz. Desulfovibrio vulgaris cell suspensions were placed between two parallel steel electrodes that are enclosed in a cylindrical glass tube, and the complex impedance of sample was measured relative to a known resistor. The measured impedance includes an electrode polarization impedance arising at the interface between electrodes and ionic solutions at low frequencies. This electrode impedance has traditionally precluded the reliable interpretation of two electrode techniques at low frequencies (< 1000 Hz). In order to obtain the true dielectric dispersion curve of sample, we adopt a simple and robust strategy to measure, analyze and remove the polarization impedance. The feasibility of this polarization removal technique was tested on water saturated glass beads. We show that the broadband dielectric response of Desulfovibrio vulgaris can be reliably determined with this approach. The measurements are modeled based on a

  8. Cloning, sequencing, and expression of the gene encoding the high-molecular-weight cytochrome c from Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Pollock, W.B.R.; Voordouw, G. ); Loutfi, M.; Bruschi, M. ); Rapp-Giles, B.J.; Wall, J.D. )

    1991-01-01

    By using a synthetic deoxyoligonucleotide probe designed to recognize the structural gene for cytochrome cc{sub 3} from Desulfovibrio vulgaris Hildenborough, a 3.7-kb XhoI genomic DNA fragment containing the cc{sub 3} gene was isolated. The gene encodes a precursor polypeptide of 58.9 kDa, with an NH{sub 2}-terminal signal sequence of 31 residues. The mature polypeptide (55.7 kDa) has 16 heme binding sites of the form C-X-X-C-H. Covalent binding of heme to these 16 sites gives a holoprotein of 65.5 kDa with properties similar to those of the high-molecular-weight cytochrome c (Hmc) isolated from the same strain by Higuchi et al. Since the data indicate that cytochrome cc{sub 3} and Hmc are the same protein, the gene has been named hmc. The Hmc polypeptide contains 31 histidinyl residues, 16 of which are integral to heme binding sites. Thus, only 15 of the 16 hemes can have bis-histidinyl coordination. A comparison of the arrangement of heme binding sites and coordinated histidines in the amino acid sequences of cytochrome c{sub 3} and Hme from D. vulgaris Hildenborough suggest that the latter contains three cytochrome c{sub 3}-like domains. Cloning of the D. vulgaris Hildenborough hmc gene into the broad-host-range vector pJRD215 and subsequent conjugational transfer of the recombinant plasmid into D. desulfuricans G200 led to expression of a periplasmic Hmc gene produce with covalently bound hemes.

  9. Multiple Roles of Desulfovibrio vulgaris to U (VI) Reduction and Long-term Stability of Uraninte (UO2)

    NASA Astrophysics Data System (ADS)

    Vannela, R.; Zhou, C.; Rittmann, B. E.

    2012-04-01

    Our current research is focused on assessing the Desulfovibrio vulgaris strain and its versatility in uranium (U) bioremediation. D.vulgaris reduces U(VI) to U(IV), which can be immobilized by precipitation to uraninite (UO2) solids. We first studied the complementary mechanisms of direct enzymatic and indirect chemical reduction of U (VI) with the help of series of batch experiments. We observed 90% removal of U (VI) by enzymatic activity within 10 hours and formation of biogenic UO2 solids. These experiments also revealed that D. vulgaris reduced U(VI) fastest under sulfate-reducing conditions in absence of aqueous Fe(II). When, Fe (II) is present, the rate of uraninite formation was significantly reduced; suggesting the retardation by aqueous Fe2+. However, X-ray diffractometry (XRD) data indicated that biogenic uraninite was far more crystallized in presence of Fe2+. This data showed that the presence of aqueous iron (II) could enhance crystallization of uraninite. These results clearly confirm the chemical reduction of U(VI) by biogenic H2S as well as direct enzymatic U(VI) reduction by D.vulgaris strain. We are also investigating the other important role of biogenic iron sulfide (FeS) solids generated by D.vulgaris to long-term U (VI) bioremediation. Iron sulfide precipitates protect UO2 against oxidative dissolution of U by serving as an effective oxidant scavenger. In this regard, we first systematically studied effects of varying experimental conditions that represent real-life scenarios. In several batch experiments, we demonstrated that, over ranges of pH (6.5 to 8.6) and concentration ratios of lactate-to-sulfate (0.5:1 to 1.9:1) and iron-to-sulfate (0.11:1 to 1:1), D. vulgaris primarily produced mackinawite form of FeS when either soluble Fe2+ or Fe3+ was used as the iron source. We observed that poorly crystalline mackinawite ((Fe1+xS) - which is a more desired type of FeS, was found when low lactate-to-sulfate ratio (0.5:1), low iron-to-sulfate ratio

  10. Contribution of rubredoxin:oxygen oxidoreductases and hybrid cluster proteins of Desulfovibrio vulgaris Hildenborough to survival under oxygen and nitrite stress.

    PubMed

    Yurkiw, Marcy A; Voordouw, Johanna; Voordouw, Gerrit

    2012-10-01

    A genomic island (GEI) of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, found to be able to migrate between two tRNA-Met loci of the genome, contains genes for rubredoxin:oxygen oxidoreductase-1 (roo1) and hybrid cluster protein-1 (hcp1) with additional copies for these genes (roo2 and hcp2) being found elsewhere on the chromosome. A suite of mutants was created in which roo2 and/or hcp2 and/or the GEI were either present or missing. The GEI and roo2 increased survival under microaerobic conditions and allowed growth in closer proximity to the air-water interface of soft agar tubes, two properties which appeared to be closely linked. When Hcp2(+) GEI(+) or Hcp2(-) GEI(+) cells, harbouring cytochrome c nitrite reductase (NrfHA) and growing on lactate and sulfate, were amended with 10 mM nitrite at mid-log phase (8-10 mM sulfide), all nitrite was reduced within 30 h with a rate of 3.0 mmol (g biomass)(-1)  h(-1) after which sulfate reduction resumed. However, Hcp2(+) GEI(-) or Hcp2(-) GEI(-) cells were unable to use lactate, causing sulfide to be used as electron donor for nitrite reduction at a sixfold lower rate. Complementation studies indicated that hcp1, not roo1, enhanced the rate of nitrite reduction under these conditions. Hcp2 enhanced the rate of nitrite reduction when, in addition to lactate, hydrogen was also present as an electron donor. These results indicate a critical role of Hcps in alleviating nitrite stress in D. vulgaris Hildenborough by maintaining the integrity of electron transport chains from lactate or H(2) to NrfHA through removal of reactive nitrogen species. It thus appears that the GEI contributes considerably to the fitness of the organism, allowing improved growth in microaerobic environments found in sulfide-oxygen gradients and in environments, containing both sulfide and nitrite, through the action of Roo1 and Hcp1 respectively.

  11. LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris

    SciTech Connect

    Zhang, Weiwen; Culley, David E.; Gritsenko, Marina A.; Moore, Ronald J.; Nie, Lei; Scholten, Johannes C.; Petritis, Konstantinos; Strittmatter, Eric F.; Camp, David G.; Smith, Richard D.; Brockman, Fred J.

    2006-11-03

    ABSTRACT In the previous study, the whole-genome gene expression profiles of D. vulgaris in response to oxidative stress and heat shock were determined. The results showed 24-28% of the responsive genes were hypothetical proteins that have not been experimentally characterized or whose function can not be deduced by simple sequence comparison. To further explore the protecting mechanisms employed in D. vulgaris against the oxidative stress and heat shock, attempt was made in this study to infer functions of these hypothetical proteins by phylogenomic profiling along with detailed sequence comparison against various publicly available databases. By this approach we were ableto assign possible functions to 25 responsive hypothetical proteins. The findings included that DVU0725, induced by oxidative stress, may be involved in lipopolysaccharide biosynthesis, implying that the alternation of lipopolysaccharide on cell surface might service as a mechanism against oxidative stress in D. vulgaris. In addition, two responsive proteins, DVU0024 encoding a putative transcriptional regulator and DVU1670 encoding predicted redox protein, were sharing co-evolution atterns with rubrerythrin in Archaeoglobus fulgidus and Clostridium perfringens, respectively, implying that they might be part of the stress response and protective systems in D. vulgaris. The study demonstrated that phylogenomic profiling is a useful tool in interpretation of experimental genomics data, and also provided further insight on cellular response to oxidative stress and heat shock in D. vulgaris.

  12. [Effect of permeabilization on sulfate reduction activity of Desulfovibrio vulgaris Hildenborough cells in the presence of different electron donors].

    PubMed

    Xu, Hui-Wei; Zhang, Xu; Li, Li-Ming; Zheng, Guang-Jie; Li, Guang-He

    2013-01-01

    The Desulfovibrio vulgaris Hildenborough (DvH) cells permeabilized with ethanol were used as biocatalysts to enhance hydrogenotrophic sulfate conversion. The effect of permeabilization extent of DvH cells on sulfate reduction was studied in the presence of different electron donors. When hydrogen was used as an electron donor, the highest level of sulfate reduction activity attained in cells treated with 10% ethanol (V/V), followed by 15% -ethanol treated cells. Furthermore, sulfate reduction activity markedly decreased when the ethanol concentration exceeded 15%. However, when lactate was used as the electron donor, the optimum ethanol concentration of the permeabilizing reagent was 20%, followed by 15% and 10%. Even when ethanol concentration reached 25%, DvH cells remained their partial activity with lactate. In a word, sulfate reduction activity of DvH cells responded differently in the presence of different donors. This was because the oxidation process of H2 and lactate occurred at different positions in DvH cells, and consequently intracellular electron transport pathway differed. To ensure the integrity of the electron transport chain between the donor and the accepter was a key factor for determining the permeabilization extent and for the application of cell permeabilization technology.

  13. Photosensitivity of the Ni-A state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F with visible light.

    PubMed

    Osuka, Hisao; Shomura, Yasuhito; Komori, Hirofumi; Shibata, Naoki; Nagao, Satoshi; Higuchi, Yoshiki; Hirota, Shun

    2013-01-04

    [NiFe] hydrogenase catalyzes reversible oxidation of molecular hydrogen. Its active site is constructed of a hetero dinuclear Ni-Fe complex, and the oxidation state of the Ni ion changes according to the redox state of the enzyme. We found that the Ni-A state (an inactive unready, oxidized state) of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F (DvMF) is light sensitive and forms a new state (Ni-AL) with irradiation of visible light. The Fourier transform infrared (FT-IR) bands at 1956, 2084 and 2094 cm(-1) of the Ni-A state shifted to 1971, 2086 and 2098 cm(-1) in the Ni-AL state. The g-values of g(x)=2.30, g(y)=2.23 and g(z)=2.01 for the signals in the electron paramagnetic resonance (EPR) spectrum of the Ni-A state at room temperature varied for -0.009, +0.012 and +0.010, respectively, upon light irradiation. The light-induced Ni-AL state converted back immediately to the Ni-A state under dark condition at room temperature. These results show that the coordination structure of the Fe site of the Ni-A state of [NiFe] hydrogenase is perturbed significantly by light irradiation with relatively small coordination change at the Ni site.

  14. Construction of Whole Genome Microarrays, and Expression Analysis of Desulfovibrio vulgaris cells in Metal-Reducing Conditions (Uranium and Chromium)

    SciTech Connect

    Fields, Matthew W.

    2005-06-01

    One of the major goals of the project is to construct whole-genome microarrays for Desulfovibrio vulgaris. Previous whole-genome microarrays constructed at ORNL have been PCR-amplimer based, and we wanted to re-evaluate the type of microarrays being built because oligonucleotide probes have several advantages. Microarrays have been generally constructed with two types of probes, PCR-generated probes that typically range in size between 200 and 2000 bp, and oligonucleotide probes with typical size of 20-70 nt. Producing PCR product-based DNA arrays can be a time-consuming procedure that includes PCR primer design, amplification, size verification, product purification, and product quantification. Also, some ORFs are difficult to amplify and thus the construction of comprehensive arrays can be a challenge. Recently, to alleviate some of the problems associated with PCR product-based microarrays, oligonucleotide microarrays that contain probes longer than 40 nt have been evaluated and used for whole genome expression studies. These microarrays should have higher specificity and are easy to construct, and can thus provide an important alternative approach to monitor gene expression. However, due to the smaller probe size, it is expected that the detection sensitivity of oligonucleotide arrays will be lower than PCR product-based probes.

  15. Secondary structures and functional requirements for thiM riboswitches from Desulfovibrio vulgaris, Erwinia carotovora and Rhodobacter spheroides.

    PubMed

    Rentmeister, Andrea; Mayer, Günter; Kuhn, Nicole; Famulok, Michael

    2008-02-01

    Abstract Bacterial thiM riboswitches contain aptamer domains that bind the metabolite thiamine pyrophosphate (TPP). Binding of TPP to the aptamer domain induces structural rearrangements that are relayed to the expression domain, thereby interfering with gene expression. Here, we report identification of three putative thiM riboswitches from different bacteria and analysis of their secondary structures. Chemical probing revealed that the riboswitches share similar secondary structures in their aptamer domains that can communicate with the highly variant expression domains in a mechanism likely involving sequestration of the Shine-Dalgarno sequence. Remarkably, the aptamer domain of the thiM gene of Desulfovibrio vulgaris binds TPP with similar affinity and selectivity as that of Escherichia coli, although nucleotides previously shown to form direct contacts to the metabolite are mutated. We also designed small RNA hairpins for each riboswitch that bind the RNA only in the absence of the metabolite. Our study shows that aptamer domains in riboswitches with high similarity in their secondary structures can communicate with a broad variety of non-related expression domains by similar mechanisms.

  16. Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR.

    PubMed Central

    Karkhoff-Schweizer, R R; Huber, D P; Voordouw, G

    1995-01-01

    The structural genes for dissimilatory sulfite reductase (desulfoviridin) from Desulfovibrio vulgaris Hilden-borough were cloned as a 7.2-kbp SacII DNA fragment. Nucleotide sequencing indicated the presence of a third gene, encoding a protein of only 78 amino acids, immediately downstream from the genes for the alpha and beta subunits (dsvA and dsvB). We designated this protein DsvD and the gene encoding it the dsvD gene. The alpha- and beta-subunit sequences are highly homologous to those of the dissimilatory sulfite reductase from Archaeoglobus fulgidus, a thermophilic archaeal sulfate reducer, which grows optimally at 83 degrees C. A gene with significant homology to dsvD was also found immediately downstream from the dsrAB genes of A. fulgidus. The remarkable conservation of gene arrangement and sequence across domain (bacterial versus archaeal) and physical (mesophilic versus thermophilic) boundaries indicates an essential role for DsvD in dissimilatory sulfite reduction and allowed the construction of conserved deoxyoligonucleotide primers for detection of the dissimilatory sulfite reductase genes in the environment. PMID:7887608

  17. Can direct extracellular electron transfer occur in the absence of outer membrane cytochromes in Desulfovibrio vulgaris?

    SciTech Connect

    Elias, Dwayne A; Zane, Mr. Grant M.; Auer, Dr. Manfred; Fields, Dr. Matthew Wayne; Wall, Judy D.; Gorby, Dr. Yuri A.

    2010-01-01

    Extracellular electron transfer has been investigated over several decades via forms of soluble electron transfer proteins that are exported for extracellular reoxidation. More recently, several organisms have been shown to reduce extracellular metals via the direct transfer of electron through appendages; also known as nanowires. They have been reported most predominantly in Shewanella and Geobacter. While the relevancy and composition of these structures in each genus has been debated, both possess outer membrane cytochrome complexes that could theoretically come into direct contact with solid phase oxidized metals. Members of the genus Desulfovibrio apparently have no such cytochromes although similar appendages are present, are electrically conductive, and are different from flagella. Upon U(VI)-reduction, the structures in Desulfovibrio become coated with U(IV). Deletion of flagellar genes did not alter soluble or amorphous Fe(III) or U(VI) reduction, or appendage appearance. Removal of the chromosomal pilA gene hampered amorphous Fe(III)-reduction by ca. 25%, but cells lacking the native plasmid, pDV1, reduced soluble Fe(III) and U(VI) at ca. 50% of the wild type rate while amorphous Fe(III)-reduction slowed to ca. 20% of the wild type rate. Appendages were present in all deletions as well as pDV1, except pilA. Gene complementation restored all activities and morphologies to wild type levels. This suggests that pilA encodes the structural component, whereas genes within pDV1 may provide the reactive members. How such appendages function without outer membrane cytochromes is under investigation.

  18. Spectroscopic characterization of the [Fe(His)(4)(Cys)] site in 2Fe-superoxide reductase from Desulfovibrio vulgaris.

    PubMed

    Clay, Michael D; Emerson, Joseph P; Coulter, Eric D; Kurtz, Donald M; Johnson, Michael K

    2003-07-01

    The electronic and vibrational properties of the [Fe(His)(4)(Cys)] site (Center II) responsible for catalysis of superoxide reduction in the two-iron superoxide reductase (2Fe-SOR) from Desulfovibrio vulgaris have been investigated using the combination of EPR, resonance Raman, UV/visible/near-IR absorption, CD, and VTMCD spectroscopies. Deconvolution of the spectral contributions of Center II from those of the [Fe(Cys)(4)] site (Center I) has been achieved by parallel investigations of the C13S variant, which does not contain Center I. The resonance Raman spectrum of ferric Center II has been assigned based on isotope shifts for (34)S and (15)N globally labeled proteins. As for the [Fe(His)(4)(Cys)] active site in 1Fe-SOR from Pyrococcus furiosus, the spectroscopic properties of ferric and ferrous Center II in D. vulgaris 2Fe-SOR are indicative of distorted octahedral and square-pyramidal coordination geometries, respectively. Differences in the properties of the ferric [Fe(His)(4)(Cys)] sites in 1Fe- and 2Fe-SORs are apparent in the rhombicity of the S=5/2 ground state ( E/ D=0.06 and 0.28 in 1Fe- and 2Fe-SORs, respectively), the energy of the CysS(-)(p(pi))-->Fe(3+)(d(pi)) CT transition (15150+/-150 cm(-1) and 15600+/-150 cm(-1) in 1Fe- and 2Fe-SORs, respectively) and in changes in the Fe-S stretching region of the resonance Raman spectrum indicative of a weaker Fe-S(Cys) bond in 2Fe-SORs. These differences are interpreted in terms of small structural perturbations in the Fe coordination sphere with changes in the Fe-S(Cys) bond strength resulting from differences in the peptide N-H.S(Cys) hydrogen bonding within a tetrapeptide bidentate "chelate". Observation of the characteristic intervalence charge transfer transition of a cyano-bridged [Fe(III)-NC-Fe(II)(CN)(5)] unit in the near-IR VTMCD spectra of ferricyanide-oxidized samples of both P. furiosus 1Fe-SOR and D. vulgaris 2Fe-SOR has confirmed the existence of novel ferrocyanide adducts of the ferric [Fe

  19. The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20

    SciTech Connect

    Price, Morgan N.; Ray, Jayashree; Wetmore, Kelly M.; Kuehl, Jennifer V.; Bauer, Stefan; Deutschbauer, Adam M.; Arkin, Adam P.

    2014-10-31

    Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants of Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible. The uncharacterized complex Hdr/flox-1 (Dde_1207:13) is sometimes important alongside Rnf and may perform an electron bifurcation to generate more reduced ferredoxin from NADH to allow further ion pumping. Similarly, during the oxidation of malate or fumarate, the electron-bifurcating transhydrogenase NfnAB-2 (Dde_1250:1) is important and may generate reduced ferredoxin to allow additional ion pumping by Rnf. During formate oxidation, the periplasmic [NiFeSe] hydrogenase HysAB is required, which suggests that hydrogen forms in the periplasm, diffuses to the cytoplasm, and is used to reduce ferredoxin, thus providing a substrate for Rnf. We found that during hydrogen utilization, the transmembrane electron transport complex Tmc is important and may move electrons from the periplasm into the cytoplasmic sulfite reduction pathway. Finally, mutants of many other putative electron carriers have no clear phenotype, which suggests that they are not important under our growth conditions, although we cannot rule out genetic redundancy.

  20. The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20

    DOE PAGES

    Price, Morgan N.; Ray, Jayashree; Wetmore, Kelly M.; ...

    2014-10-31

    Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants of Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible. The uncharacterized complex Hdr/flox-1 (Dde_1207:13) is sometimes important alongside Rnf and may perform an electron bifurcation to generate more reduced ferredoxin from NADH to allow further ion pumping. Similarly,more » during the oxidation of malate or fumarate, the electron-bifurcating transhydrogenase NfnAB-2 (Dde_1250:1) is important and may generate reduced ferredoxin to allow additional ion pumping by Rnf. During formate oxidation, the periplasmic [NiFeSe] hydrogenase HysAB is required, which suggests that hydrogen forms in the periplasm, diffuses to the cytoplasm, and is used to reduce ferredoxin, thus providing a substrate for Rnf. We found that during hydrogen utilization, the transmembrane electron transport complex Tmc is important and may move electrons from the periplasm into the cytoplasmic sulfite reduction pathway. Finally, mutants of many other putative electron carriers have no clear phenotype, which suggests that they are not important under our growth conditions, although we cannot rule out genetic redundancy.« less

  1. The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20

    PubMed Central

    Price, Morgan N.; Ray, Jayashree; Wetmore, Kelly M.; Kuehl, Jennifer V.; Bauer, Stefan; Deutschbauer, Adam M.; Arkin, Adam P.

    2014-01-01

    Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants of Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible. The uncharacterized complex Hdr/flox-1 (Dde_1207:13) is sometimes important alongside Rnf and may perform an electron bifurcation to generate more reduced ferredoxin from NADH to allow further ion pumping. Similarly, during the oxidation of malate or fumarate, the electron-bifurcating transhydrogenase NfnAB-2 (Dde_1250:1) is important and may generate reduced ferredoxin to allow additional ion pumping by Rnf. During formate oxidation, the periplasmic [NiFeSe] hydrogenase HysAB is required, which suggests that hydrogen forms in the periplasm, diffuses to the cytoplasm, and is used to reduce ferredoxin, thus providing a substrate for Rnf. During hydrogen utilization, the transmembrane electron transport complex Tmc is important and may move electrons from the periplasm into the cytoplasmic sulfite reduction pathway. Finally, mutants of many other putative electron carriers have no clear phenotype, which suggests that they are not important under our growth conditions, although we cannot rule out genetic redundancy. PMID:25400629

  2. The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20.

    PubMed

    Price, Morgan N; Ray, Jayashree; Wetmore, Kelly M; Kuehl, Jennifer V; Bauer, Stefan; Deutschbauer, Adam M; Arkin, Adam P

    2014-01-01

    Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants of Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible. The uncharacterized complex Hdr/flox-1 (Dde_1207:13) is sometimes important alongside Rnf and may perform an electron bifurcation to generate more reduced ferredoxin from NADH to allow further ion pumping. Similarly, during the oxidation of malate or fumarate, the electron-bifurcating transhydrogenase NfnAB-2 (Dde_1250:1) is important and may generate reduced ferredoxin to allow additional ion pumping by Rnf. During formate oxidation, the periplasmic [NiFeSe] hydrogenase HysAB is required, which suggests that hydrogen forms in the periplasm, diffuses to the cytoplasm, and is used to reduce ferredoxin, thus providing a substrate for Rnf. During hydrogen utilization, the transmembrane electron transport complex Tmc is important and may move electrons from the periplasm into the cytoplasmic sulfite reduction pathway. Finally, mutants of many other putative electron carriers have no clear phenotype, which suggests that they are not important under our growth conditions, although we cannot rule out genetic redundancy.

  3. Reduction of the amount of periplasmic hydrogenase in Desulfovibrio vulgaris (Hildenborough) with antisense RNA: direct evidence for an important role of this hydrogenase in lactate metabolism.

    PubMed Central

    van den Berg, W A; van Dongen, W M; Veeger, C

    1991-01-01

    To establish the function of the periplasmic Fe-only hydrogenase in the anaerobic sulfate reducer Desulfovibrio vulgaris (Hildenborough), derivatives with a reduced content of this enzyme were constructed by introduction of a plasmid that directs the synthesis of antisense RNA complementary to hydrogenase mRNA. It was demonstrated that the antisense RNA technique allowed specific suppression of the synthesis of this hydrogenase in D. vulgaris by decreasing the amount of hydrogenase mRNA but did not result in the complete elimination of the enzyme, as is usual with most conventional mutagenesis techniques. The hydrogenase content in these antisense RNA-producing D. vulgaris clones was two- to threefold lower than in the parental strain when the strains were grown in batch cultures with lactate as a substrate and sulfate as a terminal electron acceptor. Under these conditions, several differences in growth parameters were measured between the hydrogenase-suppressed clones and wild-type D. vulgaris: growth rates of the clones decreased two- to threefold, and at excess lactate, growth yields were reduced by 20%. Furthermore, the amount of hydrogen measured in the culture headspaces was reduced three- to fivefold for the clones. These observations indicate that this hydrogenase has an important function during growth on lactate and is involved in hydrogen production from protons and electrons originating from at least one of the two oxidation reactions in the conversion of lactate to acetate. The implications for the energy metabolism of D. vulgaris are discussed. Images PMID:1711025

  4. Periplasmic Cytochrome c(3) of Desulfovibrio vulgaris Is Directly Involved in H2-Mediated Metal but Not Sulfate Reduction

    SciTech Connect

    Elias, Dwayne A.; Suflita, Joseph M.; McInerney, Michael J.; Krumholz, Lee R.

    2004-01-01

    Kinetic parameters and the role of cytochrome c3 in sulfate, Fe(III), and U(VI) reduction were investigated in Desulfovibrio vulgaris Hildenborough. While sulfate reduction followed Michaelis-Menten kinetics (Km 220 uM), loss of Fe(III) and U(VI) was first-order at all concentrations tested. Initial reduction rates of all electron acceptors were similar for cells grown with H2 and sulfate, while cultures grown using lactate and sulfate had similar rates of metal loss but lower sulfate reduction activities. The similarities in metal, but not sulfate, reduction with H2 and lactate suggest divergent pathways. Respiration assays and reduced minus oxidized spectra were carried out to determine c-type cytochrome involvement in electron acceptor reduction. c-type cytochrome oxidation was immediate with Fe(III) and U(VI) in the presence of H2, lactate, or pyruvate. Sulfidogenesis occurred with all three electron donors and effectively oxidized the c-type cytochrome in lactate or pyruvate-reduced, but not H2-reduced cells. Correspondingly, electron acceptor competition assays with lactate or pyruvate as electron donors showed that Fe(III) inhibited U(VI) reduction, and U(VI) inhibited sulfate loss. However, sulfate reduction was slowed but not halted when H2 was the electron donor in the presence of Fe(III) or U(VI). U(VI) loss was still impeded by Fe(III) when H2 was used. Hence, we propose a modified pathway for the reduction of sulfate, Fe(III), and U(VI) which helps explain why these bacteria cannot grow using these metals. We further propose that cytochrome c3 is an electron carrier involved in lactate and pyruvate oxidation and is the reductase for alternate electron acceptors with higher redox potentials than sulfate.

  5. Photosensitivity of the Ni-A state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F with visible light

    SciTech Connect

    Osuka, Hisao; Shomura, Yasuhito; Komori, Hirofumi; Shibata, Naoki; Nagao, Satoshi; Higuchi, Yoshiki; Hirota, Shun

    2013-01-04

    Highlights: Black-Right-Pointing-Pointer Ni-A state of [NiFe] hydrogenase showed light sensitivity. Black-Right-Pointing-Pointer New FT-IR bands were observed with light irradiation of the Ni-A state. Black-Right-Pointing-Pointer EPR g-values of the Ni-A state shifted upon light irradiation. Black-Right-Pointing-Pointer The light-induced state converted back to the Ni-A state under the dark condition. -- Abstract: [NiFe] hydrogenase catalyzes reversible oxidation of molecular hydrogen. Its active site is constructed of a hetero dinuclear Ni-Fe complex, and the oxidation state of the Ni ion changes according to the redox state of the enzyme. We found that the Ni-A state (an inactive unready, oxidized state) of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F (DvMF) is light sensitive and forms a new state (Ni-AL) with irradiation of visible light. The Fourier transform infrared (FT-IR) bands at 1956, 2084 and 2094 cm{sup -1} of the Ni-A state shifted to 1971, 2086 and 2098 cm{sup -1} in the Ni-AL state. The g-values of g{sub x} = 2.30, g{sub y} = 2.23 and g{sub z} = 2.01 for the signals in the electron paramagnetic resonance (EPR) spectrum of the Ni-A state at room temperature varied for -0.009, +0.012 and +0.010, respectively, upon light irradiation. The light-induced Ni-AL state converted back immediately to the Ni-A state under dark condition at room temperature. These results show that the coordination structure of the Fe site of the Ni-A state of [NiFe] hydrogenase is perturbed significantly by light irradiation with relatively small coordination change at the Ni site.

  6. Periplasmic Cytochrome c3 of Desulfovibrio vulgaris Is Directly Involved in H2-Mediated Metal but Not Sulfate Reduction

    PubMed Central

    Elias, Dwayne A.; Suflita, Joseph M.; McInerney, Michael J.; Krumholz, Lee R.

    2004-01-01

    Kinetic parameters and the role of cytochrome c3 in sulfate, Fe(III), and U(VI) reduction were investigated in Desulfovibrio vulgaris Hildenborough. While sulfate reduction followed Michaelis-Menten kinetics (Km = 220 μM), loss of Fe(III) and U(VI) was first-order at all concentrations tested. Initial reduction rates of all electron acceptors were similar for cells grown with H2 and sulfate, while cultures grown using lactate and sulfate had similar rates of metal loss but lower sulfate reduction activities. The similarities in metal, but not sulfate, reduction with H2 and lactate suggest divergent pathways. Respiration assays and reduced minus oxidized spectra were carried out to determine c-type cytochrome involvement in electron acceptor reduction. c-type cytochrome oxidation was immediate with Fe(III) and U(VI) in the presence of H2, lactate, or pyruvate. Sulfidogenesis occurred with all three electron donors and effectively oxidized the c-type cytochrome in lactate- or pyruvate-reduced, but not H2-reduced cells. Correspondingly, electron acceptor competition assays with lactate or pyruvate as electron donors showed that Fe(III) inhibited U(VI) reduction, and U(VI) inhibited sulfate loss. However, sulfate reduction was slowed but not halted when H2 was the electron donor in the presence of Fe(III) or U(VI). U(VI) loss was still impeded by Fe(III) when H2 was used. Hence, we propose a modified pathway for the reduction of sulfate, Fe(III), and U(VI) which helps explain why these bacteria cannot grow using these metals. We further propose that cytochrome c3 is an electron carrier involved in lactate and pyruvate oxidation and is the reductase for alternate electron acceptors with higher redox potentials than sulfate. PMID:14711670

  7. Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses

    SciTech Connect

    Men, Yujie; Feil, Helene; Verberkmoes, Nathan C; Shah, Manesh B; Johnson, David R.; Lee, Patrick K. H.; West, Kimberlee A; Zinder, Stephen H.; Andersen, Gary L.; Alvarez-Cohen, Lisa

    2012-01-01

    Dehalococcoides ethenogenes strain 195 (DE195) was grown in a sustainable syntrophic association with Desulfovibrio vulgaris Hildenborough (DVH) as a co-culture, as well as with DVH and the hydrogenotrophic methanogen Methanobacterium congolense (MC) as a tri-culture using lactate as the sole energy and carbon source. In the co- and tri-cultures, maximum dechlorination rates of DE195 were enhanced by approximately three times (11.0 0.01 lmol per day for the co-culture and 10.1 0.3 lmol per day for the tri-culture) compared with DE195 grown alone (3.8 0.1 lmol per day). Cell yield of DE195 was enhanced in the co-culture (9.0 0.5107 cells per lmol Cl released, compared with 6.8 0.9107 cells per lmol Cl released for the pure culture), whereas no further enhancement was observed in the tri-culture (7.3 1.8107 cells per lmol Cl released). The transcriptome of DE195 grown in the co-culture was analyzed using a wholegenome microarray targeting DE195, which detected 102 significantly up- or down-regulated genes compared with DE195 grown in isolation, whereas no significant transcriptomic difference was observed between co- and tri-cultures. Proteomic analysis showed that 120 proteins were differentially expressed in the co-culture compared with DE195 grown in isolation. Physiological, transcriptomic and proteomic results indicate that the robust growth of DE195 in co- and tri-cultures is because of the advantages associated with the capabilities of DVH to ferment lactate to provide H2 and acetate for growth, along with potential benefits from proton translocation, cobalamin-salvaging and amino acid biosynthesis, whereas MC in the tri-culture provided no significant additional benefits beyond those of DVH.

  8. Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses

    SciTech Connect

    Men, Yujie; Feil, Helene; VerBerkmoes, Nathan C.; Shah, Manesh B.; Johnson, David R.; Lee, Patrick K. H.; West, Kimberlee A.; Zinder, Stephen H.; Andersen, Gary L.; Alvarez-Cohen, Lisa

    2011-09-01

    Dehalococcoides ethenogenes strain 195 (DE195) was grown in a sustainable syntrophic association with Desulfovibrio vulgaris Hildenborough (DVH) as a co-culture, as well as with DVH and the hydrogenotrophic methanogen Methanobacterium congolense (MC) as a tri-culture using lactate as the sole energy and carbon source. In the co- and tri-cultures, maximum dechlorination rates of DE195 were enhanced by approximately three times (11.0 0.01 lmol per day for the co-culture and 10.1 0.3 lmol per day for the tri-culture) compared with DE195 grown alone (3.8 0.1 lmol per day). Cell yield of DE195 was enhanced in the co-culture (9.0 0.5107 cells per lmol Cl released, compared with 6.8 0.9107 cells per lmol Cl released for the pure culture), whereas no further enhancement was observed in the tri-culture (7.3 1.8107 cells per lmol Cl released). The transcriptome of DE195 grown in the co-culture was analyzed using a wholegenome microarray targeting DE195, which detected 102 significantly up- or down-regulated genes compared with DE195 grown in isolation, whereas no significant transcriptomic difference was observed between co- and tri-cultures. Proteomic analysis showed that 120 proteins were differentially expressed in the co-culture compared with DE195 grown in isolation. Physiological, transcriptomic and proteomic results indicate that the robust growth of DE195 in co- and tri-cultures is because of the advantages associated with the capabilities of DVH to ferment lactate to provide H2 and acetate for growth, along with potential benefits from proton translocation, cobalamin-salvaging and amino acid biosynthesis, whereas MC in the tri-culture provided no significant additional benefits beyond those of DVH.

  9. Growth of the Obligate Anaerobe Desulfovibrio vulgaris Hildenborough under Continuous Low Oxygen Concentration Sparging: Impact of the Membrane-Bound Oxygen Reductases

    PubMed Central

    Ramel, Fanny; Brasseur, Gael; Pieulle, Laetitia; Valette, Odile; Hirschler-Réa, Agnès; Fardeau, Marie Laure; Dolla, Alain

    2015-01-01

    Although obligate anaerobe, the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) exhibits high aerotolerance that involves several enzymatic systems, including two membrane-bound oxygen reductases, a bd-quinol oxidase and a cc(b/o)o3 cytochrome oxidase. Effect of constant low oxygen concentration on growth and morphology of the wild-type, single (Δbd, Δcox) and double deletion (Δcoxbd) mutant strains of the genes encoding these oxygen reductases was studied. When both wild-type and deletion mutant strains were cultured in lactate/sulfate medium under constant 0.02% O2 sparging, they were able to grow but the final biomasses and the growth yield were lower than that obtained under anaerobic conditions. At the end of the growth, lactate was not completely consumed and when conditions were then switched to anaerobic, growth resumed. Time-lapse microscopy revealed that a large majority of the cells were then able to divide (over 97%) but the time to recover a complete division event was longer for single deletion mutant Δbd than for the three other strains. Determination of the molar growth yields on lactate suggested that a part of the energy gained from lactate oxidation was derived toward cells protection/repairing against oxidative conditions rather than biosynthesis, and that this part was higher in the single deletion mutant Δbd and, to a lesser extent, Δcox strains. Our data show that when DvH encounters oxidative conditions, it is able to stop growing and to rapidly resume growing when conditions are switched to anaerobic, suggesting that it enters active dormancy sate under oxidative conditions. We propose that the pyruvate-ferredoxin oxidoreductase (PFOR) plays a central role in this phenomenon by reversibly switching from an oxidative-sensitive fully active state to an oxidative-insensitive inactive state. The oxygen reductases, and especially the bd-quinol oxidase, would have a crucial function by maintaining reducing conditions

  10. Growth of the obligate anaerobe Desulfovibrio vulgaris Hildenborough under continuous low oxygen concentration sparging: impact of the membrane-bound oxygen reductases.

    PubMed

    Ramel, Fanny; Brasseur, Gael; Pieulle, Laetitia; Valette, Odile; Hirschler-Réa, Agnès; Fardeau, Marie Laure; Dolla, Alain

    2015-01-01

    Although obligate anaerobe, the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) exhibits high aerotolerance that involves several enzymatic systems, including two membrane-bound oxygen reductases, a bd-quinol oxidase and a cc(b/o)o3 cytochrome oxidase. Effect of constant low oxygen concentration on growth and morphology of the wild-type, single (Δbd, Δcox) and double deletion (Δcoxbd) mutant strains of the genes encoding these oxygen reductases was studied. When both wild-type and deletion mutant strains were cultured in lactate/sulfate medium under constant 0.02% O2 sparging, they were able to grow but the final biomasses and the growth yield were lower than that obtained under anaerobic conditions. At the end of the growth, lactate was not completely consumed and when conditions were then switched to anaerobic, growth resumed. Time-lapse microscopy revealed that a large majority of the cells were then able to divide (over 97%) but the time to recover a complete division event was longer for single deletion mutant Δbd than for the three other strains. Determination of the molar growth yields on lactate suggested that a part of the energy gained from lactate oxidation was derived toward cells protection/repairing against oxidative conditions rather than biosynthesis, and that this part was higher in the single deletion mutant Δbd and, to a lesser extent, Δcox strains. Our data show that when DvH encounters oxidative conditions, it is able to stop growing and to rapidly resume growing when conditions are switched to anaerobic, suggesting that it enters active dormancy sate under oxidative conditions. We propose that the pyruvate-ferredoxin oxidoreductase (PFOR) plays a central role in this phenomenon by reversibly switching from an oxidative-sensitive fully active state to an oxidative-insensitive inactive state. The oxygen reductases, and especially the bd-quinol oxidase, would have a crucial function by maintaining reducing conditions

  11. Interactions of polyacrylamides used for enhanced oil recovery and reservoir isolates of the sulfate-reducing bacterium Desulfovibrio

    SciTech Connect

    Sewell, G.W.

    1987-01-01

    The interactions of partially hydrolyzed polyacrylamides utilized in enhanced oil recovery as mobility control agents and reservoir isolates of Desulfovibrio were examined. Produced waters from reservoirs undergoing polymer flooding were sampled to determine the presence and numbers of sulfate-reducing bacteria. The influence of polyacrylamide on the growth of Desulfovibrio under a number of conditions was studied. Brookfield viscosity and screen factor measurements were used to screen for adverse changes in the rheological properties of polyacrylamide solutions which had been exposed to Desulfovibrio. Partially hydrolyzed polyacrylamides stimulated the growth of Desulfovibrio under laboratory conditions. The polymer may act as a nitrogen source or as an incomplete substrate under certain conditions, but is apparently not utilizable as a carbon source. Desulfovibrio caused a loss in screen factor of polyacrylamide solutions under anaerobic conditions, but no significant loss in solution viscosity was observed. No decrease in polymer concentration was detected. Labelled polyacrylamide was not incorporated in Desulfovibrio. The authors conclude that the observed screen factor losses are probably not the result of enzymatic degradation of the polymer, and are most likely a physical/chemical interaction of polymer molecules with some product of Desulfovibrio metabolism.

  12. Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus.

    PubMed

    Morais-Silva, Fabio O; Rezende, Antonio Mauro; Pimentel, Catarina; Santos, Catia I; Clemente, Carla; Varela-Raposo, Ana; Resende, Daniela M; da Silva, Sofia M; de Oliveira, Luciana Márcia; Matos, Marcia; Costa, Daniela A; Flores, Orfeu; Ruiz, Jerónimo C; Rodrigues-Pousada, Claudina

    2014-08-01

    Desulfovibrio gigas is a model organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic context of this organism was however, not yet available. The sequencing of the D. gigas genome provides insights into the integrated network of energy conserving complexes and structures present in this bacterium. Comparison with genomes of other Desulfovibrio spp. reveals the presence of two different CRISPR/Cas systems in D. gigas. Phylogenetic analysis using conserved protein sequences (encoded by rpoB and gyrB) indicates two main groups of Desulfovibrio spp, being D. gigas more closely related to D. vulgaris and D. desulfuricans strains. Gene duplications were found such as those encoding fumarate reductase, formate dehydrogenase, and superoxide dismutase. Complexes not yet described within Desulfovibrio genus were identified: Mnh complex, a v-type ATP-synthase as well as genes encoding the MinCDE system that could be responsible for the larger size of D. gigas when compared to other members of the genus. A low number of hydrogenases and the absence of the codh/acs and pfl genes, both present in D. vulgaris strains, indicate that intermediate cycling mechanisms may contribute substantially less to the energy gain in D. gigas compared to other Desulfovibrio spp. This might be compensated by the presence of other unique genomic arrangements of complexes such as the Rnf and the Hdr/Flox, or by the presence of NAD(P)H related complexes, like the Nuo, NfnAB or Mnh.

  13. Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus*

    PubMed Central

    Morais-Silva, Fabio O; Rezende, Antonio Mauro; Pimentel, Catarina; Santos, Catia I; Clemente, Carla; Varela–Raposo, Ana; Resende, Daniela M; da Silva, Sofia M; de Oliveira, Luciana Márcia; Matos, Marcia; Costa, Daniela A; Flores, Orfeu; Ruiz, Jerónimo C; Rodrigues-Pousada, Claudina

    2014-01-01

    Desulfovibrio gigas is a model organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic context of this organism was however, not yet available. The sequencing of the D. gigas genome provides insights into the integrated network of energy conserving complexes and structures present in this bacterium. Comparison with genomes of other Desulfovibrio spp. reveals the presence of two different CRISPR/Cas systems in D. gigas. Phylogenetic analysis using conserved protein sequences (encoded by rpoB and gyrB) indicates two main groups of Desulfovibrio spp, being D. gigas more closely related to D. vulgaris and D. desulfuricans strains. Gene duplications were found such as those encoding fumarate reductase, formate dehydrogenase, and superoxide dismutase. Complexes not yet described within Desulfovibrio genus were identified: Mnh complex, a v-type ATP-synthase as well as genes encoding the MinCDE system that could be responsible for the larger size of D. gigas when compared to other members of the genus. A low number of hydrogenases and the absence of the codh/acs and pfl genes, both present in D. vulgaris strains, indicate that intermediate cycling mechanisms may contribute substantially less to the energy gain in D. gigas compared to other Desulfovibrio spp. This might be compensated by the presence of other unique genomic arrangements of complexes such as the Rnf and the Hdr/Flox, or by the presence of NAD(P)H related complexes, like the Nuo, NfnAB or Mnh. PMID:25055974

  14. Study of the thiol/disulfide redox systems of the anaerobe Desulfovibrio vulgaris points out pyruvate:ferredoxin oxidoreductase as a new target for thioredoxin 1.

    PubMed

    Pieulle, Laetitia; Stocker, Pierre; Vinay, Manon; Nouailler, Matthieu; Vita, Nicolas; Brasseur, Gaël; Garcin, Edwige; Sebban-Kreuzer, Corinne; Dolla, Alain

    2011-03-11

    Sulfate reducers have developed a multifaceted adaptative strategy to survive against oxidative stresses. Along with this oxidative stress response, we recently characterized an elegant reversible disulfide bond-dependent protective mechanism in the pyruvate:ferredoxin oxidoreductase (PFOR) of various Desulfovibrio species. Here, we searched for thiol redox systems involved in this mechanism. Using thiol fluorescent labeling, we show that glutathione is not the major thiol/disulfide balance-controlling compound in four different Desulfovibrio species and that no other plentiful low molecular weight thiol can be detected. Enzymatic analyses of two thioredoxins (Trxs) and three thioredoxin reductases allow us to propose the existence of two independent Trx systems in Desulfovibrio vulgaris Hildenborough (DvH). The TR1/Trx1 system corresponds to the typical bacterial Trx system. We measured a TR1 apparent K(m) value for Trx1 of 8.9 μM. Moreover, our results showed that activity of TR1 was NADPH-dependent. The second system named TR3/Trx3 corresponds to an unconventional Trx system as TR3 used preferentially NADH (K(m) for NADPH, 743 μM; K(m) for NADH, 5.6 μM), and Trx3 was unable to reduce insulin. The K(m) value of TR3 for Trx3 was 1.12 μM. In vitro experiments demonstrated that the TR1/Trx1 system was the only one able to reactivate the oxygen-protected form of Desulfovibrio africanus PFOR. Moreover, ex vivo pulldown assays using the mutant Trx1(C33S) as bait allowed us to capture PFOR from the DvH extract. Altogether, these data demonstrate that PFOR is a new target for Trx1, which is probably involved in the protective switch mechanism of the enzyme.

  15. Desulfovibrio vulgaris bacterioferritin uses H(2)O(2) as a co-substrate for iron oxidation and reveals DPS-like DNA protection and binding activities.

    PubMed

    Timóteo, Cristina G; Guilherme, Márcia; Penas, Daniela; Folgosa, Filipe; Tavares, Pedro; Pereira, Alice S

    2012-08-15

    A gene encoding Bfr (bacterioferritin) was identified and isolated from the genome of Desulfovibrio vulgaris cells, and overexpressed in Escherichia coli. In vitro, H(2)O(2) oxidizes Fe(2+) ions at much higher reaction rates than O(2). The H(2)O(2) oxidation of two Fe(2+) ions was proven by Mössbauer spectroscopy of rapid freeze-quenched samples. On the basis of the Mössbauer parameters of the intermediate species we propose that D. vulgaris Bfr follows a mineralization mechanism similar to the one reported for vertebrate H-type ferritins subunits, in which a diferrous centre at the ferroxidase site is oxidized to diferric intermediate species, that are subsequently translocated into the inner nanocavity. D. vulgaris recombinant Bfr oxidizes and stores up to 600 iron atoms per protein. This Bfr is able to bind DNA and protect it against hydroxyl radical and DNase deleterious effects. The use of H(2)O(2) as an oxidant, combined with the DNA binding and protection activities, seems to indicate a DPS (DNA-binding protein from starved cells)-like role for D. vulgaris Bfr.

  16. Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio.

    PubMed

    Cao, Junwei; Gayet, Nicolas; Zeng, Xiang; Shao, Zongze; Jebbar, Mohamed; Alain, Karine

    2016-10-01

    A novel sulfate-reducing bacterium, strain J2T, was isolated from a serpentinized peridotite sample from the Indian Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J2T clustered with the genus Desulfovibrio within the family Desulfovibrionaceae, but it showed low similarity (87.95 %) to the type species Desulfovibrio desulfuricans DSM 642T. It was most closely related to Desulfovibrio portus MSL79T (96.96 %), followed by Desulfovibrio aespoeensis Aspo-2T (96.11 %), Desulfovibrio piezophilus C1TLV30T (96.04 %) and Desulfovibrio profundus DSM 11384T (95.17 %). Other available sequences shared less than 93.33 % 16S rRNA gene sequence similarity. Cells were Gram-staining-negative, anaerobic, motile vibrios (2-6×0.4-0.6 µm). Growth was observed at salinities ranging from 0.2 to 6 % (optimum 2.5 %), from pH 5 to 8 (optimum pH 6.5-7) and at temperatures between 9 and 40 °C (optimum 30-35 °C). J2T was piezophilic, growing optimally at 10 MPa (range 0-30 MPa). J2T used lactate, malate, pyruvate, formate and hydrogen as energy sources. Sulfate, thiosulfate, sulfite, fumarate and nitrate were used as terminal electron acceptors. Lactate and pyruvate were fermented. The main fatty acids were iso-C15 : 0, anteiso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and iso-C17 : 0. The DNA G+C content of strain J2T was 63.5 mol%. The combined genotypic and phenotypic data show that strain J2T represents a novel species of a novel genus in the family Desulfovibrionaceae, for which the name Pseudodesulfovibrio indicus gen. nov., sp. nov. is proposed, with the type strain J2T (=MCCC 1A01867T = DSM 101483T). We also propose the reclassification of D. piezophilus as Pseudodesulfovibrio piezophilus comb. nov., D. profundus as Pseudodesulfovibrio profundus comb. nov., D. portus as Pseudodesulfovibrio portus comb. nov. and D. aespoeensis as Pseudodesulfovibrio aespoeensis comb. nov.

  17. Final Report Construction of Whole Genome Microarrays, and Expression Analysis of Desulfovibrio vulgaris cells in Metal-Reducing Conditions

    SciTech Connect

    M.W. Fields; J.D. Wall; J. Keasling; J. Zhou

    2008-05-15

    We continue to utilize the oligonucleotide microarrays that were constructed through funding with this project to characterize growth responses of Desulfovibrio vulgaris relevant to metal-reducing conditions. To effectively immobilize heavy metals and radionuclides via sulfate-reduction, it is important to understand the cellular responses to adverse factors observed at contaminated subsurface environments (e.g., nutrients, pH, contaminants, growth requirements and products). One of the major goals of the project is to construct whole-genome microarrays for Desulfovibrio vulgaris. First, in order to experimentally establish the criteria for designing gene-specific oligonucleotide probes, an oligonucleotide array was constructed that contained perfect match (PM) and mismatch (MM) probes (50mers and 70mers) based upon 4 genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were examined. Little hybridization was observed at a probe-target identity of <85% for both 50mer and 70mer probes. 33 to 48% of the PM signal intensities were detected at a probe-target identity of 94% for 50mer oligonucleotides, and 43 to 55% for 70mer probes at a probe-target identity of 96%. When the effects of sequence identity and continuous stretch were considered independently, a stretch probe (>15 bases) contributed an additional 9% of the PM signal intensity compared to a non-stretch probe (< 15 bases) at the same identity level. Cross-hybridization increased as the length of continuous stretch increased. A 35-base stretch for 50mer probes or a 50-base stretch for 70mer probes had approximately 55% of the PM signal. Mismatches should be as close to the middle position of an oligonucleotide probe as possible to minimize cross-hybridization. Little cross-hybridization was observed for probes with a minimal binding free energy greater than -30 kcal/mol for 50mer probes or -40 kcal/mol for 70mer probes. Based on the

  18. Comparison of Transcriptional Heterogeneity of Eight Genes between Batch Desulfovibrio vulgaris Biofilm and Planktonic Culture at a Single-Cell Level

    PubMed Central

    Qi, Zhenhua; Chen, Lei; Zhang, Weiwen

    2016-01-01

    Sulfate-reducing bacteria (SRB) biofilm formed on metal surfaces can change the physicochemical properties of metals and cause metal corrosion. To enhance understanding of differential gene expression in Desulfovibrio vulgaris under planktonic and biofilm growth modes, a single-cell based RT-qPCR approach was applied to determine gene expression levels of 8 selected target genes in four sets of the 31 individual cells isolated from each growth condition (i.e., biofilm formed on a mild steel (SS) and planktonic cultures, exponential and stationary phases). The results showed obvious gene-expression heterogeneity for the target genes among D. vulgaris single cells of both biofilm and planktonic cultures. In addition, an increased gene-expression heterogeneity in the D. vulgaris biofilm when compared with the planktonic culture was also observed for seven out of eight selected genes at exponential phase, and six out of eight selected genes at stationary phase, respectively, which may be contributing to the increased complexity in terms of structures and morphology in the biofilm. Moreover, the results showed up-regulation of DVU0281 gene encoding exopolysaccharide biosynthesis protein, and down-regulation of genes involved in energy metabolism (i.e., DVU0434 and DVU0588), stress responses (i.e., DVU2410) and response regulator (i.e., DVU3062) in the D. vulgaris biofilm cells. Finally, the gene (DVU2571) involved in iron transportation was found down-regulated, and two genes (DVU1340 and DVU1397) involved in ferric uptake repressor and iron storage were up-regulated in D. vulgaris biofilm, suggesting their possible roles in maintaining normal metabolism of the D. vulgaris biofilm under environments of high concentration of iron. This study showed that the single-cell based analysis could be a useful approach in deciphering metabolism of microbial biofilms. PMID:27199927

  19. Comparison of Transcriptional Heterogeneity of Eight Genes between Batch Desulfovibrio vulgaris Biofilm and Planktonic Culture at a Single-Cell Level.

    PubMed

    Qi, Zhenhua; Chen, Lei; Zhang, Weiwen

    2016-01-01

    Sulfate-reducing bacteria (SRB) biofilm formed on metal surfaces can change the physicochemical properties of metals and cause metal corrosion. To enhance understanding of differential gene expression in Desulfovibrio vulgaris under planktonic and biofilm growth modes, a single-cell based RT-qPCR approach was applied to determine gene expression levels of 8 selected target genes in four sets of the 31 individual cells isolated from each growth condition (i.e., biofilm formed on a mild steel (SS) and planktonic cultures, exponential and stationary phases). The results showed obvious gene-expression heterogeneity for the target genes among D. vulgaris single cells of both biofilm and planktonic cultures. In addition, an increased gene-expression heterogeneity in the D. vulgaris biofilm when compared with the planktonic culture was also observed for seven out of eight selected genes at exponential phase, and six out of eight selected genes at stationary phase, respectively, which may be contributing to the increased complexity in terms of structures and morphology in the biofilm. Moreover, the results showed up-regulation of DVU0281 gene encoding exopolysaccharide biosynthesis protein, and down-regulation of genes involved in energy metabolism (i.e., DVU0434 and DVU0588), stress responses (i.e., DVU2410) and response regulator (i.e., DVU3062) in the D. vulgaris biofilm cells. Finally, the gene (DVU2571) involved in iron transportation was found down-regulated, and two genes (DVU1340 and DVU1397) involved in ferric uptake repressor and iron storage were up-regulated in D. vulgaris biofilm, suggesting their possible roles in maintaining normal metabolism of the D. vulgaris biofilm under environments of high concentration of iron. This study showed that the single-cell based analysis could be a useful approach in deciphering metabolism of microbial biofilms.

  20. Spectroscopic evidence for and characterization of a trinuclear ferroxidase center in bacterial ferritin from Desulfovibrio vulgaris Hildenborough.

    PubMed

    Pereira, Alice S; Timóteo, Cristina G; Guilherme, Márcia; Folgosa, Filipe; Naik, Sunil G; Duarte, Américo G; Huynh, Boi Hanh; Tavares, Pedro

    2012-07-04

    Ferritins are ubiquitous and can be found in practically all organisms that utilize Fe. They are composed of 24 subunits forming a hollow sphere with an inner cavity of ~80 Å in diameter. The main function of ferritin is to oxidize the cytotoxic Fe(2+) ions and store the oxidized Fe in the inner cavity. It has been established that the initial step of rapid oxidation of Fe(2+) (ferroxidation) by H-type ferritins, found in vertebrates, occurs at a diiron binding center, termed the ferroxidase center. In bacterial ferritins, however, X-ray crystallographic evidence and amino acid sequence analysis revealed a trinuclear Fe binding center comprising a binuclear Fe binding center (sites A and B), homologous to the ferroxidase center of H-type ferritin, and an adjacent mononuclear Fe binding site (site C). In an effort to obtain further evidence supporting the presence of a trinuclear Fe binding center in bacterial ferritins and to gain information on the states of the iron bound to the trinuclear center, bacterial ferritin from Desulfovibrio vulgaris (DvFtn) and its E130A variant was loaded with substoichiometric amounts of Fe(2+), and the products were characterized by Mössbauer and EPR spectroscopy. Four distinct Fe species were identified: a paramagnetic diferrous species, a diamagnetic diferrous species, a mixed valence Fe(2+)Fe(3+) species, and a mononuclear Fe(2+) species. The latter three species were detected in the wild-type DvFtn, while the paramagnetic diferrous species was detected in the E130A variant. These observations can be rationally explained by the presence of a trinuclear Fe binding center, and the four Fe species can be properly assigned to the three Fe binding sites. Further, our spectroscopic data suggest that (1) the fully occupied trinuclear center supports an all ferrous state, (2) sites B and C are bridged by a μ-OH group forming a diiron subcenter within the trinuclear center, and (3) this subcenter can afford both a mixed valence Fe(2

  1. Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: Global transcriptomic and proteomic analyses

    SciTech Connect

    Men, Y.; Feil, H.; VerBerkmoes, N.C.; Shah, M.B.; Johnson, D.R.; Lee, P.K.H; West, K.A.; Zinder, S.H.; Andersen, G.L.; Alvarez-Cohen, L.

    2011-03-01

    Dehalococcoides ethenogenes strain 195 (DE195) was grown in a sustainable syntrophic association with Desulfovibrio vulgaris Hildenborough (DVH) as a co-culture, as well as with DVH and the hydrogenotrophic methanogen Methanobacterium congolense (MC) as a tri-culture using lactate as the sole energy and carbon source. In the co- and tri-cultures, maximum dechlorination rates of DE195 were enhanced by approximately three times (11.0±0.01 lmol per day for the co-culture and 10.1±0.3 lmol per day for the tri-culture) compared with DE195 grown alone (3.8±0.1 lmol per day). Cell yield of DE195 was enhanced in the co-culture (9.0±0.5 x 107 cells per lmol Cl{sup -} released, compared with 6.8±0.9x 107 cells per lmol Cl{sup -} released for the pure culture), whereas no further enhancement was observed in the tri-culture (7.3±1.8x 107 cells per lmol Cl{sup -} released). The transcriptome of DE195 grown in the co-culture was analyzed using a whole-genome microarray targeting DE195, which detected 102 significantly up- or down-regulated genes compared with DE195 grown in isolation, whereas no significant transcriptomic difference was observed between co- and tri-cultures. Proteomic analysis showed that 120 proteins were differentially expressed in the co-culture compared with DE195 grown in isolation. Physiological, transcriptomic and proteomic results indicate that the robust growth of DE195 in co- and tri-cultures is because of the advantages associated with the capabilities of DVH to ferment lactate to provide H2 and acetate for growth, along with potential benefits from proton translocation, cobalamin-salvaging and amino acid biosynthesis, whereas MC in the tri-culture provided no significant additional benefits beyond those of DVH.

  2. Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses.

    PubMed

    Men, Yujie; Feil, Helene; Verberkmoes, Nathan C; Shah, Manesh B; Johnson, David R; Lee, Patrick K H; West, Kimberlee A; Zinder, Stephen H; Andersen, Gary L; Alvarez-Cohen, Lisa

    2012-02-01

    Dehalococcoides ethenogenes strain 195 (DE195) was grown in a sustainable syntrophic association with Desulfovibrio vulgaris Hildenborough (DVH) as a co-culture, as well as with DVH and the hydrogenotrophic methanogen Methanobacterium congolense (MC) as a tri-culture using lactate as the sole energy and carbon source. In the co- and tri-cultures, maximum dechlorination rates of DE195 were enhanced by approximately three times (11.0±0.01 μmol per day for the co-culture and 10.1±0.3 μmol per day for the tri-culture) compared with DE195 grown alone (3.8±0.1 μmol per day). Cell yield of DE195 was enhanced in the co-culture (9.0±0.5 × 10(7) cells per μmol Cl(-) released, compared with 6.8±0.9 × 10(7) cells per μmol Cl(-) released for the pure culture), whereas no further enhancement was observed in the tri-culture (7.3±1.8 × 10(7) cells per μmol Cl(-) released). The transcriptome of DE195 grown in the co-culture was analyzed using a whole-genome microarray targeting DE195, which detected 102 significantly up- or down-regulated genes compared with DE195 grown in isolation, whereas no significant transcriptomic difference was observed between co- and tri-cultures. Proteomic analysis showed that 120 proteins were differentially expressed in the co-culture compared with DE195 grown in isolation. Physiological, transcriptomic and proteomic results indicate that the robust growth of DE195 in co- and tri-cultures is because of the advantages associated with the capabilities of DVH to ferment lactate to provide H(2) and acetate for growth, along with potential benefits from proton translocation, cobalamin-salvaging and amino acid biosynthesis, whereas MC in the tri-culture provided no significant additional benefits beyond those of DVH.

  3. Solution NMR structure, backbone dynamics, and heme-binding properties of a novel cytochrome c maturation protein CcmE from Desulfovibrio vulgaris.

    PubMed

    Aramini, James M; Hamilton, Keith; Rossi, Paolo; Ertekin, Asli; Lee, Hsiau-Wei; Lemak, Alexander; Wang, Huang; Xiao, Rong; Acton, Thomas B; Everett, John K; Montelione, Gaetano T

    2012-05-08

    Cytochrome c maturation protein E, CcmE, plays an integral role in the transfer of heme to apocytochrome c in many prokaryotes and some mitochondria. A novel subclass featuring a heme-binding cysteine has been identified in archaea and some bacteria. Here we describe the solution NMR structure, backbone dynamics, and heme binding properties of the soluble C-terminal domain of Desulfovibrio vulgaris CcmE, dvCcmE'. The structure adopts a conserved β-barrel OB fold followed by an unstructured C-terminal tail encompassing the CxxxY heme-binding motif. Heme binding analyses of wild-type and mutant dvCcmE' demonstrate the absolute requirement of residue C127 for noncovalent heme binding in vitro.

  4. Fractionation of Sulfur Isotopes by Desulfovibrio vulgaris Mutants Lacking Periplasmic Hydrogenases or the Type I Tetraheme Cytochrome c3

    NASA Astrophysics Data System (ADS)

    Sim, M.; Ono, S.; Bosak, T.

    2012-12-01

    A large fraction of anaerobic mineralization of organic compounds relies on microbial sulfate reduction. Sulfur isotope fractionation by these microbes has been widely used to trace the biogeochemical cycling of sulfur and carbon, but intracellular mechanisms behind the wide range of fractionations observed in nature and cultures are not fully understood. In this study, we investigated the influence of electron transport chain components on the fractionation of sulfur isotopes by culturing Desulfovibrio vulgaris Hildenborough mutants lacking hydrogenases or type I tetraheme cytochrome c3 (Tp1-c3). The mutants were grown both in batch and continuous cultures. All tested mutants grew on lactate or pyruvate as the sole carbon and energy sources, generating sulfide. Mutants lacking cytoplasmic and periplasmic hydrogenases exhibited similar growth physiologies and sulfur isotope fractionations to their parent strains. On the other hand, a mutant lacking Tp1-c3 (ΔcycA) fractionated the 34S/32S ratio more than the wild type, evolving H2 in the headspace and exhibiting a lower specific respiration rate. In the presence of high concentrations of pyruvate, the growth of ΔcycA relied largely on fermentation rather than sulfate reduction, even when sulfate was abundant, producing the largest sulfur isotope effect observed in this study. Differences between sulfur isotope fractionation by ΔcycA and the wild type highlight the effect of electron transfer chains on the magnitude of sulfur isotope fractionation. Because Tp1-c3 is known to exclusively shuttle electrons from periplasmic hydrogenases to transmembrane complexes, electron transfers in the absence of Tp1-c3 should bypass the periplasmic hydrogen cycling, and the loss of reducing equivalents in the form of H2 can impair the flow of electrons from organic acids to sulfur, increasing isotope fractionation. Larger fractionation by ΔcycA can inform interpretations of sulfur isotope data at an environmental scale as well

  5. Subcellular localization of proteins in the anaerobic sulfate reducer Desulfovibrio vulgaris via SNAP-tag labeling and photoconversion

    SciTech Connect

    Gorur, A.; Leung, C. M.; Jorgens, D.; Tauscher, A.; Remis, J. P.; Ball, D. A.; Chhabra, S.; Fok, V.; Geller, J. T.; Singer, M.; Hazen, T. C.; Juba, T.; Elias, D.; Wall, J.; Biggin, M.; Downing, K. H.; Auer, M.

    2010-06-01

    Systems Biology studies the temporal and spatial 3D distribution of macromolecular complexes with the aim that such knowledge will allow more accurate modeling of biological function and will allow mathematical prediction of cellular behavior. However, in order to accomplish accurate modeling precise knowledge of spatial 3D organization and distribution inside cells is necessary. And while a number of macromolecular complexes may be identified by its 3D structure and molecular characteristics alone, the overwhelming number of proteins will need to be localized using a reporter tag. GFP and its derivatives (XFPs) have been traditionally employed for subcelllar localization using photoconversion approaches, but this approach cannot be taken for obligate anaerobic bacteria, where the intolerance towards oxygen prevents XFP approaches. As part of the GTL-funded PCAP project (now ENIGMA) genetic tools have been developed for the anaerobe sulfate reducer Desulfovibrio vulgaris that allow the high-throughput generation of tagged-protein mutant strains, with a focus on the commercially available SNAP-tag cell system (New England Biolabs, Ipswich, MA), which is based on a modified O6-alkylguanine-DNA alkyltransferase (AGT) tag, that has a dead-end reaction with a modified O6-benzylguanine (BG) derivative and has been shown to function under anaerobic conditions. After initial challenges with respect to variability, robustness and specificity of the labeling signal we have optimized the labeling. Over the last year, as a result of the optimized labeling protocol, we now obtain robust labeling of 20 out of 31 SNAP strains. Labeling for 13 strains were confirmed at least five times. We have also successfully performed photoconversion on 5 of these 13 strains, with distinct labeling patterns for different strains. For example, DsrC robustly localizes to the periplasmic portion of the inner membrane, where as a DNA-binding protein localizes to the center of the cell, where the

  6. Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris.

    PubMed

    Valverde, Angel; Igual, José M; Peix, Alvaro; Cervantes, Emilio; Velázquez, Encarna

    2006-11-01

    The species Phaseolus vulgaris is a promiscuous legume nodulated by several species of the family Rhizobiaceae. During a study of rhizobia nodulating this legume in Portugal, we isolated several strains that nodulate P. vulgaris effectively and also Macroptilium atropurpureum and Leucaena leucocephala, but they form ineffective nodules in Medicago sativa. According to phylogenetic analysis of the 16S rRNA gene sequence, the strains from this study belong to the genus Rhizobium, with Rhizobium rhizogenes and Rhizobium tropici as the closest related species, with 99.9 and 99.2% similarity, respectively, between the type strains of these species and strain P1-7T. The nodD and nifH genes carried by strain P1-7T are phylogenetically related to those of other species nodulating Phaseolus. This strain does not carry virulence genes present in the type strain of R. rhizogenes, ATCC 11325T. Analysis of the recA and atpD genes confirms this phylogenetic arrangement, showing low similarity with respect to those of R. rhizogenes ATCC 11325T (91.9 and 94.1% similarity, respectively) and R. tropici IIB CIAT 899T (90.6% and 91.8% similarity, respectively). The intergenic spacer (ITS) of the strains from this study is phylogenetically divergent from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, with 85.9 and 82.8% similarity, respectively, with respect to strain P1-7T. The tRNA profile and two-primer random amplified polymorphic DNA pattern of strain P1-7T are also different from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T. The strains isolated in this study can be also differentiated from R. rhizogenes and R. tropici by several phenotypic characteristics. The results of DNA-DNA hybridization showed means of 28 and 25% similarity between strain P1-7T and R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, respectively. All these data showed that the strains isolated in this study belong to a novel species of the genus Rhizobium, for which we propose

  7. Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH.

    PubMed

    Christensen, G A; Zane, G M; Kazakov, A E; Li, X; Rodionov, D A; Novichkov, P S; Dubchak, I; Arkin, A P; Wall, J D

    2015-01-01

    Although the enzymes for dissimilatory sulfate reduction by microbes have been studied, the mechanisms for transcriptional regulation of the encoding genes remain unknown. In a number of bacteria the transcriptional regulator Rex has been shown to play a key role as a repressor of genes producing proteins involved in energy conversion. In the model sulfate-reducing microbe Desulfovibrio vulgaris Hildenborough, the gene DVU_0916 was observed to resemble other known Rex proteins. Therefore, the DVU_0916 protein has been predicted to be a transcriptional repressor of genes encoding proteins that function in the process of sulfate reduction in D. vulgaris Hildenborough. Examination of the deduced DVU_0916 protein identified two domains, one a winged helix DNA-binding domain common for transcription factors, and the other a Rossman fold that could potentially interact with pyridine nucleotides. A deletion of the putative rex gene was made in D. vulgaris Hildenborough, and transcript expression studies of sat, encoding sulfate adenylyl transferase, showed increased levels in the D. vulgaris Hildenborough Rex (RexDvH) mutant relative to the parental strain. The RexDvH-binding site upstream of sat was identified, confirming RexDvH to be a repressor of sat. We established in vitro that the presence of elevated NADH disrupted the interaction between RexDvH and DNA. Examination of the 5' transcriptional start site for the sat mRNA revealed two unique start sites, one for respiring cells that correlated with the RexDvH-binding site and a second for fermenting cells. Collectively, these data support the role of RexDvH as a transcription repressor for sat that senses the redox status of the cell.

  8. Development of a Model, Metal-reducing Microbial Community for a System Biology Level Assessment of Desulfovibrio vulgaris as part of a Community

    SciTech Connect

    Elias, Dwayne; Schadt, Christopher; Miller, Lance; Phelps, Tommy; Brown, S. D.; Arkin, Adam; Hazen, Terry; Drake, Megin; Yang, Z.K.; Podar, Mircea

    2010-05-17

    One of the largest experimental gaps is between the simplicity of pure cultures and the complexity of open environmental systems, particularly in metal-contaminated areas. These microbial communities form ecosystem foundations, drive biogeochemical processes, and are relevant for biotechnology and bioremediation. A model, metal-reducing microbial community was constructed as either syntrophic or competitive to study microbial cell to cell interactions, cell signaling and competition for resources. The microbial community was comprised of the metal-reducing Desulfovibrio vulgaris Hildenborough and Geobacter sulfurreducens PCA. Additionally, Methanococcus maripaludis S2 was added to study complete carbon reduction and maintain a low hydrogen partial pressure for syntrophism to occur. Further, considerable work has been published on D. vulgaris and the D. vulgaris/ Mc. maripaludis co-culture both with and without stress. We are extending this work by conducting the same stress conditions on the model community. Additionally, this comprehensive investigation includes physiological and metabolic analyses as well as specially designed mRNA microarrays with the genes for all three organisms on one slide so as to follow gene expression changes in the various cultivation conditions as well as being comparable to the co- and individual cultures. Further, state-of -the-art comprehensive AMT tag proteomics allows for these comparisons at the protein level for a systems biology assessment of a model, metal-reducing microbial community. Preliminary data revealed that lactate oxidation by D. vulgaris was sufficient to support both G. sulfurreducens and M. maripaludis via the excretion of H2 and acetate. Fumarate was utilized by G. sulfurreducens and reduced to succinate since neither of the other two organisms can reduce fumarate. Methane was quantified, suggesting acetate and H2 concentrations were sufficient for M. maripaludis. Steady state community cultivation will allow for

  9. Pathway confirmation and flux analysis of central metabolicpathways in Desulfovibrio vulgaris Hildenborough using GasChromatography-Mass Spectrometry and Fourier Transform-Ion CyclotronResonance Mass Spectrometry

    SciTech Connect

    Tang, Yinjie; Pingitore, Francesco; Mukhopadhyay, Aindrila; Phan,Richard; Hazen, Terry C.; Keasling, Jay D.

    2007-03-15

    Flux distribution in central metabolic pathways ofDesulfovibrio vulgaris Hildenborough was examined using 13C tracerexperiments. Consistent with the current genome annotation andindependent evidence from enzyme activity assays, the isotopomer resultsfrom both GC-MS and Fourier Transform-Ion Cyclotron Resonance massspectrometry (FT-ICR MS) indicate the lack of oxidatively functional TCAcycle and an incomplete pentose phosphate pathway. Results from thisstudy suggest that fluxes through both pathways are limited tobiosynthesis. The data also indicate that>80 percent of the lactatewas converted to acetate and the reactions involved are the primary routeof energy production (NAD(P)H and ATP production). Independent of the TCAcycle, direct cleavage of acetyl-CoA to CO and 5,10-methyl-THF also leadsto production of NADH and ATP. Although the genome annotation implicatesa ferredoxin-dependentoxoglutarate synthase, isotopic evidence does notsupport flux through this reaction in either the oxidative or reductivemode; therefore, the TCA cycle is incomplete. FT-ICR MS was used tolocate the labeled carbon distribution in aspartate and glutamate andconfirmed the presence of an atypical enzyme for citrate formationsuggested in previous reports (the citrate synthesized by this enzyme isthe isotopic antipode of the citrate synthesized by the (S)-citratesynthase). These findings enable a better understanding of the relationbetween genome annotation and actual metabolic pathways in D. vulgaris,and also demonstrate FT-ICR MS as a powerful tool for isotopomeranalysis, overcoming problems in both GC-MS and NMRspectroscopy.

  10. Isolation and characterization of a bacteriophage lytic for Desulfovibrio salexigens, a salt-requiring, sulfate-reducing bacterium

    SciTech Connect

    Kamimura, Kazuo; Araki, Michio )

    1989-03-01

    A bacteriophage that lysed Desulfovibrio salexigens cells was isolated from marine sediments and preliminarily characterized by electron microscopy and electrophoretic analysis of structural proteins and genomic nucleic acid. The bacteriophage had an icosahedral head and a long flexible tail, and the buoyant density of the bacteriophage particles was 1.468 g/ml in cesium chloride. The particles consisted of a double-stranded DNA molecule about 33 kilobase pairs long and at least 11 structural proteins.

  11. Structure of the O-specific polysaccharide of the bacterium Proteus vulgaris O23.

    PubMed

    Perepelov, A V; Shashkov, A S; Babichka, D; Senchenkova, S N; Bartodziejska, B; Rozalski, A; Knirel, Y A

    2000-09-01

    An acidic O-specific polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of the bacterium Proteus vulgaris O23 (strain PrK 44/57) and found to contain 2-acetamido-2-deoxy-D-galactose, 2-acetamido-2-deoxy-D-glucose, and D-galacturonic acid. Based on 1H- and 13C-NMR spectroscopic studies, including two-dimensional correlation spectroscopy (COSY), total correlation spectroscopy (TOCSY), nuclear Overhauser effect spectroscopy (NOESY), and 1H,13C heteronuclear multiple-quantum coherence (HMQC) experiments, the following structure of the branched tetrasaccharide repeating unit of the polysaccharide was established: [figure], where the degree of O-acetylation of the terminal GalA residue at position 4 is about 80%. A structural similarity of the O-specific polysaccharides of P. vulgaris O23 and P. mirabilis O23 is discussed.

  12. Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: Zero-Inflated Poisson regression models to predict abundance of undetected proteins

    SciTech Connect

    Nie, Lei; Wu, Gang; Brockman, Fred J.; Zhang, Weiwen

    2006-05-04

    Abstract Advances in DNA microarray and proteomics technologies have enabled high-throughput measurement of mRNA expression and protein abundance. Parallel profiling of mRNA and protein on a global scale and integrative analysis of these two data types could provide additional insight into the metabolic mechanisms underlying complex biological systems. However, because protein abundance and mRNA expression are affected by many cellular and physical processes, there have been conflicting results on the correlation of these two measurements. In addition, as current proteomic methods can detect only a small fraction of proteins present in cells, no correlation study of these two data types has been done thus far at the whole-genome level. In this study, we describe a novel data-driven statistical model to integrate whole-genome microarray and proteomic data collected from Desulfovibrio vulgaris grown under three different conditions. Based on the Poisson distribution pattern of proteomic data and the fact that a large number of proteins were undetected (excess zeros), Zero-inflated Poisson models were used to define the correlation pattern of mRNA and protein abundance. The models assumed that there is a probability mass at zero representing some of the undetected proteins because of technical limitations. The models thus use abundance measurements of transcripts and proteins experimentally detected as input to generate predictions of protein abundances as output for all genes in the genome. We demonstrated the statistical models by comparatively analyzing D. vulgaris grown on lactate-based versus formate-based media. The increased expressions of Ech hydrogenase and alcohol dehydrogenase (Adh)-periplasmic Fe-only hydrogenase (Hyd) pathway for ATP synthesis were predicted for D. vulgaris grown on formate.

  13. Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: A quantitative analysis

    SciTech Connect

    Nie, Lei; Wu, Gang; Zhang, Weiwen

    2006-12-01

    The modest correlation between mRNA expression and protein abundance in large scale datasets is explained in part by experimental challenges, such as technological limitations, and in part by fundamental biological factors in the transcription and translation processes. Among various factors affecting the mRNA-protein correlation, the roles of biological factors related to translation are poorly understood. In this study, using experimental mRNA expression and protein abundance data collected from Desulfovibrio vulgaris by DNA microarray and LC-MS/MS proteomic analysis, we quantitatively examined the effects of several translational-efficiency-related sequence features on mRNA-protein correlation. Three classes of sequence features were investigated according to different translational stages: (1) initiation: Shine-Dalgarno sequences, start codon identity and start codon context; (2) elongation: codon usage and amino acid usage; and (3) termination: stop codon identity and stop codon context. Surprisingly, although it is widely accepted that translation initiation is a rate-limiting step for translation, our results showed that the mRNA-protein correlation was affected the most by the features at elongation stages, codon usage and amino acid composition (7.4-12.6% and 5.3-9.3% of the total variation of mRNA-protein correlation, respectively), followed by stop codon context and the Shine-Dalgarno sequence (2.5-4.2% and 2.3%, respectively). Taken together, all sequence features contributed to 18.4-21.8% of the total variation of mRNA-protein correlation. As the first comprehensive quantitative analysis of the mRNA-protein correlation in bacterial D. vulgaris, our results suggest that the traditional view of the relative importance of various sequence features in prokaryotic protein translation might be questionable.

  14. Fermentative hydrogen production in an up-flow anaerobic biofilm reactor inoculated with a co-culture of Clostridium acetobutylicum and Desulfovibrio vulgaris.

    PubMed

    Barca, Cristian; Ranava, David; Bauzan, Marielle; Ferrasse, Jean-Henry; Giudici-Orticoni, Marie-Thérèse; Soric, Audrey

    2016-12-01

    Dark fermentation systems often show low H2 yields and unstable H2 production, as the result of the variability of microbial dynamics and metabolic pathways. Recent batch investigations have demonstrated that an artificial consortium of two anaerobic bacteria, Clostridium acetobutylicum and Desulfovibrio vulgaris Hildenborough, may redirect metabolic fluxes and improve H2 yields. This study aimed at evaluating the scale-up from batch to continuous H2 production in an up-flow anaerobic packed-bed reactor (APBR) continuously fed with a glucose-medium. The effects of various parameters, including void hydraulic retention time (HRTv), pH, and alkalinity, on H2 production performances and metabolic pathways were investigated. The results demonstrated that a stable H2 production was reached after 3-4days of operation. H2 production rates increased significantly with decreasing HRTv from 4 to 2h. Instead, H2 yields remained almost stable despite the change in HRTv, indicating that the decrease in HRTv did not affect the global metabolism.

  15. Control of interspecies electron flow during anaerobic digestion: significance of formate transfer versus hydrogen transfer during syntrophic methanogenesis in flocs. [Methanobacterium formicicum; Desulfovibrio vulgaris

    SciTech Connect

    Thiele, J.H.; Zeikus, J.G.

    1988-01-01

    Microbial formate production and consumption during syntrophic conversion of ethanol or lactate to methane was examined in purified flocs and digestor contents obtained from a whey-processing digestor. Formate production by digestor contents or purified digestor flocs was dependent on CO/sub 2/ and either ethanol or lactate but not H/sub 2/ gas as an electron donor. Floc preparations accumulated fourfold-higher levels of formate (40 ..mu..M) than digestor contents, and the free flora was the primary site for formate cleavage to CO/sub 2/ and H/sub 2/ (90 ..mu..M formate per h). Inhibition of methanogenesis by CHCl/sub 3/ resulted in formate accumulation and suppression of syntrophic ethanol oxidation. H/sub 2/ gas was an insignificant intermediary metabolite of syntrophic ethanol conversion by flocs, and it exogenous addition neither stimulated methanogenes nor inhibited the initial rate of ethanol oxidation. These results demonstrated that >90% of the syntrophic ethanol conversion to methane by mixed cultures containing primarily Desulfovibrio vulgaris and Methanobacterium formicicum was mediated via interspecies formate transfer and the <10% was mediated via interspecies H/sub 2/ transfer. The results are discussed in relation to biochemical thermodynamics. A model is presented which describes the dynamics of a bicarbonate-formate electron shuttle mechanism for control of carbon and electron flow during syntrophic methanogenesis and provides a novel mechanism for energy conservation by syntrophic acetogens.

  16. First isolation of Desulfovibrio from the human vaginal flora.

    PubMed

    Ichiishi, Suguru; Tanaka, Kaori; Nakao, Kenichi; Izumi, Koji; Mikamo, Hiroshige; Watanabe, Kunitomo

    2010-06-01

    Four Desulfovibrio species, including 2 subtypes of 1 species, namely, Desulfovibrio piger, Desulfovibrio desulfuricans MB subtype and Essex 6 subtype, Desulfovibrio fairfieldensis, and Desulfovibrio vulgaris, have been isolated from the human oral and intestinal flora, but not previously from the vaginal flora. They are opportunistic pathogens and have been considered as possible environmental and etiologic agents involved in ulcerative colitis and chronic periodontitis. We isolated Desulfovibrio intestinalis from vaginal specimens of four Japanese women; a species which has not been previously isolated from humans. The vaginal isolates were highly resistant to cefoxitin, piperacillin, and piperacillin-tazobactam but were susceptible to the other antimicrobial agents tested. Our findings suggested that vaginal Desulfovibrio species may be involved in gynecological or obstetric pathology, and provides additional information of the medical relevance on human Desulfovibrio species.

  17. Effect of the deletion of qmoABC and the promoter-distal gene encoding a hypothetical protein on sulfate reduction in Desulfovibrio vulgaris Hildenborough.

    PubMed

    Zane, Grant M; Yen, Huei-che Bill; Wall, Judy D

    2010-08-01

    The pathway of electrons required for the reduction of sulfate in sulfate-reducing bacteria (SRB) is not yet fully characterized. In order to determine the role of a transmembrane protein complex suggested to be involved in this process, a deletion in Desulfovibrio vulgaris Hildenborough was created by marker exchange mutagenesis that eliminated four genes putatively encoding the QmoABC complex and a hypothetical protein (DVU0851). The Qmo (quinone-interacting membrane-bound oxidoreductase) complex is proposed to be responsible for transporting electrons to the dissimilatory adenosine-5'-phosphosulfate reductase in SRB. In support of the predicted role of this complex, the deletion mutant was unable to grow using sulfate as its sole electron acceptor with a range of electron donors. To explore a possible role for the hypothetical protein in sulfate reduction, a second mutant was constructed that had lost only the gene that codes for the DVU0851 protein. The second constructed mutant grew with sulfate as the sole electron acceptor; however, there was a lag that was not present with the wild-type or complemented strain. Neither deletion strain was significantly impaired for growth with sulfite or thiosulfate as the terminal electron acceptor. Complementation of the Delta(qmoABC-DVU0851) mutant with all four genes or only the qmoABC genes restored its ability to grow by sulfate respiration. These results confirmed the prediction that the Qmo complex is in the electron pathway for sulfate reduction and revealed that no other transmembrane complex could compensate when Qmo was lacking.

  18. Effect of the deletion of qmoABC and the promoter distal gene encoding a hypothetical protein on sulfate-reduction in Desulfovibrio vulgaris Hildenborough

    SciTech Connect

    Zane, Grant M.; Yen, Huei-chi Bill; Wall, Judy D.

    2010-03-18

    The pathway of electrons required for the reduction of sulfate in sulfate-reducing bacteria (SRB) is not yet fully characterized. In order to determine the role of a transmembrane protein complex suggested to be involved in this process, a deletion of Desulfovibrio vulgaris Hildenborough was created by marker exchange mutagenesis that eliminated four genes putatively encoding the QmoABC complex and a hypothetical protein (DVU0851). The Qmo complex (quinone-interacting membrane-bound oxidoreductase) is proposed to be responsible for transporting electrons to the dissimilatory adenosine-5?phosphosulfate (APS) reductase in SRB. In support of the predicted role of this complex, the deletion mutant was unable to grow using sulfate as its sole electron acceptor with a range of electron donors. To explore a possible role for the hypothetical protein in sulfate reduction, a second mutant was constructed that had lost only the gene that codes for DVU0851. The second constructed mutant grew with sulfate as the sole electron acceptor; however, there was a lag that was not present with the wild-type or complemented strain. Neither deletion strain was significantly impaired for growth with sulfite or thiosulfate as terminal electron acceptor. Complementation of the D(qmoABC-DVU0851) mutant with all four genes or only the qmoABC genes restored its ability to grow by sulfate respiration. These results confirmed the prediction that the Qmo complex is in the electron pathway for sulfate-reduction and revealed that no other transmembrane complex could compensate when Qmo was lacking.

  19. Diverse Oxidative Stress Resistance Mechanisms in Sulfate-reducing Bacteria as Revealed by Global Analysis of the Impact of H2O2 Exposure on Desulfovibrio vulgaris Hildenborough

    NASA Astrophysics Data System (ADS)

    Zhou, A.; Mukhopadhyay, A.; He, Z.; Hemme, C. L.; Keasling, J. D.; Arkin, A. P.; Hazen, T. C.; Wall, J. D.; Zhou, J.

    2008-12-01

    Desulfovibrio vulgaris Hildenborough (DvH) plays important roles in the bioremediation of toxic metals. It has been shown aero-tolerant. In order to understand the molecular mechanism of DvH oxidative stress response, mid-log DvH cells were subjected to 1 mM of H2O2 and the transcriptomic changes were examined at 30, 60, 120, 240 and 480 min. The microarray data demonstrated that the gene expression was extensively affected with 29% of genes in the genome significantly up- or down-regulated after 120-min H2O2 treatment. In response to elevated cellular H2O2, expression of thiol-peroxidase genes ahpC and bcp were increased in addition to the significant induction of many thioredoxin reductase and thioredoxin genes, which represent the thiol switch in the oxidative stress response. Increased gene expression PerR regulon genes including PerR itself provided evidence for the regulatory role of PerR in oxidative stress response. The role of Fur was suggested by the significant up-regulation of Fur regulon genes. In terms of the H2O2 scavenging enzymes, different from the stress response to air where both rbr and rbr2 were induced, only rbr2 was up-regulated in response to H2O2; together with up-regulated rdl, they might be the additional players for the detoxification of H2O2. Superoxide scavenging enzyme katA was significantly down-regulated, which is in contrast to its role in facultative microbes such as E.coli and B. subtilis. The links between the up- regulated genes involved in H2O2 scavenging, protein fate, DNA metabolism and lipid metabolism and the down-regulated genes involved in sulfate reduction, energy production and translation were demonstrated by the gene co-expression network. The proteomics data provided further evidence in translation level and complemented the transcriptomics data. Taken together, the cellular response of D. vulgaris Hildenborough to H2O2 was the up-regulation of detoxification, protein and DNA repair systems and the down

  20. Rhizobium hidalgonense sp. nov., a nodule endophytic bacterium of Phaseolus vulgaris in acid soil.

    PubMed

    Yan, Jun; Yan, Hui; Liu, Li Xue; Chen, Wen Feng; Zhang, Xiao Xia; Verástegui-Valdés, Myrthala M; Wang, En Tao; Han, Xiao Zeng

    2017-01-01

    One Gram-negative, aerobic, motile, rod-shaped bacterium, designated as FH14(T), was isolated from nodules of Phaseolus vulgaris grown in Hidalgo State of Mexico. Results based upon 16S rRNA gene (≥99.8 % similarities to known species), concatenated sequence (recA, atpD and glnII) analysis of three housekeeping genes (≤93.4 % similarities to known species) and average nucleotide identity (ANI) values of genome sequence (ranged from 87.6 to 90.0 % to related species) indicated the distinct position of strain FH14(T) within the genus Rhizobium. In analyses of symbiotic genes, only nitrogen fixation gene nifH was amplified that had nucleotide sequence identical to those of the bean-nodulating strains in R. phaseoli and R. vallis, while nodulation gene nodC gene was not amplified. The failure of nodulation to its original host P. vulgaris and other legumes evidenced the loss of its nodulation capability. Strain FH14(T) contained summed feature 8 (C18:1 ω6c/C18:1 ω7c, 59.96 %), C16:0 (10.6 %) and summed feature 2 (C12:0 aldehyde/unknown 10.928, 10.24 %) as the major components of cellular fatty acids. Failure to utilize alaninamide, and utilizing L-alanine, L-asparagine and γ-amino butyric acid as carbon source, distinguished the strain FH14(T) from the type strains for the related species. The genome size and DNA G+C content of FH14(T) were 6.94 Mbp and 60.8 mol %, respectively. Based on those results, a novel specie in Rhizobium, named Rhizobium hidalgonense sp. nov., was proposed, with FH14(T) (=HAMBI 3636(T) = LMG 29288(T)) as the type strain.

  1. Two Component Signal Transduction in Desulfovibrio Species

    SciTech Connect

    Luning, Eric; Rajeev, Lara; Ray, Jayashree; Mukhopadhyay, Aindrila

    2010-05-17

    The environmentally relevant Desulfovibrio species are sulfate-reducing bacteria that are of interest in the bioremediation of heavy metal contaminated water. Among these, the genome of D. vulgaris Hildenborough encodes a large number of two component systems consisting of 72 putative response regulators (RR) and 64 putative histidinekinases (HK), the majority of which are uncharacterized. We classified the D. vulgaris Hildenborough RRs based on their output domains and compared the distribution of RRs in other sequenced Desulfovibrio species. We have successfully purified most RRs and several HKs as His-tagged proteins. We performed phospho-transfer experiments to verify relationships between cognate pairs of HK and RR, and we have also mapped a few non-cognate HK-RR pairs. Presented here are our discoveries from the Desulfovibrio RR categorization and results from the in vitro studies using purified His tagged D. vulgaris HKs and RRs.

  2. Salimesophilobacter vulgaris gen. nov., sp. nov., an anaerobic bacterium isolated from paper-mill wastewater.

    PubMed

    Zhang, Yan-Zhou; Fang, Ming-Xu; Zhang, Wen-Wu; Li, Tian-Tian; Wu, Min; Zhu, Xu-Fen

    2013-04-01

    A novel anaerobic, heterotrophic bacterium, designated strain Zn2(T), was isolated from the wastewater of a paper mill in Zhejiang, China. Cells were gram-type-positive rods, 0.5-0.8 µm wide and 2-4 µm long, and were motile by a lateral flagellum. The ranges of temperature and pH for growth were 10-50 °C and pH 6.0-9.5. Optimal growth occurred at 35 °C and pH 7.3-7.5. The strain did not require NaCl for growth, but its inclusion in the medium improved growth (optimum concentration 6 %). Substrates utilized as sole carbon sources were peptone, tryptone, Casamino acids, D-xylose, salicin, glycerol, formate, acetate and propionate. The main products of carbohydrate fermentation were acetate, formate, propionate and lactate. Elemental sulfur, thiosulfate and Fe(III) were used as electron acceptors, but sulfate, sulfite, nitrate, nitrite and Mn(IV) were not. Growth was inhibited by the addition of 10 µg ampicillin, penicillin, tetracycline or chloramphenicol ml(-1). iso-C15 : 0, C14 : 0, C16 : 0, C16 : 1 cis9 and C18 : 1 cis9 were the major fatty acids. Strain Zn2(T) did not contain any detectable menaquinones or ubiquinones. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, two unknown phospholipids and four unknown glycolipids. The genomic DNA G+C content was 37 mol%, as determined by HPLC. 16S rRNA gene sequence analysis revealed that strain Zn2(T) was a member of family Clostridiaceae, and was most closely related to the type strains of Geosporobacter subterraneus, Thermotalea metallivorans and Caminicella sporogenes, showing 91.2, 90.3 and 91.1 % sequence similarity, respectively. On the basis of its phenotypic and genotypic properties, strain Zn2(T) is suggested to represent a novel species of a new genus, for which the name Salimesophilobacter vulgaris gen. nov., sp. nov. is proposed. The type strain of Salimesophilobacter vulgaris is Zn2(T) ( = DSM 24770(T)

  3. Genome of ‘Ca. Desulfovibrio trichonymphae', an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut

    PubMed Central

    Kuwahara, Hirokazu; Yuki, Masahiro; Izawa, Kazuki; Ohkuma, Moriya; Hongoh, Yuichi

    2017-01-01

    The cellulolytic protist Trichonympha agilis in the termite gut permanently hosts two symbiotic bacteria, ‘Candidatus Endomicrobium trichonymphae' and ‘Candidatus Desulfovibrio trichonymphae'. The former is an intracellular symbiont, and the latter is almost intracellular but still connected to the outside via a small pore. The complete genome of ‘Ca. Endomicrobium trichonymphae' has previously been reported, and we here present the complete genome of ‘Ca. Desulfovibrio trichonymphae'. The genome is small (1 410 056 bp), has many pseudogenes, and retains biosynthetic pathways for various amino acids and cofactors, which are partially complementary to those of ‘Ca. Endomicrobium trichonymphae'. An amino acid permease gene has apparently been transferred between the ancestors of these two symbionts; a lateral gene transfer has affected their metabolic capacity. Notably, ‘Ca. Desulfovibrio trichonymphae' retains the complex system to oxidize hydrogen by sulfate and/or fumarate, while genes for utilizing other substrates common in desulfovibrios are pseudogenized or missing. Thus, ‘Ca. Desulfovibrio trichonymphae' is specialized to consume hydrogen that may otherwise inhibit fermentation processes in both T. agilis and ‘Ca. Endomicrobium trichonymphae'. The small pore may be necessary to take up sulfate. This study depicts a genome-based model of a multipartite symbiotic system within a cellulolytic protist cell in the termite gut. PMID:27801909

  4. Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: Combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundance

    SciTech Connect

    Wu, Gang; Nie, Lei; Zhang, Weiwen

    2006-05-26

    ABSTRACT-The context-dependent expression of genes is the core for biological activities, and significant attention has been given to identification of various factors contributing to gene expression at genomic scale. However, so far this type of analysis has been focused whether on relation between mRNA expression and non-coding sequence features such as upstream regulatory motifs or on correlation between mRN abundance and non-random features in coding sequences (e.g. codon usage and amino acid usage). In this study multiple regression analyses of the mRNA abundance and all sequence information in Desulfovibrio vulgaris were performed, with the goal to investigate how much coding and non-coding sequence features contribute to the variations in mRNA expression, and in what manner they act together...

  5. Functional genomic study of the environmentally important Desulfovibrio /Methanococcus syntrophic co-culture.

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, A.

    2008-12-01

    The use of microbe-oriented bioremediation for ameliorating extensive environmental pollution has fostered fundamental and applied studies of environmentally relevant microorganisms such as Desulfovibrio vulgaris, Shewanella oneidensis and Geobacter metallireducens.. Concurrently, there has been an increasing appreciation that the physiology of these organisms in pure culture is not necessarily representative of its activities in the environment. To enable a better understanding of microbial physiology under more environmentally relevant conditions, the syntrophic growth between the sulfate reducing bacterium, D. vulgaris and the hydrogenotrophic methanogen, Methanococcus maripaludis serves as an ideal system for laboratory studies. Cell wide analyses using transcript, proteomics and metabolite analysis have been widely used to understand cellular activity at a molecular level. Using D. vulgaris and M. maripaludis arrays, and the iTRAQ proteomics method, we studied the physiology of the D. vulgaris / M. maripaludis syntrophic co- cultures. The results from this study allowed us to identify differences in cellular response in mono-culture vs. co-culture growth for both D. vulgaris and M. maripaludis.

  6. Enzymatic redox chemistry: A proposed reaction pathway for the six-electron reduction of SO sub 3 sup 2 minus to S sup 2 minus by the assimilatory-type sulfite reductase from Desulfovibrio vulgaris (Hildenborough)

    SciTech Connect

    Tan, Jian; Cowan, J.A. )

    1991-09-10

    A detailed reaction pathway for the six-electron reduction of SO{sub 3}{sup 2{minus}} to S{sup 2{minus}} by the assimilatory-type sulfite reductase (SiR) from Desulfovibrio vulgaris (Hildenborough) has been deduced from experiments with {sup 35}S-labeled enzyme and the relative reaction rates of nitrogenous substrates. The ligand bridging the prosthetic (Fe{sub 4}S{sub 4})-siroheme center is apparently exchanged by {sup 35}S{sup 2{minus}} in both oxidized and reduced enzyme. This {sup 35}S{sup 2{minus}} label was retained in the course of SO{sub 3}{sup 2{minus}} reduction, implicating substrate binding to the nonbridging axial site of the siroheme. A reaction mechanism is proposed in which SO{sub 3}{sup 2{minus}} binds to Fe{sup 2+} through the sulfur atom, followed by a series of two-electron reductive cleavages of S-O bonds. Protonation of oxygen facilitates bond cleavage, giving hydroxide as leaving group. The bridge remains intact throughout the course of the reaction, providing an efficient coupling pathway for electron transfer between the cluster and siroheme.

  7. Purification, crystallization and preliminary X-ray diffraction analysis of adenosine triphosphate sulfurylase (ATPS) from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774

    SciTech Connect

    Gavel, Olga Yu.; Kladova, Anna V.; Bursakov, Sergey A.; Dias, João M.; Texeira, Susana; Shnyrov, Valery L.; Moura, José J. G.; Moura, Isabel; Romão, Maria J.; Trincão, José

    2008-07-01

    Native zinc-containing ATP sulfurylase from D. desulfuricans ATCC 27774 was purified to homogeneity and crystallized. Diffraction data were collected to 2.5 Å resolution. Native zinc/cobalt-containing ATP sulfurylase (ATPS; EC 2.7.7.4; MgATP:sulfate adenylyltransferase) from Desulfovibrio desulfuricans ATCC 27774 was purified to homogeneity and crystallized. The orthorhombic crystals diffracted to beyond 2.5 Å resolution and the X-ray data collected should allow the determination of the structure of the zinc-bound form of this ATPS. Although previous biochemical studies of this protein indicated the presence of a homotrimer in solution, a dimer was found in the asymmetric unit. Elucidation of this structure will permit a better understanding of the role of the metal in the activity and stability of this family of enzymes.

  8. Identification of Molecular and Cellular Responses of Desulfovibrio vulgaris Biofilms under Culture Conditions Relevant to Field Conditions for Bioreduction of Toxic Metals and Radionuclides

    SciTech Connect

    Judy D. Wall

    2011-06-09

    Our findings demonstrated that D. vulgaris surface-adhered populations produce extracellular structures, and that that the cells have altered carbon and energy flux compared to planktonic cells. Biofilms did not have greatly increased carbohydrate accumulation. Interestingly genes present on the native plasmid found in D. vulgaris Hildenborough were necessary for wild type biofilm formation. In addition, extracellular appendages dependent on functions or proteins encoded by flaG or fliA also contributed to biofilm formation. Studies with SRB biofilms have indicated that the reduction and precipitation of metals can occur within the biofilm matrix; however, little work has been done to elucidate the physiological state of surface-adhered cells during metal reduction (Cr6+, U6+) and how this process is affected by nutrient feed levels (i.e., the stimulant).

  9. FT-IR Characterization of the Light-Induced Ni-L2 and Ni-L3 States of [NiFe] Hydrogenase from Desulfovibrio vulgaris Miyazaki F.

    PubMed

    Tai, Hulin; Nishikawa, Koji; Inoue, Seiya; Higuchi, Yoshiki; Hirota, Shun

    2015-10-29

    Different light-induced Ni-L states of [NiFe] hydrogenase from its Ni-C state have previously been observed by EPR spectroscopy. Herein, we succeeded in detecting simultaneously two Ni-L states of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F by FT-IR spectroscopy. A new light-induced νCO band at 1890 cm(-1) and νCN bands at 2034 and 2047 cm(-1) were detected in the FT-IR spectra of the H2-activated enzyme under N2 atmosphere at basic conditions, in addition to the 1910 cm(-1) νCO band and 2047 and 2061 cm(-1) νCN bands of the Ni-L2 state. The new bands were attributed to the Ni-L3 state by comparison of the FT-IR and EPR spectra. The νCO and νCN frequencies of the Ni-L3 state are the lowest frequencies observed among the corresponding frequencies of standard-type [NiFe] hydrogenases in various redox states. These results indicate that a residue, presumably Ni-coordinating Cys546, is protonated and deprotonated in the Ni-L2 and Ni-L3 states, respectively. Relatively small ΔH (6.4 ± 0.8 kJ mol(-1)) and ΔS (25.5 ± 10.3 J mol(-1) K(-1)) values were obtained for the conversion from the Ni-L2 to Ni-L3 state, which was in agreement with the previous proposals that deprotonation of Cys546 is important for the catalytic reaction of the enzyme.

  10. Empirical Establishment of Oligonucleotide Probe Design Criteria; Use of Microarrays with Different Probe Sizes for Monitoring Gene Expression; Temporal Transcriptomic Analysis as Desulfovibrio vulgaris Hildenborough Transitions into Stationary Phase during Electron Donor Depletion

    SciTech Connect

    He, Q.; He, Z.; Huang, K. H.; Alm, E. J.; Wan, X. F.; Hazen, T. C.; Arkin, A. P.; Wall, J. D.; Zhou, J. Z.; Fields, M. W.

    2005-07-15

    In order to experimentally establish the criteria for designing gene-specific and group-specific oligonucleotide probes, an oligonucleotide array was constructed that contained perfect match (PM) and mismatch (MM) probes (50mers and 70mers) based upon 4 genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were examined. Little hybridization was observed at a probe-target identity of <85% for both 50mer and 70mer probes........Based on the experimental results, a set of criteria are suggested for the design of gene-specific and group-specific oligonucleotide probes, and these criteria should provide valuable information for the development of new software and algorithms for microarray-based studies.; Microarrays with oligonucleotides of different lengths were used to monitor gene expression at a wholegenome level. To determine what length of oligonucleotide is a better alternative to PCR-generated probes, the performance of oligonucleotide probes was systematically compared to that of their PCR-generated counterparts for 96 genes from Shewanella oneidensis MR-1 in terms of overall signal intensity, numbers of genes detected, specificity, sensitivity, and differential gene expression under experimental conditions. .......To evaluate differential gene expression under experimental conditions, S. oneidensis MR-1 cells were exposed to low- or high-pH conditions for 30 and 60 min, and the transcriptional profiles detected by oligonucleotide probes (50-mer, 60-mer, and 70-mer) were closely correlated with those detected by the PCR probes. The results demonstrated that 70-mer oligonucleotides can provide the performance most comparable to the performance obtained with PCR-generated probes.; Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the

  11. Overproduction of the rbo gene product from Desulfovibrio species suppresses all deleterious effects of lack of superoxide dismutase in Escherichia coli.

    PubMed Central

    Pianzzola, M J; Soubes, M; Touati, D

    1996-01-01

    In an attempt to isolate the superoxide dismutase (SOD) gene from the anaerobic sulfate-reducing bacterium Desulfoarculus baarsii, a DNA fragment was isolated which functionally complemented an Escherichia coli mutant (sodA sodB) deficient in cytoplasmic SODs. This region carries two open reading frames with sequences which are very similar to that of the rbo-rub operon from Desulfovibrio vulgaris. Independent expression of the rbo and rub genes from ptac showed that expression of rbo was responsible for the observed phenotype. rbo overexpression suppressed all deleterious effects of SOD deficiency in E. coli, including inactivation by superoxide of enzymes containing 4Fe-4S clusters and DNA damage produced via the superoxide-enhanced Fenton reaction. Thus, rbo restored to the sodA sodB mutant the ability to grow on minimal medium without the addition of branched amino acids, and growth on gluconate and succinate carbon sources was no longer impaired. The spontaneous mutation rate, which is elevated in SOD-deficient mutants, returned to the wild-type level in the presence of Rbo, which also restored aerobic viability of sodA sodB recA mutants. Rbo from Desulfovibrio vulgaris, but not Desulfovibrio gigas desulforedoxin, which corresponds to the NH2-terminal domain of Rbo, complemented sod mutants. The physiological role of Rbo in sulfate-reducing bacteria is unknown. In E. coli, Rbo may permit the bacterium to avoid superoxide stress by maintaining functional (reduced) superoxide sensitive 4Fe-4S clusters. It would thereby restore enzyme activities and prevent the release of iron that occurs after cluster degradation and presumably leads to DNA damage. PMID:8955290

  12. Electron transfer pathways of formate-driven H2 production in Desulfovibrio.

    PubMed

    Martins, Mónica; Mourato, Cláudia; Morais-Silva, Fabio O; Rodrigues-Pousada, Claudina; Voordouw, Gerrit; Wall, Judy D; Pereira, Inês A C

    2016-09-01

    The potential of sulfate-reducing bacteria (SRB) as biocatalysts for H2 production from formate was recently demonstrated, but the electron transfer pathways involved were not described. In the present work, we analyzed the H2 production capacity of five Desulfovibrio strains: Desulfovibrio vulgaris, Desulfovibrio desulfuricans, Desulfovibrio alaskensis, Desulfovibrio fructosivorans, and Desulfovibrio gigas. D. vulgaris showed the highest H2 productivity (865 mL Lmedium (-1)), and D. gigas the lowest one (374 mL Lmedium (-1) of H2). The electron transfer pathways involved in formate-driven H2 production by these two organisms were further investigated through the study of deletion mutants of hydrogenases (Hases) and formate dehydrogenases (Fdhs). In D. vulgaris, the periplasmic FdhAB is the key enzyme for formate oxidation and two pathways are apparently involved in the production of H2 from formate: a direct one only involving periplasmic enzymes and a second one that involves transmembrane electron transfer and may allow energy conservation. In the presence of selenium, the Hys [NiFeSe] Hase is the main periplasmic enzyme responsible for H2 production, and the cytoplasmic Coo Hase is apparently involved in the ability of D. vulgaris to grow by converting formate to H2, in sparging conditions. Contrary to D. vulgaris, H2 production in D. gigas occurs exclusively by the direct periplasmic route and does not involve the single cytoplasmic Hase, Ech. This is the first report of the metabolic pathways involved in formate metabolism in the absence of sulfate in SRB, revealing that the electron transfer pathways are species-specific.

  13. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater

    SciTech Connect

    Ramsay, Bradley D.; Hwang, Chiachi; Woo, Hannah L.; Carroll, Sue L.; Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Samuel; Peters, Lin; Chertkov, Olga; Held, Brittany; Detter, John C.; Han, Cliff S.; Tapia, Roxanne; Land, Miriam L.; Hauser, Loren J.; Kyrpides, Nikos C.; Ivanova, Natalia N.; Mikhailova, Natalia; Pagani, Loanna; Woyke, Tanja; Arkin, Adam P.; Dehal, Paramvir; Chivian, Dylan; Criddle, Craig S.; Wu, Weimin; Chakraborty, Romy; Hazen, Terry C.; Fields, Matthew W.

    2015-03-12

    Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.

  14. Probable new species of Desulfovibrio isolated from a pyogenic liver abscess.

    PubMed Central

    Tee, W; Dyall-Smith, M; Woods, W; Eisen, D

    1996-01-01

    A fastidious, slowly growing, spiral gram-negative bacterium was isolated from the liver abscess of an 82-year-old man with a 3-week history of febrile illness. The organism was an obligate anaerobe that grew at 37 and 42 degrees C but not at 25 degrees C. Its vibrioid or spiral morphology on Gram staining, rapid progressive motility, electron micrograph features, and biochemical tests were all consistent with the organism belonging to the genus Desulfovibrio. 16S rRNA gene sequencing of this organism demonstrated a 97% similarity to Desulfovibrio desulfuricans with 45 nucleotide differences, suggesting that it is a new species of Desulfovibrio. PMID:8784584

  15. Investigating the role of CheA-3 in Dusulfovibrio Vulgaris Hildenborough

    SciTech Connect

    Ray, Jayashee; Keller, Kimberley; Krierim, Bernhard; Auer, Manfred; Keasling, Jay; Wall, Judy; Mukhopadhyay, Aindrila

    2010-05-22

    Multiple sets of chemotaxis genes including three cheA homologs were identified in the genome sequence of the anaerobic bacterium Desulfovibrio vulgaris Hildenborough. Each CheA is a histidine kinase (HK) and part of a two component signal transduction system. Knock out mutants in the three cheA genes were created using single cross-over homologous recombination insertion. We studied the phenotypes of the cheA mutants in detail and discovered that ?cheA-3 has a non swarming/swimming phenotype both in the soft agar plates and Palleroni chamber assays. CheA-3 shows similarity to the Shewanella oneidensis CheA-3 and the Vibrio cholerae CheA-2 that are responsible for chemotaxis in the respective organisms. We did not find any morphological or structural differences between the three Delta cheA mutants and the wild type cells in electron microscopy. Our results from these studies are presented.

  16. Genetic basis for nitrate resistance in Desulfovibrio strains

    PubMed Central

    Korte, Hannah L.; Fels, Samuel R.; Christensen, Geoff A.; Price, Morgan N.; Kuehl, Jennifer V.; Zane, Grant M.; Deutschbauer, Adam M.; Arkin, Adam P.; Wall, Judy D.

    2014-01-01

    Nitrate is an inhibitor of sulfate-reducing bacteria (SRB). In petroleum production sites, amendments of nitrate and nitrite are used to prevent SRB production of sulfide that causes souring of oil wells. A better understanding of nitrate stress responses in the model SRB, Desulfovibrio vulgaris Hildenborough and Desulfovibrio alaskensis G20, will strengthen predictions of environmental outcomes of nitrate application. Nitrate inhibition of SRB has historically been considered to result from the generation of small amounts of nitrite, to which SRB are quite sensitive. Here we explored the possibility that nitrate might inhibit SRB by a mechanism other than through nitrite inhibition. We found that nitrate-stressed D. vulgaris cultures grown in lactate-sulfate conditions eventually grew in the presence of high concentrations of nitrate, and their resistance continued through several subcultures. Nitrate consumption was not detected over the course of the experiment, suggesting adaptation to nitrate. With high-throughput genetic approaches employing TnLE-seq for D. vulgaris and a pooled mutant library of D. alaskensis, we determined the fitness of many transposon mutants of both organisms in nitrate stress conditions. We found that several mutants, including homologs present in both strains, had a greatly increased ability to grow in the presence of nitrate but not nitrite. The mutated genes conferring nitrate resistance included the gene encoding the putative Rex transcriptional regulator (DVU0916/Dde_2702), as well as a cluster of genes (DVU0251-DVU0245/Dde_0597-Dde_0605) that is poorly annotated. Follow-up studies with individual D. vulgaris transposon and deletion mutants confirmed high-throughput results. We conclude that, in D. vulgaris and D. alaskensis, nitrate resistance in wild-type cultures is likely conferred by spontaneous mutations. Furthermore, the mechanisms that confer nitrate resistance may be different from those that confer nitrite resistance

  17. Structural and serological studies of the O-antigen of the bacterium Proteus vulgaris OX2 (serogroup O2) used in the Weil-Felix test.

    PubMed

    Cedzynski, M; Knirel YuA; Amano, K I; Swierzko, A S; Paramonov, N A; Senchenkova, S N; Kaca, W

    1997-01-01

    Based on monosaccharide analysis and 1H- and 13C-NMR spectroscopy, the following structure of the O-specific polysaccharide chain of Proteus vulgaris OX2 lipopolysaccharide (LPS), which defines the O2 specificity of Proteus, was established: [formula: see text] where L-QuiNAc is N-acetyl-L-quinovosamine (2-acetamido-2,6-dideoxy-L-glucose). Various strains of P. vulgaris OX2 used in the Weil-Felix test for serodiagnosis of rickettsiosis (spotted fevers, except for Rocky Mountain spotted fever) were shown to produce LPS with the same O-specific polysaccharide, which differs structurally and serologically from LPS of P. vulgaris OX19 used as antigen for serodiagnosis of typhus and Rocky Mountain spotted fever. O-Acetyl groups present in the polysaccharide are not important for manifesting the immunospecificity. ELISA confirmed that the epitope responsible for the cross-reactivity between sera from patients with Japanese spotted fever and P. vulgaris OX2 cells is located on the P. vulgaris LPS. At the same time, no cross-reaction was observed between rabbit anti-P. vulgaris OX2 antibodies and the spotted fever group (SFG) rickettsial cells. Therefore, human anti-SFG rickettsial antibodies and rabbit anti-P. vulgaris OX2 antibodies may bind to distinct epitopes on P. vulgaris OX2 LPS, and no epitope recognized by rabbit anti-P. vulgaris OX2 antibodies is present on the LPS or any other surface antigen of SFG rickettsiae.

  18. The Complete Genome Sequence and Updated Annotation of Desulfovibrio alaskensis G20

    SciTech Connect

    Hauser, Loren John; Wall, Judy D.; Brown, Steven D; Land, Miriam L; Bruce, David; Detter, J. Chris; Frank, Larimer; Goodwin, Lynne A.; Han, Cliff; Lapidus, Alla L.; Nolan, Matt; Palumbo, Anthony Vito; Pitluck, Samual; Keller, Kimberly L; Rapp-Giles, Barbara J; Price, Morgan N.; Lin, Monica; Tapia, Roxanne; Copeland, A; Cheng, Jan-Fang

    2011-01-01

    Desulfovibrio alaskensis G20 (formerly desulfuricans G20) is a Gram-negative mesophilic sulfate-reducing bacterium (SRB), known to corrode ferrous metals and to reduce toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms. We present the 3.7 Mb genome sequence to provide insights into its physiology.

  19. Complete Genome Sequence and Updated Annotation of Desulfovibrio alaskensis G20

    DOE PAGES

    Hauser, Loren J.; Land, Miriam L.; Brown, Steven D.; ...

    2011-06-17

    Desulfovibrio alaskensis G20 (formerly desulfuricans G20) is a Gram-negative mesophilic sulfate-reducing bacterium (SRB), known to corrode ferrous metals and to reduce toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms. We present the 3.7 Mb genome sequence to provide insights into its physiology.

  20. Genome sequence of the mercury-methylating strain Desulfovibrio desulfuricans ND132.

    PubMed

    Brown, Steven D; Gilmour, Cynthia C; Kucken, Amy M; Wall, Judy D; Elias, Dwayne A; Brandt, Craig C; Podar, Mircea; Chertkov, Olga; Held, Brittany; Bruce, David C; Detter, John C; Tapia, Roxanne; Han, Cliff S; Goodwin, Lynne A; Cheng, Jan-Fang; Pitluck, Samuel; Woyke, Tanja; Mikhailova, Natalia; Ivanova, Natalia N; Han, James; Lucas, Susan; Lapidus, Alla L; Land, Miriam L; Hauser, Loren J; Palumbo, Anthony V

    2011-04-01

    Desulfovibrio desulfuricans strain ND132 is an anaerobic sulfate-reducing bacterium (SRB) capable of producing methylmercury (MeHg), a potent human neurotoxin. The mechanism of methylation by this and other organisms is unknown. We present the 3.8-Mb genome sequence to provide further insight into microbial mercury methylation.

  1. Complete Genome Sequence of Mercury-Methylating Desulfovibrio desulfuricans ND132

    SciTech Connect

    Brown, Steven D; Gilmour, C C; Kucken, A M; Wall, Judy D.; Brandt, Craig C; Elias, Dwayne A; Podar, Mircea; Chertkov, Olga; Held, Brittany; Bruce, David; Detter, J C; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Land, Miriam L; Hauser, Loren John; Palumbo, Anthony Vito

    2011-01-01

    Desulfovibrio desulfuricans strain ND132 is an anaerobic sulfate-reducing bacterium (SRB) capable of producing methylmercury (MeHg), a potent human neurotoxin. The mechanism of methylation by this and other organisms is unknown. We present the 3.8-Mb genome sequence to provide further insight into microbial mercury methylation.

  2. Genome Sequence of Mercury-Methylating and Pleomorphic Desulfovibrio africanus strain Walvis Bay

    SciTech Connect

    Brown, Steven D; Wall, Judy D.; Kucken, A M; Gilmour, C C; Podar, Mircea; Brandt, Craig C; Teshima, Hazuki; Detter, J C; Han, Cliff; Land, Miriam L; Lucas, Susan; Han, James; Pennacchio, Len; Nolan, Matt; Pitluck, Samual; Woyke, Tanja; Goodwin, Lynne A.; Palumbo, Anthony Vito; Elias, Dwayne A

    2011-01-01

    Desulfovibrio africanus strain Walvis Bay is an anaerobic sulfate-reducing bacterium capable of producing methylmercury (MeHg), a potent human neurotoxin. The mechanism of methylation by this and other organisms is unknown. We present the 4.2-Mb genome sequence to provide further insight into microbial mercury methylation and sulfate-reducing bacteria.

  3. Regulation, sensory domains and roles of two Desulfovibrio desulfuricans ATCC27774 Crp family transcription factors, HcpR1 and HcpR2, in response to nitrosative stress.

    PubMed

    Cadby, Ian T; Ibrahim, Susan A; Faulkner, Matthew; Lee, David J; Browning, Douglas; Busby, Stephen J; Lovering, Andrew L; Stapleton, Melanie R; Green, Jeffrey; Cole, Jeffrey A

    2016-12-01

    In silico analyses identified a Crp/Fnr family transcription factor (HcpR) in sulfate-reducing bacteria that controls expression of the hcp gene, which encodes the hybrid cluster protein and contributes to nitrosative stress responses. There is only one hcpR gene in the model sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, but two copies in Desulfovibrio desulfuricans 27774, which can use nitrate as an alternative electron acceptor to sulfate. Structures of the D. desulfuricans hcpR1, hcpR2 and hcp operons are reported. We present evidence that hcp expression is regulated by HcpR2, not by HcpR1, and that these two regulators differ in both their DNA-binding site specificity and their sensory domains. HcpR1 is predicted to be a b-type cytochrome. HcpR1 binds upstream of the hcpR1 operon and its synthesis is regulated coordinately with hcp in response to NO. In contrast, hcpR2 expression was not induced by nitrate, nitrite or NO. HcpR2 is an iron-sulfur protein that reacts with NO and O2 . We propose that HcpR1 and HcpR2 use different sensory mechanisms to regulate subsets of genes required for defense against NO-induced nitrosative stress, and that diversification of signal perception and DNA recognition by these two proteins is a product of D. desulfuricans adaptation to its particular environmental niche.

  4. Properties of aromatic residues in ferricytochrome c3 of desulforvibrio vulgaris Miyazaki F studied by 1H NMR

    NASA Astrophysics Data System (ADS)

    Park, Jang-Su; Enoki, Minoru; Ohbu, Ayako; Fan, Kejung; Niki, Katsumi; Akutsu, Hideo; Kyogoku, Yoshimasa

    1991-01-01

    Conditions for the specific labelling of the tetrahaeme protein cytochrome c3 of Desulfovibrio vulgaris Miyazaki F during culture of this sulphate-reducing bacterium in a minimal medium were established. Phenylalanine and tyrosine residues were specifically deuterated at more than 85% efficiency. Cytochrome c3 has nine histidine, three tyrosine and two phenylalamine residues. Eight histidine imidazoles are ligated to four haeme groups. Using the deuterated cytochrome c3, aromatic proton signals of phenylalanine and tyrosine residues in the fully oxidized state were identified. However, the signals of one phenylalanine residue were missing and this was tentatively assigned to Phe20. The aromatic proton signals of His67 were also assigned p2H titration. Its pk1 was much higher than that for the free histidine residue. No tyrosine residue was ionized up to p2H 12.

  5. Methods for Engineering Sulfate Reducing Bacteria of the Genus Desulfovibrio

    SciTech Connect

    Chhabra, Swapnil R; Keller, Kimberly L.; Wall, Judy D.

    2011-03-15

    Sulfate reducing bacteria are physiologically important given their nearly ubiquitous presence and have important applications in the areas of bioremediation and bioenergy. This chapter provides details on the steps used for homologous-recombination mediated chromosomal manipulation of Desulfovibrio vulgaris Hildenborough, a well-studied sulfate reducer. More specifically, we focus on the implementation of a 'parts' based approach for suicide vector assembly, important aspects of anaerobic culturing, choices for antibiotic selection, electroporation-based DNA transformation, as well as tools for screening and verifying genetically modified constructs. These methods, which in principle may be extended to other sulfate-reducing bacteria, are applicable for functional genomics investigations, as well as metabolic engineering manipulations.

  6. Draft Genome Sequence of Desulfovibrio BerOc1, a Mercury-Methylating Strain

    PubMed Central

    Gassie, Claire; Bouchez, Oliver; Klopp, Christophe; Guyoneaud, Rémy

    2017-01-01

    ABSTRACT Desulfovibrio BerOc1 is a sulfate-reducing bacterium isolated from the Berre lagoon (French Mediterranean coast). BerOc1 is able to methylate and demethylate mercury. The genome size is 4,081,579 bp assembled into five contigs. We identified the hgcA and hgcB genes involved in mercury methylation, but not those responsible for mercury demethylation. PMID:28104657

  7. Draft Genome Sequence of Desulfovibrio BerOc1, a Mercury-Methylating Strain.

    PubMed

    Goñi Urriza, Marisol; Gassie, Claire; Bouchez, Oliver; Klopp, Christophe; Guyoneaud, Rémy

    2017-01-19

    Desulfovibrio BerOc1 is a sulfate-reducing bacterium isolated from the Berre lagoon (French Mediterranean coast). BerOc1 is able to methylate and demethylate mercury. The genome size is 4,081,579 bp assembled into five contigs. We identified the hgcA and hgcB genes involved in mercury methylation, but not those responsible for mercury demethylation.

  8. Crystallization and preliminary X-ray analysis of a class II release factor RF3 from a sulfate-reducing bacterium

    SciTech Connect

    Kihira, Kiyohito; Numata, Shuko; Kitamura, Masaya; Kondo, Jun; Terawaki, Shinichi; Shomura, Yasuhito; Komori, Hirofumi; Shibata, Naoki; Higuchi, Yoshiki

    2008-07-01

    Class II release factor 3 (RF3) from the sulfate-reducing bacterium D. vulgaris Miyazaki F has been overexpressed, purified and crystallized in complex with GDP. Class II release factor 3 (RF3) from the sulfate-reducing bacterium Desulfovibrio vulgaris Miyazaki F, which promotes rapid dissociation of a class I release factor, has been overexpressed, purified and crystallized in complex with GDP at 293 K using the sitting-drop vapour-diffusion method. A data set was collected to 1.8 Å resolution from a single crystal at 100 K using synchrotron radiation. The crystal belongs to space group P1, with unit-cell parameters a = 47.39, b = 82.80, c = 148.29 Å, α = 104.21, β = 89.78, γ = 89.63°. The asymmetric unit contains four molecules of the RF3–GDP complex. The Matthews coefficient was calculated to be 2.3 Å{sup 3} Da{sup −1} and the solvent content was estimated to be 46.6%.

  9. Genetic transfer in Desulfovibrio desulfuricans

    PubMed Central

    Rapp, Barbara J.; Wall, Judy D.

    1987-01-01

    An apparently defective bacteriophage capable of mediating transduction has been identified in culture filtrates of Desulfovibrio desulfuricans (American Type Culture Collection 27774). Phage-mediated intraspecies transfer of antibiotic resistance markers occurs with a frequency of 10-5 to 10-6 per recipient cell. The vector contains linear fragments of double-stranded DNA of about 13.5 kilobase pairs, which appear to be random pieces of bacterial DNA. As yet, neither induction nor plaque formation has been observed. To our knowledge, a system of genetic exchange has not been described before for a member of the sulfate-reducing bacteria. Images PMID:16578824

  10. Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth.

    PubMed

    Meyer, Birte; Kuehl, Jennifer; Deutschbauer, Adam M; Price, Morgan N; Arkin, Adam P; Stahl, David A

    2013-03-01

    Mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers linked by interspecies electron transfer in syntrophic consortia that may include sulfate-reducing species (e.g., Desulfovibrio). Physiological differences and various gene repertoires implicated in syntrophic metabolism among Desulfovibrio species suggest considerable variation in the biochemical basis of syntrophy. In this study, comparative transcriptional and mutant analyses of Desulfovibrio alaskensis strain G20 and Desulfovibrio vulgaris strain Hildenborough growing syntrophically with Methanococcus maripaludis on lactate were used to develop new and revised models for their alternative electron transfer and energy conservation systems. Lactate oxidation by strain G20 generates a reduced thiol-disulfide redox pair(s) and ferredoxin that are energetically coupled to H(+)/CO(2) reduction by periplasmic formate dehydrogenase and hydrogenase via a flavin-based reverse electron bifurcation process (electron confurcation) and a menaquinone (MQ) redox loop-mediated reverse electron flow involving the membrane-bound Qmo and Qrc complexes. In contrast, strain Hildenborough uses a larger number of cytoplasmic and periplasmic proteins linked in three intertwining pathways to couple H(+) reduction to lactate oxidation. The faster growth of strain G20 in coculture is associated with a kinetic advantage conferred by the Qmo-MQ-Qrc loop as an electron transfer system that permits higher lactate oxidation rates under elevated hydrogen levels (thereby enhancing methanogenic growth) and use of formate as the main electron-exchange mediator (>70% electron flux), as opposed to the primarily hydrogen-based exchange by strain Hildenborough. This study further demonstrates the absence of a conserved gene core in Desulfovibrio that would determine the ability for a syntrophic lifestyle.

  11. Variation among Desulfovibrio Species in Electron Transfer Systems Used for Syntrophic Growth

    PubMed Central

    Meyer, Birte; Kuehl, Jennifer; Deutschbauer, Adam M.; Price, Morgan N.; Arkin, Adam P.

    2013-01-01

    Mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers linked by interspecies electron transfer in syntrophic consortia that may include sulfate-reducing species (e.g., Desulfovibrio). Physiological differences and various gene repertoires implicated in syntrophic metabolism among Desulfovibrio species suggest considerable variation in the biochemical basis of syntrophy. In this study, comparative transcriptional and mutant analyses of Desulfovibrio alaskensis strain G20 and Desulfovibrio vulgaris strain Hildenborough growing syntrophically with Methanococcus maripaludis on lactate were used to develop new and revised models for their alternative electron transfer and energy conservation systems. Lactate oxidation by strain G20 generates a reduced thiol-disulfide redox pair(s) and ferredoxin that are energetically coupled to H+/CO2 reduction by periplasmic formate dehydrogenase and hydrogenase via a flavin-based reverse electron bifurcation process (electron confurcation) and a menaquinone (MQ) redox loop-mediated reverse electron flow involving the membrane-bound Qmo and Qrc complexes. In contrast, strain Hildenborough uses a larger number of cytoplasmic and periplasmic proteins linked in three intertwining pathways to couple H+ reduction to lactate oxidation. The faster growth of strain G20 in coculture is associated with a kinetic advantage conferred by the Qmo-MQ-Qrc loop as an electron transfer system that permits higher lactate oxidation rates under elevated hydrogen levels (thereby enhancing methanogenic growth) and use of formate as the main electron-exchange mediator (>70% electron flux), as opposed to the primarily hydrogen-based exchange by strain Hildenborough. This study further demonstrates the absence of a conserved gene core in Desulfovibrio that would determine the ability for a syntrophic lifestyle. PMID:23264581

  12. Mechanism of Uranium Reduction and Immobilization in Desulfovibrio vulgaris Biofilms.

    PubMed

    Stylo, Malgorzata; Neubert, Nadja; Roebbert, Yvonne; Weyer, Stefan; Bernier-Latmani, Rizlan

    2015-09-01

    The prevalent formation of noncrystalline U(IV) species in the subsurface and their enhanced susceptibility to reoxidation and remobilization, as compared to crystalline uraninite, raise concerns about the long-term sustainability of the bioremediation of U-contaminated sites. The main goal of this study was to resolve the remaining uncertainty concerning the formation mechanism of noncrystalline U(IV) in the environment. Controlled laboratory biofilm systems (biotic, abiotic, and mixed biotic-abiotic) were probed using a combination of U isotope fractionation and X-ray absorption spectroscopy (XAS). Regardless of the mechanism of U reduction, the presence of a biofilm resulted in the formation of noncrystalline U(IV). Our results also show that biotic U reduction is the most effective way to immobilize and reduce U. However, the mixed biotic-abiotic system resembled more closely an abiotic system: (i) the U(IV) solid phase lacked a typically biotic isotope signature and (ii) elemental sulfur was detected, which indicates the oxidation of sulfide coupled to U(VI) reduction. The predominance of abiotic U reduction in our systems is due to the lack of available aqueous U(VI) species for direct enzymatic reduction. In contrast, in cases where bicarbonate is present at a higher concentration, aqueous U(VI) species dominate, allowing biotic U reduction to outcompete the abiotic processes.

  13. Pemphigus vulgaris

    MedlinePlus

    ... this page: //medlineplus.gov/ency/article/000882.htm Pemphigus vulgaris To use the sharing features on this page, please enable JavaScript. Pemphigus vulgaris (PV) is an autoimmune disorder of the ...

  14. Orange protein from Desulfovibrio alaskensis G20: insights into the Mo-Cu cluster protein-assisted synthesis.

    PubMed

    Carepo, Marta S P; Carreira, Cíntia; Grazina, Raquel; Zakrzewska, Małgorzata E; Dolla, Alain; Aubert, Corinne; Pauleta, Sofia R; Moura, José J G; Moura, Isabel

    2016-03-01

    A novel metalloprotein containing a unique [S2MoS2CuS2MoS2](3-) cluster, designated as Orange Protein (ORP), was isolated for the first time from Desulfovibrio gigas, a sulphate reducer. The orp operon is conserved in almost all sequenced Desulfovibrio genomes and in other anaerobic bacteria, however, so far D. gigas ORP had been the only ORP characterized in the literature. In this work, the purification of another ORP isolated form Desulfovibrio alaskensis G20 is reported. The native protein is monomeric (12443.8 ± 0.1 Da by ESI-MS) and contains also a MoCu cluster with characteristic absorption bands at 337 and 480 nm, assigned to S-Mo charge transfer bands. Desulfovibrio alaskensis G20 recombinant protein was obtained in the apo-form from E. coli. Cluster reconstitution studies and UV-visible titrations with tetrathiomolybdate of the apo-ORP incubated with Cu ions indicate that the cluster is incorporated in a protein metal-assisted synthetic mode and the protein favors the 2Mo:1Cu stoichiometry. In Desulfovibrio alaskensis G20, the orp genes are encoded by a polycistronic unit composed of six genes whereas in Desulfovibrio vulgaris Hildenborough the same genes are organized into two divergent operons, although the composition in genes is similar. The gene expression of ORP (Dde_3198) increased 6.6 ± 0.5 times when molybdate was added to the growth medium but was not affected by Cu(II) addition, suggesting an involvement in molybdenum metabolism directly or indirectly in these anaerobic bacteria.

  15. Structural studies on Desulfovibrio gigas cytochrome c3 by two-dimensional 1H-nuclear-magnetic-resonance spectroscopy.

    PubMed Central

    Piçarra-Pereira, M A; Turner, D L; LeGall, J; Xavier, A V

    1993-01-01

    Several aromatic amino acid residues and haem resonances in the fully reduced form of Desulfovibrio gigas cytochrome c3 are assigned, using two-dimensional 1H n.m.r., on the basis of the interactions between the protons of the aromatic amino acids and the haem protons as well as the intrahaem distances known from the X-ray structure [Kissinger (1989) Ph.D. Thesis, Washington State University]. The interhaem interactions observed in the n.m.r. spectra are in full agreement with the D. gigas X-ray structure and also with the n.m.r. data from Desulfovibrio vulgaris (Hildenborough) [Turner, Salgueiro, LeGall and Xavier (1992) Eur. J. Biochem. 210, 931-936]. The good correlation between the calculated ring-current shifts and the observed chemical shifts strongly supports the present assignments. Observation of the two-dimensional nuclear-Overhauser-enhancement spectra of the protein in the reduced, intermediate and fully oxidized stages led to the ordering of the haems in terms of their midpoint redox potentials and their identification in the X-ray structure. The first haem to oxidize is haem I, followed by haems II, III and IV, numbered according to the Cys ligand positions in the amino acid sequences [Mathews (1985) Prog. Biophys. Mol. Biol. 54, 1-56]. Although the haem core architecture is the same for the different Desulfovibrio cytochromes c3, the order of redox potentials is different. PMID:8397514

  16. Structural studies on Desulfovibrio gigas cytochrome c3 by two-dimensional 1H-nuclear-magnetic-resonance spectroscopy.

    PubMed

    Piçarra-Pereira, M A; Turner, D L; LeGall, J; Xavier, A V

    1993-09-15

    Several aromatic amino acid residues and haem resonances in the fully reduced form of Desulfovibrio gigas cytochrome c3 are assigned, using two-dimensional 1H n.m.r., on the basis of the interactions between the protons of the aromatic amino acids and the haem protons as well as the intrahaem distances known from the X-ray structure [Kissinger (1989) Ph.D. Thesis, Washington State University]. The interhaem interactions observed in the n.m.r. spectra are in full agreement with the D. gigas X-ray structure and also with the n.m.r. data from Desulfovibrio vulgaris (Hildenborough) [Turner, Salgueiro, LeGall and Xavier (1992) Eur. J. Biochem. 210, 931-936]. The good correlation between the calculated ring-current shifts and the observed chemical shifts strongly supports the present assignments. Observation of the two-dimensional nuclear-Overhauser-enhancement spectra of the protein in the reduced, intermediate and fully oxidized stages led to the ordering of the haems in terms of their midpoint redox potentials and their identification in the X-ray structure. The first haem to oxidize is haem I, followed by haems II, III and IV, numbered according to the Cys ligand positions in the amino acid sequences [Mathews (1985) Prog. Biophys. Mol. Biol. 54, 1-56]. Although the haem core architecture is the same for the different Desulfovibrio cytochromes c3, the order of redox potentials is different.

  17. Isolation and characterization of a new Cu-Fe protein from Desulfovibrio aminophilus DSM12254.

    PubMed

    Rivas, Maria G; Mota, Cristiano S; Pauleta, Sofia R; Carepo, Marta S P; Folgosa, Filipe; Andrade, Susana L A; Fauque, Guy; Pereira, Alice S; Tavares, Pedro; Calvete, Juan J; Moura, Isabel; Moura, José J G

    2009-10-01

    The isolation and characterization of a new metalloprotein containing Cu and Fe atoms is reported. The as-isolated Cu-Fe protein shows an UV-visible spectrum with absorption bands at 320 nm, 409 nm and 615 nm. Molecular mass of the native protein along with denaturating electrophoresis and mass spectrometry data show that this protein is a multimer consisting of 14+/-1 subunits of 15254.3+/-7.6 Da. Mössbauer spectroscopy data of the as-isolated Cu-Fe protein is consistent with the presence of [2Fe-2S](2+) centers. Data interpretation of the dithionite reduced protein suggest that the metallic cluster could be constituted by two ferromagnetically coupled [2Fe-2S](+) spin delocalized pairs. The biochemical properties of the Cu-Fe protein are similar to the recently reported molybdenum resistance associated protein from Desulfovibrio, D. alaskensis. Furthermore, a BLAST search from the DNA deduced amino acid sequence shows that the Cu-Fe protein has homology with proteins annotated as zinc resistance associated proteins from Desulfovibrio, D. alaskensis, D. vulgaris Hildenborough, D. piger ATCC 29098. These facts suggest a possible role of the Cu-Fe protein in metal tolerance.

  18. Microcalorimetric studies of the growth of sulfate-reducing bacteria: comparison of the growth parameters of some Desulfovibrio species.

    PubMed Central

    Traore, A S; Hatchikian, C E; Le Gall, J; Belaich, J P

    1982-01-01

    We performed a comparative study of the growth energetics of some species of Desulfovibrio by measuring microcalorimetric and molar growth yield values. Lactate and pyruvate were used as energy sources for sulfate reduction. On lactate-sulfate media Desulfovibrio desulfuricans Norway, Desulfovibrio gigas, and Desulfovibrio africanus exhibited molar growth yields of 4.1 +/- 0.6, 3.7 +/- 1.7, and 1.8 +/- 0.1 g/mol, respectively, whereas on pyruvate-sulfate media the molar growth yields were higher (8.5 +/- 0.8, 7.7 +/- 1.6, and 3.5 +/- 0.5 g/mol, respectively). Thus, we found that D. africanus was the least efficient species in converting energy into cell material. The uncoupling of energy in this strain was obvious since its catabolic activities were high compared with those of the two other strains. The enthalpy changes associated with lactate and pyruvate metabolism were -49 +/- 0.7 and -70.2 +/- 6.0 jK/mol, respectively, for D. desulfuricans, -76.6 +/- 1.8 and -91.2 +/- 1.1 kJ/mol, respectively, for D. gigas, and -78.8 +/- 7.2 and -88.0 +/- 6.2 kJ/mol, respectively, for D. africanus. D. gigas and D. africanus produced only acetate, CO2 and hydrogen sulfide as metabolic end products. In addition to these normal end products, D. desulfuricans Norway produced a small amount of butanol. This butanol production was interpreted as reflecting a regulatory system of electron flow during the catabolism of both substrates. Such metabolism was comparable to that reported for D. vulgaris, which lost part of the reducing power of its energy sources through hydrogen evolution. PMID:7056697

  19. Crystallization and preliminary crystallographic analysis of the pyruvate-ferredoxin oxidoreductase from Desulfovibrio africanus.

    PubMed

    Pieulle, L; Chabrière, E; Hatchikian, C; Fontecilla-Camps, J C; Charon, M H

    1999-01-01

    For the first time, crystals of a pyruvate-ferredoxin oxidoreductase (PFOR) suitable for X-ray analysis have been obtained. This enzyme catalyzes, in anaerobic organisms, the crucial energy-yielding reaction of pyruvate decarboxylation to acetylCoA. Polyethylene glycol and divalent metal cations have been used to crystallize the PFOR from the sulfate-reducing bacterium Desulfovibrio africanus. Two different orthorhombic (P212121 ) crystal forms have been grown with unit-cell dimensions a = 86.1, b = 146.7, c = 212.5 A and a = 84.8, b = 144.9, c = 203.0 A. Both crystals diffract to 2.3 A resolution using synchrotron radiation.

  20. Transposon mutagenesis in Desulfovibrio desulfuricans: Development of a random mutagenesis tool from Tn7

    SciTech Connect

    Wall, J.D.; Murnan, T.; Argyle, J.

    1996-10-01

    The transposons Tn5, Tn7, Tn9, and Tn10 or their derivatives have been examined for transposition in the sulfate-reducing bacterium Desulfovibrio desulfuricans G20. Tn7 inserted with a frequency of 10{sup {minus}4} to 10{sup {minus}3} into a unique attachment site that shows strong homology with those sites identified in other gram-negative bacteria. Inactivation of the tnsD gene in Tn7, encoding the function directing insertion into the unique site, yielded a derivative that transposed essentially randomly with a frequency of ca. 10{sup {minus}6} per donor. Derivatives of Tn5, but not wild-type Tn5, were also found to undergo random transposition at a similar frequency. No evidence was obtained for transposition of Tn9 or Tn10. 34 refs., 5 figs., 2 tabs.

  1. Cloning and sequencing of the genes encoding the large and small subunits of the periplasmic (NiFeSe) hydrogenase of Desulfovibrio baculatus

    SciTech Connect

    Menon, N.K.; Peck, H.D. Jr.; Le Gall, J.; Przybyla, A.E.

    1987-12-01

    The genes coding for the large and small subunits of the periplasmic hydrogenase from Desulfovibrio baculatus have been cloned and sequenced. The genes are arranged in an operon with the small subunit gene preceding the large subunit gene. The small subunit gene codes for a 32 amino acid leader sequence supporting the periplasmic localization of the protein, however no ferredoxin-like or other characteristic iron-sulfur coordination sites were observed. The periplasmic hydrogenases from D. baculatus (an NiFeSe protein) and D. vulgaris (an Fe protein) exhibit no homology suggesting that they are structurally different, unrelated entities.

  2. Acne vulgaris.

    PubMed

    Robertson, Kevin M

    2004-08-01

    Acne vulgaris is a common inflammatory skin condition that presents management difficulties to cosmetic surgeons. Acute management and treatment focuses on early diagnosis as well as treatment with topical agents, oral antibiotics, hormonal therapy,and nonablative chemical peel and laser applications. The treatment of postinflammatory scarring must be individualized to address potential macular dyschromia, cystic lesions,epithelial bridges, or deep pitted scars. A review of interventional options is presented to apply to the spectrum of acne scarring as well as a review of the literature to address objectively published reports on efficacy.

  3. Anaerobic degradation of lactate by syntrophic associations of methanosarcina barkeri and desulfovibrio species and effect of H2 on acetate degradation

    SciTech Connect

    McInerney, M.J.; Bryant, M.P.

    1981-02-01

    When grown in the absence of added sulfate, cocultures of Desulfovibrio desulfuricans or Desulfovibrio vulgaris with Methanobrevibacter smithii (Methanobacterium ruminantium), which uses H2 and CO2 for methanogenesis, degraded lactate, with the production of acetate and CH4. When D. desulfuricans or D. vulgaris was grown in the absence of added sulfate in coculture with Methanosarcina barkeri (type strain), which uses both H2-CO2 and acetate for methanogenesis, lactate was stoichiometrically degraded to CH4 and presumably to CO2. During the first 12 days of incubation of the D. desulfuricans-M. barkeri coculture, lactate was completely degraded, with almost stoichiometric production of acetate and CH4. Later, acetate was degraded to CH4 and presumably to CO2. In experiments in which 20 mM acetate and 0 to 20 mM lactate were added to D. desulfuricans-M. barkeri cocultures, no detectable degradation of acetate occurred until the lactate was catabolized. The ultimate rate of acetate utilization for methanogenesis was greater for those cocultures receiving the highest levels of lactate. A small amount of H2 was detected in cocultures which contained D. desulfuricans and M. barkeri until after all lactate was degraded. The addition of H2, but not of lactate, to the growth medium inhibited acetate degradation by pure cultures of M. barkeri. Pure cultures of M. barkeri produced CH4 from acetate at a rate equivalent to that observed for cocultures containing M. barkeri. Inocula of M. barkeri grown with H2-CO2 as the methanogenic substrate produced CH4 from acetate at a rate equivalent to that observed for acetate-grown inocula when grown in a rumen fluid-vitamin-based medium but not when grown in a yeast extract-based medium. The results suggest that H2 produced by the Desulfovibrio species during growth with lactate inhibited acetate degradation by M. barkeri. (Refs. 26).

  4. Degradation of nitrocellulose-based paint by Desulfovibrio desulfuricans ATCC 13541.

    PubMed

    Giacomucci, L; Toja, F; Sanmartín, P; Toniolo, L; Prieto, B; Villa, F; Cappitelli, F

    2012-09-01

    Nitrocellulose is one of the most commonly used compounds in ammunition and paint industries and its recalcitrance to degradation has a negative impact on human health and the environment. In this study the capability of Desulfovibrio desulfuricans ATCC 13541 to degrade nitrocellulose as binder in paint was assayed for the first time. Nitrocellulose-based paint degradation was followed by monitoring the variation in nitrate, nitrite and ammonium content in the culture medium using Ultraviolet-Visible spectroscopy. At the same time cell counts and ATP assay were performed to estimate bacterial density and activity in all samples. Infrared spectroscopy and colorimetric measurements of paint samples were performed to assess chemical and colour changes due to the microbial action. Microscope observations of nitrocellulose-based paint samples demonstrated the capability of the bacterium to adhere to the paint surface and change the paint adhesive characteristics. Finally, preliminary studies of nitrocellulose degradation pathway were conducted by assaying nitrate- and nitrite reductases activity in D. desulfuricans grown in presence or in absence of paint. We found that D. desulfuricans ATCC 13541 is able to transform nitrocellulose as paint binder and we hypothesised ammonification as degradation pathway. The results suggest that D. desulfuricans ATCC 13541 is a good candidate as a nitrocellulose-degrading bacterium.

  5. The influence of desulfovibrio desulfuricans on neptunium chemistry.

    SciTech Connect

    Soderholm, L.; Williams, C.; Antonio, M. R.; Tischler, M. L.; Markos, M.

    1999-12-20

    The role of biotic Np(V) reduction is studied in light of its potential role in the environmental immobilization of this hazardous radionuclide. The speciation of Np in Desulfovibrio desulfuricans cultures is compared with Np speciation in the spent medium and in the uninoculated medium. Precipitates formed in all three samples. Optical spectroscopy and X-ray absorption near edge structure (XANES) were used to determine that Np(V) is almost quantitatively reduced in all three samples and that the precipitate is an amorphous Np(IV) species. These results demonstrate that the reduction of Np is independent of Desulfovibrio desulfuricans. The underlying chemistry associated with these results is discussed.

  6. Acne vulgaris.

    PubMed

    Wilson, B B

    1989-09-01

    Acne vulgaris is a disease of the pilosebaceous unit that affects nearly all persons to some degree during the teenage years. It is a disease that should be treated because of the anxiety and disfigurement it causes in the affected patient. Acne therapy is directed against the three probable pathogenic processes in acne: (1) abnormal keratinization of the sebaceous follicle, (2) excessive production of sebum, and (3) proliferation of bacteria in the follicle. Superficial acne consisting of comedones and small papulopustules will frequently respond to topical therapy such as retinoic acid, benzoyl peroxide, and topical antibiotics. Deeper lesions require systemic antibiotics of which tetracycline is the drug of choice. Severe, recalcitrant cystic acne usually responds well to the oral retinoid, isotretinoin. The severe teratogenic effects of isotretinoin on a developing fetus make this a risky drug to prescribe for women with childbearing potential. In such cases the greatest precautions should be taken to avoid pregnancy during a course of isotretinoin. Such precautions include pregnancy testing, contraceptive counseling, and the use of at least two effective forms of birth control in sexually active women.

  7. Propionibacterium acnes in the pathogenesis and immunotherapy of acne vulgaris.

    PubMed

    Liu, Pei-Feng; Hsieh, Yao-Dung; Lin, Ya-Ching; Two, Aimee; Shu, Chih-Wen; Huang, Chun-Ming

    2015-01-01

    Acne vulgaris, a multi-factorial disease, is one of the most common skin diseases, affecting an estimated 80% of Americans at some point during their lives. The gram-positive and anaerobic Propionibacterium acnes (P. acnes) bacterium has been implicated in acne inflammation and pathogenesis. Therapies for acne vulgaris using antibiotics generally lack bacterial specificity, promote the generation of antibiotic-resistant bacterial strains, and cause adverse effects. Immunotherapy against P. acnes or its antigens (sialidase and CAMP factor) has been demonstrated to be effective in mice, attenuating P. acnes-induced inflammation; thus, this method may be applied to develop a potential vaccine targeting P. acnes for acne vulgaris treatment. This review summarizes reports describing the role of P. acnes in the pathogenesis of acne and various immunotherapy-based approaches targeting P. acnes, suggesting the potential effectiveness of immunotherapy for acne vulgaris as well as P. acnes-associated diseases.

  8. Reduction of uranium by Desulfovibrio desulfuricans

    USGS Publications Warehouse

    Lovley, D.R.; Phillips, E.J.P.

    1992-01-01

    The possibility that sulfate-reducing microorganisms contribute to U(VI) reduction in sedimentary environments was investigated. U(VI) was reduced to U(IV) when washed cells of sulfate-grown Desulfovibrio desulfuricans were suspended in a bicarbonate buffer with lactate or H2 as the electron donor. There was no U(VI) reduction in the absence of an electron donor or when the cells were killed by heat prior to the incubation. The rates of U(VI) reduction were comparable to those in respiratory Fe(III)-reducing microorganisms. Azide or prior exposure of the cells to air did not affect the ability of D. desulfuricans to reduce U(VI). Attempts to grow D. desulfuricans with U(VI) as the electron acceptor were unsuccessful. U(VI) reduction resulted in the extracellular precipitation of the U(IV) mineral uraninite. The presence of sulfate had no effect on the rate of U(VI) reduction. Sulfate and U(VI) were reduced simultaneously. Enzymatic reduction of U(VI) by D. desulfuricans was much faster than nonenzymatic reduction of U(VI) by sulfide, even when cells of D. desulfuricans were added to provide a potential catalytic surface for the nonenzymatic reaction. The results indicate that enzymatic U(VI) reduction by sulfate-reducing microorganisms may be responsible for the accumulation of U(IV) in sulfidogenic environments. Furthermore, since the reduction of U(VI) to U(IV) precipitates uranium from solution, D. desulfuricans might be a useful organisms for recovering uranium from contaminated waters and waste streams.

  9. Metabolism of polyethylene glycol by two anaerobic bacteria, Desulfovibrio desulfuricans and a Bacteroides sp

    SciTech Connect

    Dwyer, D.F.; Tiedje, J.M.

    1986-10-01

    Two anaerobic bacteria were isolated from polyethylene glycol (PEG)-degrading, methanogenic, enrichment cultures obtained from a municipal sludge digester. One isolate, identified as Desulfovibrio desulfuricans (strain DG2), metabolized oligomers ranging from ethylene glycol (EG) to tetraethylene glycol. The other isolate, identified as a Bacteroides sp. (strain PG1), metabolized diethylene glycol and polymers of PEG up to an average molecular mass of 20,000 g/mol (PEG 20000; HO-(CH/sub 2/-CH/sub 2/-O-)/sub n/H). Both strains produced acetaldehyde as an intermediate, with acetate, ethanol, and hydrogen as end products. In coculture with a Methanobacterium sp., the end products were acetate and methane. Polypropylene glycol (HO-(CH/sub 2/-CH/sub 2/-CH/sub 2/-O-)/sub n/H) was not metabolized by either bacterium, and methanogenic enrichments could not be obtained on this substrate. Cell extracts of both bacteria dehydrogenated EG, PEGs up to PEG 400 in size, acetaldehyde, and other mono- and dihydroxylated compounds. Extracts of Bacteroides strain PGI could not dehydrogenate long polymers of PEG (less than or equal to1000 g/mol), but the bacterium grew with PEG 1000 or PEG 20000 as a substrate and therefore possesses a mechanism for PEG depolymerization not present in cell extracts. In contrast, extracts of D. desulfuricans DG2 dehydrogenated long polymers of PEG, but whole cells did not grow with these polymerase substrates. This indicated that the bacterium could not convert PEG to a product suitable for uptake.

  10. Complete Genome Sequence of Desulfovibrio piger FI11049

    PubMed Central

    Nueno Palop, Carmen; Mayer, Melinda J.; Crost, Emmanuelle; Narbad, Arjan

    2017-01-01

    ABSTRACT The complete genome sequence of Desulfovibrio piger FI11049 was determined. The genome consists of a single circular chromosome of 2,807,531 bp encoding seven rRNA operons, 76 tRNA genes, and 2,535 coding genes. PMID:28209813

  11. DsrJ, an essential part of the DsrMKJOP transmembrane complex in the purple sulfur bacterium Allochromatium vinosum, is an unusual triheme cytochrome c.

    PubMed

    Grein, Fabian; Venceslau, Sofia S; Schneider, Lilian; Hildebrandt, Peter; Todorovic, Smilja; Pereira, Inês A C; Dahl, Christiane

    2010-09-28

    The DsrMKJOP transmembrane complex has a most important function in dissimilatory sulfur metabolism, not only in many sulfur-oxidizing organisms but also in sulfate-reducing prokaryotes. Here, we focused on an individual component of this complex, the triheme cytochrome c DsrJ from the purple sulfur bacterium Allochromatium vinosum. In A. vinosum, the signal peptide of DsrJ is not cleaved off but serves as a membrane anchor. Sequence analysis suggested the presence of three heme c species with bis-His, His/Met, and possibly a very unusual His/Cys ligation. A. vinosum DsrJ produced as a recombinant protein in Escherichia coli indeed contained three hemes, and electron paramagnetic resonance (EPR) spectroscopy provided evidence of possible, but only partial, His/Cys heme ligation in one of the hemes. This heme shows heterogeneous coordination, with Met being another candidate ligand. Cysteine 46 was replaced with serine using site-directed mutagenesis, with the mutant protein showing a small decrease in the magnitude of the EPR signal attributed to His/Cys coordination, but identical UV-vis and RR spectra. The redox potentials of the hemes in the wild-type protein were determined to be -20, -200, and -220 mV and were found to be virtually identical in the mutant protein. However, in vivo the same ligand exchange led to a dramatically altered phenotype, highlighting the importance of Cys46. Our results suggest that Cys46 may be involved in catalytic sulfur chemistry rather than electron transfer. Additional in vivo experiments showed that DsrJ can be functionally replaced in A. vinosum by the homologous protein from the sulfate reducer Desulfovibrio vulgaris.

  12. System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions

    PubMed Central

    Schubotz, Florence; de Santiago-Torio, Ana; Kuehl, Jennifer V.; Carlson, Hans K.; Watson, Nicki; Daye, Mirna; Summons, Roger E.; Arkin, Adam P.; Deutschbauer, Adam M.

    2016-01-01

    The prevalence of lipids devoid of phosphorus suggests that the availability of phosphorus limits microbial growth and activity in many anoxic, stratified environments. To better understand the response of anaerobic bacteria to phosphate limitation and starvation, this study combines microscopic and lipid analyses with the measurements of fitness of pooled barcoded transposon mutants of the model sulfate reducing bacterium Desulfovibrio alaskensis G20. Phosphate-limited G20 has lower growth rates and replaces more than 90% of its membrane phospholipids by a mixture of monoglycosyl diacylglycerol (MGDG), glycuronic acid diacylglycerol (GADG) and ornithine lipids, lacks polyphosphate granules, and synthesizes other cellular inclusions. Analyses of pooled and individual mutants reveal the importance of the high-affinity phosphate transport system (the Pst system), PhoR, and glycolipid and ornithine lipid synthases during phosphate limitation. The phosphate-dependent synthesis of MGDG in G20 and the widespread occurrence of the MGDG/GADG synthase among sulfate reducing ∂-Proteobacteria implicate these microbes in the production of abundant MGDG in anaerobic environments where the concentrations of phosphate are lower than 10 μM. Numerous predicted changes in the composition of the cell envelope and systems involved in transport, maintenance of cytoplasmic redox potential, central metabolism and regulatory pathways also suggest an impact of phosphate limitation on the susceptibility of sulfate reducing bacteria to other anthropogenic or environmental stresses. PMID:28030630

  13. Percolative Conduction in Biological Conductor: Cytochrome c3 Anhydrous Film of Desulfovibrio vulgaris, Miyazaki Strain

    NASA Astrophysics Data System (ADS)

    Kimura, Keisaku; Inokuchi, Hiroo

    1982-07-01

    Electrical conductivity of the thin film of cytochrome c3, electron carrier protein of anaerobic bacteria, was measured as a function of ferri- to ferro-ratio. At the initial reduction stage of ferric cytochrome c3, the conductivity was gradually increased and was explained by doping effect. This was the first observation of doping effect for biological molecules. At 0.95 ferro-ratio, the conductivity was abruptly increased. The observation was analysed by the percolation theory which predicts that there is very strong heme-heme interaction between fully reduced cytochrome c3 molecules in a condensed phase. The anomalous physico-chemical behaviors of ferrocytochrome c3 film such as very low ionization potential and intermolecular heme-heme interaction observed by Mössbauer spectroscopy were also discussed in relation to the present results.

  14. Large-Scale, Continuous-Flow Production of Stressed Biomass (Desulfovibrio vulgaris Hildenborough)

    SciTech Connect

    Geller, Jil T.; Borglin, Sharon E.; Fortney, Julian L.; Lam, Bonita R.; Hazen, Terry C.; Biggin, Mark D.

    2010-05-01

    The Protein Complex Analysis Project (PCAP, http://pcap.lbl.gov/), focuses on high-throughput analysis of microbial protein complexes in the anaerobic, sulfate-reducing organism, DesulfovibriovulgarisHildenborough(DvH).Interest in DvHas a model organism for bioremediation of contaminated groundwater sites arises from its ability to reduce heavy metals. D. vulgarishas been isolated from contaminated groundwater of sites in the DOE complex. To understand the effect of environmental changes on the organism, midlog-phase cultures are exposed to nitrate and salt stresses (at the minimum inhibitory concentration, which reduces growth rates by 50percent), and compared to controls of cultures at midlogand stationary phases. Large volumes of culture of consistent quality (up to 100 liters) are needed because of the relatively low cell density of DvHcultures (one order of magnitude lower than E. coli, for example) and PCAP's challenge to characterize low-abundance membrane proteins. Cultures are grown in continuous flow stirred tank reactors (CFSTRs) to produce consistent cell densities. Stressor is added to the outflow from the CFSTR, and the mixture is pumped through a plug flow reactor (PFR), to provide a stress exposure time of 2 hours. Effluent is chilled and held in large carboys until it is centrifuged. A variety of analyses -- including metabolites, total proteins, cell density and phospholipidfatty-acids -- track culture consistency within a production run, and differences due to stress exposure and growth phase for the different conditions used. With our system we are able to produce the requisite 100 L of culture for a given condition within a week.

  15. High Throughput Identification, Purification and Structural Characterization of Water Soluble Protein Complexes in Desulfovibrio vulgaris

    SciTech Connect

    Dong,, Ming; Han, Bong-Gyoon; Liu, Hui-Hai; Malik, J.; Geller, Jil; Yang, Li; Choi, M.; Chandonia, John-Marc; Arbelaez, Pablo; Sterling, H. J.; Typke, Dieter; Shatsky, Max; Brenner, Steve; Fisher, Susan; Williams, Evan; Szakal, Evelin; Allen, S.; Hall, S. C.; Hazen, Terry; Witkowska, H. E.; Jin, Jiming; Glaeser, Robert; Biggin, Mark

    2010-05-17

    Our scheme for the tagless purification of water soluble complexes. 10 g of protein from a crude bacterial extract is first fractionated by ammonium sulfate precipitation and then by a series of chromatographic steps: anion exchange (IEX), hydrophobic interaction (HIC), and finally size exclusion (Gel Filtration). Fractions from the last chromatography step are trypsin digested and peptides labeled with iTRAQ reagents to allow multiplexing and quantitation during mass spectrometric analysis. Elution profiles of identified proteins are then subjected to clustering analysis.

  16. Analyzing the metabolic capabilities of Desulfovibrio speciesthrough genetic manipulation.

    SciTech Connect

    Bender, K.; Yen, H.-C.; Wall, J.D.

    2005-12-31

    Sulfate-reducing bacteria (SRB) are an environmentallysignificant group belonging to the anaerobic delta-Proteobacteria thatrespire sulfate for growth. From an industrial stand point, SRB pose athreat through corrosion of ferrous metals and production of toxicsulfides. The more positive aspects of the metabolism of the SRB includea robust but poorly understood hydrogen metabolism that is of interest toalternative energy studies. SRB also immobilize a number of heavy metalsthrough sulfide precipitation or through changing the redox state of themetal and thus its solubility. When metals are made less soluble, as isthe case with chromium (Cr(VI) to Cr(III)) or uranium (U(VI) to U(IV)),toxicity is reduced by limiting biological availability. Despite theeconomic and environmental impacts associated with SRB activities, ourcurrent knowledge of their metabolism is inadequate. Among the SRB,members of the Desulfovibrio genus have received most attention becausethese strains are most readily grown in pure culture. Therefore,Desulfovibrio strains have been the focus of biochemical and biophysicalanalyses, however, genetic studies have been more difficult. Over thelast 15 years, progress has been made in developing techniques for DNAtransformation, gene mutagenesis and over expression, and proteintagging. Since the last genetics of SRB review by van Dongen, 10 yearshave passed (van Dongen, 1995) and the complete genome sequences of a fewstrains are now available (Heidelberg, et al., 2004). This reviewhighlights the current advances in the genetic manipulation ofDesulfovibrio species and the potential use of these tools inunderstanding the metabolism of sulfate reducers for biotechnologicalpurposes.

  17. Corrosive Metabolic Activity of Desulfovibrio sp. on 316L Stainless Steel

    NASA Astrophysics Data System (ADS)

    Arkan, Simge; Ilhan-Sungur, Esra; Cansever, Nurhan

    2016-12-01

    The present study investigated the effects of chemical parameters (SO4 2-, PO4 3-, Cl-, pH) and the contents of extracellular polymeric substances (EPS) regarding the growth of Desulfovibrio sp. on the microbiologically induced corrosion of 316L stainless steel (SS). The experiments were carried out in laboratory-scaled test and control systems. 316L SS coupons were exposed to Desulfovibrio sp. culture over 720 h. The test coupons were removed at specific sampling times for enumeration of Desulfovibrio sp., determination of the corrosion rate by the weight loss measurement method and also for analysis of carbohydrate and protein in the EPS. The chemical parameters of the culture were also established. Biofilm/film formation and corrosion products on the 316L SS surfaces were investigated by scanning electron microscopy and energy-dispersive x-ray spectrometry analyses in the laboratory-scaled systems. It was found that Desulfovibrio sp. led to the corrosion of 316L SS. Both the amount of extracellular protein and chemical parameters (SO4 2- and PO4 3-) of the culture caused an increase in the corrosion of metal. There was a significantly positive relationship between the sessile and planktonic Desulfovibrio sp. counts ( p < 0.01). It was detected that the growth phases of the sessile and planktonic Desulfovibrio sp. were different from each other and the growth phases of the sessile Desulfovibrio sp. vary depending on the subspecies of Desulfovibrio sp. and the type of metal when compared with the other published studies.

  18. The Effect of Desulfovibrio sp. Biofilms on Corrosion Behavior of Copper in Sulfide-Containing Solutions

    NASA Astrophysics Data System (ADS)

    Güngör, Nihal Doğruöz; Çotuk, Ayşın; Dışpınar, Derya

    2015-03-01

    This study aims to detect the effect of Desulfovibrio sp. on copper in terms of biofilm formation and corrosion in 722 h. In that way, appropriate strategies to inhibit microbiological corrosion in copper systems with Desulfovibrio sp. can be evaluated. For this purpose, experiments were performed in 1 L glass model system containing 28 copper coupons and pure culture of the sulfate-reducing bacteria (SRB) strain Desulfovibrio sp. in Postgate's medium C. Also, a control system with copper coupons but without Desulfovibrio sp. containing sterile Postgate's medium was studied concurrently with the test system. The test coupons were collected from systems at certain time intervals, namely 24, 168, 360, and 720 h. The samples were then subjected to several characterization analyses such as measurement of Desulfovibrio sp. numbers, corrosion resistance, EPS extraction, carbohydrate analysis, SEM, and EDS. During the experiments, the maximum Desulfovibrio sp. count in biofilm samples was found at 360 h. Carbohydrate and copper concentrations in biofilm were increased over time. EDS analysis revealed Cu, S, C, O, and Cl peaks on the surface of the samples. For the control coupons, only Cu peaks were observed. The results obtained from this study showed that copper was corroded by Desulfovibrio sp. in the model system under laboratory conditions.

  19. The toxicity of lead to Desulfovibrio desulfuricans G20 in the presence of goethite and quartz

    SciTech Connect

    Sani, Rajesh K.; Rastogi, Gurdeep; Moberly, J.; Dohnalkova, Alice; Ginn, Timothy R.; Spycher, Nicolas; Shende, Rajesh; Peyton, Brent

    2010-04-01

    An aqueous mixture of goethite, quartz, and lead chloride (PbCl2) was treated with the sulfatereducing bacterium, Desulfovibrio desulfuricans G20 (D. desulfuricans G20), in a medium specifically designed to assess metal toxicity. In the presence of 26 μM of soluble Pb, together with the goethite and quartz, D. desulfuricans G20 grew after a lag time of 5 days compared to 2 days in Pb-, goethite-, and quartz-free treatments. In the absence of goethite and quartz, however, with 26 μM soluble Pb, no measurable growth was observed. Results showed that D. desulfuricans G20 first removed Pb from solutions then growth began resulting in black precipitates of Pb and iron sulfides. Transmission electron microscopic analyses of thin sections of D. desulfuricans G20 treated with 10 μM PbCl2 in goethite- and quartz-free treatment showed the presence of a dense deposit of lead sulfide precipitates both in the periplasm and cytoplasm. However, thin sections of D. desulfuricans G20 treated with goethite, quartz, and PbCl2 (26 μM soluble Pb) showed the presence of a dense deposit of iron sulfide precipitates both in the periplasm and cytoplasm. Energy-dispersive X-ray spectroscopy, selected area electron diffraction patterns, or X-ray diffraction analyses confirmed the structure of precipitated Pb inside the cell as galena (PbS) in goethite- and quartz-free treatments, and iron sulfides in treatments with goethite, quartz, and PbCl2. Overall results suggest that even at the same soluble Pb concentration (26 μM), in the presence of goethite and quartz, apparent Pb toxicity to D. desulfuricans G20 decreased significantly. Further, accumulation of lead/iron sulfides inside D. desulfuricans G20 cells depended on the presence of goethite and quartz.

  20. Lupus vulgaris of external nose.

    PubMed

    Bhandary, Satheesh Kumar; Ranganna, B Usha

    2008-12-01

    Lupus vulgaris is the commonest form of cutaneous tuberculosis which commonly involve trunk and buttocks. Lupus vulgaris affecting nose and face, are rarely reported in India. This study reports an unusual case of lupus vulgaris involving the external nose that showed dramatic outcome after six months of anti- tubercular treatment.

  1. Lupus vulgaris: difficulties in diagnosis.

    PubMed

    Rhodes, Julia; Caccetta, Tony Philip; Tait, Clare

    2013-05-01

    Lupus vulgaris is one of the most common forms of cutaneous tuberculosis. It presents a diagnostic challenge due to its paucibacillary nature. This is a report of a case of a delayed diagnosis of lupus vulgaris, presenting as perianal and peristomal plaques, followed by a review of the diagnostic tools for lupus vulgaris and their limitations.

  2. The First Genomic and Proteomic Characterization of a Deep-Sea Sulfate Reducer: Insights into the Piezophilic Lifestyle of Desulfovibrio piezophilus

    PubMed Central

    Pradel, Nathalie; Ji, Boyang; Gimenez, Grégory; Talla, Emmanuel; Lenoble, Patricia; Garel, Marc; Tamburini, Christian; Fourquet, Patrick; Lebrun, Régine; Bertin, Philippe; Denis, Yann; Pophillat, Matthieu; Barbe, Valérie; Ollivier, Bernard; Dolla, Alain

    2013-01-01

    Desulfovibrio piezophilus strain C1TLV30T is a piezophilic anaerobe that was isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents a unique model for studying the adaptation of sulfate-reducing bacteria to hydrostatic pressure. Here, we report the 3.6 Mbp genome sequence of this piezophilic bacterium. An analysis of the genome revealed the presence of seven genomic islands as well as gene clusters that are most likely linked to life at a high hydrostatic pressure. Comparative genomics and differential proteomics identified the transport of solutes and amino acids as well as amino acid metabolism as major cellular processes for the adaptation of this bacterium to hydrostatic pressure. In addition, the proteome profiles showed that the abundance of key enzymes that are involved in sulfate reduction was dependent on hydrostatic pressure. A comparative analysis of orthologs from the non-piezophilic marine bacterium D. salexigens and D. piezophilus identified aspartic acid, glutamic acid, lysine, asparagine, serine and tyrosine as the amino acids preferentially replaced by arginine, histidine, alanine and threonine in the piezophilic strain. This work reveals the adaptation strategies developed by a sulfate reducer to a deep-sea lifestyle. PMID:23383081

  3. Cosubstrate independent mineralization of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by a Desulfovibrio species under anaerobic conditions.

    PubMed

    Arnett, Clint M; Adrian, Neal R

    2009-02-01

    Past handling practices associated with the manufacturing and processing of the high explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has resulted in extensive environmental contamination. In-situ biodegradation is a promising technology for remediating RDX contaminated sites but often relies on the addition of a cosubstrate. A sulfate-reducing bacterium isolated from an RDX-degrading enrichment culture was studied for its ability to grow on RDX as a sole source of carbon and nitrogen and for its ability to mineralize RDX in the absence of a cosubstrate. The results showed the isolate degraded 140 muM RDX in 63 days when grown on RDX as a carbon source. Biomass within the carbon limited culture increased 9-fold compared to the RDX unamended controls. When the isolate was incubated with RDX as sole source of nitrogen it degraded 160 muM RDX in 41 days and exhibited a 4-fold increase in biomass compared to RDX unamended controls. Radiolabeled studies under carbon limiting conditions with (14)C-hexahydro-1,3,5-trinitro-1,3,5-triazine confirmed mineralization of the cyclic nitramine. After 60 days incubation 26% of the radiolabel was recovered as (14)CO(2), while in the control bottles less than 1% of the radiolabel was recovered as (14)CO(2). Additionally, approximately 2% of the radiolabeled carbon was found to be associated with the biomass. The 16S rDNA gene was sequenced and identified the isolate as a novel species of Desulfovibrio, having a 95.1% sequence similarity to Desulfovibrio desulfuricans. This is the first known anaerobic bacterium capable of mineralizing RDX when using it as a carbon and energy source for growth.

  4. Psoriasiform lupus vulgaris.

    PubMed

    Padmavathy, L; Rao, L Lakshmana; Ethirajan, N; Dhanlaklshmi, M

    2008-04-01

    Tuberculosis is a major public health problem in both developing and developed countries. Cutaneous Tuberculosis constitutes a minor proportion of extra-pulmonary manifestations of Tuberculosis. Lupus Vulgaris (LV) is one of the clinical variants of Cutaneous Tuberculosis. A case of a large plaque type psoriasiform lesion of lupus vulgaris on the thigh, of 15 years' duration, in an 18-year-old girl is reported. This case highlights the ignorance level among the patients and consequent failure to avail proper anti-tuberculous treatment despite campaign in print and audio visual media.

  5. Genes for Uranium Bioremediation in the Anaerobic Sulfate-Reducing Bacteria: Desulfovibrio mutants with altered sensitivity to oxidative stress

    SciTech Connect

    Payne, Rayford B.; Ringbauer, Joseph A., Jr.; Wall, Judy D.

    2006-04-05

    Sulfate-reducing bacteria of the genus Desulfovibrio are ubiquitous in anaerobic environments such as groundwater, sediments, and the gastrointestinal tract of animals. Because of the ability of Desulfovibrio to reduce radionuclides and metals through both enzymatic and chemical means, they have been proposed as a means to bioremediate heavy metal contaminated sites. Although classically thought of as strict anaerobes, Desulfovibrio species are surprisingly aerotolerant. Our objective is to understand the response of Desulfovibrio to oxidative stress so that we may more effectively utilize them in bioremediation of heavy metals in mixed aerobic-anaerobic environments. The enzymes superoxide dismutase, superoxide reductase, catalase, and rubrerythrin have been shown by others to be involved in the detoxification of reactive oxygen species in Desulfovibrio. Some members of the genus Desulfovibrio can even reduce molecular oxygen to water via a membrane bound electron transport chain with the concomitant production of ATP, although their ability to grow with oxygen as the sole electron acceptor is still questioned.

  6. Inoculation lupus vulgaris.

    PubMed

    Sehgal, V N; Jain, S; Gupta, R

    1992-01-01

    An 11-years-old girl with lupus vulgaris on the right buttock following inoculation is described. The diagnosis was formed by the history, morphological characteristics, Mantoux test, histopathology, and was supported by an affirmative response to short course intensive chemotherapy (6 months). This route of infection acquires special significance with the worldwide-spread of HIV infection.

  7. Kinetic analysis of microbial sulfate reduction by Desulfovibrio desulfuricans in an anaerobic upflow porous media biofilm reactor

    SciTech Connect

    Chen, Chingi; Mueller, R.F.; Griebe, T. . National Science Foundation Engineering Research Center for Biofilm Engineering)

    1994-02-20

    An anaerobic upflow porous media biofilm reactor was designed to study the kinetics and stoichiometry of hydrogen sulfide production by the sulfate-reducing bacterium (SRB) Desulfovibrio desulfuricans (ATCC 5575) as the first step for the modeling and control of formation souring (H[sub 2]S) in oil field porous media. The initial indication of souring was the appearance of well-separated black spots (precipitates of iron sulfide) in the sand bed. Analysis of the pseudo-steady state column shows that there were concentration gradients for lactate and hydrogen sulfide along the column. The results indicate that most of the lactate was consumed at the front part of the column. Measurements of SRB biomass on the solid phase (sand) and in the liquid phase indicate that the maximum concentration of SRB biomass resided at the front part of the column while the maximum in the liquid phase occurred further downstream. The stoichiometry regarding lactate consumption and hydrogen sulfide production observed in the porous media reactor was different from that in a chemostat. After analyzing the radial dispersion coefficient for the SRB in porous media and kinetics of microbial growth, it was deduced that transport phenomena dominate the souring process in the porous media reactor system.

  8. Pemphigus vulgaris and disseminated nocardiosis.

    PubMed

    Martín, F J; Pérez-Bernal, A M; Camacho, F

    2000-09-01

    Infectious diseases, in particular septicaemia from Staphylococcus aureus, Proteus vulgaris and Pseudomonas aeruginosa, are the most severe and frequent complications for the immunosuppressive therapy of pemphigus. Infection by Nocardia asteroides in subjects with pemphigus vulgaris is rare. We report the sixth case found of such an association; the subject died of disseminated nocardiosis while receiving steroids and immunosuppressive drugs, 4 years after being diagnosed with chronic pemphigus vulgaris.

  9. Lung and lupus vulgaris.

    PubMed

    Mukta, V; Jayachandran, K

    2011-04-01

    Lupus vulgaris is chronic, postprimary, paucibacillary cutaneous tuberculosis found in individuals with moderate immunity and high degree of tuberculin sensitivity. Eighty percent of the lesions are on the head and neck. We present the case of a 38 year old lady who was admitted with complaints of worsening breathlessness and low grade fever of one month duration. Examination showed multiple, nontender skin ulcers on bilateral lumbar areas, two oozing serosanguinous discharge and others scarred in the centre. Respiratory system examination and chest X-ray revealed right sided pleural effusion. On investigation, pleural fluid was tuberculous in nature. Skin biopsy from the edge of ulcer was also suggestive of tuberculosis. Patient is doing well on antituberculous drugs. This case highlights the importance of cutaneous manifestations of systemic disease and is an example of the unusual presentation of lupus vulgaris in a case of pleural effusion.

  10. [Cefaclor induced pemphigus vulgaris].

    PubMed

    Scardina, G A; Conti, N M; Messina, P

    2004-01-01

    Pemphigus is a chronic disease with an outcome that is not without risk. It is characterised by loss of the intraepithelial cell-cell relationship (acantholysis). Underlying the disease is an autoimmune disorder in which the desmosomes are damaged by antibodies directed against particular molecules called desmogleins (particularly 3 and 1). Various types of pemphigus have been described with different antibody profiles and clinical signs. In the present paper, a case of pemphigus vulgaris associated with the medication cefaclor monohydrate is reported. Histological and immunological evaluation of the biopsy sample led to a diagnosis of pemphigus vulgaris. The patient, who was not hospitalised, was treated with corticosteroids and systemic immunosuppressors. At present she is being controlled by low doses of systemic corticosteroids. Early diagnosis and the timely introduction of the therapeutic protocol permitted complete remission of the lesions observed at the level of the oral and conjunctival mucosa, preventing the involvement of other locations.

  11. Pemphigus vulgaris in pregnancy.

    PubMed

    Salzberg, Kelsey W; Gero, Melanie J; Ragsdale, Bruce D

    2014-10-01

    We report the case of a 34-year-old woman who was diagnosed with pemphigus vulgaris (PV) during pregnancy. The patient presented with widespread blistering dermatitis and associated burning and pruritus. At 6 weeks' gestation the patient was admitted to the hospital to expedite her diagnosis and initiate treatment. A skin biopsy revealed suprabasal acantholysis, and direct immunofluorescence demonstrated diffuse intercellular IgG in the epidermis and basal intercellular C3, which confirmed the diagnosis of PV. Treatment with corticosteroids was instituted after discussions with the patient about possible adverse effects to the fetus. Pemphigus vulgaris is rare in pregnancy and active PV presents potential threats of fetal spread and transient lesion production, which is associated with increased mortality and morbidity in the fetus. Our patient had active PV and required treatment throughout her pregnancy. The pregnancy progressed to premature delivery of the neonate without skin lesions or apparent complications.

  12. Coexistence of a sulphate-reducing Desulfovibrio species and the dehalorespiring Desulfitobacterium frappieri TCE1 in defined chemostat cultures grown with various combinations of sulfate and tetrachloroethene.

    PubMed

    Drzyzga, O; Gerritse, J; Dijk, J A; Elissen, H; Gottschal, J C

    2001-02-01

    A two-member co-culture consisting of the dehalorespiring Desulfitobacterium frappieri TCE1 and the sulphate-reducing Desulfovibrio sp. strain SULF1 was obtained via anaerobic enrichment from soil contaminated with tetrachloroethene (PCE). In this co-culture, PCE dechlorination to cis-dichloroethene was due to the activity of the dehalorespiring bacterium only. Chemostat experiments with lactate as the primary electron donor for both strains along with varying sulphate and PCE concentrations showed that the sulphate-reducing strain outnumbered the dehalogenating strain at relatively high ratios of sulphate/PCE. Stable co-cultures with both organisms present at similar cell densities were observed when both electron acceptors were supplied in the reservoir medium in nearly equimolar amounts. In the presence of low sulphate/PCE ratios, the Desulfitobacterium sp. became the numerically dominant strain within the chemostat co-culture. Surprisingly, in the absence of sulphate, strain SULF1 did not disappear completely from the co-culture despite the fact that there was no electron acceptor provided with the medium to be used by this sulphate reducer. Therefore, we propose a syntrophic association between the sulphate-reducing and the dehalorespiring bacteria via interspecies hydrogen transfer. The sulphate reducer was able to sustain growth in the chemostat co-culture by fermenting lactate and using the dehalogenating bacterium as a 'biological electron acceptor'. This is the first report describing growth of a sulphate-reducing bacterium in a defined two-member continuous culture by syntrophically coupling the electron and hydrogen transfer to a dehalorespiring bacterium.

  13. Methanogenesis from choline by a coculture of Desulfovibrio sp. and Methanosarcina barkeri

    SciTech Connect

    Fiebig, K.; Gottschalk, G.

    1983-01-01

    A sulfate-reducing vibrio was isolated from a methanogenic enrichment with choline as the sole added organic substrate. This oganism was identified as a member of the genus Desulfovibrio and was designated Desulfovibrio strain G1. In a defined medium devoid of sulfate, a pure culture of Desulfovibrio strain G1 fermented choline to trimethylamine, acetate, and ethanol. In the presence of sulfate, more acetate and less ethanol were formed from choline than in the absence of sulfate. When grown in a medium containing sulfate, a coculture of Desulfovibrio strain G1 and Methanosarcina barkeri strain Fusaro degraded chloline almost completely to methane, ammonia, and hydrogen sulfide and presumably to carbon dioxide. Methanogenesis occurred in two distinct phases separated by a lag of about 6 days. During the first phase of methanogenesis choline was completely converted to trimethylamine, acetate, hydrogen sulfide, and traces of ethanol by the desulfovibrio.M. barkeri fermented trimethylamine to methane, ammonia, and presumably carbon dioxide via dimethyl- and methylamine as intermediates. Simultaneously, about 60% of the acetate expected was metabolized. In the second phase of methanogenesis, the residual acetate was almost completely catabolized.

  14. Biomolecular and Isotopic Signatures Related to Cr(VI) Reduction by a Sulfate-Reducing Bacterium Isolated from the Hanford 100H Aquifer

    NASA Astrophysics Data System (ADS)

    Han, R.; Qin, L.; Geller, J. T.; Chakraborty, R.; Christensen, J. N.; Beller, H. R.

    2011-12-01

    Chromium contamination of groundwater is widespread within the Dept. of Energy (DOE) complex. At DOE's Hanford 100H area, we have conducted Cr bioremediation (in situ reductive immobilization) studies involving injection of a lactate-containing polymer, and have observed sequential use of the dissolved electron acceptors present in groundwater (namely, oxygen, nitrate, and sulfate). Sulfate-reducing bacteria are of particular interest for chromate reduction because they can reduce Cr(VI) enzymatically (e.g., using cytochrome c3 or thioredoxin reductase) and abiotically with hydrogen sulfide, the end product of their respiration. In this poster, we use studies of a sulfate-reducing bacterium isolated from the Hanford 100H aquifer, Desulfovibrio vulgaris strain RCH1, to explore (a) isotopic signatures that might allow us to distinguish between enzymatic and sulfide-mediated Cr(VI) reduction and (b) biomolecular signatures (gene or transcript copy number of diagnostic genes) that might be used as proxies of in situ metabolic rates. In order to differentiate between the mechanisms of Cr reduction by sulfate reducers, we analyzed the isotopic fractionation during Cr(VI) reduction by strain RCH1. Cell suspension studies of strain RCH1 demonstrated that Cr(VI) reduction could occur in the presence of lactate (electron donor) alone or with both lactate and sulfate. Cr(VI) reduction in the presence of lactate and sulfate was 25-30% more rapid than enzymatic Cr reduction when only lactate was added, suggesting that biogenic hydrogen sulfide increases the specific rate of Cr(VI) reduction beyond purely enzymatic activity. Cr isotopic measurements showed different fractionation behavior for the lactate-only and lactate+sulfate systems, with fractionation (epsilon) values of 2.3 and 1.66 per mil, respectively. In order to determine whether gene or transcript copy number for diagnostic sulfate and chromate reduction genes could serve as proxies to estimate in situ metabolic

  15. Extracellular iron-sulfur precipitates from growth of Desulfovibrio desulfuricans

    SciTech Connect

    Antonio, M. R.; Tischler, M. L.; Witzcak, D.

    1999-12-20

    The authors have examined extracellular iron-bearing precipitates resulting from the growth of Desulfovibrio desulfuricans in a basal medium with lactate as the carbon source and ferrous sulfate. Black precipitates were obtained when D. desulfuricans was grown with an excess of FeSO{sub 4}. When D. desulfuricans was grown under conditions with low amounts of FeSO{sub 4}, brown precipitates were obtained. The precipitates were characterized by iron K-edge XAFS (X-ray absorption fine structure), {sup 57}Fe Moessbauer-effect spectroscopy, and powder X-ray diffraction. Both were noncrystalline and nonmagnetic (at room temperature) solids containing high-spin Fe(III). The spectroscopic data for the black precipitates indicate the formation of an iron-sulfur phase with 6 nearest S neighbors about Fe at an average distance of 2.24(1) {angstrom}, whereas the brown precipitates are an iron-oxygen-sulfur phase with 6 nearest O neighbors about Fe at an average distance of 1.95(1) {angstrom}.

  16. [Antagonistic interrelationships of Bifidobacterium bifidum i Proteus vulgaris in vitro in the digestive tract of gnotobiotic chicks].

    PubMed

    Timoshko, M A; Vil'shanskaia, F L; Pospelova, V V; Rakhimova, N G

    1979-07-01

    The antagonistic relations between Bacterium bifidum, strain I/850 phi, and Proteus vulgaris, strain F-30, were studied. These organisms, when introduced together in equal doses into the digestive tract of gnotobiotic chickens in a single administration, were shown to create certain ecological correlations in various organs with the prevalence of bifidobacteria which exerted no negative influence on Proteus vulgaris. The additional daily administration of bifidobacteria for 3 days running in doses 1000 times as great as the initial dose, the content of both dibifobacteria and Proteus vulgaris in the intestine being at that time at its maximum, resulted in the suppression of the growth of Proteus vulgaris. Our findings indicate that the influence of the pH of the medium should be considered in order to obtain the evidence of significantly pronounced antagonistic relations between the two organisms in vitro.

  17. Characterization of the structure and redox behaviour of cytochrome c3 from Desulfovibrio baculatus by 1H-nuclear-magnetic-resonance spectroscopy.

    PubMed Central

    Coutinho, I B; Turner, D L; LeGall, J; Xavier, A V

    1993-01-01

    Complete assignment of the aromatic and haem proton resonances in the cytochromes c3 isolated from Desulfovibrio baculatus strains (Norway 4, DSM 1741) and (DSM 1743) was achieved using one- and two-dimensional 1H n.m.r. Nuclear Overhauser enhancements observed between haem and aromatic resonances and between resonances due to different haems, together with the ring-current contributions to the chemical shifts of haem resonances, support the argument that the haem core architecture is conserved in the various cytochromes c3, and that the X-ray structure of the D. baculatus cytochrome c3 is erroneous. The relative orientation of the haems for both cytochromes was determined directly from n.m.r. data. The n.m.r. structures have a resolution of approximately 0.25 nm and are found to be in close agreement with the X-ray structure from D. vulgaris cytochrome c3. The proton assignments were used to relate the highest potential to a specific haem in the three-dimensional structure by monitoring the chemical-shift variation of several haem resonances throughout redox titrations followed by 1H n.m.r. The haem with highest redox potential is not the same as that in other cytochromes c3. PMID:8397513

  18. Propionate-degrading bacterium, Syntrophobacter wolinii sp. nov. gen. nov. , from methanogenic ecosystems

    SciTech Connect

    Boone, D.R.; Bryant, M.P.

    1980-09-01

    A new genus and species of a nonmotile gram-negative rod, Syntrophobacter wolinii, is the first bacterium described which degrades propionate only in coculture with an H/sub 2/-using organism and in the absence of light or exogenous electron acceptors such as O/sub 2/, sulfate, or nitrate. It was isolated from methanogenic enrichments from an anaerobic municipal sewage digestor, using anaerobic roll tubes containing a medium with propionate as the energy source in association with an H/sub 2/-using, sulfate-reducing Desulfovibrio sp. which cannot utilize fatty acids other than formate. S. wolinii produced acetate and, presumably, CO/sub 2/ and H/sub 2/ (or formate) from propionate. In media without sulfate and with Methanospirillum hungatei, a methanogen that uses only H/sub 2/-CO/sub 2/ or formate as an energy source, acetate, methane, and, presumably, CO/sub 2/ were produced from propionate and only small amounts of Desulfovibrio sp. were present. Isolation in coculture with the methanogen was not successful. S. wolinii does not use other saturated fatty acids as energy sources. 2 figures, 3 tables.

  19. Kinetic analysis of microbial sulfate reduction by desulfovibrio desulfuricans in an anaerobic upflow porous media biofilm reactor.

    PubMed

    Chen, C I; Mueller, R F; Griebe, T

    1994-02-20

    An anaerobic upflow porous media biofilm reactor was designed to study the kinetics and stoichiometry of hydrogen sulfide production by the sulfate-reducing bacterium (SRB) Desulfovibrio desulfuricans (ATCC 5575) as the first step for the modeling and control of formation souring (H(2)S) in oil field porous media. The reactor was a packed bed (50 x 5.5 cm) tubular reactor. Sea sand (140 to 375 mum) was used as the porous media. The initial indication of souring was the appearance of well-separated black spots (precipitates of iron sulfide) in the sand bed. The blackened zones expanded radially and upward through the column. New spots also appeared and expanded into the cone shapes. Lactate (substrate) was depleted and hydrogen sulfide appeared in the effluent.Analysis of the pseudo-steady state column shows that there were concentration gradients for lactate and hydrogen sulfide along the column. The results indicate that most of the lactate was consumed at the front part of the column. Measurements of SRB biomass on the solid phase (sand) and in the liquid phase indicate that the maximum concentration of SRB biomass resided at the front part of the column while the maximum in the liquid phase occurred further downstream. The stoichiometry regarding lactate consumption and hydrogen sulfide production observed in the porous media reactor was different from that in a chemostat. After analyzing the radial dispersion coefficient for the SRB in porous media and kinetics of microbial growth, it was deduced that transport phenomena dominate the souring process in our porous media reactor system. (c) 1994 John Wiley & Sons, Inc.

  20. Hydrogen production and deuterium-proton exchange reactions catalyzed by Desulfovibrio nickel(II)-substituted rubredoxins

    PubMed Central

    Saint-Martin, Pascal; Lespinat, Paul A.; Fauque, Guy; Berlier, Yves; LeGall, Jean; Moura, Isabel; Teixeira, Miguel; Xavier, Antonio V.; Moura, Jose J. G.

    1988-01-01

    The nickel tetrahedral sulfur-coordinated core formed upon metal replacement of the native iron in Desulfovibrio sp. rubredoxins is shown to mimic the reactivity pattern of nickel-containing hydrogenases with respect to hydrogen production, deuterium-proton exchange, and inhibition by carbon monoxide. PMID:16594005

  1. Ultrafast fluorescence dynamics of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) and its site-directed mutated proteins

    NASA Astrophysics Data System (ADS)

    Chosrowjan, Haik; Taniguchi, Seiji; Mataga, Noboru; Tanaka, Fumio; Todoroki, Daisuke; Kitamura, Masaya

    2008-09-01

    Ultrafast fluorescence dynamics of FMN in FMN-binding protein (FMN-bp), and its mutated proteins, W32Y and W32A, were investigated by the fluorescence up-conversion method. Fluorescence lifetimes were 167 fs (96%) and 1.5 ps (4%) in wild-type FMN-bp (WT), and 3.4 ps (23%), 18.2 ps (74%), and 96 ps (3%) at 530 nm in W32Y, and 30.1 ps in W32A. The fluorescence lifetime of W32A, in which Trp-32 was absent, was about 140 times longer than that of WT. Tyr-32 in W32Y was not so effective quencher as Trp-32 in WT. This was explained in terms of different ionization potentials of quenchers and average donor-acceptor distances in the protein.

  2. Co(III)EDTA- Reduction by Desulfovibrio vulgaris and Propagation of Reactions Involving Dissolved Sulfide and Polysulfides.

    SciTech Connect

    Blessing, T.C.; B.W. Wielinga; M.J. Morra; S. Fendorf

    2001-04-15

    The migration of 60Co is driven by Co(III)EDTA- complexes. Here we document the bacterial mediated reduction of Co(III) to Co(II)EDTA2- complexes, which are far less mobile within the environment. Additionally, we demonstrate that sulfate promotes reduction via production of reactive polysulfides rather than acting as a competitive electron acceptor.

  3. Phaseolus vulgaris - recalcitrant potential.

    PubMed

    Hnatuszko-Konka, Katarzyna; Kowalczyk, Tomasz; Gerszberg, Aneta; Wiktorek-Smagur, Aneta; Kononowicz, Andrzej K

    2014-11-15

    Since the ability to genetically engineer plants was established, researchers have modified a great number of plant species to satisfy agricultural, horticultural, industrial, medicinal or veterinary requirements. Almost thirty years after the first approaches to the genetic modification of pulse crops, it is possible to transform many grain legumes. However, one of the most important species for human nutrition, Phaseolus vulgaris, still lacks some practical tools for genomic research, such as routine genetic transformation. Its recalcitrance towards in vitro regeneration and rooting significantly hampers the possibilities of improvement of the common bean that suffers from many biotic and abiotic constraints. Thus, an efficient and reproducible system for regeneration of a whole plant is desired. Although noticeable progress has been made, the rate of recovery of transgenic lines is still low. Here, the current status of tissue culture and recent progress in transformation methodology are presented. Some major challenges and obstacles are discussed and some examples of their solutions are presented.

  4. [Acne vulgaris: endocrine aspects].

    PubMed

    Dekkers, O M; Thio, B H; Romijn, J A; Smit, J W A

    2006-06-10

    Androgens play an important part in the development of acne vulgaris. Androgen levels in patients with acne are higher than those in controls and people with the androgen insensitivity syndrome do not develop acne. Local factors other than androgen plasma levels, also play a part in the development of acne. The skin contains enzymes that convert precursor hormones to the more potent androgens such as testosterone and dihydrotestosterone. Androgen synthesis can therefore be regulated locally. The effects of androgens on the skin are the result of circulating androgens and enzyme activity in local tissues and androgen receptors. Acne is a clinical manifestation of some endocrine diseases. The polycystic ovary syndrome has the highest prevalence. In women with acne that persists after puberty, in 10-200% of cases polycystic ovary syndrome is later diagnosed. The mechanism of hormonal anti-acne therapy may work by blocking the androgen-production (oestrogens) or by blocking the androgen receptor (cyproterone, spironolactone).

  5. Brain abscesses during Proteus vulgaris bacteremia.

    PubMed

    Bloch, Jennifer; Lemaire, Xavier; Legout, Laurence; Ferriby, Didier; Yazdanpanah, Yazdan; Senneville, Eric

    2011-08-01

    Proteus vulgaris is only rarely the cause of multiple septic metastases. We describe multiple brain abscesses due to P. vulgaris in an immunocompetent patient successfully treated by antibiotic therapy and colonectomy.

  6. Pemphigus Vulgaris Presented with Cheilitis

    PubMed Central

    Safaie Naraghi, Zahra; Behrangi, Elham

    2014-01-01

    Background. Pemphigus vulgaris is an autoimmune blistering disease affecting the mucous membrane and skin. In 50 to 70% of cases, the initial manifestations of pemphigus vulgaris are oral lesions which may be followed by skin lesions. But it is unusual for the disease to present with initial and solitary persistent lower lip lesions without progression to any other location. Main Observations. We report a 41-year-old woman with dry crusted lesions only on the lower lip, clinically resembling actinic cheilitis and erosive lichen planus, but histopathological evaluation showed unexpected results of suprabasal acantholysis and cleft compatible with pemphigus vulgaris. We treated her with intralesional triamcinolone 10 mg/mL for 2 sessions and 2 g cellcept daily. Patient showed excellent response and lesions resolved completely within 2 months. In one-year follow-up, there was no evidence of relapse or any additional lesion on the other sites. Conclusion. Cheilitis may be the initial and sole manifestation of pemphigus vulgaris. Localized and solitary lesions of pemphigus vulgaris can be treated and controlled without systemic corticosteroids. PMID:25328720

  7. Desulfovibrio frigidus sp. nov. and Desulfovibrio ferrireducens sp. nov., psychrotolerant bacteria isolated from Arctic fjord sediments (Svalbard) with the ability to reduce Fe(III).

    PubMed

    Vandieken, Verona; Knoblauch, Christian; Jørgensen, Bo Barker

    2006-04-01

    Strains 18T, 61T and 77 were isolated from two permanently cold fjord sediments on the west coast of Svalbard. The three psychrotolerant strains, with temperature optima at 20-23 degrees C, were able to grow at the freezing point of sea water, -2 degrees C. The strains oxidized important fermentation products such as hydrogen, formate and lactate with sulfate as the electron acceptor. Sulfate could be replaced by sulfite, thiosulfate or elemental sulfur. Poorly crystalline and soluble Fe(III) compounds were reduced in sulfate-free medium, but no growth occurred under these conditions. In the absence of electron acceptors, fermentative growth was possible. The pH optimum for the strains was around 7.1. The DNA G+C contents were 43.3 and 42.0 mol% for strains 18T and 61T, respectively. Strains 18T, 61T and 77 were most closely related to Desulfovibrio hydrothermalis (95.0-95.7 % 16S rRNA gene sequence similarity). Strains 18T and 77, exhibiting 99.9 % sequence similarity, represent a novel species for which the name Desulfovibrio frigidus sp. nov. is proposed. The type strain is strain 18T (=DSM 17176T = JCM 12924T). Strain 61T was closely related to strains 18T and 77 (97.6 and 97.5 % 16S rRNA gene sequence similarity), but on the basis of DNA-DNA hybridization strain 61T represents a novel species for which the name Desulfovibrio ferrireducens sp. nov. is proposed. The type strain is strain 61T (=DSM 16995T = JCM 12925T).

  8. Microbial reduction of structural iron in interstratified illite-smectite minerals by a sulfate-reducing bacterium.

    PubMed

    Liu, D; Dong, H; Bishop, M E; Zhang, J; Wang, H; Xie, S; Wang, S; Huang, L; Eberl, D D

    2012-03-01

    Clay minerals are ubiquitous in soils, sediments, and sedimentary rocks and could coexist with sulfate-reducing bacteria (SRB) in anoxic environments, however, the interactions of clay minerals and SRB are not well understood. The objective of this study was to understand the reduction rate and capacity of structural Fe(III) in dioctahedral clay minerals by a mesophilic SRB, Desulfovibrio vulgaris and the potential role in catalyzing smectite illitization. Bioreduction experiments were performed in batch systems, where four different clay minerals (nontronite NAu-2, mixed-layer illite-smectite RAr-1 and ISCz-1, and illite IMt-1) were exposed to D. vulgaris in a non-growth medium with and without anthraquinone-2,6-disulfonate (AQDS) and sulfate. Our results demonstrated that D. vulgaris was able to reduce structural Fe(III) in these clay minerals, and AQDS enhanced the reduction rate and extent. In the presence of AQDS, sulfate had little effect on Fe(III) bioreduction. In the absence of AQDS, sulfate increased the reduction rate and capacity, suggesting that sulfide produced during sulfate reduction reacted with the phyllosilicate Fe(III). The extent of bioreduction of structural Fe(III) in the clay minerals was positively correlated with the percentage of smectite and mineral surface area of these minerals. X-ray diffraction, and scanning and transmission electron microscopy results confirmed formation of illite after bioreduction. These data collectively showed that D. vulgaris could promote smectite illitization through reduction of structural Fe(III) in clay minerals.

  9. Microbial reduction of structural iron in interstratified illite-smectite minerals by a sulfate-reducing bacterium

    USGS Publications Warehouse

    Liu, D.; Dong, H.; Bishop, M.E.; Zhang, Jiahua; Wang, Hongfang; Xie, S.; Wang, Shaoming; Huang, L.; Eberl, D.D.

    2012-01-01

    Clay minerals are ubiquitous in soils, sediments, and sedimentary rocks and could coexist with sulfate-reducing bacteria (SRB) in anoxic environments, however, the interactions of clay minerals and SRB are not well understood. The objective of this study was to understand the reduction rate and capacity of structural Fe(III) in dioctahedral clay minerals by a mesophilic SRB, Desulfovibrio vulgaris and the potential role in catalyzing smectite illitization. Bioreduction experiments were performed in batch systems, where four different clay minerals (nontronite NAu-2, mixed-layer illite-smectite RAr-1 and ISCz-1, and illite IMt-1) were exposed to D. vulgaris in a non-growth medium with and without anthraquinone-2,6-disulfonate (AQDS) and sulfate. Our results demonstrated that D. vulgaris was able to reduce structural Fe(III) in these clay minerals, and AQDS enhanced the reduction rate and extent. In the presence of AQDS, sulfate had little effect on Fe(III) bioreduction. In the absence of AQDS, sulfate increased the reduction rate and capacity, suggesting that sulfide produced during sulfate reduction reacted with the phyllosilicate Fe(III). The extent of bioreduction of structural Fe(III) in the clay minerals was positively correlated with the percentage of smectite and mineral surface area of these minerals. X-ray diffraction, and scanning and transmission electron microscopy results confirmed formation of illite after bioreduction. These data collectively showed that D. vulgaris could promote smectite illitization through reduction of structural Fe(III) in clay minerals. ?? 2011 Blackwell Publishing Ltd.

  10. Accumulation fatty acids of in Chlorella vulgaris under heterotrophic conditions in relation to activity of acetyl-CoA carboxylase, temperature, and co-immobilization with Azospirillum brasilense

    NASA Astrophysics Data System (ADS)

    Leyva, Luis A.; Bashan, Yoav; Mendoza, Alberto; de-Bashan, Luz E.

    2014-10-01

    The relation between fatty acid accumulation, activity of acetyl-CoA carboxylase (ACC), and consequently lipid accumulation was studied in the microalgae Chlorella vulgaris co-immobilized with the plant growth-promoting bacterium Azospirillum brasilense under dark heterotrophic conditions with Na acetate as a carbon source. In C. vulgaris immobilized alone, cultivation experiments for 6 days showed that ACC activity is directly related to fatty acid accumulation, especially in the last 3 days. In co-immobilization experiments, A. brasilense exerted a significant positive effect over ACC activity, increased the quantity in all nine main fatty acids, increased total lipid accumulation in C. vulgaris, and mitigated negative effects of nonoptimal temperature for growth. No correlation between ACC activity and lipid accumulation in the cells was established for three different temperatures. This study demonstrated that the interaction between A. brasilense and C. vulgaris has a significant effect on fatty acid and lipid accumulation in the microalgae.

  11. Nickel and platinum group metal nanoparticle production by Desulfovibrio alaskensis G20.

    PubMed

    Capeness, M J; Edmundson, M C; Horsfall, L E

    2015-12-25

    Desulfovibrio alaskensis G20 is an anaerobic sulfate reducing bacteria. While Desulfovibrio species have previously been shown to reduce palladium and platinum to the zero-state, forming nanoparticles in the process; there have been no reports that D. alaskensis is able to form these nanoparticles. Metal nanoparticles have properties that make them ideal for use in many industrial and medical applications, such as their size and shape giving them higher catalytic activity than the bulk form of the same metal. Nanoparticles of the platinum group metals in particular are highly sought after for their catalytic ability and herein we report the formation of both palladium and platinum nanoparticles by D. alaskensis and the biotransformation of solvated nickel ions to nanoparticle form.

  12. Reduction of U(VI) and Toxic Metals by Desulfovibrio Cytochrome C3

    SciTech Connect

    Wall, Judy D

    2013-04-11

    The central objective of our proposed research was twofold: 1) to investigate the structure-function relationship of Desulfovibrio desulfuricans (now Desulfovibrio alaskensis G20) cytochrome c3 with uranium and 2) to elucidate the mechanism for uranium reduction in vitro and in vivo. Physiological analysis of a mutant of D. desulfuricans with a mutation of the gene encoding the type 1 tetraheme cytochrome c3 had demonstrated that uranium reduction was negatively impacted while sulfate reduction was not if lactate were the electron donor. This was thought to be due to the presence of a branched pathway of electron flow from lactate leading to sulfate reduction. Our experimental plan was to elucidate the structural and mechanistic details of uranium reduction involving cytochrome c3.

  13. Signalling pathways in pemphigus vulgaris.

    PubMed

    Li, Xiaoguang; Ishii, Norito; Ohata, Chika; Furumura, Minao; Hashimoto, Takashi

    2014-03-01

    Acantholysis in pemphigus vulgaris is induced by binding of autoantibodies to desmoglein 3 (Dsg3). The roles of signalling pathways on development of acantholysis have recently been extensively studied. In the study by Sayar et al., recently published in Exp Dermatol, epidermal growth factor receptor (EGFR) signalling was activated in both in vivo and in vitro pemphigus vulgaris experimental models. However, while EGFR inhibitors suppressed activity of p38 mitogen-activated protein kinase (p38MAPK) linearly, they suppressed activity of c-Myc and acantholysis in a non-linear, V-shaped relationship. These findings indicated complicated interactions among EGFR, p38MAPK and c-Myc in pemphigus vulgaris pathology.

  14. Pemphigus Vulgaris with Tense Bullae

    PubMed Central

    Nguyen, Emilie T; Lin, Shinko K; Wu, Jashin J

    2015-01-01

    We report a case of a 51-year-old woman with a history of type II diabetes mellitus and dyslipidemia presenting with pain, swelling, and crusting of the lips. One year after onset of mucosal lesions, she developed an abdominal eruption with several tense vesicles and bullae on an erythematous base. The hematoxylin and eosin stain sample was consistent with a diagnosis of pemphigus vulgaris. The tense bullae of our patient highlight a rare phenotype of pemphigus vulgaris, which fits the mucocutaneous type because of involvement of the oral mucosa, with the exception of the findings of tense bullae. PMID:25663209

  15. Pemphigus vulgaris with tense bullae.

    PubMed

    Nguyen, Emilie T; Lin, Shinko K; Wu, Jashin J

    2015-01-01

    We report a case of a 51-year-old woman with a history of type II diabetes mellitus and dyslipidemia presenting with pain, swelling, and crusting of the lips. One year after onset of mucosal lesions, she developed an abdominal eruption with several tense vesicles and bullae on an erythematous base. The hematoxylin and eosin stain sample was consistent with a diagnosis of pemphigus vulgaris. The tense bullae of our patient highlight a rare phenotype of pemphigus vulgaris, which fits the mucocutaneous type because of involvement of the oral mucosa, with the exception of the findings of tense bullae.

  16. Analysis and comparison of nucleotide sequences encoding the genes for [NiFe] and [NiFeSe] hydrogenases from Desulfovibrio gigas and Desulfovibrio baculatus.

    PubMed Central

    Voordouw, G; Menon, N K; LeGall, J; Choi, E S; Peck, H D; Przybyla, A E

    1989-01-01

    The nucleotide sequences encoding the [NiFe] hydrogenase from Desulfovibrio gigas and the [NiFeSe] hydrogenase from Desulfovibrio baculatus (N.K. Menon, H.D. Peck, Jr., J. LeGall, and A.E. Przybyla, J. Bacteriol. 169:5401-5407, 1987; C. Li, H.D. Peck, Jr., J. LeGall, and A.E. Przybyla, DNA 6:539-551, 1987) were analyzed by the codon usage method of Staden and McLachlan. The reported reading frames were found to contain regions of low codon probability which are matched by more probable sequences in other frames. Renewed nucleotide sequencing showed the probable frames to be correct. The corrected sequences of the two small and large subunits share a significant degree of sequence homology. The small subunit, which contains 10 conserved cysteine residues, is likely to coordinate at least 2 iron-sulfur clusters, while the finding of a selenocysteine codon (TGA) near the 3' end of the [NiFeSe] large-subunit gene matched by a regular cysteine codon (TGC) in the [NiFe] large-subunit gene indicates the presence of some of the ligands to the active-site nickel in the large subunit. PMID:2651421

  17. Disseminated lupus vulgaris.

    PubMed

    Garg, Taru; Ramchander; Shrihar, Rashmi; Gupta, Tanvi Pal; Aggarwal, Shilpi

    2011-01-01

    follicular plugging and multiple epithelioid cell granulomas, rimmed by lymphocytes in the deeper portion of the dermis, mainly peri-appendageal. Stain for acid-fast bacteria was negative. Cultures from the skin lesions were negative. The patient was diagnosed as having lupus vulgaris with multiple lesions of varying morphology at different sites with pulmonary tuberculosis and healed lymph node involvement.

  18. Enhanced activity of ADP glucose pyrophosphorylase and formation of starch induced by Azospirillum brasilense in Chlorella vulgaris.

    PubMed

    Choix, Francisco J; Bashan, Yoav; Mendoza, Alberto; de-Bashan, Luz E

    2014-05-10

    ADP-glucose pyrophosphorylase (AGPase) regulates starch biosynthesis in higher plants and microalgae. This study measured the effect of the bacterium Azospirillum brasilense on AGPase activity in the freshwater microalga Chlorella vulgaris and formation of starch. This was done by immobilizing both microorganisms in alginate beads, either replete with or deprived of nitrogen or phosphorus and all under heterotrophic conditions, using d-glucose or Na-acetate as the carbon source. AGPase activity during the first 72h of incubation was higher in C. vulgaris when immobilized with A. brasilense. This happened simultaneously with higher starch accumulation and higher carbon uptake by the microalgae. Either carbon source had similar effects on enzyme activity and starch accumulation. Starvation either by N or P had the same pattern on AGPase activity and starch accumulation. Under replete conditions, the population of C. vulgaris immobilized alone was higher than when immobilized together, but under starvation conditions A. brasilense induced a larger population of C. vulgaris. In summary, adding A. brasilense enhanced AGPase activity, starch formation, and mitigation of stress in C. vulgaris.

  19. Growth and aroma contribution of Microbacterium foliorum, Proteus vulgaris and Psychrobacter sp. during ripening in a cheese model medium.

    PubMed

    Deetae, Pawinee; Spinnler, Henry-Eric; Bonnarme, Pascal; Helinck, Sandra

    2009-02-01

    The growth and aroma contribution of Microbacterium foliorum, Proteus vulgaris and Psychrobacter sp., some common but rarely mentioned cheese bacteria, were investigated in a cheese model deacidified by Debaryomyces hansenii during the ripening process. Our results show that these bacteria had distinct growth and cheese flavour production patterns during the ripening process. P. vulgaris had the greatest capacity to produce not only the widest variety but also the highest quantities of volatile compounds with low olfactive thresholds, e.g. volatile sulphur compounds and branched-chain alcohols. Such compounds produced by P. vulgaris increased after 21 days of ripening and reached a maximum at 41 days. The three bacteria studied exhibited various degrees of caseinolytic, aminopeptidase and deaminase activities. Moreover, P. vulgaris had a greater capacity for hydrolysing casein and higher deaminase activity. Our results show that P. vulgaris, a Gram-negative bacterium naturally present on the surface of ripened cheeses, could produce high concentrations of flavour compounds from amino acid degradation during the ripening process. Its flavouring role in cheese cannot be neglected. Moreover, it could be a useful organism for producing natural flavours as dairy ingredients.

  20. Extensive keloid formation after pemphigus vulgaris.

    PubMed

    Sako, Eric Y; Workwick, Scott

    2015-11-18

    Pemphigus vulgaris is an immunobullous disease characterized by intraepidermal blister formation. These blisters eventually rupture, leaving erosions that are slow to heal, often leaving hyperpigmented patches, but no scars. We describe a case of a 67- year-old man with pemphigus vulgaris who suffered severe keloidal scarring after the pemphigus lesions became infected. His keloids were treated with intralesional corticosteroids with some improvement. Pemphigus vulgaris, a process confined to the epidermis, may lead to scarring in predisposed individuals, particularly if infection occurs.

  1. [Therapy-resistant "psoriasis vulgaris"].

    PubMed

    Kempter, W; Stein, A; Bauer, A; Wozel, G

    2009-04-01

    A 61-year-old patient had a 25-year history of erythematous scaling lesions, diagnosed and treated as psoriasis vulgaris. He presented with a growing nodule within the erythematous plaque. Biopsy shows epithelioid cell granulomas with prominent Langhans giant cells. There was no sign of a squamous cell carcinoma. The tuberculin test was strongly positive and M. tuberculosis complex was detected in the biopsy material by PCR. He was diagnosed with lupus vulgaris, the most frequent form of cutaneous tuberculosis. Other types include tuberculosis verrucosa cutis, tuberculosis cutis orificialis and disseminated military tuberculosis. The patient was treated with rifampicin, isoniazid, pyrazinamide and ethambutol for two months, following a four month treatment with rifampicin and isoniazid. The skin lesions rapidly resolved under antituberculotic treatment.

  2. Immobilizing U from solution by immobilized sulfate-reducing bacteria of desulfovibrio desulfuricans

    NASA Astrophysics Data System (ADS)

    Xu, Hulfang; Barton, Larry L.

    2000-07-01

    As determined by transmission electron microscopy, the reduction of uranyl accetate by immobilized cells of Desulfovibrio desulfuricans results in the production of black uraninite nanocrystals precipitated outside the cell. Some nanocrystals are associated with outer membranes of the cell as revealed from cross sections of these metabolically active sulfate-reducing bacteria. The nanocrystals have an average diameter of 5 nm and have anhedral shape. It is proposed that cytochrome in these cells has an important role in the reduction of uranyl through transferring electron from molecular hydrogen or lactic acid to uranyl ions.

  3. Reduction of U(VI) and Toxic Metals by Desulfovibrio Cytochrome c3

    SciTech Connect

    Wall, Judy D.

    2003-06-01

    The project, ''Reduction of U(VI) and toxic metals by Desulfovibrio cytochrome c3'', is designed to obtain spectroscopic information for or against a functional interaction of cytochrome c3 and uranium in the whole cells. That is, is the cytochrome c3 the uranium reductase? Our approach has been to start with purified cytochrome and determine any unique spectral disturbances during electron flow to U(VI). Then we will attempt to identify these signals emanating from cells actively reducing uranium. This project is being carried out in collaboration with Dr. William Woodruff at the Los Alamos National Laboratory where the spectral experiments are being carried out.

  4. Single Bacterium Detection Using Sers

    NASA Astrophysics Data System (ADS)

    Gonchukov, S. A.; Baikova, T. V.; Alushin, M. V.; Svistunova, T. S.; Minaeva, S. A.; Ionin, A. A.; Kudryashov, S. I.; Saraeva, I. N.; Zayarny, D. A.

    2016-02-01

    This work is devoted to the study of a single Staphylococcus aureus bacterium detection using surface-enhanced Raman spectroscopy (SERS) and resonant Raman spectroscopy (RS). It was shown that SERS allows increasing sensitivity of predominantly low frequency lines connected with the vibrations of Amide, Proteins and DNA. At the same time the lines of carotenoids inherent to this kind of bacterium are well-detected due to the resonance Raman scattering mechanism. The reproducibility and stability of Raman spectra strongly depend on the characteristics of nanostructured substrate, and molecular structure and size of the tested biological object.

  5. Sulfur isotope fractionation during the evolutionary adaptation of a sulfate-reducing bacterium.

    PubMed

    Pellerin, André; Anderson-Trocmé, Luke; Whyte, Lyle G; Zane, Grant M; Wall, Judy D; Wing, Boswell A

    2015-04-01

    Dissimilatory sulfate reduction is a microbial catabolic pathway that preferentially processes less massive sulfur isotopes relative to their heavier counterparts. This sulfur isotope fractionation is recorded in ancient sedimentary rocks and generally is considered to reflect a phenotypic response to environmental variations rather than to evolutionary adaptation. Modern sulfate-reducing microorganisms isolated from similar environments can exhibit a wide range of sulfur isotope fractionations, suggesting that adaptive processes influence the sulfur isotope phenotype. To date, the relationship between evolutionary adaptation and isotopic phenotypes has not been explored. We addressed this by studying the covariation of fitness, sulfur isotope fractionation, and growth characteristics in Desulfovibrio vulgaris Hildenborough in a microbial evolution experiment. After 560 generations, the mean fitness of the evolved lineages relative to the starting isogenic population had increased by ∼ 17%. After 927 generations, the mean fitness relative to the initial ancestral population had increased by ∼ 20%. Growth rate in exponential phase increased during the course of the experiment, suggesting that this was a primary influence behind the fitness increases. Consistent changes were observed within different selection intervals between fractionation and fitness. Fitness changes were associated with changes in exponential growth rate but changes in fractionation were not. Instead, they appeared to be a response to changes in the parameters that govern growth rate: yield and cell-specific sulfate respiration rate. We hypothesize that cell-specific sulfate respiration rate, in particular, provides a bridge that allows physiological controls on fractionation to cross over to the adaptive realm.

  6. Genetic diversity of Desulfovibrio spp. in environmental samples analyzed by denaturing gradient gel electrophoresis of [NiFe] hydrogenase gene fragments.

    PubMed Central

    Wawer, C; Muyzer, G

    1995-01-01

    The genetic diversity of Desulfovibrio species in environmental samples was determined by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified [NiFe] hydrogenase gene fragments. Five different PCR primers were designed after comparative analysis of [NiFe] hydrogenase gene sequences from three Desulfovibrio species. These primers were tested in different combinations on the genomic DNAs of a variety of hydrogenase-containing and hydrogenase-lacking bacteria. One primer pair was found to be specific for Desulfovibrio species only, while the others gave positive results with other bacteria also. By using this specific primer pair, we were able to amplify the [NiFe] hydrogenase genes of DNAs isolated from environmental samples and to detect the presence of Desulfovibrio species in these samples. However, only after DGGE analysis of these PCR products could the number of different Desulfovibrio species within the samples be determined. DGGE analysis of PCR products from different bioreactors demonstrated up to two bands, while at least five distinguishable bands were detected in a microbial mat sample. Because these bands most likely represent as many Desulfovibrio species present in these samples, we conclude that the genetic diversity of Desulfovibrio species in the natural microbial mat is far greater than that in the experimental bioreactors. PMID:7793940

  7. The FlxABCD-HdrABC proteins correspond to a novel NADH dehydrogenase/heterodisulfide reductase widespread in anaerobic bacteria and involved in ethanol metabolism in Desulfovibrio vulgaris Hildenborough.

    PubMed

    Ramos, Ana Raquel; Grein, Fabian; Oliveira, Gonçalo P; Venceslau, Sofia S; Keller, Kimberly L; Wall, Judy D; Pereira, Inês A C

    2015-07-01

    Flavin-based electron bifurcation (FBEB) is an important mechanism for the energy metabolism of anaerobes. A new family of NADH dehydrogenases, the flavin oxidoreductase (FlxABCD, previously called FloxABCD), was proposed to perform FBEB in sulphate-reducing organisms coupled with heterodisulfide reductase (HdrABC). We found that the hdrABC-flxABCD gene cluster is widespread among anaerobic bacteria, pointing to a general and important role in their bioenergetics. In this work, we studied FlxABCD of Desulfovibrio vulgaris Hildenborough. The hdr-flx genes are part of the same transcriptional unit and are increased in transcription during growth in ethanol-sulfate, and to a less extent during pyruvate fermentation. Two mutant strains were generated: one where expression of the hdr-flx genes was interrupted and another lacking the flxA gene. Both strains were unable to grow with ethanol-sulfate, whereas growth was restored in a flxA-complemented strain. The mutant strains also produced very reduced amounts of ethanol compared with the wild type during pyruvate fermentation. Our results show that in D. vulgaris, the FlxABCD-HdrABC proteins are essential for NADH oxidation during growth on ethanol, probably involving a FBEB mechanism that leads to reduction of ferredoxin and the small protein DsrC, while in fermentation they operate in reverse, reducing NAD(+) for ethanol production.

  8. Survey of large protein complexes D. vulgaris reveals great structural diversity

    SciTech Connect

    Han, B.-G.; Dong, M.; Liu, H.; Camp, L.; Geller, J.; Singer, M.; Hazen, T. C.; Choi, M.; Witkowska, H. E.; Ball, D. A.; Typke, D.; Downing, K. H.; Shatsky, M.; Brenner, S. E.; Chandonia, J.-M.; Biggin, M. D.; Glaeser, R. M.

    2009-08-15

    An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.

  9. Autoimmunity to desmocollin 3 in pemphigus vulgaris.

    PubMed

    Mao, Xuming; Nagler, Arielle R; Farber, Sara A; Choi, Eun Jung; Jackson, Lauren H; Leiferman, Kristin M; Ishii, Norito; Hashimoto, Takashi; Amagai, Masayuki; Zone, John J; Payne, Aimee S

    2010-12-01

    Pemphigus vulgaris is a blistering disease associated with autoantibodies to the desmosomal adhesion protein, desmoglein 3. Genetic deficiency of desmoglein 3 in mice mimics autoimmunity to desmoglein 3 in pemphigus vulgaris, with mucosal-dominant blistering in the suprabasal layer of the epidermis. Mice with an epidermal-specific deletion of desmocollin 3, the other major desmosomal cadherin isoform expressed in the basal epidermis, develop suprabasal blisters in skin that are histologically identical to those observed in pemphigus vulgaris, suggesting that desmocollin 3 might be a target of autoantibodies in some pemphigus vulgaris patients. We now demonstrate that desmocollin 3 is an autoantigen in pemphigus vulgaris, illustrated in a patient with mucosal-dominant blistering. Six of 38 pemphigus vulgaris and one of 85 normal serum samples immunoprecipitate desmocollin 3 (P = 0.003). Incubation of patient IgG with human keratinocytes causes loss of intercellular adhesion, and adsorption with recombinant desmocollin 3 specifically prevents this pathogenic effect. Additionally, anti-desmocollin 3 sera cause loss of keratinocyte cell surface desmocollin 3, but not desmoglein 3 by immunofluorescence, indicating distinct cellular pathogenic effects in anti-desmocollin and anti-desmoglein pemphigus, despite their identical clinical presentations. These data demonstrate that desmocollin 3 is a pathogenic autoantigen in pemphigus vulgaris and suggest that pemphigus vulgaris is a histological reaction pattern that may result from autoimmunity to desmoglein 3, desmocollin 3, or both desmosomal cadherins.

  10. Sporotrichoid lupus vulgaris: A rare presentation.

    PubMed

    Maheshwari, Anshul; Tiwari, Siddhi; Mathur, Deepak K; Bhargava, Puneet

    2015-01-01

    Lupus vulgaris is the most common presentation of cutaneous tuberculosis in India and can present as papular, nodular, plaque, ulcerative, vegetating, and tumid forms. Unusual variants include the frambesiform, gangrenous, ulcerovegetating, lichen simplex chronicus, myxomatous, and sporotrichoid types. We describe a rare sporotrichoid presentation of lupus vulgaris on the leg of a 28-year-old female of 12 years duration.

  11. Pemphigus vulgaris with solitary toxic thyroid nodule.

    PubMed

    Alfishawy, Mostafa; Anwar, Karim; Elbendary, Amira; Daoud, Ahmed

    2014-01-01

    Background. Pemphigus vulgaris is an autoimmune vesiculobullous disease, affecting the skin and mucous membranes. It is reported to be associated with other autoimmune diseases including autoimmune thyroid diseases. However we report herein a case of pemphigus vulgaris associated with autonomous toxic nodule. Case Presentation. A 51-year-old woman was evaluated for blisters and erosions that develop on her trunk, face, and extremities, with a five-year history of progressively enlarging neck mass, and a past medical history of pemphigus vulgaris seven years ago. The condition was associated with palpitation, dyspnea, and heat intolerance. Thyroid function tests and thyroid scan were compatible with the diagnosis of thyrotoxicosis due to autonomous toxic nodule. Exacerbation of pemphigus vulgaris was proved by skin biopsy from the patient which revealed histologic picture of pemphigus vulgaris. Conclusion. Autoimmune thyroid diseases are reported to associate pemphigus vulgaris. To our knowledge, this case is the first in the English literature to report association between pemphigus vulgaris and autonomous toxic nodule and highlights the possibility of occurrence of pemphigus vulgaris with a nonautoimmune thyroid disease raising the question: is it just a coincidence or is there an explanation for the occurrence of both conditions together?

  12. Lupus vulgaris with squamous cell carcinoma.

    PubMed

    Motswaledi, Mojakgomo Hendrick; Doman, Chantal

    2007-12-01

    Tuberculosis is still a significant problem in developing countries. Cutaneous forms of tuberculosis account for approximately 10% of all cases of extrapulmonary tuberculosis. Cutaneous tuberculosis may be because of true infection with Mycobacterium tuberculosis or because of tuberculids. Tuberculids are immunological reactions to haematogenously spread antigenic components of M. tuberculosis. True cutaneous tuberculosis may be because of inoculation or haematogenous spread of M. tuberculosis to the skin. Lupus vulgaris is the commonest form of true cutaneous tuberculosis. Other forms of true cutaneous tuberculosis are tuberculous chancre, tuberculosis verrucosa cutis, scrofuloderma, periorificial tuberculosis and miliary tuberculosis of the skin. Lupus vulgaris is usually chronic and progressive. It occurs in patients with moderate to high immunity against M. tuberculosis as evidenced by strongly positive tuberculin test. Long-standing cases of lupus vulgaris may be complicated by squamous cell carcinoma (SCC). We describe a patient who had undiagnosed lupus vulgaris for 35 years until she developed SCC on the lesion of lupus vulgaris.

  13. Syntrophic Growth of Desulfovibrio alaskensis Requires Genes for H2 and Formate Metabolism as Well as Those for Flagellum and Biofilm Formation

    PubMed Central

    Bradstock, Peter; Sheik, Cody S.; Diao, Yiwei; Gazioglu, Ozcan; Gorby, Yuri; McInerney, Michael J.

    2015-01-01

    In anaerobic environments, mutually beneficial metabolic interactions between microorganisms (syntrophy) are essential for oxidation of organic matter to carbon dioxide and methane. Syntrophic interactions typically involve a microorganism degrading an organic compound to primary fermentation by-products and sources of electrons (i.e., formate, hydrogen, or nanowires) and a partner producing methane or respiring the electrons via alternative electron accepting processes. Using a transposon gene mutant library of the sulfate-reducing Desulfovibrio alaskensis G20, we screened for mutants incapable of serving as the electron-accepting partner of the butyrate-oxidizing bacterium, Syntrophomonas wolfei. A total of 17 gene mutants of D. alaskensis were identified as incapable of serving as the electron-accepting partner. The genes identified predominantly fell into three categories: membrane surface assembly, flagellum-pilus synthesis, and energy metabolism. Among these genes required to serve as the electron-accepting partner, the glycosyltransferase, pilus assembly protein (tadC), and flagellar biosynthesis protein showed reduced biofilm formation, suggesting that each of these components is involved in cell-to-cell interactions. Energy metabolism genes encoded proteins primarily involved in H2 uptake and electron cycling, including a rhodanese-containing complex that is phylogenetically conserved among sulfate-reducing Deltaproteobacteria. Utilizing an mRNA sequencing approach, analysis of transcript abundance in wild-type axenic and cocultures confirmed that genes identified as important for serving as the electron-accepting partner were more highly expressed under syntrophic conditions. The results imply that sulfate-reducing microorganisms require flagellar and outer membrane components to effectively couple to their syntrophic partners; furthermore, H2 metabolism is essential for syntrophic growth of D. alaskensis G20. PMID:25616787

  14. Isolation of sulfate-reducing bacteria from the terrestrial deep subsurface and description of Desulfovibrio cavernae sp. nov.

    PubMed

    Sass, Henrik; Cypionka, Heribert

    2004-09-01

    Deep subsurface sandstones in the area of Berlin (Germany) located 600 to 1060 m below the surface were examined for the presence of viable microorganisms. The in situ temperatures at the sampling sites ranged from 37 to 45 degrees C. Investigations focussed on sulfate-reducing bacteria able to grow on methanol and triethylene glycol, which are added as chemicals to facilitate the long-term underground storage of natural gas. Seven strains were isolated from porewater brines in the porous sandstone. Three of them were obtained with methanol (strains H1M, H3M, and B1M), three strains with triethylene glycol (strains H1T, B1T, and B2T) and one strain with a mixture of lactate, acetate and butyrate (strain H1-13). Due to phenotypic properties six isolates could be identified as members of the genus Desulfovibrio, and strain B2T as a Desulfotomaculum. The salt tolerance and temperature range for growth indicated that the isolates originated from the indigenous deep subsurface sandstones. They grew in mineral media reflecting the in situ ionic composition of the different brines, which contained 1.5 to 190 g NaCl x l(-1) and high calcium and magnesium concentrations. The Desulfovibrio strains grew at temperatures between 20 and 50 degrees C, while the Desulfotomaculum strain was thermophilic and grew between 30 and 65 degrees C. The strains utilized a broad spectrum of electron donors and acceptors. They grew with carbon compounds like lactate, pyruvate, formate, n-alcohols (C1-C5), glycerol, ethylene glycol, malate, succinate, and fumarate. Some strains even utilized glucose as electron donor and carbon source. All strains were able to use sulfate, sulfite and nitrate as electron acceptors. Additionally, three Desulfovibrio strains reduced manganese oxide, the Desulfotomaculum strain reduced manganese oxide, iron oxide, and elemental sulfur. The 16S rRNA analysis revealed that the isolates belong to three different species. The strains H1T, H3M and B1M could be

  15. Diagnosis and clinical features of pemphigus vulgaris.

    PubMed

    Venugopal, Supriya S; Murrell, Dédée F

    2012-05-01

    Autoimmune bullous diseases are associated with autoimmunity against structural components that maintain cell-cell and cell-matrix adhesion in the skin and mucous membranes. They include those where the skin blisters at the basement membrane zone and those where the skin blisters within the epidermis (pemphigus vulgaris, pemphigus foliaceus, and other subtypes of pemphigus). The variants of pemphigus are determined according to the level of intraepidermal split formation. There are 5 main variants of pemphigus: pemphigus vulgaris, pemphigus foliaceus, pemphigus erythematosus, drug-induced pemphigus, and paraneoplastic pemphigus. This review focuses only on pemphigus vulgaris.

  16. Diagnosis and clinical features of pemphigus vulgaris.

    PubMed

    Venugopal, Supriya S; Murrell, Dédée F

    2011-07-01

    Autoimmune bullous diseases are associated with autoimmunity against structural components that maintain cell-cell and cell-matrix adhesion in the skin and mucous membranes. They include those where the skin blisters at the basement membrane zone and those where the skin blisters within the epidermis (pemphigus vulgaris, pemphigus foliaceus, and other subtypes of pemphigus). The variants of pemphigus are determined according to the level of intraepidermal split formation. There are 5 main variants of pemphigus: pemphigus vulgaris, pemphigus foliaceus, pemphigus erythematosus, drug-induced pemphigus, and paraneoplastic pemphigus. This review focuses only on pemphigus vulgaris.

  17. Hypertrophic lupus vulgaris: an unusual presentation.

    PubMed

    Jain, Vijay K; Aggarwal, Kamal; Jain, Sarika; Singh, Sunita

    2009-07-01

    Lupus vulgaris is the most common form of cutaneous tuberculosis occurring in previously sensitized individuals with a high degree of tuberculin sensitivity. Various forms including plaque, ulcerative, hypertrophic, vegetative, papular, and nodular forms have been described. A 30-year-old male patient presented with a very large hypertrophic lupus vulgaris lesion over left side of chest since 22 years. Histopathological examination showed granulomatous infiltration without caseation necrosis. The Mantoux reaction was strongly positive. Hypertrophic lupus vulgaris of such a giant size and that too at an unusual site is extremely rare and hence is being reported.

  18. Determination of kinetic coefficients for the simultaneous reduction of sulfate and uranium by Desulfovibrio desulfuricans bacteria

    SciTech Connect

    Tucker, M.D.

    1995-05-01

    Uranium contamination of groundwaters and surface waters near abandoned mill tailings piles is a serious concern in many areas of the western United States. Uranium usually exists in either the U(IV) or the U(VI) oxidation state. U(VI) is soluble in water and, as a result, is very mobile in the environment. U(IV), however, is generally insoluble in water and, therefore, is not subject to aqueous transport. In recent years, researchers have discovered that certain anaerobic microorganisms, such as the sulfate-reducing bacteria Desulfovibrio desulfuricans, can mediate the reduction of U(VI) to U(IV). Although the ability of this microorganism to reduce U(VI) has been studied in some detail by previous researchers, the kinetics of the reactions have not been characterized. The purpose of this research was to perform kinetic studies on Desulfovibrio desulficans bacteria during simultaneous reduction of sulfate and uranium and to determine the phase in which uranium exists after it has been reduced and precipitated from solution. The studies were conducted in a laboratory-scale chemostat under substrate-limited growth conditions with pyruvate as the substrate. Kinetic coefficients for substrate utilization and cell growth were calculated using the Monod equation. The maximum rate of substrate utilization (k) was determined to be 4.70 days{sup {minus}1} while the half-velocity constant (K{sub s}) was 140 mg/l COD. The yield coefficient (Y) was determined to be 0.17 mg cells/mg COD while the endogenous decay coefficient (k{sub d}) was calculated as 0.072 days{sup {minus}1}. After reduction, U(IV) Precipitated from solution in the uraninite (UO{sub 2}) phase. Uranium removal efficiency as high as 90% was achieved in the chemostat.

  19. Phaseolus vulgaris endornavirus 1 and Phaseolus vulgaris endornavirus 2 infecting common bean Phaseolus vulgaris genotypes show differential infection patterns between gene pools

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We investigated the occurrence of two plant endornaviruses, Phaseolus vulgaris endornavirus 1 (PvEV-1) and Phaseolus vulgaris endornavirus 2 (PvEV-2), in breeding-lines, cultivars, landraces, and wild genotypes of common bean (Phaseolus vulgaris) as well as other Phaseolus species collected from two...

  20. Berberis Vulgaris and Berberine: An Update Review.

    PubMed

    Imenshahidi, Mohsen; Hosseinzadeh, Hossein

    2016-11-01

    Berberine is an isoquinoline alkaloid present in several plants, including Coptis sp. and Berberis sp. Berberine is a customary component in Chinese medicine, and is characterized by a diversity of pharmacological effects. An extensive search in electronic databases (PubMed, Scopus, Ovid, Wiley, ProQuest, ISI, and Science Direct) were used to identify the pharmacological and clinical studies on Berberis vulgaris and berberine, during 2008 to 2015, using 'berberine' and 'Berberis vulgaris' as search words. We found more than 1200 new article studying the properties and clinical uses of berberine and B. vulgaris, for treating tumor, diabetes, cardiovascular disease, hyperlipidemia, inflammation, bacterial and viral infections, cerebral ischemia trauma, mental disease, Alzheimer disease, osteoporosis, and so on. In this article, we have updated the pharmacological effects of B. vulgaris and its active constituent, berberine. Copyright © 2016 John Wiley & Sons, Ltd.

  1. [Childhood pemphigus vulgaris, a case report].

    PubMed

    Bellelli, Ana G; Mantero, Natalia M; Rueda, María L; Navacchia, Daniel; Cao, Gabriel; De Lillo, Leonardo; Grees, Susana A

    2016-12-01

    Pemphigus vulgaris is a chronic disease that is characterized by flaccid blisters and erosions, caused by immunoglobulin G autoantibodies against epidermal components. It is highly unusual in the pediatric population; it represents the 1.4 - 2.9% of the total cases. We present a case of pemphigus vulgaris in a 12 year old girl, which has implied a challenge both in its diagnosis and in its treatment.

  2. Diclofenac: a new trigger of pemphigus vulgaris?

    PubMed

    Matz, H; Bialy-Golan, A; Brenner, S

    1997-01-01

    Many drugs have been shown to induce pemphigus, including thiol and nonthiol drugs. We present a case of pemphigus vulgaris where a nonsteroidal anti-inflammatory medication, diclofenac in suppositories and topical gel preparations, is suspected of having triggered the disease. The temporal relationship between drug and outbreak of disease together with the positive migration inhibition factor test to diclofenac point to the possible involvement of this drug in triggering pemphigus vulgaris.

  3. Pemphigus vulgaris presenting with multiple lesion morphologies.

    PubMed

    Song, Philip In; Divito, Sherrie J; Kroshinsky, Daniela

    2014-12-14

    Pemphigus vulgaris is an uncommon intraepidermal blistering disorder that typically presents with flaccid bullae or erosions. We report a patient with pemphigus vulgaris who presented with several unusual clinical features: tense bullae with dependently layered pus, true target lesions coalescing into annular configurations, and diffuse desquamation that initially raised concern for toxic epidermal necrolysis. We discuss the differential diagnosis and implications of these morphological findings.

  4. Neonatal and infantile acne vulgaris: an update.

    PubMed

    Serna-Tamayo, Cristian; Janniger, Camila K; Micali, Giuseppe; Schwartz, Robert A

    2014-07-01

    Acne may present in neonates, infants, and small children. Neonatal and infantile acne vulgaris are not considered to be rare. The presentation of acne in this patient population sometimes represents virilization and may portend later development of severe adolescent acne. Neonatal and infantile acne vulgaris must be distinguished from other cutaneous disorders seen in newborns and infants. Infantile acne tends to be more pleomorphic and inflammatory, thus requiring more vigorous therapy than neonatal acne.

  5. Nail involvement in pemphigus vulgaris.

    PubMed

    Engineer, L; Norton, L A; Ahmed, A R

    2000-09-01

    Nail involvement in pemphigus vulgaris is relatively rare. We describe a case of severe pemphigus involving both the skin and oral mucosa in which an acute exacerbation was preceded by the onset of nail involvement of all 4 extremities. Nail involvement occurred in the form of hemorrhagic paronychia of multiple digits. Oral, cutaneous, and nail manifestations of the disease were all well controlled by systemic therapy. A review of the literature on nail involvement in pemphigus reveals that this involvement may be manifested in multiple ways, with chronic paronychia and onychomadesis being the most common. Involvement of the nail occurs most frequently either as part of the initial presentation, or just before or concurrent with a flare of pre-existing disease. Nail involvement, when it occurs, is usually present when the disease is severe. Topical therapy is insufficient, and systemic therapy is warranted. In the majority of cases, nail recovery is complete, with no residual damage.

  6. Pemphigus vulgaris affecting 19 nails.

    PubMed

    Patsatsi, A; Sotiriou, E; Devliotou-Panagiotidou, D; Sotiriadis, D

    2009-03-01

    A 60-year-old woman presented with painful erosions in the oral mucosa, pharynx, perineum and perianal area, and multiple plaques with thick adherent crusts on the scalp. Most (nine) of the patient's fingernails had alterations in colour, affecting more than half of the nail plate, and all the toenails had severe inflammation of the nail folds, haemorrhagic paronychia and subungual or intraungual haemorrhage. A diagnosis of pemphigus vulgaris (PV) was made based on histology and on direct and indirect immunofluorescence findings. Groups of acantholytic cells were also observed in a Tzanck smear obtained from a subungual lesion. Onychomadesis in most of the fingernails and in all the toenails developed gradually. The patient was hospitalized and treated with oral corticosteroids. Complete recovery without residual damage to the nails and persistent remission was achieved. Nail involvement in PV is rarely described and is always of interest, as its presentation varies widely.

  7. Pemphigus vulgaris: approach to treatment.

    PubMed

    Sinha, Animesh A; Hoffman, Melissa B; Janicke, Elise C

    2015-04-01

    The therapeutic management of pemphigus vulgaris (PV) is centered around immunosuppression, which can be generalized, as in the use of corticosteroids or steroid sparing agents, or specific, as in therapeutic blockage of autoantibody production, certain cytokines, or signaling pathways. Currently, the backbone of treatment for PV, particularly, first line therapy, remains systemic corticosteroids. Although very effective, the significant side effects of long-term corticosteroid usage are well documented. Adjunctive therapies aim to eliminate, or at least decrease, the necessary dose of corticosteroids. Specifically, azathioprine, cyclophosphamide, methotrexate, cyclosporine, mycophenolate mofetil and dapsone are now widely used in PV. Intravenous immunoglobulin (IVIG), plasmapheresis, immunoadsorption, and most recently, rituximab, are other members of the therapeutic armamentarium. However, despite the widening range of treatment options in PV, well-controlled clinical trials and consensus guidelines are lacking.

  8. Elongated magnetite nanoparticle formation from a solid ferrous precursor in a magnetotactic bacterium

    PubMed Central

    Menguy, Nicolas; Gonzalez, Teresa Perez; Morin, Guillaume; Widdrat, Marc; Faivre, Damien

    2016-01-01

    Magnetotactic bacteria are aquatic microorganisms that intracellularly mineralize ferrimagnetic nanoparticles enabling the cells to align with the geomagnetic field. The bacteria produce a magnetic mineral of species-specific phase (magnetite Fe(II)Fe(III)2O4 or greigite Fe(II)Fe(III)2S4), size, morphology and particle assembly. Several species produce crystals of unusual elongated particle shapes, which break the symmetry of the thermodynamically favoured isometric morphology. Such morphologies are thought to affect domain size and orientation of the internal magnetization. Therefore, they are interesting study objects to develop new synthetic strategies for the morphological control of nanoparticles. We investigate the formation of such irregularly shaped nanomagnets in the species Desulfovibrio magneticus RS-1. In contrast to previously described organisms, this bacterium accumulates iron predominantly as Fe(II) rather than Fe(III) consistent with an alternative oxidative biomineralization route. Further, using high-resolution electron microscopy, we observe an epitaxial relationship between precursor and the final mineral phase supporting the notion of a solid-state transformation pathway. The precursor is likely a green rust previously thought to convert to magnetite only by dissolution and re-precipitation. Our findings represent a novel observation in the interconversion of iron (oxyhydr)oxide materials and suggest that solid-state growth processes could be required to produce irregularly shaped, elongated magnetite nanocrystals. PMID:27881802

  9. Rhizobium azibense sp. nov., a nitrogen fixing bacterium isolated from root-nodules of Phaseolus vulgaris.

    PubMed

    Mnasri, Bacem; Liu, Tian Yan; Saidi, Sabrine; Chen, Wen Feng; Chen, Wen Xin; Zhang, Xiao Xia; Mhamdi, Ridha

    2014-05-01

    Three microbial strains isolated from common beans, 23C2T (Tunisia), Gr42 (Spain) and IE4868 (Mexico), which have been identified previously as representing a genomic group closely related to Rhizobium gallicum, are further studied here. Their 16S rRNA genes showed 98.5-99% similarity with Rhizobium loessense CCBAU 7190BT, R. gallicum R602spT, Rhizobium mongolense USDA 1844T and Rhizobium yanglingense CCBAU 71623T. Phylogenetic analysis based on recA, atpD, dnaK and thrC sequences showed that the novel strains were closely related and could be distinguished from the four type strains of the closely related species. Strains 23C2T, Gr42 and IE4868 could be also differentiated from their closest phylogenetic neighbours by their phenotypic and physiological properties and their fatty acid contents. All three strains harboured symbiotic genes specific to biovar gallicum. Levels of DNA-DNA relatedness between strain 23C2T and the type strains of R. loessense, R. mongolense, R. gallicum and R. yanglingense ranged from 58.1 to 61.5%. The DNA G+C content of the genomic DNA of strain 23C2T was 59.52%. On the basis of these data, strains 23C2T, Gr42 and IE4868 were considered to represent a novel species of the genus Rhizobium for which the name Rhizobium azibense is proposed. Strain 23C2T (=CCBAU 101087T=HAMBI3541T) was designated as the type strain.

  10. Conversion of cellulose to methane and carbon dioxide by triculture of acetivibrio cellulolyticus, desulfovibrio sp. , and methanosarcina barkeri

    SciTech Connect

    Laube, V.M.; Martin, S.M.

    1981-01-01

    The fermentation of cellulose by monocultures of Acetivibrio cellulolyticus and cocultures of A. cellulolyticus-Methanosarcina barkeri, A. cellulolyticus-Desulfovibrio sp., and A. cellulolyticus-M. barkeri-Desulfovibrio sp. was studied. The monoculture produced ethanol, acetate, H, and CO. More acetate and less ethanol was formed by the cocultures than by the monoculture. Acetate was utilized by M. barkeri in coculture with A. cellulolyticus after a lag period, whereas ethanol was metabolized by the sulfate reducer only under conditions of low H partial pressure, i.e., when cocultured with A. cellulolyticus-M. barkeri or when grown together with the methanogen. Only the 3-component culture carried out the rapid conversion of cellulose to CO2 and CH4. Furthermore, this culture hydrolyzed the most cellulose-85% of that initially present. This amount was increased to 90% by increasing the population of M. barkeri in the triculture. CH4 production was also increased, and a quicker fermentation rate was achieved.

  11. Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium

    PubMed Central

    Rajeev, Lara; Luning, Eric G.; Altenburg, Sara; Zane, Grant M.; Baidoo, Edward E. K.; Catena, Michela; Keasling, Jay D.; Wall, Judy D.; Fields, Matthew W.; Mukhopadhyay, Aindrila

    2014-01-01

    We surveyed the eight putative cyclic-di-GMP-modulating response regulators (RRs) in Desulfovibrio vulgaris Hildenborough that are predicted to function via two-component signaling. Using purified proteins, we examined cyclic-di-GMP (c-di-GMP) production or turnover in vitro of all eight proteins. The two RRs containing only GGDEF domains (DVU2067, DVU0636) demonstrated c-di-GMP production activity in vitro. Of the remaining proteins, three RRs with HD-GYP domains (DVU0722, DVUA0086, and DVU2933) were confirmed to be Mn2+-dependent phosphodiesterases (PDEs) in vitro and converted c-di-GMP to its linear form, pGpG. DVU0408, containing both c-di-GMP production (GGDEF) and degradation domains (EAL), showed c-di-GMP turnover activity in vitro also with production of pGpG. No c-di-GMP related activity could be assigned to the RR DVU0330, containing a metal-dependent phosphohydrolase HD-OD domain, or to the HD-GYP domain RR, DVU1181. Studies included examining the impact of overexpressed cyclic-di-GMP-modulating RRs in the heterologous host E. coli and led to the identification of one RR, DVU0636, with increased cellulose production. Evaluation of a transposon mutant in DVU0636 indicated that the strain was impaired in biofilm formation and demonstrated an altered carbohydrate:protein ratio relative to the D. vulgaris wild type biofilms. However, grown in liquid lactate/sulfate medium, the DVU0636 transposon mutant showed no growth impairment relative to the wild-type strain. Among the eight candidates, only the transposon disruption mutant in the DVU2067 RR presented a growth defect in liquid culture. Our results indicate that, of the two diguanylate cyclases (DGCs) that function as part of two-component signaling, DVU0636 plays an important role in biofilm formation while the function of DVU2067 has pertinence in planktonic growth. PMID:25120537

  12. Lupus vulgaris: report of two cases.

    PubMed

    Wozniacka, Anna; Schwartz, Robert A; Sysa-Jedrzejowska, Anna; Borun, Marta; Arkuszewska, Cecylia

    2005-04-01

    Although there has been a steady decline in the incidence of tuberculosis in recent years, it persists in some regions, and where AIDS is especially prevalent, the number of new cases has been increasing. Thus, cutaneous tuberculosis has re-emerged in areas with a high incidence of HIV infection and multidrug-resistant pulmonary tuberculosis. Lupus vulgaris has been and remains the most common form of cutaneous tuberculosis. Cutaneous manifestations of disseminated tuberculosis are unusual, being seen in less than 0.5% of cases. Scrofuloderma, tuberculosis verrucosa cutis and lupus vulgaris comprise most cutaneous tuberculosis cases. Bacillus Calmette-Guerin (BCG) is derived from an attenuated strain of Mycobacterium bovis and is employed beneficially as a relatively safe vaccination in Poland and other countries in which the prevalence of tuberculosis is high. However, BCG vaccination may produce complications, including disseminated BCG and lupus vulgaris, the latter seen in one of our two patients in whom lupus vulgaris at the inoculation site followed a second vaccination with BCG 12 years after the initial one. A similar phenomenon has been described after immunotherapy with BCG vaccination. Re-infection (secondary) inoculation cutaneous tuberculosis may also occur as a result of BCG vaccination, producing either lupus vulgaris or tuberculosis verrucosa cutis, probably depending upon the patient's degree of cell-mediated immunity. However, most lupus vulgaris cases are not associated with vaccination with BCG, as occurred in our first patient. For those who do develop lupus vulgaris, it can be persistent for a long period, in some cases for many decades. In the second patient we describe a lengthy duration and cutaneous reactivation at distant sites after more than 40 years.

  13. Sunflower Seed and Acne Vulgaris

    PubMed Central

    Mohebbipour, Alireza; Sadeghi-Bazargani, Homayoun; Mansouri, Mona

    2015-01-01

    Background: Regardless of the overall association between diet and acne which cannot be easily ignored, there might be an association between specific nutrients and acne development or improvement. Objectives: The aim of this study was to assess the effect of dietary intake of sunflower seeds on acne severity and the pattern of acne lesions. Patients and Methods: In a randomized controlled trial, 50 patients aged 15 - 30 years old with acne vulgaris were enrolled through consecutive convenient sampling, in a dermatology clinic in Ardabil, Iran. They were randomly allocated into two trial arms. Those in the control group were asked to stop eating sunflower seeds if they did before. In the intervention group, they consumed 25 g sunflower-containing food daily for seven days. The primary outcome of interest was 10% increase/decrease in the baseline acne severity index (ASI), sustained to the end of the follow-up period on day 14. Results: The mean ASI did not change significantly through the study period in the control group, but it increased in the sunflower group from 62 at the baseline to 86.8 after two weeks (P < 0.001). The ASI mean change was 24.8 in the sunflower group compared to 4.9 in the control group (P < 0.001). The global acne grading score (GAGS) did not significantly change in any of the groups and the difference in the change of GAGS was not significant between the groups (2.4 in the sunflower group versus 1.6 in the control group). Twenty two subjects (88%) in the sunflower group versus 9 (36%) in the control group had at least 10% increment in ASI throughout the follow-up period (P < 0.001). The relative risk of developing the primary outcome in taking the sunflower seed intervention was 2.4 (95% CI: 1.4 - 4.2). The observed risk difference was 0.52 (95% CI: 0.29 - 0.75). Conclusions: Sunflower seed intake appears to aggravate acne vulgaris; however, further evidence is needed to ban sunflower seed intake in patients with acne. Considering the

  14. A "MICROTUBULE" IN A BACTERIUM

    PubMed Central

    van Iterson, Woutera; Hoeniger, Judith F. M.; van Zanten, Eva Nijman

    1967-01-01

    A study of the anchorage of the flagella in swarmers of Proteus mirabilis led to the incidental observation of microtubules. These microtubules were found in thin sections and in whole mount preparations of cells from which most of the content had been released by osmotic shock before staining negatively with potassium phosphotungstate (PTA). The microtubules are in negatively stained preparations about 200 A wide, i.e. somewhat thicker than the flagella (approximately 130 A). They are thus somewhat thinner than most microtubules recorded for other cells. They are referred to as microtubules because of their smooth cylindrical wall, or cortex, surrounding a hollow core which is readily filled with PTA when stained negatively. Since this is probably the first time that such a structure is described inside a bacterium, we do not know for certain whether it represents a normal cell constituent or an abnormality, for instance of the type of "polysheaths" (16). PMID:10976198

  15. Ocular involvement in pemphigus vulgaris.

    PubMed

    Akhyani, Maryam; Keshtkar-Jafari, Alireza; Chams-Davatchi, Cheyda; Lajevardi, Vahide; Beigi, Sara; Aghazadeh, Nessa; Rayati Damavandi, Maede; Arami, Shabnam

    2014-07-01

    Pemphigus vulgaris (PV) is an autoimmune disorder affecting the skin and mucous membranes. Ocular involvement in PV has been reported but its prevalence and clinical characteristics are not well defined. This prospective cross-sectional study of 103 PV patients was designed to determine the prevalence, clinical types and epidemiological trends of ocular involvement in a population of Iranian patients with PV. Ocular involvement was present in 17 (16.5%) patients. Conjunctivitis was the most prevalent type of ocular involvement (9/17, 52.9%), followed by erosion of the palpebral conjunctiva (7/17, 41.2%). Erosion of the bulbar conjunctiva was noted in only one patient (5.9%). The most commonly reported symptoms were eye irritation (76.5%) and redness (76.5%). No significant relation was found between ocular involvement and disease activity (partial remission or relapse). Mucoid discharge was significantly more common in patients with conjunctival erosions as compared to patients with conjunctivitis (P = 0.038). We conclude that ocular involvement is not rare in PV; 16.5% of PV patients develop ocular disease independent of the disease activity and extension. Conjunctivitis is the most common type of involvement, however, palpebral conjunctival erosion is more frequent than previously realized.

  16. Twins with neonatal pemphigus vulgaris born to a mother with pemphigus vulgaris: a case report.

    PubMed

    Itsukaichi, Mina; Takakuwa, Koichi; Yamaguchi, Masayuki; Serikawa, Takehiro; Tanaka, Kenichi; Kojima, Kinuko; Sakakibara, Seiichi; Usuda, Tohei; Matsunaga, Masamichi; Hashimoto, Tsuyoshi

    2013-01-01

    Dichorionic diamniotic twins were born at 37 weeks of gestation by cesarean section to a 34-year-old primigravid Japanese woman because the first twin was in breech presentation. The mother had been diagnosed with pemphigus vulgaris prior to her pregnancy. In addition to a high antidesmoglein 3 autoantibody titer, flaccid bullae and erosions on both of the twins' lips and in their oral cavities at 13 days of age led to the diagnosis of neonatal pemphigus vulgaris. This case highlights the need for awareness that pemphigus vulgaris may not occur immediately after birth.

  17. Pathway confirmation and flux analysis of central metabolicpathways in Desulfovibrio vulgaris Hildenborough using gaschromatography-mass spectrometry and fourier transform-ion cyclotronresonance mass spectrometry

    SciTech Connect

    Tang, Yinjie; Pingitore, Francesco; Mukhopadhyay, Aindrila; Phan,Richard; Hazen, Terry C.; Keasling, Jay D.

    2006-07-11

    It has been proposed that during growth under anaerobic oroxygen-limited conditions Shewanella oneidensis MR-1 uses theserine-isocitrate lyase pathway common to many methylotrophic anaerobes,in which formaldehyde produced from pyruvate is condensed with glycine toform serine. The serine is then transformed through hydroxypyruvate andglycerate to enter central metabolism at phosphoglycerate. To examine itsuse of the serine-isocitrate lyase pathway under anaerobic conditions, wegrew S. oneidensis MR-1 on [1-13C]lactate as the sole carbon source witheither trimethylamine N-oxide (TMAO) or fumarate as an electron acceptor.Analysis of cellular metabolites indicates that a large percentage(>75 percent) of lactate was partially oxidized to either acetate orpyruvate. The 13C isotope distributions in amino acids and other keymetabolites indicate that, under anaerobic conditions, a complete serinepathway is not present, and lactate is oxidized via a highly reversibleserine degradation pathway. The labeling data also suggest significantactivity in the anaplerotic (malic enzyme and phosphoenolpyruvatecarboxylase) and glyoxylate shunt (isocitrate lyase and malate synthase)reactions. Although the tricarboxylic acid (TCA) cycle is often observedto be incomplete in many other anaerobes (absence of 2-oxoglutaratedehydrogenase activity), isotopic labeling supports the existence of acomplete TCA cycle in S. oneidensis MR-1 under TMAO reductioncondition.

  18. Pemphigus vulgaris in three adolescents: the course of the disease.

    PubMed

    Popadic, Svetlana; Medenica, Ljiljana; Skiljevic, Dusan; Djakovic, Zorana; Nikolic, Milos

    2011-08-01

    We report three adolescents with pemphigus vulgaris whose disease started at the age of 13, 15 and 14 years, respectively. The course of the disease and the treatment approaches were reviewed. Pemphigus vulgaris during childhood and adolescence is a very rare disease in this part of Europe. Among 410 pemphigus vulgaris patients that we treated during the 20-year period, only three patients (0.73%) were under the age of 18 years. According to our experience, the course of pemphigus vulgaris in patients before the age of 18 years is comparable with the course of pemphigus vulgaris in adults.

  19. A case of exfoliative esophagitis with pemphigus vulgaris.

    PubMed

    Fukuchi, M; Otake, S; Naitoh, H; Shoji, H; Yamagishi, J; Suzuki, M; Yanoma, T; Kuwano, H

    2011-04-01

    Autoimmune blistering skin diseases, including pemphigus vulgaris, rarely involve the esophagus. We report a case of exfoliative esophagitis with pemphigus vulgaris. A sloughing esophageal cast observed by endoscopy was dissected esophageal squamous epithelium in all layers. Our case is the fifth case of pemphigus vulgaris associated with esophageal cast formation recorded in the medical literature. Prednisolone was administered, and both the pemphigus vulgaris and exfoliative esophagitis improved. Upon findings of exfoliative esophagitis by endoscopic examination, we should consider the coexistence of blistering skin diseases, including pemphigus vulgaris.

  20. [Pemphigus chronicus vulgaris--case report].

    PubMed

    Spoljar, Sanja; Cavka, Mira; Tvorić, Anamarija

    2012-10-01

    Pemphigus vulgaris is a rare, chronic, autoimmune blistering skin disease of adulthood. In 50 percent of patients, mucous membrane erosions of the oral cavity are the presenting sign. Typically, patients develop flaccid blisters and erosions on the normal appearing skin and mucous membranes. Mucous membranes in other areas may also be involved. The disease is caused by IgG autoantibodies to the desmosomes inducing the loss of cell adhesion between keratinocytes, and subsequent intraepidermal blister formation. Antigens are desmoglein 3 (Dsg3) and desmoglein 1 (Dsg1) transmembrane glycoproteins. Desmoglein 3 is expressed in the lower portion of the epidermis. Alone, it is sufficient to keep mucosal surfaces intact. Desmoglein 1 is expressed more intensely in the superficial layers. Pemphigus vulgaris can be divided into two subgroups, the mucosal type and mucocutaneous type. The characteristic histologic finding is intraepidermal blister. Acantholytic keratinocytes as well as clusters of epidermal cells are seen in the blister cavity. Direct immunofluorescence examination (DIF) of perilesional skin shows a deposit of IgG, rarely IgA, and complement components (C3, C1q,C4) between the epidermal cells. The titers of circulating antibodies measured with indirect immunofluorescence examination (IIF) often correlate with the disease course. There are sporadic cases of pemphigus vulgaris associated with the use of drugs, in particular D-penicillamine and captopril. Pemphigus vulgaris has rarely evolved into pemphigus foliaceus, and vice versa. Very uncommon, pemphigus vulgaris or pemphigus foliaceus has been associated with bullous pemphigoid in the same patient. We present an unusual case of pemphigus vulgaris in an adult female patient.

  1. THERAPEUTIC AGENTS IN ACNE VULGARIS. I. TETRACYCLINE.

    PubMed

    STEWART, W D; MADDIN, S; NELSON, A J; DANTO, J L

    1963-11-23

    A total of 120 consecutive patients with pustular and cystic acne vulgaris were selected for study. Patients were assigned a placebo and a tetracycline medication in a random method. Of the 53 patients who were given tetracycline, 45 showed some response, which was fair in 19 and excellent in 26. Of the 55 patients who received placebo, 24 showed no response while 31 showed some improvement. No side effects were reported. The difference in response between the two groups is statistically significant. It is concluded that administration of 250 mg. tetracycline four times daily, even for periods as short as two weeks, enhances the likelihood of improvement of cystic or pustular acne vulgaris.

  2. Lupus vulgaris: unusual presentations over the face.

    PubMed

    Khandpur, S; Reddy, B S N

    2003-11-01

    Lupus vulgaris (LV) is the most common morphological variant of cutaneous tuberculosis. However, the occurrence of bizarre clinical presentations over atypical sites often leads to misdiagnosis and inappropriate treatment causing significant morbidity. This report seeks to highlight two unusual cases of lupus vulgaris occurring on the face of immunocompetent women and remarkably mimicking periorbital cellulitis and basal cell carcinoma, respectively. The diagnosis was confirmed by histopathology, an enzyme-linked immunosorbent assay (ELISA) test for Mycobacterium tuberculosis and polymerase chain reaction (PCR). With four-drug antitubercular therapy, both patients had a dramatic response.

  3. Bismuth(III) deferiprone effectively inhibits growth of Desulfovibrio desulfuricans ATCC 27774.

    PubMed

    Barton, Larry L; Lyle, Daniel A; Ritz, Nathaniel L; Granat, Alex S; Khurshid, Ali N; Kherbik, Nada; Hider, Robert; Lin, Henry C

    2016-04-01

    Sulfate-reducing bacteria have been implicated in inflammatory bowel diseases and ulcerative colitis in humans and there is an interest in inhibiting the growth of these sulfide-producing bacteria. This research explores the use of several chelators of bismuth to determine the most effective chelator to inhibit the growth of sulfate-reducing bacteria. For our studies, Desulfovibrio desulfuricans ATCC 27774 was grown with nitrate as the electron acceptor and chelated bismuth compounds were added to test for inhibition of growth. Varying levels of inhibition were attributed to bismuth chelated with subsalicylate or citrate but the most effective inhibition of growth by D. desulfuricans was with bismuth chelated by deferiprone, 3-hydroxy-1,2-dimethyl-4(1H)-pyridone. Growth of D. desulfuricans was inhibited by 10 μM bismuth as deferiprone:bismuth with either nitrate or sulfate respiration. Our studies indicate deferiprone:bismuth has bacteriostatic activity on D. desulfuricans because the inhibition can be reversed following exposure to 1 mM bismuth for 1 h at 32 °C. We suggest that deferiprone is an appropriate chelator for bismuth to control growth of sulfate-reducing bacteria because deferiprone is relatively nontoxic to animals, including humans, and has been used for many years to bind Fe(III) in the treatment of β-thalassemia.

  4. Role of Morphological Growth State and Gene Expression in Desulfovibrio africanus strain Walvis Bay Mercury Methylation

    SciTech Connect

    Moberly, James G; Miller, Carrie L; Brown, Steven D; Biswas, Abir; Brandt, Craig C; Palumbo, Anthony Vito; Elias, Dwayne A

    2012-01-01

    The biogeochemical transformations of mercury are a complex process, with the production of methylmercury, a potent human neurotoxin, repeatedly demonstrated in sulfate- and Fe(III)- reducing as well as methanogenic bacteria. However, little is known regarding the morphology, genes or proteins involved in methylmercury generation. Desulfovibrio africanus strain Walvis Bay is a Hg-methylating -proteobacterium with a sequenced genome and has unusual pleomorphic forms. In this study, a relationship between the pleomorphism and Hg methylation was investigated. Proportional increases in the sigmoidal (regular) cell form corresponded with increased net MeHg production, but decreased when the pinched cocci (persister) form became the major morphotype. D. africanus microarrays indicated that the ferrous iron transport genes (feoAB), as well as ribosomal genes and several genes whose products are predicted to have metal binding domains (CxxC), were up-regulated during exposure to Hg in the exponential phase. While no specific methylation pathways were identified, the finding that Hg may interfere with iron transport and the correlation of growth-phase dependent morphology with MeHg production are notable. The identification of these relationships between differential gene expression, morphology, and the growth phase dependence of Hg transformations suggests that actively growing cells are primarily responsible for methylation, and so areas with ample carbon and electron-acceptor concentrations may also generate a higher proportion of methylmercury than more oligotrophic environments. The observation of increased iron transporter expression also suggests that Hg methylation may interfere with iron biogeochemical cycles.

  5. The role of Rnf in ion gradient formation in Desulfovibrio alaskensis

    PubMed Central

    Wang, Luyao; Bradstock, Peter; Li, Chuang; McInerney, Michael J.

    2016-01-01

    Rnf is a membrane protein complex that has been shown to be important in energy conservation. Here, Desulfovibrio alaskensis G20 and Rnf mutants of G20 were grown with different electron donor and acceptor combinations to determine the importance of Rnf in energy conservation and the type of ion gradient generated. The addition of the protonophore TCS strongly inhibited lactate-sulfate dependent growth whereas the sodium ionophore ETH2120 had no effect, indicating a role for the proton gradient during growth. Mutants in rnfA and rnfD were more sensitive to the protonophore at 5 µM than the parental strain, suggesting the importance of Rnf in the generation of a proton gradient. The electrical potential (ΔΨ), ΔpH and proton motive force were lower in the rnfA mutant than in the parental strain of D.alaskensis G20. These results provide evidence that the Rnf complex in D. alaskensis functions as a primary proton pump whose activity is important for growth. PMID:27114876

  6. Impact of Desulfovibrio alaskensis biofilms on corrosion behaviour of carbon steel in marine environment.

    PubMed

    Wikieł, Agata J; Datsenko, Iaryna; Vera, Mario; Sand, Wolfgang

    2014-06-01

    Sulfate reducing prokaryotes are associated with the steel deterioration. They build heterogeneous biofilms, capable of accelerating corrosion processes. In this study metabolic activity and the biofilm development of Desulfovibrio alaskensis were correlated to electrochemical response of carbon steel surface. In the exponential growth phase sulfide concentration reached its maximum of about 10mM. This phenomenon was responsible for the parallel increase in the corrosion potential (Ecorr) up to -720mV (vs. SCE). Subsequently, during the intensive biofilm formation and development another Ecorr peak (-710mV vs. SCE) occurred. Decrease in Ecorr was registered during the biofilm maturation and kept stable, being 20mV lower than in the control. While carbon steel was protected from the microbial attachment and exposed to metabolic products, only one potential maximum (-730mV vs. SCE) was recorded. Here Ecorr variations coincided with sulfide concentration changes and kept at 120mV lower vs. the control. Weight loss examinations revealed corrosion rates, which did not exceed 0.05mm/y. Confocal microscopy suggested the importance of extracellular proteins in the biofilm formation. Above 150 proteins were detected in the EPS matrix. Surface effects of biofilm and metabolic products were visualised, revealing the role of attached microorganisms in the localised corrosion.

  7. Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria

    PubMed Central

    Nakazawa, Hidekazu; Arakaki, Atsushi; Narita-Yamada, Sachiko; Yashiro, Isao; Jinno, Koji; Aoki, Natsuko; Tsuruyama, Ai; Okamura, Yoshiko; Tanikawa, Satoshi; Fujita, Nobuyuki; Takeyama, Haruko; Matsunaga, Tadashi

    2009-01-01

    Magnetotactic bacteria are ubiquitous microorganisms that synthesize intracellular magnetite particles (magnetosomes) by accumulating Fe ions from aquatic environments. Recent molecular studies, including comprehensive proteomic, transcriptomic, and genomic analyses, have considerably improved our hypotheses of the magnetosome-formation mechanism. However, most of these studies have been conducted using pure-cultured bacterial strains of α-proteobacteria. Here, we report the whole-genome sequence of Desulfovibrio magneticus strain RS-1, the only isolate of magnetotactic microorganisms classified under δ-proteobacteria. Comparative genomics of the RS-1 and four α-proteobacterial strains revealed the presence of three separate gene regions (nuo and mamAB-like gene clusters, and gene region of a cryptic plasmid) conserved in all magnetotactic bacteria. The nuo gene cluster, encoding NADH dehydrogenase (complex I), was also common to the genomes of three iron-reducing bacteria exhibiting uncontrolled extracellular and/or intracellular magnetite synthesis. A cryptic plasmid, pDMC1, encodes three homologous genes that exhibit high similarities with those of other magnetotactic bacterial strains. In addition, the mamAB-like gene cluster, encoding the key components for magnetosome formation such as iron transport and magnetosome alignment, was conserved only in the genomes of magnetotactic bacteria as a similar genomic island-like structure. Our findings suggest the presence of core genetic components for magnetosome biosynthesis; these genes may have been acquired into the magnetotactic bacterial genomes by multiple gene-transfer events during proteobacterial evolution. PMID:19675025

  8. Inhibition of Desulfovibrio gigas hydrogenase with copper salts and other metal ions.

    PubMed

    Fernandez, V M; Rua, M L; Reyes, P; Cammack, R; Hatchikian, E C

    1989-11-06

    The effect of several transition metals on the activity of Desulfovibrio gigas hydrogenase has been studied. Co(II) and Ni(II) at a concentration of 1 mM did not modify the activity of the enzyme; nor did they affect the pattern of activation/deactivation. Cu(II) inhibited the active hydrogenase, prepared by treatment with hydrogen, but had little effect on the 'unready' enzyme unless a reductant such as ascorbate was present, in which case inactivation took place either in air or under argon. Hg(II) also inactivated the enzyme irreversible in the 'unready' state without the requirement for reductants. The reaction of H2 uptake with methyl viologen was much more sensitive to inhibition than the H2/tritium exchange activity. EPR spectra of this preparation showed that the rates of decline were [3Fe-4S] signal greater than H2-uptake activity greater than Ni-A signal. Similar results were obtained when the protein was treated with Hg(II). The results demonstrate that the [3Fe-4S] cluster is not essential for H2-uptake activity with methyl viologen, but the integrity of [4Fe-4S] clusters is probably necessary to catalyze the reduction of methyl viologen with hydrogen. D. gigas hydrogenase was found to be highly resistant to digestion by proteases.

  9. Photodynamic therapy of acne vulgaris.

    NASA Astrophysics Data System (ADS)

    Ershova, Ekaterina Y.; Karimova, Lubov N.; Kharnas, Sergey S.; Kuzmin, Sergey G.; Loschenov, Victor B.

    2003-06-01

    Photodynamic therapy (PDT) with topical 5-aminolevulinic acid (ALA) was tested for the treatment of acne vulgaris. Patients with acne were treated with ALA plus red light. Ten percent water solution of ALA was applied with 1,5-2 h occlusion and then 18-45 J/cm2 630 nm light was given. Bacterial endogenous porphyrins fluorescence also was used for acne therapy. Treatment control and diagnostics was realized by fluorescence spectra and fluorescence image. Light sources and diagnostic systems were used: semiconductor laser (λ=630 nm, Pmax=1W), (LPhT-630-01-BIOSPEC); LED system for PDT and diagnostics with fluorescent imager (λ=635 nm, P=2W, p=50 mW/cm2), (UFPh-630-01-BIOSPEC); high sensitivity CCD video camera with narrow-band wavelength filter (central wavelength 630 nm); laser electronic spectrum analyzer for fluorescent diagnostics and photodynamic therapy monitoring (LESA-01-BIOSPEC). Protoporphyrin IX (PP IX) and endogenous porphyrins concentrations were measured by fluorescence at wavelength, correspondingly, 700 nm and 650 nm. It was shown that topical ALA is converted into PP IX in hair follicles, sebaceous glands and acne scars. The amount of resulting PP IX is sufficient for effective PDT. There was good clinical response and considerable clearance of acne lesion. ALA-PDT also had good cosmetic effect in treatment acne scars. PDT with ALA and red light assist in opening corked pores, destroying Propionibacterium acnes and decreasing sebum secretion. PDT treatment associated with several adverse effects: oedema and/or erytema for 3-5 days after PDT, epidermal exfoliation from 5th to 10th day and slight pigmentation during 1 month after PDT. ALA-PDT is effective for acne and can be used despite several side effects.

  10. Complementary therapies for acne vulgaris

    PubMed Central

    Cao, Huijuan; Yang, Guoyan; Wang, Yuyi; Liu, Jian Ping; Smith, Caroline A; Luo, Hui; Liu, Yueming

    2015-01-01

    Background Acne is a chronic skin disease characterised by inflamed spots and blackheads on the face, neck, back, and chest. Cysts and scarring can also occur, especially in more severe disease. People with acne often turn to complementary and alternative medicine (CAM), such as herbal medicine, acupuncture, and dietary modifications, because of their concerns about the adverse effects of conventional medicines. However, evidence for CAM therapies has not been systematically assessed. Objectives To assess the effects and safety of any complementary therapies in people with acne vulgaris. Search methods We searched the following databases from inception up to 22 January 2014: the Cochrane Skin Group Specialised Register, the Cochrane Central Register of Controlled Trials (CENTRAL; 2014, Issue 1), MEDLINE (from 1946), Embase (from 1974), PsycINFO (from 1806), AMED (from 1985), CINAHL (from 1981), Scopus (from 1966), and a number of other databases listed in the Methods section of the review. The Cochrane CAM Field Specialised Register was searched up to May 2014. We also searched five trials registers and checked the reference lists of articles for further references to relevant trials. Selection criteria We included parallel-group randomised controlled trials (or the first phase data of randomised cross-over trials) of any kind of CAM, compared with no treatment, placebo, or other active therapies, in people with a diagnosis of acne vulgaris. Data collection and analysis Three authors collected data from each included trial and evaluated the methodological quality independently. They resolved disagreements by discussion and, as needed, arbitration by another author. Main results We included 35 studies, with a total of 3227 participants. We evaluated the majority as having unclear risk of selection, attrition, reporting, detection, and other biases. Because of the clinical heterogeneity between trials and the incomplete data reporting, we could only include four

  11. Autoinoculation lupus vulgaris of the perineum.

    PubMed

    Sehgal, V N; Chaudhry, A K; Gupta, R

    1991-08-01

    The case of a young heterosexual male, with a 7 year history of an asymptomatic progressive plaque over the right side of the perineum is described, which 4 years later involved the left perineum and scrotal skin, indicating autoinoculation. The diagnosis of lupus vulgaris was made by strongly positive tuberculin test, histopathology, and a favourable response to a short course of intensive antitubercular therapy.

  12. Ichthyosis vulgaris: the filaggrin mutation disease.

    PubMed

    Thyssen, J P; Godoy-Gijon, E; Elias, P M

    2013-06-01

    Ichthyosis vulgaris is caused by loss-of-function mutations in the filaggrin gene (FLG) and is characterized clinically by xerosis, scaling, keratosis pilaris, palmar and plantar hyperlinearity, and a strong association with atopic disorders. According to the published studies presented in this review article, FLG mutations are observed in approximately 7·7% of Europeans and 3·0% of Asians, but appear to be infrequent in darker-skinned populations. This clinical review article provides an overview of ichthyosis vulgaris epidemiology, related disorders and pathomechanisms. Not only does ichthyosis vulgaris possess a wide clinical spectrum, recent studies suggest that carriers of FLG mutations may have a generally altered risk of developing common diseases, even beyond atopic disorders. Mechanistic studies have shown increased penetration of allergens and chemicals in filaggrin-deficient skin, and epidemiological studies have found higher levels of hand eczema, irritant contact dermatitis, nickel sensitization and serum vitamin D levels. When relevant, individuals should be informed about an increased risk of developing dermatitis when repeatedly or continuously exposed to nickel or irritants. Moreover, with our current knowledge, individuals with ichthyosis vulgaris should be protected against neonatal exposure to cats to prevent atopic dermatitis and should abstain from smoking to prevent asthma. Finally, they should be advised against excessive exposure to factors that decrease skin barrier functions and increase the risk of atopic dermatitis.

  13. Squamous cell carcinoma associated with lupus vulgaris.

    PubMed

    Gooptu, C; Marks, N; Thomas, J; James, M P

    1998-05-01

    Squamous cell carcinomas are known to arise in certain chronic, scarring dermatoses and also to be associated with exposure to ultraviolet radiation. We now report a case arising in a plaque of lupus vulgaris, the patient having received radiation from a Finsen lamp as a child for a tuberculous abscess in that region.

  14. Viable endospores of Thermoactinomyces vulgaris in lake sediments as indicators of agricultural history.

    PubMed Central

    Nilsson, M; Renberg, I

    1990-01-01

    Bacteria of the genus Thermoactinomyces form endospores with an extreme longevity in natural habitats. We isolated Thermoactinomyces sacchari from 9,000-year-old varved (annually laminated) sediment; thus, T. sacchari is probably one of the oldest known living organisms. More importantly, we tested and verified the hypothesis that there is a relationship between concentrations of dormant, viable endospores of T. vulgaris in lake sediments and the extent of agriculture in the catchments of the lakes. In surface sediments, low concentrations were recorded in forest lakes and the concentrations increased with increasing areas of cultivated land around the lakes. In varved sediment cores from three lakes, we found a temporal relationship between records of T. vulgaris endospores and the pollen of plants indicating agriculture. Endospores were very rare in sediments deposited before agriculture, ca. 1100 A.D. From then to between 1300 and 1700 A.D., a period with restricted cultivation, low but more regular rates of accumulation of endospores were recorded. High endospore accumulation rates were found with the subsequent agricultural expansion. This investigation confirms suggestions that this bacterium could be used as a paleoindicator for agricultural activity and be complementary to pollen analyses. Viable bacteria in continuous records of lake sediments are also potential material for evolutionary studies. PMID:2202253

  15. Metabolic Interfaces of Mercury Methylation Proteins in Desulfovibrio sp. ND132

    NASA Astrophysics Data System (ADS)

    Wall, J. D.; Bridou, R.; Smith, S. D.; Mok, K.; Widner, F.; Johs, A.; Parks, J.; Pierce, E. M.; Elias, D. A.; Gilmour, C. C.; Taga, M.

    2015-12-01

    Two genes necessary for microbial production of the neurotoxin methylmercury have been identified; hgcA encoding a corrinoid methyltransferase and hgcB, a ferredoxin-like protein. To date, all microbes possessing orthologs of these genes that have been tested are capable of methylating mercury; whereas, organisms lacking hgcA and hgcB are not. Also of interest is the observation that confirmed mercury-methylating microbes are all considered anaerobes although not members of a specific phylogenetic group. They are found scattered in the genomes of methanogens, Firmicutes, and Deltaproteobacteria. Methylation has not been demonstrated to provide protection of the microbes to mercury exposure. To determine the source of evolutionary pressure for acquisition and maintenance of these genes, we are seeking to understand whether there is a second function of the proteins. We are seeking evidence for the metabolic source(s) of the methyl group and for competing reactions. We have found that deletion of the metH gene encoding a tetrahydrofolate methyltransferase in Desulfovibrio sp. ND132 decreases the mercury methylation capacity by ca. 95%, consistent with an interpretation that this enzyme is involved in the pathway for the methyl group for HgcA. In addition, the corrinoid present in HgcA and the MetH of ND132 is strictly dependent on nicotinate nucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase encoded by the cobT gene, linking methionine biosynthesis with mercury methylation at a second level. Additional methyl transferases have not been found to be necessary for this function. While earlier evidence was provided for an involvement of the CO dehydrogenase/acetylCoA synthase, this enzyme is not universally present in methylating strains unlike the pathway for methionine synthesis.

  16. Hydrogenase Activity of Mineral-Associated and Suspended Populations of Desulfovibrio desulfuricans Essex 6

    SciTech Connect

    C.L. Reardon; T.S. Magnuson; E.S. Boyd; W.D. Leavitt; D.W. Reed; G.G. Geesey

    2014-02-01

    The interactions between sulfate-reducing microorganisms and iron oxides influence a number of important redox-sensitive biogeochemical processes including the formation of iron sulfides. Enzymes, such as hydrogenase which catalyze the reversible oxidation of molecular hydrogen, are known to mediate electron transfer to metals and may contribute to the formation and speciation of ferrous sulfides formed at the cell–mineral interface. In the present study, we compared the whole cell hydrogenase activity of Desulfovibrio desulfuricans strain Essex 6 growing as biofilms on hematite (hematite-associated) or as suspended populations using different metabolic pathways. Hematite-associated cells exhibited significantly greater hydrogenase activity than suspended populations during sulfate respiration but not during pyruvate fermentation. The enhanced activity of the hematite-associated, sulfate-grown cells appears to be dependent on iron availability rather than a general response to surface attachment since the activity of glass-associated cells did not differ from that of suspended populations. Hydrogenase activity of pyruvate-fermenting cells was stimulated by addition of iron as soluble Fe(II)Cl2 and, in the absence of added iron, both sulfate-reducing and pyruvate-fermenting cells displayed similar rates of hydrogenase activity. These data suggest that iron exerts a stronger influence on whole cell hydrogenase activity than either metabolic pathway or mode of growth. The location of hydrogenase to the cell envelope and the enhanced activity at the hematite surface in sulfate-reducing cells may influence the redox conditions that control the species of iron sulfides on the mineral surface.

  17. Effects of cellular sorption on mercury bioavailability and methylmercury production by Desulfovibrio desulfuricans ND132

    DOE PAGES

    Liu, Yu-Rong; Lu, Xia; Zhao, Linduo; ...

    2016-11-14

    Microbial conversion of inorganic mercury (IHg) to methylmercury (MeHg) is a significant environmental concern because of the bioaccumulation and biomagnification of toxic MeHg in the food web. Laboratory incubation studies have shown that, despite the presence of large quantities of IHg in cell cultures, MeHg biosynthesis often reaches a plateau or a maximum within hours or a day by an as yet unexplained mechanism. In this paper, we report that mercuric Hg(II) can be taken up rapidly by cells of Desulfovibrio desulfuricans ND132, but a large fraction of the Hg(II) is unavailable for methylation because of strong cellular sorption. Thiols,more » such as cysteine, glutathione, and penicillamine, added either simultaneously with Hg(II) or after cells have been exposed to Hg(II), effectively desorb or mobilize the bound Hg(II), leading to a substantial increase in MeHg production. The amount of thiol-desorbed Hg(II) is strongly correlated to the amount of MeHg produced (r = 0.98). Furthermore, cells do not preferentially take up Hg(II)–thiol complexes, but Hg(II)–ligand exchange between these complexes and the cell-associated proteins likely constrains Hg(II) uptake and methylation. Finally, we suggest that, aside from aqueous chemical speciation of Hg(II), binding and exchange of Hg(II) between cells and complexing ligands such as thiols and naturally dissolved organics in solution is an important controlling mechanism of Hg(II) bioavailability, which should be considered when predicting MeHg production in the environment.« less

  18. A New Model for Electron Flow for Sulfate Reduction in Desulfovibrio alaskensis G20

    SciTech Connect

    Keller, Kimberly L; Rapp-Giles, Barbara J; Semkiw, Elizabeth M.; Porat, Iris; Brown, Steven D; Wall, Judy D.

    2013-01-01

    To understand the energy conversion activities of the anaerobic sulfate-reducing bacteria, it is necessary to identify the components involved in electron flow. The importance of the abundant type I tetraheme cytochrome c3 (TpIc3) as an electron carrier during sulfate respiration was questioned by the previous isolation of a null mutation in the encoding gene, cycA, in Desulfovibrio alaskensis G20. Whereas respiratory growth of the CycA mutant with lactate and sulfate was little affected, growth with pyruvate and sulfate was significantly impaired. We have explored the phenotype of the CycA mutant through physiological tests and transcriptomic and proteomic analyses. Data reported here show that electrons from pyruvate oxidation do not reach adenylyl sulfate reductase, the enzyme catalyzing the first redox reaction during sulfate reduction, in the absence of either CycAor the type I cytochrome c3:menaquinone oxidoreductase, QrcABCD transmembrane complex. In contrast to the wild type, neither CycA and QrcA mutants do not grow with H2 or formate and sulfate as electron acceptor. Transcriptomic and proteomic analyses of the CycA mutant showed that transcripts and enzymes for the pathway from pyruvate to succinate were strongly decreased in the CycA mutant regardless of growth mode. Neither the CycA nor the QrcA mutant grew on fumarate alone, consistent with the omics results and a redox regulation of gene expression. We conclude that TpIc3 and the Qrc complex are essential D. alaskensis components for transfer of electrons released in the periplasm to reach the cytoplasmic adenylyl sulfate reductase and present a model that may explain the CycA phenotype through confurcation of electrons.

  19. New Model for Electron Flow for Sulfate Reduction in Desulfovibrio alaskensis G20

    SciTech Connect

    Rapp-Giles, Barbara J; Keller, Kimberly L; Porat, Iris; Brown, Steven D; Semkiw, Elizabeth M.; Wall, Judy D.

    2014-01-01

    To understand the energy conversion activities of the anaerobic sulfate-reducing bacteria, it is necessary to identify the components involved in electron flow. The importance of the abundant type I tetraheme cytochrome c3 (TpIc3) as an electron carrier during sulfate respiration was questioned by the previous isolation of a null mutation in the gene encoding TpIc3, cycA, in Desulfovibrio alaskensis G20. Whereas respiratory growth of the CycA mutant with lactate and sulfate was little affected, growth with pyruvate and sulfate was significantly impaired. We have explored the phenotype of the CycA mutant through physiological tests and transcriptomic and proteomic analyses. Data reported here show that electrons from pyruvate oxidation do not reach adenylyl sulfate reductase, the enzyme catalyzing the first redox reaction during sulfate reduction, in the absence of either CycA or the type I cytochrome c3:menaquinone oxidoreductase transmembrane complex, QrcABCD. In contrast to the wild type, the CycA and QrcA mutants did not grow with H2 or formate and sulfate as the electron acceptor. Transcriptomic and proteomic analyses of the CycA mutant showed that transcripts and enzymes for the pathway from pyruvate to succinate were strongly decreased in the CycA mutant regardless of the growth mode. Neither the CycA nor the QrcA mutant grew on fumarate alone, consistent with the omics results and a redox regulation of gene expression. We conclude that TpIc3 and the Qrc complex are D. alaskensis components essential for the transfer of electrons released in the periplasm to reach the cytoplasmic adenylyl sulfate reductase and present a model that may explain the CycA phenotype through confurcation of electrons.

  20. New Model for Electron Flow for Sulfate Reduction in Desulfovibrio alaskensis G20

    SciTech Connect

    Keller, Kimberly L.; Rapp-Giles, Barbara J.; Semkiw, Elizabeth S.; Porat, Iris; Brown, Steven D.; Wall, Judy D.

    2014-02-01

    To understand the energy conversion activities of the anaerobic sulfate-reducing bacteria, it is necessary to identify the components involved in electron flow. The importance of the abundant type I tetraheme cytochrome c3 (TpIc3) as an electron carrier during sulfate respiration was questioned by the previous isolation of a null mutation in the gene encoding TpIc3, cycA, in Desulfovibrio alaskensis G20. Whereas respiratory growth of the CycA mutant with lactate and sulfate was little affected, growth with pyruvate and sulfate was significantly impaired. We have explored the phenotype of the CycA mutant through physiological tests and transcriptomic and proteomic analyses. Data reported here show that electrons from pyruvate oxidation do not reach adenylyl sulfate reductase, the enzyme catalyzing the first redox reaction during sulfate reduction, in the absence of either CycA or the type I cytochrome c3:menaquinone oxidoreductase transmembrane complex, QrcABCD. In contrast to the wild type, the CycA and QrcA mutants did not grow with H2 or formate and sulfate as the electron acceptor. Transcriptomic and proteomic analyses of the CycA mutant showed that transcripts and enzymes for the pathway from pyruvate to succinate were strongly decreased in the CycA mutant regardless of the growth mode. Neither the CycA nor the QrcA mutant grew on fumarate alone, consistent with the omics results and a redox regulation of gene expression. We conclude that TpIc3 and the Qrc complex are D. alaskensis components essential for the transfer of electrons released in the periplasm to reach the cytoplasmic adenylyl sulfate reductase and present a model that may explain the CycA phenotype through confurcation of electrons.

  1. Transhydrogenase and Growth Substrate Influence Lipid Hydrogen Isotope Ratios in Desulfovibrio alaskensis G20

    PubMed Central

    Leavitt, William D.; Flynn, Theodore M.; Suess, Melanie K.; Bradley, Alexander S.

    2016-01-01

    Microbial fatty acids preserve metabolic and environmental information in their hydrogen isotope ratios (2H/1H). This ratio is influenced by parameters that include the 2H/1H of water in the microbial growth environment, and biosynthetic fractionations between water and lipid. In some microbes, this biosynthetic fractionation has been shown to vary systematically with central energy metabolism, and controls on fatty acid 2H/1H may be linked to the intracellular production of NADPH. We examined the apparent fractionation between media water and the fatty acids produced by Desulfovibrio alaskensis G20. Growth was in batch culture with malate as an electron donor for sulfate respiration, and with pyruvate and fumarate as substrates for fermentation and for sulfate respiration. A larger fractionation was observed as a consequence of respiratory or fermentative growth on pyruvate than growth on fumarate or malate. This difference correlates with opposite apparent flows of electrons through the electron bifurcating/confurcating transhydrogenase NfnAB. When grown on malate or fumarate, mutant strains of D. alaskensis G20 containing transposon disruptions in a copy of nfnAB show different fractionations than the wild type strain. This phenotype is muted during fermentative growth on pyruvate, and it is absent when pyruvate is a substrate for sulfate reduction. All strains and conditions produced similar fatty acid profiles, and the 2H/1H of individual lipids changed in concert with the mass-weighted average. Unsaturated fatty acids were generally depleted in 2H relative to their saturated homologs, and anteiso-branched fatty acids were generally depleted in 2H relative to straight-chain fatty acids. Fractionation correlated with growth rate, a pattern that has also been observed in the fractionation of sulfur isotopes during dissimilatory sulfate reduction by sulfate-reducing bacteria. PMID:27445998

  2. Bioaccessibility of carotenoids from Chlorella vulgaris and Chlamydomonas reinhardtii.

    PubMed

    Gille, Andrea; Trautmann, Andreas; Posten, Clemens; Briviba, Karlis

    2015-08-01

    Microalgae can contribute to a balanced diet because of their composition. Beside numerous essential nutrients, carotenoids are in the focus for food applications. The bioavailability of carotenoids from photoautotrophic-cultivated Chlorella vulgaris (C. vulgaris) and Chlamydomonas reinhardtii (C. reinhardtii) was compared. An in vitro digestion model was used to investigate carotenoid bioaccessibility. Furthermore, the effect of sonication on bioaccessibility was assessed. Lutein was the main carotenoid in both species. C. reinhardtii showed higher amounts of lutein and β-carotene than C. vulgaris. In contrast to C. reinhardtii, no β-carotene and only 7% of lutein were bioaccessible in nonsonicated C. vulgaris. Sonication increased the bioaccessibility of carotenoids from C. vulgaris to a level comparable with C. reinhardtii (β-carotene: ≥ 10%; lutein: ≥ 15%). Thus, C. reinhardtii represents a good carotenoid source for potential use in foods without processing, while the application of processing methods, like sonication, is necessary for C. vulgaris.

  3. Optimization of liquid media and biosafety assessment for algae-lysing bacterium NP23.

    PubMed

    Liao, Chunli; Liu, Xiaobo; Shan, Linna

    2014-09-01

    To control algal bloom caused by nutrient pollution, a wild-type algae-lysing bacterium was isolated from the Baiguishan reservoir in Henan province of China and identified as Enterobacter sp. strain NP23. Algal culture medium was optimized by applying a Placket-Burman design to obtain a high cell concentration of NP23. Three minerals (i.e., 0.6% KNO3, 0.001% MnSO4·H2O, and 0.3% K2HPO4) were found to be independent factors critical for obtaining the highest cell concentration of 10(13) CFU/mL, which was 10(4) times that of the control. In the algae-lysing experiment, the strain exhibited a high lysis rate for the 4 algae test species, namely, Chlorella vulgari, Scenedesmus, Microcystis wesenbergii, and Chlorella pyrenoidosa. Acute toxicity and mutagenicity tests showed that the bacterium NP23 had no toxic and mutagenic effects on fish, even in large doses such as 10(7) or 10(9) CFU/mL. Thus, Enterobacter sp. strain NP23 has strong potential application in the microbial algae-lysing project.

  4. A case of pemphigus vulgaris with esophageal involvement.

    PubMed

    Amichai, B; Grunwald, M H; Gasper, N; Finkelstein, E; Halevy, S

    1996-03-01

    Esophageal involvement in pemphigus vulgaris is rare, found more in women than in men, and can be the only manifestation of pemphigus. Esophageal involvement had been reported only among patients with pemphigus vulgaris and not in patients with other forms of pemphigus. We describe a case of pemphigus vulgaris in which the esophagus was severely involved with only few oral lesions and no involvement of the skin or oropharynx.

  5. Psoriasiform lupus vulgaris with 30 years duration.

    PubMed

    Reich, Adam; Kobierzycka, Monika; Cisło, Maria; Schwartz, Robert A; Szepietowski, Jacek C

    2006-01-01

    Lupus vulgaris is a progressive form of cutaneous tuberculosis occurring in a person with a moderate to high degree of immunity. It is the most common type of cutaneous tuberculosis. Lupus vulgaris can be mimicked by several other skin conditions, and a 69-y-old female is described with an extremely long history of extensive infiltrative skin lesions with abundant scaling. The lesions were localized on the right arm and forearm, and on the right lateral surface of the chest. The diascopic test was positive. Moreover, a large atrophic scar was seen in the region of right cubital fossa resulting in contracture of the right elbow joint. The histopathology strongly suggested the diagnosis of tuberculosis. The final diagnosis of tuberculosis was confirmed by PCR examination. A polychemotherapeutic regimen (ethambutol 1250 mg/d, rifampicin 600 mg/d and isoniazid 300 mg/d) was successfully employed for the treatment of skin lesions.

  6. Disseminated lupus vulgaris presenting as granulomatous folliculitis.

    PubMed

    Hruza, G J; Posnick, R B; Weltman, R E

    1989-01-01

    A 69-year-old man presented with a 3-year history of scattered, grouped, asymptomatic follicular papules, pustules, and nodules tending toward coalescence into large geographic aggregates. Repeated cutaneous biopsy specimens showed granulomatous folliculitis with negative Ziehl-Neelsen stains. Finally, biopsy material submitted for mycobacterial culture grew Mycobacterium tuberculosis. No evidence of active systemic tuberculosis was found. The patient had a very rare form of tuberculosis, disseminated lupus vulgaris, presenting with granulomatous folliculitis, which is usually not seen in lupus vulgaris. The lesions resolved after an 18-month course of isoniazid and rifampin. The unusual clinical and histologic presentation as well as occasional partial remissions following a variety of nonspecific empiric therapies delayed diagnosis despite multiple evaluations. This case illustrates the importance of obtaining mycobacterial cultures from skin biopsy specimens in addition to special stains whenever cutaneous tuberculosis is suspected.

  7. Giant lupus vulgaris: A rare presentation.

    PubMed

    Sacchidanand, S; Sharavana, S; Mallikarjun, M; Nataraja, H V

    2012-01-01

    Cutaneous tuberculosis continues to be an important public health problem even with the availability of highly effective anti-tuberculous drugs. It constitutes 0.1% of all cases of extrapulmonary tuberculosis. Lupus vulgaris is the most common form of cutaneous tuberculosis that occurs in previously sensitized individuals with a moderate degree of immunity against tubercle bacilli. The different types of lupus vulgaris include plaque, ulcerative, vegetative, papular and nodular, and tumor forms. A 40-year-old man presented with large multiple plaques over right upper limb, right side of chest and back, and right lower limb for the past 30 years. Histopathology showed numerous noncaseating granulomas with Langhan's type of giant cells. The Mantoux test showed strong positivity and there was excellent response to anti-tuberculous treatment. This case is being reported because of its extreme chronicity of 30 years duration, unusually large size and multiplicity of lesions.

  8. Management of pemphigus vulgaris: challenges and solutions

    PubMed Central

    Gregoriou, Stamatis; Efthymiou, Ourania; Stefanaki, Christina; Rigopoulos, Dimitris

    2015-01-01

    The main objective in the treatment of pemphigus vulgaris is to control the disease, prevent relapses, and avoid adverse events associated with the prolonged use of steroids and immunosuppressive agents. Systemic corticosteroids remain the gold standard treatment for pemphigus vulgaris. Azathioprine and mycophenolate mofetil are the first line of steroid-sparing treatment. Rituximab is extremely effective in recalcitrant pemphigus, when other treatments fail to control the disease. The European Dermatology Forum recommends tapering prednisolone by 25% every 2 weeks after the consolidation phase, and a 5 mg reduction every 4 weeks when the dose is reduced to <20 mg. If the patient relapses, options include increasing steroids back to the previous dose, adding an immunosuppressant if using steroid monotherapy, or replacing a first-line immunosuppressant by another if already on combination therapy. PMID:26543381

  9. Pemphigus vulgaris: a rare cause of dysphagia.

    PubMed

    Al-Janabi, Ali; Greenfield, Simon

    2015-10-22

    Pemphigus vulgaris is a rare autoimmune blistering disease of the skin and mucous membranes. The case reported presented unusually with dyspepsia that was not responsive to protein pump inhibitor (PPI) therapy. This progressed to severe dysphagia and odynophagia. An esophagogastroduodenoscopy showed extensive ulceration of the esophagus, and direct immunofluorescence of an esophageal biopsy showed bright intercellular staining with C3 and IgG, confirming the diagnosis of pemphigus vulgaris. Immunological remission was achieved after a number of courses of pulsed intravenous methylprednisolone and cyclophosphamide. The patient has remained in remission for 5 years, but has required regular dilation of esophageal strictures for symptom relief. During this period, a chronic lymphocytosis was incidentally noted on routine blood tests, and chronic lymphocytic leukaemia was diagnosed. It is essential to investigate PPI-resistant symptoms, dysphagia and odynophagia, as they may indicate a serious underlying cause.

  10. Coagulation-membrane filtration of Chlorella vulgaris.

    PubMed

    Lee, Duu-Jong; Liao, Guan-Yu; Chang, Yin-Ru; Chang, Jo-Shu

    2012-03-01

    Filtration-based separation of Chlorella vulgaris, a species with excellent potential for CO(2) capture and lipid production, was investigated using a surface-modified hydrophilic polytetrafluoroethylene (PTFE) membrane. Coagulation using polyaluminum chloride (PACl) attained maximum turbidity removal at 200 mg L(-1) as Al(2)O(3). The membrane filtration flux at 1 bar increased as the PACl dose increased, regardless of overdosing in the coagulation stage. The filtered cake at the end of filtration tests peaked in solid content at 10 mg L(-1) as Al(2)O(3), reaching 34% w/w, roughly two times that of the original suspension. Differential scanning calorimetry (DSC) tests demonstrate that the cake with minimum water-solid binding strength produced the driest filter cake. Coagulation using 10 mg L(-1) PACl as Al(2)O(3), followed by PTFE membrane filtration at 1 bar, is an effective process for harvesting C. vulgaris from algal froth.

  11. Lupus vulgaris--a case report.

    PubMed

    Munn, S E; Basarab, T; Russell Jones, R

    1995-01-01

    Although lupus vulgaris is the most common form of cutaneous tuberculosis seen in Europe, the incidence has steadily declined and it is now rarely seen. We report a case in a 69-year-old lady who presented with a 10-year history of a slowly growing plaque on the left cheek. Skin biopsy confirmed caseating granulomata, and acid-fast bacilli were seen. She was commenced on triple antituberculous therapy with good effect.

  12. Clindamycin phosphate 1% gel in acne vulgaris.

    PubMed

    Rizer, R L; Sklar, J L; Whiting, D; Bucko, A; Shavin, J; Jarratt, M

    2001-01-01

    A 12-week study compared Clindagel, a unique water-based gel formulation of clindamycin phosphate 1%, administered once daily, and Cleocin T, a slightly different gel formulation indicated for twice-daily use, in the treatment of acne vulgaris. Clindagel was safe and effective and equivalent to Cleocin T gel, albeit with a better tolerability profile. Clindagel is a viable alternative to Cleocin T gel.

  13. The Psychosocial Impact of Acne Vulgaris

    PubMed Central

    Hazarika, Neirita; Archana, M

    2016-01-01

    Background: Acne vulgaris causes erythematous papulopustular lesions in active stage and often leave behind residual scarring and pigmentation. Its onset in adolescence may add to the emotional and psychological challenges experienced during this period. Aims: To assess the impact of acne on the various psychosocial domains of daily life. Materials and Methods: This was a prospective, cross-sectional study done in the dermatology out-patient department of a tertiary care hospital from January to March 2015. A total of 100 consecutive, newly diagnosed patients of acne vulgaris, aged 15 years and above were included in this study. The relationship between acne vulgaris and its sequelae was analyzed with ten different domains of daily life by using dermatology life quality index (DLQI) questionnaire. Results: Females (56%), 15–20 year olds (61%), facial lesions (60%), and Grade II acne (70%) were most common. Acne scars were noted in 75% patients, whereas 79% cases had post-acne hyperpigmentation. Thirty-seven percent patients had DLQI scores of (6–10) interpreted as moderate effect on patient's life. Statistically significant correlation (P < 0.05) found were as follows: Physical symptoms with grade of acne; embarrassment with site and grade of acne; daily activities with grade of acne and post-acne pigmentation; choice of clothes with site of acne; social activities with gender, site and grade of acne; effect on work/study with grade of acne; interpersonal problems with site and post-acne pigmentation; sexual difficulties with grade of acne. Limitation: It was a hospital-based study with small sample size. Conclusion: Significant impact of acne and its sequelae was noted on emotions, daily activities, social activities, study/work, and interpersonal relationships. Assurance and counseling along with early treatment of acne vulgaris is important to reduce disease-related psychosocial sequelae and increase the efficacy of treatment. PMID:27688440

  14. Characterization of the nickel-iron periplasmic hydrogenase from Desulfovibrio fructosovorans.

    PubMed

    Hatchikian, C E; Traore, A S; Fernandez, V M; Cammack, R

    1990-02-14

    The periplasmic hydrogenase from Desulfovibrio fructosovorans grown on fructose/sulfate medium was purified to homogeneity. It exhibits a molecular mass of 88 kDa and is composed of two different subunits of 60 kDa and 28.5 kDa. The absorption spectrum of the enzyme is characteristic of an iron-sulfur protein and its absorption coefficients at 400 and 280 nm are 50 and 180 mM-1 cm-1, respectively. D. fructosovorans hydrogenase contains 11 +/- 1 iron atoms, 0.9 +/- 0.15 nickel atom and 12 +/- 1 acid-labile sulfur atoms/molecule but does not contain selenium. The amino acid composition of the protein and of its subunits, as well as the N-terminal sequences of the small and large subunits, have been determined. The cysteine residues of the protein are distributed between the large (9 residues) and the small subunits (11 residues). Electron spin resonance (ESR) properties of the enzyme are consistent with the presence of nickel(III), [3Fe-4S] and [4Fe-4S] clusters. The hydrogenase of D. fructosovorans isolated under aerobic conditions required an incubation with hydrogen or other reductants in order to express its full catalytic activity. H2 uptake and H2 evolution activities doubled after a 3-h incubation under reducing conditions. Comparison with the (NiFe) hydrogenase from D. gigas shows great structural similarities between the two proteins. However, there are significant differences between the catalytic properties of the two enzymes which can be related to the respective state of their nickel atom. ESR showed a higher proportion of the Ni-B species (g = 2.33, 2.16, 2.01) which can be related to a more facile conversion to the ready state. The periplasmic location of the enzyme and the presence of hydrogenase activity in other cellular compartments are discussed in relation to the ability of D. fructosovorans to participate actively in interspecies hydrogen transfer.

  15. Adaptive evolution of Desulfovibrio alaskensis G20 for developing resistance to perchlorate

    NASA Astrophysics Data System (ADS)

    Mehta-Kolte, M. G.; Youngblut, M.; Redford, S.; Gregoire, P.; Carlson, H. K.; Coates, J. D.

    2015-12-01

    Due to its toxic, explosive, and corrosive nature, inadvertent biological H2S production by sulfate reducing microorganisms (SRM) poses significant health and industrial operational risks. Anthropogenic sources are dominated by the oil industry where H2S in reservoir gases and fluids has an associated annual cost estimated at $90 billion globally. Our previous studies have identified perchlorate (ClO4-) as a selective and potent inhibitor of SRM in pure culture and complex microbial ecosystems. However, constant addition of inhibitors like perchlorate to natural ecosystems may result in a new adaptive selective pressure on SRM populations. With this in mind we investigated the ability of Desulfovibrio alaskensis G20, a model oil reservoir SRM, to adapt to perchlorate and develop a resistance. Serial transfers of three parallel cultures with increasing concentrations of perchlorate up to 100 mM were generated and compared to wild-type strains that were transferred for same number of generations in absence of perchlorate. Genome sequencing revealed that all three adapted strains had single non-synonymous single-nucleotide polymorphisms in the same gene, Dde_2265, the sulfate adenylytransferase (ATP sulfurylase (ATPS)) (EC 2.7.7.4). ATPS catalyzes the first committed step in sulfate reduction and is essential in all SRM. IC50s against growth for these evolved strains demonstrated a three-fold increased resistance to perchlorate compared to wild-type controls. These evolved strains also had 5x higher transcriptional abundance of Dde_2265 compared to the wild-type strain. Biochemical characterization of the purified ATPS enzyme from both wild-type and the evolved strain showed that the mutant ATPS from the evolved strain was resistant to perchlorate inhibition of ATP turnover with a KI for perchlorate that was 3x greater relative to the wild-type ATPS. These results demonstrate that a single-base pair mutation in ATPS can have a significant impact on developing

  16. Metabolism of H2 by Desulfovibrio alaskensis G20 during syntrophic growth on lactate.

    PubMed

    Li, Xiangzhen; McInerney, Michael J; Stahl, David A; Krumholz, Lee R

    2011-10-01

    Syntrophic growth involves the oxidation of organic compounds and subsequent transfer of electrons to an H(2)- or formate-consuming micro-organism. In order to identify genes involved specifically in syntrophic growth, a mutant library of Desulfovibrio alaskensis G20 was screened for loss of the ability to grow syntrophically with Methanospirillum hungatei JF-1. A collection of 20 mutants with an impaired ability to grow syntrophically was obtained. All 20 mutants grew in pure culture on lactate under sulfidogenic conditions at a rate and to a maximum OD(600) similar to those of the parental strain. The largest number of mutations that affected syntrophic growth with lactate was in genes encoding proteins involved in H(2) oxidation, electron transfer, hydrogenase post-translational modification, pyruvate degradation and signal transduction. The qrcB gene, encoding a quinone reductase complex (Qrc), and cycA, encoding the periplasmic tetrahaem cytochrome c(3) (TpIc(3)), were required by G20 to grow syntrophically with lactate. A mutant in the hydA gene, encoding an Fe-only hydrogenase (Hyd), is also impaired in syntrophic growth with lactate. The other mutants grew more slowly than the parental strain in syntrophic culture with M. hungatei JF-1. qrcB and cycA were shown previously to be required for growth of G20 pure cultures with H(2) and sulfate. Washed cells of the parental strain produced H(2) from either lactate or pyruvate, but washed cells of qrcB, cycA and hydA mutants produced H(2) at rates similar to the parental strain from pyruvate and did not produce significant amounts of H(2) from lactate. Real-time quantitative PCR assays showed increases in expression of the above three genes during syntrophic growth compared with pure-culture growth with lactate and sulfate. Our work shows that Hyd, Qrc and TpIc(3) are involved in H(2) production during syntrophic lactate metabolism by D. alaskensis G20 and emphasizes the importance of H(2) production for

  17. Inhibition of lentivirus replication by aqueous extracts of Prunella vulgaris

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Prunella vulgaris has been used historically in Chinese and Native American medicine. Various members of the mint family, including Prunella, have been reported to have antiviral activity. To characterize the anti-lentiviral activities of P. vulgaris, we tested water and ethanol extracts for their...

  18. Lupus vulgaris secondary to single BCG vaccination. A case report.

    PubMed

    Selimoğlu, M A; Erdem, T; Parlak, M; Eşrefoğlu, M

    1998-01-01

    A 10-year-old girl with lupus vulgaris following single BCG vaccination is reported. She had a 15 x 20 cm painless lesion covering her left shoulder, axilla, triceps and biceps region. PPD test was positive. Histopathological picture was identical to lupus vulgaris.

  19. Variation in the Breeding System of Prunella vulgaris L.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Prunella vulgaris (Lamiaceae), commonly known as selfheal, is a perennial herb with a long history of use in traditional medicine. Recent studies have found that P. vulgaris possesses anti-inflammatory, antiviral and anti-bacterial properties, which may lead to increased commercial demand. To date...

  20. Evidence for selenocysteine coordination to the active site nickel in the [NiFeSe]hydrogenases from Desulfovibrio baculatus.

    PubMed Central

    Eidsness, M K; Scott, R A; Prickril, B C; DerVartanian, D V; Legall, J; Moura, I; Moura, J J; Peck, H D

    1989-01-01

    Ni and Se x-ray absorption spectroscopic studies of the [NiFeSe]hydrogenases from Desulfovibrio baculatus are described. The Ni site geometry is pseudo-octahedral with a coordinating ligand composition of 3-4 (N,O) at 2.06 A, 1-2 (S,Cl) at 2.17 A, and 1 Se at 2.44 A. The Se coordination environment consists of 1 C at 2.0 A and a heavy scatterer M (M = Ni or Fe) at approximately 2.4 A. These results are interpreted in terms of a selenocysteine residue coordinated to the Ni site. The possible role of the Ni-Se site in the catalytic activation of H2 is discussed. PMID:2521386

  1. Novel Waddlia Intracellular Bacterium in Artibeus intermedius Fruit Bats, Mexico

    PubMed Central

    Pierlé, Sebastián Aguilar; Morales, Cirani Obregón; Martínez, Leonardo Perea; Ceballos, Nidia Aréchiga; Rivero, Juan José Pérez; Díaz, Osvaldo López; Brayton, Kelly A.

    2015-01-01

    An intracellular bacterium was isolated from fruit bats (Artibeus intermedius) in Cocoyoc, Mexico. The bacterium caused severe lesions in the lungs and spleens of bats and intracytoplasmic vacuoles in cell cultures. Sequence analyses showed it is related to Waddlia spp. (order Chlamydiales). We propose to call this bacterium Waddlia cocoyoc. PMID:26583968

  2. Culturable Populations of Sporomusa spp. and Desulfovibrio spp. in the Anoxic Bulk Soil of Flooded Rice Microcosms

    PubMed Central

    Rosencrantz, Dirk; Rainey, Frederick A.; Janssen, Peter H.

    1999-01-01

    Most-probable-number (MPN) counts were made of homoacetogenic and other bacteria present in the anoxic flooded bulk soil of laboratory microcosms containing 90- to 95-day-old rice plants. MPN counts with substrates known to be useful for the selective enrichment or the cultivation of homoacetogenic bacteria (betaine, ethylene glycol, 2,3-butanediol, and 3,4,5-trimethoxybenzoate) gave counts of 2.3 × 103 to 2.8 × 105 cells per g of dry soil. Homoacetogens isolated from the terminal positive steps of these dilution cultures belonged to the genus Sporomusa. Counts with succinate, ethanol, and lactate gave much higher MPNs of 5.9 × 105 to 3.4 × 107 cells per g of dry soil and led to the isolation of Desulfovibrio spp. Counting experiments on lactate and ethanol which included Methanospirillum hungatei in the medium gave MPNs of 2.3 × 106 to 7.5 × 108 cells per g of dry soil and led to the isolation of Sporomusa spp. The latter strains could grow with betaine, ethylene glycol, 2,3-butanediol, and/or 3,4,5-trimethoxybenzoate, but apparently most cells of Sporomusa spp. did not initiate growth in counting experiments with those substrates. Spores apparently accounted for 2.2% or less of the culturable bacteria. It appears that culturable Desulfovibrio spp. and Sporomusa spp. were present in approximately equal numbers in the bulk soil. Multiple, phylogenetically-distinct, phenotypically-different, strains of each genus were found in the same soil system. PMID:10427044

  3. Addressing Free Radical Oxidation in Acne Vulgaris

    PubMed Central

    Criscito, Maressa C.; Schlesinger, Todd E.; Verdicchio, Robert; Szoke, Ernest

    2016-01-01

    Objective: Comparatively little attention has been paid to the role of free radical oxidation in acne vulgaris. Here, using the traditional abnormalities cited for acne, the authors address the role of free radical oxidation throughout the pathogenesis by detailing the chemistry that may contribute to clinical changes. To probe the effects of free radical oxidation and test an antioxidant, they conducted a preliminary study of topically applied vitamin E. Methods: Seventeen patients with mild-to-moderate acne vulgaris were evaluated over an eight-week period in two private dermatology practices in this open-label study. All patients enrolled were on the same baseline regimen of salicylic acid and benzoyl peroxide. This regimen was then supplemented with topical vitamin E in sunflower seed oil. Results: At the end of the eight-week period, all patients demonstrated clinical improvement, as indicated by a reduction in the number of lesions and global mean difference. A statistically significant reduction was noted as early as Week 2. Enrolled patients also expressed a positive experience due to good tolerability and easy application. Conclusion: Although the exact pathogenesis of acne vulgaris remains unknown, the presence of excessive reactive oxygen species can be implicated in each of the major abnormalities involved. This presence, along with the positive results of the authors’ preliminary study, demonstrates the need for more exploration on the use of topical antioxidants in limiting free radical oxidation in the acne model. This paper is designed to stimulate academic discussion regarding a new way of thinking about the disease state of acne. PMID:26962389

  4. Insulin resistance in severe acne vulgaris

    PubMed Central

    Cengiz, Fatma Pelin; Kemeriz, Funda

    2015-01-01

    Introduction Acne vulgaris is a pilosebaceous gland disease that usually affects people from puberty to young adulthood. It is seen especially on the face, neck, trunk and arms. Its severity differs from patient to patient and its pathogenesis is multifactorial. The main pathogenic factors of acne are high sebaceous gland secretion, follicular hyperproliferation, high androgen effects, propionibacterium acnes colonization and inflammation. Diet is always thought a probable reason for acne and many studies are done about acne and diet. Aim To determine the effect of insulin resistance in severe acne vulgaris. Material and methods Two hundred and forty-three acne vulgaris patients and 156 healthy controls were enrolled into the study. The blood levels of insulin and glucose were measured. Homeostasis Model Assessment (HOMA) Index was calculated. The values were compared with the control group. Results All of the patients were in the severe acne group according to their scores on the global acne scoring scale. While fasting blood glucose levels were not different between the groups (p > 0.05, 82.91 ±9.76 vs. 80.26 ±8.33), the fasting insulin levels were significantly higher in the patient group than in the control group (p < 0.001, 14.01 ±11.94 vs. 9.12 ±3.53). Additionally, there was a highly significant difference between the patient and control groups in terms of HOMA values (p < 0.001, 2.87 ±2.56 vs. 1.63 ±0.65). Conclusions These results suggest that insulin resistance may have a role in the pathogenesis of acne. PMID:26366152

  5. Disseminated lupus vulgaris: a case report.

    PubMed

    Can, Burce; Zindanci, Ilkin; Turkoglu, Zafer; Kavala, Mukaddes; Ulucay, Vasfiye; Demir, Filiz Topaloglu

    2014-01-01

    Lupus vulgaris is a secondary form of cutaneous tuberculosis which persists for years if not treated. The head and neck are the most commonly affected sites. While less frequently arms and legs, and rarely the trunk and the scalp are involved. Herein, we describe a 73-year-old man with a 5-year history of slowly growing, atrophic, some eroded and ulcerated, red-brown plaques on his forehead, nose, cheeks, ear lobes, trunk and extremites. All of his disseminated lesions healed after antituberculosis therapy.

  6. A new pyrroloquinazoline alkaloid from Linaria vulgaris.

    PubMed

    Hua, Huiming; Cheng, Maosheng; Li, Xian; Pei, Yuehu

    2002-10-01

    A new alkaloid, 1,2,3,9-tetrahydropyrrolo(2,1-b)quinazolin-1-carboxylic acid (1), together with eight known compounds, 7-hydroxy vasicine (2), benzyl alcohol beta-D-(2'-O-beta-xylopyranosyl)glucopyranoside (3), benzyl alcohol O-beta-D-glucopyranoside (4), benzyl alcohol O-beta-D-primveroside (5), 3,5-dimethyl-4-hydroxy benzaldehyde (6), gluco-syringic acid (7), syringin (8), and liriodendrin (9), were isolated from the plants of Linaria vulgaris. Their structures were established by spectroscopic methods.

  7. Pemphigus vulgaris and amyotrophic lateral sclerosis

    PubMed Central

    Mokhtari, Fatemeh; Matin, Marzieh; Rajati, Fatemeh

    2016-01-01

    Pemphigus vulgaris (PV) is an autoimmune bullous and erosive mucocutaneous disease. Rarely, it occurs in patients with other autoimmune disease. The relation between PV and neurological disorders is unclear and needs to be more studied. Here, we report a case of amyotrophic lateral sclerosis (ALS), followed by dermatologic involvement. Histopathological evidence and direct immunofluorescence are consistent with PV. Systemic corticosteroid and azathioprine were effective in the treatment of mucocutaneous lesions. PV seems to be accidentally associated with ALS. Expression of major histocompatibility complex Class II in autoimmune disease and production of autoantibodies have been proposed to describe the association of PV with ALS. PMID:28163728

  8. Pemphigus vulgaris presenting as gingival involvement.

    PubMed

    Javali, Mukhatar Ahmed; Zainab, Heena

    2012-09-01

    Pemphigus vulgaris (PV) is an autoimmune blistering disease affecting the mucous membrane and skin. Typically, oral lesions appear before skin lesions, and in a majority of the cases only oral lesions are present. The dentist may then be the first to recognize and diagnose this disease. It is unusual for PV to present over the gingiva as a primary site of involvement. Diagnosis is based on clinical presentation and confirmed by histopathological study. Early diagnosis and management can prevent the uneven life- threatening effects of this potentially chronic mucocutaneous disorder. The case serves to enhance our awareness of the gingiva as a site at which systemic disease can manifest itself.

  9. Nootropic effect of meadowsweet (Filipendula vulgaris) extracts.

    PubMed

    Shilova, I V; Suslov, N I

    2015-03-01

    The effects of the extracts of the aboveground parts of Filipendula vulgaris Moench on the behavior and memory of mice after hypoxic injury and their physical performance in the open-field test were studied using the models of hypoxia in a sealed volume, conditioned passive avoidance response (CPAR), and forced swimming with a load. The extracts improved animal resistance to hypoxia, normalized orientation and exploration activities, promoted CPAR retention after hypoxic injury, and increased physical performance. Aqueous extract of meadowsweet had the most pronounced effect that corresponded to the effect of the reference drug piracetam. These effects were probably caused by modulation of hippocampal activity.

  10. Hormonal treatment of acne vulgaris: an update

    PubMed Central

    Elsaie, Mohamed L

    2016-01-01

    Acne vulgaris is a common skin condition associated with multiple factors. Although mostly presenting alone, it can likewise present with features of hyperandrogenism and hormonal discrepancies. Of note, hormonal therapies are indicated in severe, resistant-to-treatment cases and in those with monthly flare-ups and when standard therapeutic options are inappropriate. This article serves as an update to hormonal pathogenesis of acne, discusses the basics of endocrinal evaluation for patients with suspected hormonal acne, and provides an overview of the current hormonal treatment options in women. PMID:27621661

  11. Molecular biology of coal bio-desulfurization. [Rhodococcus rhodochrous, Desulfovibrio desulfuricans

    SciTech Connect

    Young, K.D.; Gallagher, J.R.

    1992-04-30

    Genes cloned from Rhodococcus rhodochrous IGTS8 can transfer the DBT desulfurization phenotype to a different species (R. Fascians). The product was identified as 2-phenylphenol by gas chromatography. This result parallels the results we have previously reported for the activity of these genes in a DBT-negative mutant of IGTS8. Thus, the evidence is strong that we have identified and cloned the entire set of genes that are responsible for this very specific desulfurization reaction. Sequencing of these genes has commenced. A genomic library was constructed from the bacterium, Besulfovibrio desulfuricans. Screening has not yet identified a clone that carries the desulfurization genes from that organism. Two open reading frames, doxH and doxJ, in the C18 DBT degradation pathway were mutated and are now believed to be dispensable to that pathway. Finally, progress was made toward beginning to sequence the DBT dixoygenase genes from strain A15.

  12. Characterization of an alkaline lipase from Proteus vulgaris K80 and the DNA sequence of the encoding gene.

    PubMed

    Kim, H K; Lee, J K; Kim, H; Oh, T K

    1996-01-01

    A facultatively anaerobic bacterium producing an extracellular alkaline lipase was isolated from the soil collected near a sewage disposal plant in Korea and identified to be a strain of Proteus vulgaris. The molecular mass of the purified lipase K80 was estimated to be 31 kDa by SDS-PAGE. It was found to be an alkaline enzyme having maximum hydrolytic activity at pH 10, while fairly stable in a wide pH range from 5 to 11. The gene for lipase K80 was cloned in Escherichia coli. Sequence analysis showed an open reading frame of 861 bp coding for a polypeptide of 287 amino acid residues. The deduced amino acid sequence of the lipase gene had 46.3% identity to the lipase from Pseudomonas fragi.

  13. Paradigms: examples from the bacterium Xylella fastidiosa.

    PubMed

    Purcell, Alexander

    2013-01-01

    The history of advances in research on Xylella fastidiosa provides excellent examples of how paradigms both advance and limit our scientific understanding of plant pathogens and the plant diseases they cause. I describe this from a personal perspective, having been directly involved with many persons who made paradigm-changing discoveries, beginning with the discovery that a bacterium, not a virus, causes Pierce's disease of grape and other plant diseases in numerous plant species, including important crop and forest species.

  14. Pneumonia caused by a previously undescribed bacterium.

    PubMed Central

    Hopfer, R L; Mills, K; Fainstein, V; Fischer, H E; Luna, M P

    1982-01-01

    A new and as yet unidentified bacterium was isolated from the lung tissue of a cancer patient with bilateral pneumonia. Clinically, the pneumonia was consistent with legionellosis; the organism cultured from the lung grew only on the charcoal-yeast extract agar routinely used for Legionella isolation. Subsequent testing, however, showed the organism to be quite distinct from the known Legionella species in its biochemical, antigenic, and growth characteristics. Images PMID:7130363

  15. Characterization of a novel extremely alkalophilic bacterium

    NASA Technical Reports Server (NTRS)

    Souza, K. A.; Deal, P. H.

    1977-01-01

    A new alkalophilic bacterium, isolated from a natural spring of high pH is characterized. It is a Gram-positive, non-sporulating, motile rod requiring aerobic and alkaline conditions for growth. The characteristics of this organism resemble those of the coryneform group of bacteria; however, there are no accepted genera within this group with which this organism can be closely matched. Therefore, a new genus may be warranted.

  16. Lupus vulgaris: unusual presentation on face.

    PubMed

    Pilani, A; Vora, R V

    2014-01-01

    Lupus vulgaris is a variant of cutaneous tuberculosis. As the disease has potential to mutilate when left untreated, leaving deforming scars and disfigurement, an early diagnosis is of paramount importance. Though the common type is plaque type, rarely mutilating and vegetative forms also are found. A 28 year old female, labourer presented with progressive annular plaque over right side of cheek extending upto right lower lid and ala of nose. There were two satellite plaques near the right side of giant lesion. On diascopy apple jelly nodule was seen. There was no regional lymhadenopathy. Histopathological examination showed many granulomas in upper dermis extending to deep dermis comprising of epitheloid cells with langhans' type of giant cells, lymphocytic infiltration & focal necrosis suggestive of lupus vulgaris. The consequences of failing to make an early diagnosis can be disastrous for the patients, as the progression of the disease can lead to necrosis, destruction of bones and cartilage leading to permanent deformity. Thus it is vital for clinicians to have a high index of suspicion of such atypical forms and take biopsy samples for histological and bacteriological studies.

  17. [Severe eye involvement in pemphigus vulgaris].

    PubMed

    Baykal, H E; Pleyer, U; Sönnichsen, K; Thiel, H J; Zierhut, M

    1995-12-01

    Pemphigus vulgaris (PV) is an immune-mediated vesiculobullous disease of the skin and mucous membranes. Generally, patients with PV present first with oral lesions, which may precede the cutaneous lesions, such as bullae and erosions, by several months. An ocular manifestation is unusual. The most common ophthalmologic involvement in pemphigus is conjunctivitis, but without progressive scarring such as occurs in ocular cictricial pemphigoid. Corneal involvement is very rare. CASE REPORT. We report on severe ocular involvement in a 56-year-old male Turkish patient with PV. Ophthalmologic findings included conjunctival cicatrization, corneal ulceration and corneal perforation, despite immunosuppressive therapy with azathioprine and corticosteroids. A penetrating keratoplasty was performed, but rapidly failed because of corneal vascularization. CONCLUSION. If a chronic bullous dermatosis leads to severe eye involvement, PV should be considered in the differential diagnosis besides ocular cicatricial pemphigoid. Pemphigus vulgaris can be differentiated on the basis of clinical findings and histopathological and immunohistological features. Generally, PV can be treated with steroids or with a combination of an immunosuppressant and steroids. However, the combination of prednisone and azathioprine could not prevent corneal perforation in our patient.

  18. [Squamous cell carcinoma in lupus vulgaris].

    PubMed

    Kimmritz, Jens; Hermes, Barbara; Schewe, Christiane; Haas, Norbert

    2004-02-01

    Lupus vulgaris and carcinoma in lupo have become rare events that take place in the developed countries only under special circumstances. A 53-year-old woman developed such a carcinoma. She suffered from alcoholism, a well known risk factor for tuberculosis. The diagnosis of lupus vulgaris was confirmed by biopsy when an erythematous lesion on her arm that had been present for 25 years enlarged and subsequently ulcerated. Chemotherapy was discontinued because of lack of compliance and the ulcer grew markedly over the following 16 months. Therefore the entire lesion was excised. Histology showed a squamous cell carcinoma within the ulcer. Neither further systemic manifestations of tuberculosis nor metastases of the carcinoma were found. Under continuous combined antituberculous therapy, the patient remained free of symptoms. This case underlines the problems associated with a disease that has been nearly forgotten in the western countries. It also shows that alcoholism is a risk factor for tuberculosis, along with debilitating diseases such as lymphoma and AIDS as well as immunosuppressive therapy.

  19. [Microstructural changes in hardened beans (Phaseolus vulgaris)].

    PubMed

    Mujica, Maria Virginia; Granito, Marisela; Soto, Naudy

    2015-06-01

    (Phaseolus vulgaris). The hardening of Phaseolus vulgaris beans stored at high temperature and high relative humidity is one of the main constraints for consumption. The objective of this research was to evaluate by scanning electron microscopy, structural changes in cotyledons and testa of the hardened beans. The freshly harvested grains were stored for twelve months under two conditions: 5 ° C-34% RH and 37 ° C-75% RH, in order to promote hardening. The stored raw and cooked grains were lyophilized and fractured. The sections of testa and cotyledons were observed in an electron microscope JSM-6390. After twelve months, grains stored at 37 ° C-75% RH increased their hardness by 503%, whereas there were no significant changes in grains stored at 5 ° C-34% RH. At the microstructural level, the cotyledons of the raw grains show clear differences in appearance of the cell wall, into the intercellular space size and texture matrix protein. There were also differences in compaction of palisade and sub-epidermal layer in the testa of raw grains. After cooking, cotyledon cells of the soft grains were well separated while these ofhard grains were seldom separated. In conclusion, the found differences in hard and soft grains showed a significant participation of both structures, cotyledons and testa, in the grains hardening.

  20. Oxidative Stress in Patients With Acne Vulgaris

    PubMed Central

    Arican, Ozer; Belge Kurutas, Ergul; Sasmaz, Sezai

    2005-01-01

    Acne vulgaris is one of the common dermatological diseases and its pathogenesis is multifactorial. In this study, we aim to determine the effects of oxidative stress in acne vulgaris. Forty-three consecutive acne patients and 46 controls were enrolled. The parameters of oxidative stress such as catalase (CAT), glucose-6-phosphate dehydrogenase (G6PD), superoxide dismutase (SOD), and malondialdehyde (MDA) in the venous blood of cases were measured spectrophotometrically. The values compared with control group, the relation between the severity and distribution of acne, and the correlation of each enzyme level were researched. CAT and G6PD levels in patients were found to be statistically decreased, and SOD and MDA levels were found to be statistically increased (P < .001). However, any statistical difference and correlation could not be found between the severity and distribution of lesions and the mean levels of enzymes. In addition, we found that each enzyme is correlated with one another. Our findings show that oxidative stress exists in the acne patients. It will be useful to apply at least one antioxidant featured drug along with the combined acne treatment. PMID:16489259

  1. Role of olfaction in Octopus vulgaris reproduction.

    PubMed

    Polese, Gianluca; Bertapelle, Carla; Di Cosmo, Anna

    2015-01-01

    The olfactory system in any animal is the primary sensory system that responds to chemical stimuli emanating from a distant source. In aquatic animals "Odours" are molecules in solution that guide them to locate food, partners, nesting sites, and dangers to avoid. Fish, crustaceans and aquatic molluscs possess sensory systems that have anatomical similarities to the olfactory systems of land-based animals. Molluscs are a large group of aquatic and terrestrial animals that rely heavily on chemical communication with a generally dispersed sense of touch and chemical sensitivity. Cephalopods, the smallest class among extant marine molluscs, are predators with high visual capability and well developed vestibular, auditory, and tactile systems. Nevertheless they possess a well developed olfactory organ, but to date almost nothing is known about the mechanisms, functions and modulation of this chemosensory structure in octopods. Cephalopod brains are the largest of all invertebrate brains and across molluscs show the highest degree of centralization. The reproductive behaviour of Octopus vulgaris is under the control of a complex set of signal molecules such as neuropeptides, neurotransmitters and sex steroids that guide the behaviour from the level of individuals in evaluating mates, to stimulating or deterring copulation, to sperm-egg chemical signalling that promotes fertilization. These signals are intercepted by the olfactory organs and integrated in the olfactory lobes in the central nervous system. In this context we propose a model in which the olfactory organ and the olfactory lobe of O. vulgaris could represent the on-off switch between food intake and reproduction.

  2. Effects of trifluoromethyl ketones on the motility of Proteus vulgaris.

    PubMed

    Wolfart, Krisztina; Molnar, Annamaria; Kawase, Masami; Motohashi, Noboru; Molnar, Joseph

    2004-09-01

    In the present study, we showed the inhibition of motility by trifluoromethyl ketone (TF) derivatives (1-8) in Proteus vulgaris (P. vulgaris) cultures. Among them, 1-(2-benzoxazoyl)-3,3,3-trifluoro-2-propanone (1) showed a much stronger inhibitory effect on the motility of P. vulgaris than other TF compounds at 10% MIC. Our results suggest the possibility of an inhibitory action of TF compounds on the proton motive forces by affecting the action of biological motor and proton efflux in the membranes, resulting in a reduction of the ratio of running and the increased number of tumbling and non-motile cells.

  3. Experimental infection of octopus vulgaris (Cuvier, 1797) with Photobacterium damsela subsp. piscicida. Immunohistochemical tracking of antigen and tissue responses.

    PubMed

    Bakopoulos, Vasileios; White, Daniella; Valsamidis, Michail-Aggelos; Vasilaki, Feli

    2017-01-17

    Adult common octopus individuals were intramuscularly infected with Photobacterium damsela subsp. piscicida in order to investigate if this species is sensitive to this common and important fish pathogen. The fate of the bacterial antigens and the tissue responses of Octopus vulgaris were studied employing immunohistochemical techniques. Strong reaction at the site of injection was evident from day 2 post-infection that continued until day 14. Great numbers of hemocytes that were attracted at the site of infection were involved in phagocytosis of bacteria. Very early in the infection, a transition of cells to fibroblasts and an effort to isolate the infection was observed. During the course of the study, very large necrotic cells were seen at the site of infection, whereas during the later stages hemocytes with phagocytosed bacteria were observed in well-defined pockets inside the muscle tissue. None of the internal organs tested for the presence of the bacterium were positive with the exception of the digestive gland where antigen staining was observed which was not associated with hemocyte infiltration. The high doses of bacterial cells used in this experimental infection and the lack of disease signs from Octopus vulgaris suggest that, under normal conditions, octopus is resistant to Photobacterium damsela subsp. piscicida.

  4. Effects of Ag and Cu ions on the microbial corrosion of 316L stainless steel in the presence of Desulfovibrio sp.

    PubMed

    Unsal, Tuba; Ilhan-Sungur, Esra; Arkan, Simge; Cansever, Nurhan

    2016-08-01

    The utilization of Ag and Cu ions to prevent both microbial corrosion and biofilm formation has recently increased. The emphasis of this study lies on the effects of Ag and Cu ions on the microbial corrosion of 316L stainless steel (SS) induced by Desulfovibrio sp. Electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization were used to analyze the corrosion behavior. The biofilm formation, corrosion products and Ag and Cu ions on the surfaces were investigated using scanning electron microscopy (SEM), energy dispersive X-ray spectrometry (EDS) and elemental mapping. Through circuit modeling, EIS results were used to interpret the physicoelectric interactions between the electrode, biofilm and culture interfaces. EIS results indicated that the metabolic activity of Desulfovibrio sp. accelerated the corrosion rate of SS in both conditions with and without ions. However, due to the retardation in the growth of Desulfovibrio sp. in the presence of Ag and Cu ions, significant decrease in corrosion rate was observed in the culture with the ions. In addition, SEM and EIS analyses revealed that the presence of the ions leads to the formation on the SS of a biofilm with different structure and morphology. Elemental analysis with EDS detected mainly sulfide- and phosphorous-based corrosion products on the surfaces.

  5. Plant Anticancer Agents XXXIII. Constituents of Passerina vulgaris1.

    PubMed

    Ji-Xian, G; Handa, S S; Pezzuto, J M; Kinghorn, A D; Farnsworth, N R

    1984-06-01

    Two lignans of known structure, (+)-syringaresinol, a cytotoxic agent, and (+)-nortrachelogenin, a compound with demonstrated antileukemic activity, were isolated from a biologically active extract of the stems of PASSERINA VULGARIS.

  6. Lupus vulgaris of external nose--a case report.

    PubMed

    Arunkumar, J S; Naveen, K N; Prasad, K C; Santhosh, S G; Hegde, J S

    2013-02-01

    Lupus vulgaris is the most common morphological variant of cutaneous tuberculosis accounting for approximately 59% of cases of cutaneous tuberculosis in India. We present a case of lupus vulgaris of external nose diagnosed early and treated with CAT-3 RNTCP regimen for six months without any nasal deformity except for a small scar over the dorsum of the nose. Patient followed up for one year after completion of the prescribed regimen, there being no recurrence of the lesion.

  7. Uropathogenic properties of Proteus mirabilis and Proteus vulgaris.

    PubMed

    Peerbooms, P G; Verweij, A M; MacLaren, D M

    1985-02-01

    A group of faecal isolates of Proteus vulgaris and P. mirabilis was studied for the presence of possible virulence factors such as growth rates in urine and broth, haemolysin production, hydrophobicity, sensitivity to the bactericidal activity of human serum and cell invasiveness. Differences were found in haemolysin production, cell invasiveness and experimental virulence in a mouse model. These differences might explain why P. mirabilis is much more common in human urinary-tract infections than P. vulgaris.

  8. [Squamous epithelial carcinoma as a complication of lupus vulgaris].

    PubMed

    Betti, R; Tolomio, E; Vergani, R; Crosti, C

    2002-02-01

    Lupus vulgaris represents a type of cutaneous tuberculosis that, if not correctly treated, presents a progressive chronic development whose long-term complications include cutaneous neoplasms. We report on a 55-year-old man presenting a 10-year-old ulcerated and bleeding lupus vulgaris lesion on the left cheek containing a squamous cell carcinoma. Reviewing the literature, we search for possible causes of delay in diagnosis that even now allowed therapy only after discovery of the tumoral complication.

  9. Pemphigus vulgaris and infections: a retrospective study on 155 patients.

    PubMed

    Esmaili, Nafiseh; Mortazavi, Hossein; Noormohammadpour, Pedram; Boreiri, Majid; Soori, Tahereh; Vasheghani Farahani, Iman; Mohit, Mitra

    2013-01-01

    Background. Autoimmune process and immunosuppressive therapy of pemphigus vulgaris would predispose the patients to infections. Aim. We aimed to study the prevalence of infection and pathogenic agents in pemphigus vulgaris patients admitted to dermatology service. Material and methods. This retrospective study was conducted on 155 pemphigus vulgaris patients (68 males, 87 females) admitted to dermatology service between 2009 and 2011. In this study, the diagnosis of pemphigus vulgaris was confirmed by light microscopic and direct immunofluorescence findings. Data were collected through a questionnaire. Results. Of 155 pemphigus vulgaris patients, 33 had infection at admission and 9 acquired nosocomial infection. In addition, 37 cases of oral candidiasis and 15 cases of localized herpes simplex were recorded. Totally, 94 cases of infection were recorded. The occurrence of infection was significantly related to the severity of disease, number of hospital admissions, and presence of diabetes mellitus. The most common pathogenic germs isolated from cultures were Staphylococcus aureus and Escherichia coli. Conclusion. Severity of pemphigus vulgaris and diabetes were directly related with tendency to infections. Staphylococcus aureus and Escherichia coli were the most common pathogenic agents. Due to limitations of retrospective study, a prospective study is recommended.

  10. Pemphigus Vulgaris and Infections: A Retrospective Study on 155 Patients

    PubMed Central

    Esmaili, Nafiseh; Noormohammadpour, Pedram; Boreiri, Majid; Soori, Tahereh; Vasheghani Farahani, Iman; Mohit, Mitra

    2013-01-01

    Background. Autoimmune process and immunosuppressive therapy of pemphigus vulgaris would predispose the patients to infections. Aim. We aimed to study the prevalence of infection and pathogenic agents in pemphigus vulgaris patients admitted to dermatology service. Material and methods. This retrospective study was conducted on 155 pemphigus vulgaris patients (68 males, 87 females) admitted to dermatology service between 2009 and 2011. In this study, the diagnosis of pemphigus vulgaris was confirmed by light microscopic and direct immunofluorescence findings. Data were collected through a questionnaire. Results. Of 155 pemphigus vulgaris patients, 33 had infection at admission and 9 acquired nosocomial infection. In addition, 37 cases of oral candidiasis and 15 cases of localized herpes simplex were recorded. Totally, 94 cases of infection were recorded. The occurrence of infection was significantly related to the severity of disease, number of hospital admissions, and presence of diabetes mellitus. The most common pathogenic germs isolated from cultures were Staphylococcus aureus and Escherichia coli. Conclusion. Severity of pemphigus vulgaris and diabetes were directly related with tendency to infections. Staphylococcus aureus and Escherichia coli were the most common pathogenic agents. Due to limitations of retrospective study, a prospective study is recommended. PMID:23844280

  11. Essential Oil Characterization of Thymus vulgaris from Various Geographical Locations

    PubMed Central

    Satyal, Prabodh; Murray, Brittney L.; McFeeters, Robert L.; Setzer, William N.

    2016-01-01

    Thyme (Thymus vulgaris L.) is a commonly used flavoring agent and medicinal herb. Several chemotypes of thyme, based on essential oil compositions, have been established, including (1) linalool; (2) borneol; (3) geraniol; (4) sabinene hydrate; (5) thymol; (6) carvacrol, as well as a number of multiple-component chemotypes. In this work, two different T. vulgaris essential oils were obtained from France and two were obtained from Serbia. The chemical compositions were determined using gas chromatography–mass spectrometry. In addition, chiral gas chromatography was used to determine the enantiomeric compositions of several monoterpenoid components. The T. vulgaris oil from Nyons, France was of the linalool chemotype (linalool, 76.2%; linalyl acetate, 14.3%); the oil sample from Jablanicki, Serbia was of the geraniol chemotype (geraniol, 59.8%; geranyl acetate, 16.7%); the sample from Pomoravje District, Serbia was of the sabinene hydrate chemotype (cis-sabinene hydrate, 30.8%; trans-sabinene hydrate, 5.0%); and the essential oil from Richerenches, France was of the thymol chemotype (thymol, 47.1%; p-cymene, 20.1%). A cluster analysis based on the compositions of these essential oils as well as 81 additional T. vulgaris essential oils reported in the literature revealed 20 different chemotypes. This work represents the first chiral analysis of T. vulgaris monoterpenoids and a comprehensive description of the different chemotypes of T. vulgaris. PMID:28231164

  12. Plastid transformation in sugar beet: Beta vulgaris.

    PubMed

    De Marchis, Francesca; Bellucci, Michele

    2014-01-01

    Chloroplast biotechnology has assumed great importance in the past 20 years and, thanks to the numerous advantages as compared to conventional transgenic technologies, has been applied in an increasing number of plant species but still very much limited. Hence, it is of utmost importance to extend the range of species in which plastid transformation can be applied. Sugar beet (Beta vulgaris L.) is an important industrial crop of the temperate zone in which chloroplast DNA is not transmitted trough pollen. Transformation of the sugar beet genome is performed in several research laboratories; conversely sugar beet plastome genetic transformation is far away from being considered a routine technique. We describe here a method to obtain transplastomic sugar beet plants trough biolistic transformation. The availability of sugar beet transplastomic plants should avoid the risk of gene flow between these cultivated genetic modified sugar beet plants and the wild-type plants or relative wild species.

  13. Lupus vulgaris in a young girl.

    PubMed

    Goyal, Tarang; Varshney, Anupam; Bakshi, S K

    2013-01-01

    With the estimated global burden of TB being 8.8 million incident cases and 1.1 million deaths from TB in HIV-negative cases and additional 0.35 million deaths in HIV-associated cases,1 the total number of cutaneous TB cases ( < 1-2 % of total cases) becomes significant. With the WHO setting up public-private mix partnerships and a millenium development goal of a 50% reduction in the total number of incident cases, the case detection and reporting of unusual cutaneous TB cases becomes very important. We present a case of lupus vulgaris in a young girl with rapid progression of a large plaque with hypertrophic features in the periphery. The case is unusual due to its rapid progression, unusual site and extensive giant form which have never been reported previously.

  14. Dispersed ozone flotation of Chlorella vulgaris.

    PubMed

    Cheng, Ya-Ling; Juang, Yu-Chuan; Liao, Guan-Yu; Ho, Shih-Hsin; Yeh, Kuei-Ling; Chen, Chun-Yen; Chang, Jo-Shu; Liu, Jhy-Chern; Lee, Duu-Jong

    2010-12-01

    Flotation separation of Chlorella vulgaris, a species with excellent potential for CO(2) capture and lipid production, was studied using dispersed ozone gas. Pure oxygen aeration did not yield flotation. Conversely, applying ozone effectively separation algae from broth through flotation. The ozone dose applied for sufficient algal flotation is <0.05 mg/g biomass, much lower than those used in practical drinking waterworks (0.1-0.3 mg/g suspended solids). Main products, lipid C16:0, was effectively collected in the flotage phase. The algae removal rate, surface charge, and hydrophobicity of algal cells, and proteins and polysaccharides contents of algogenic organic matter (AOM) were determined. Certain quantities of proteins were present in the cultivated algal suspension, hence, minimal quantity of ozone was required to release intracellular proteins as surfactants to lead to effective flotation.

  15. Pemphigus vulgaris: gingival involvement. A case report.

    PubMed

    Weinberg, M A; Abitbol, T E

    1995-01-01

    Pemphigus is an autoimmune disease in which intraepithelial vesicles and bullae of the skin and oral mucosa are produced by the action of autoantibodies against specific desmosomal proteins of squamous epithelium. Usually, oral lesions will appear before skin lesions, and in a majority of the cases only oral lesions are present. The dentist may then be the first to make and early diagnosis. The importance of this case report is to alert the dentist that subtle gingival lesions can be recognized and treated early in such a life-threatening disease. Diagnosis is based on the clinical presentation and confirmed by histologic study and direct immunofluorescence. This case describes the clinical signs, symptoms, histology, and immunofluorescence of pemphigus vulgaris of the gingiva.

  16. Pregnancy-Associated "Cutaneous Type" Pemphigus Vulgaris.

    PubMed

    Rangel, Javier

    2016-01-01

    The development of pemphigus, including pemphigus vulgaris (PV) and pemphigus foliaceus, during pregnancy is rare. PV manifests with mucosal and/or cutaneous erosions with flaccid bullae that are histologically characterized by suprabasilar acantholysis. In contrast, pemphigus foliaceus manifests with cutaneous-only involvement and superficial epidermal acantholysis. Enzyme-linked immunosorbent assay specific for autoantibodies against desmoglein 1 and desmoglein 3 aids in the diagnosis and differentiation between pemphigus subtypes. High-dose systemic corticosteroids are first-line agents in management of PV, yet their potential long-term use raises complex management issues associated with pregnancy and fetal risk. Here we report a rare case of cutaneous-limited PV in association with pregnancy.

  17. Pemphigus vulgaris-associated interstitial lung disease.

    PubMed

    Bai, Yi-Xiu; Chu, Jin-Gang; Xiao, Ting; Chen, Hong-Duo

    2016-07-01

    Autoimmune bullous diseases (AIBDs)-associated interstitial lung disease (ILD) is extremely rare. Pemphigus vulgaris (PV) is an intraepidermal autoimmune blistering disease caused by circulating autoantibodies against desmoglein. To date, PV-associated ILD has rarely been reported in English literature. We report a rare association of PV and ILD. A 53-year-old Chinese female with PV for 8 months developed ILD after a relapse of PV for 2 months due to discontinuation of oral prednisone by herself. She was successfully treated by systemic methylprednisolone. Taken previously reported bullous pemphigoid-associated ILD and linear IgA/IgG bullous dermatosis-associated ILD together, in general, AIBDs-associated ILD occurs when AIBDs relapse or are not controlled, responds well to systemic corticosteroids, and has a relatively better prognosis when compared with rheumatoid arthritis- or dermatomyositis-associated ILD.

  18. Acne vulgaris and rosacea: evaluation and management.

    PubMed

    Webster, G F

    2001-01-01

    Acne vulgaris, commonly termed acne, is an extremely common disease. It can be found in nearly all teenagers to some degree as well as in women in their 30s. Regardless of severity, acne often has a greater psychologic effect than cutaneous effect. Indeed, most patients overestimate the severity of their disease, while most physicians underestimate its impact on their patients. Studies have shown that people with severe acne as teens are less employable as adults and that self-esteem is low. When combined with other adolescent tensions, acne can be a difficult disease to treat. Rosacea, which usually starts in the late 20s, may affect the eyes as well as the skin. This article describes the pathogenesis of acne and rosacea and treatment approaches the primary care physician can use.

  19. [The pathogenesis of acne vulgaris (author's transl)].

    PubMed

    Gloor, M; Habedank, W D

    1976-05-14

    Stickl's method of oral treatment of acne vulgaris with antigens has been carried out on 26 test persons. During the treatment the number of comedones increased significantly and the number of papules decreased significantly. Biochemically, a significant increase of the free fatty acids and a significant decrease of the triglycerides could be demonstrated in the skin surface lipids, the total amount remaining unchanged. The following important conclusions for the pathogenesis of acne may be drawn: 1. The living conditions for Corynebacterium acnes on the surface of the skin or in the ducts of sebaceous glands respectively are influenced by the immunological system of the host. 2. The free fatty acids have a comedogenic effect in vivo. 3. The free fatty acids are not responsible for the development of inflammatory acne efflorescences.

  20. Setting the target for pemphigus vulgaris therapy

    PubMed Central

    Ellebrecht, Christoph T.

    2017-01-01

    Despite the rising incidence of autoimmunity, therapeutic options for patients with autoimmune disease still rely on decades-old immunosuppressive strategies that risk severe and potentially fatal complications. Thus, novel therapeutic approaches for autoimmune diseases are greatly needed in order to minimize treatment-related toxicity. Such strategies would ideally target only the autoreactive immune components to preserve beneficial immunity. Here, we review how several decades of basic, translational, and clinical research on the immunology of pemphigus vulgaris (PV), an autoantibody-mediated skin disease, have enabled the development of targeted immunotherapeutic strategies. We discuss research to elucidate the pathophysiology of PV and how the knowledge afforded by these studies has led to the preclinical and clinical testing of targeted approaches to neutralize autoantibodies, to induce antigen-specific tolerance, and to specifically eliminate autoreactive B cells in PV. PMID:28289723

  1. Does Octopus vulgaris have preferred arms?

    PubMed

    Byrne, Ruth A; Kuba, Michael J; Meisel, Daniela V; Griebel, Ulrike; Mather, Jennifer A

    2006-08-01

    Previous behavioral studies in Octopus vulgaris revealed lateralization of eye use. In this study, the authors expanded the scope to investigate arm preferences. The octopus's generalist hunting lifestyle and the structure of their arms suggest that these animals have no need to designate specific arms for specific tasks. However, octopuses also show behaviors, like exploration, in which only single or small groups of arms are involved. Here the authors show that octopuses had a strong preference for anterior arm use to reach for and explore objects, which points toward a task division between anterior and posterior arms. Four out of 8 subjects also showed a lateral bias. In addition, octopuses had a preference for a specific arm to reach into a T maze to retrieve a food reward. These findings give evidence for limb-specialization in an animal whose 8 arms were believed to be equipotential.

  2. Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms

    NASA Technical Reports Server (NTRS)

    Jackson, B. E.; Bhupathiraju, V. K.; Tanner, R. S.; Woese, C. R.; McInerney, M. J.

    1999-01-01

    Strain SBT is a new, strictly anaerobic, gram-negative, nonmotile, non-sporeforming, rod-shaped bacterium that degrades benzoate and certain fatty acids in syntrophic association with hydrogen/formate-using microorganisms. Strain SBT produced approximately 3 mol of acetate and 0.6 mol of methane per mol of benzoate in coculture with Methanospirillum hungatei strain JF1. Saturated fatty acids, some unsaturated fatty acids, and methyl esters of butyrate and hexanoate also supported growth of strain SBT in coculture with Desulfovibrio strain G11. Strain SBT grew in pure culture with crotonate, producing acetate, butyrate, caproate, and hydrogen. The molar growth yield was 17 +/- 1 g cell dry mass per mol of crotonate. Strain SBT did not grow with fumarate, iron(III), polysulfide, or oxyanions of sulfur or nitrogen as electron acceptors with benzoate as the electron donor. The DNA base composition of strain SBT was 43.1 mol% G+C. Analysis of the 16 S rRNA gene sequence placed strain SBT in the delta-subdivision of the Proteobacteria, with sulfate-reducing bacteria. Strain SBT was most closely related to members of the genus Syntrophus. The clear phenotypic and genotypic differences between strain SBT and the two described species in the genus Syntrophus justify the formation of a new species, Syntrophus aciditrophicus.

  3. Theoretical study of the catalytic mechanism of DNA-(N4-cytosine)-methyltransferase from the bacterium Proteus vulgaris.

    PubMed

    Aranda, Juan; Roca, Maite; López-Canut, Violeta; Tuñón, Iñaki

    2010-07-01

    In this paper the reaction mechanism for methylation of cytosine at the exocyclic N4 position catalyzed by M.PvuII has been explored by means of hybrid quantum mechanics/molecular mechanics (QM/MM) methods. A reaction model was prepared by placing a single cytosine base in the active site of the enzyme. In this model the exocyclic amino group of the base establishes hydrogen bond interactions with the hydroxyl oxygen atom of Ser53 and the carbonyl oxygen atom of Pro54. The reaction mechanism involves a direct methyl transfer from AdoMet to the N4 atom and a proton transfer from this atom to Ser53, which in turn transfers a proton to Asp96. Different timings for the proton transfers and methylation steps have been explored at the AM1/MM and B3LYP/MM levels including localization and characterization of stationary structures. At our best estimate the reaction proceeds by means of a simultaneous but asynchronous proton transfer from Ser53 to Asp96 and from N4 of cytosine to Ser53 followed by a direct methyl transfer from AdoMet to the exocyclic N4 of cytosine.

  4. Detection of Salmonella bacterium in drinking water using microring resonator.

    PubMed

    Bahadoran, Mahdi; Noorden, Ahmad Fakhrurrazi Ahmad; Mohajer, Faeze Sadat; Abd Mubin, Mohamad Helmi; Chaudhary, Kashif; Jalil, Muhammad Arif; Ali, Jalil; Yupapin, Preecha

    2016-01-01

    A new microring resonator system is proposed for the detection of the Salmonella bacterium in drinking water, which is made up of SiO2-TiO2 waveguide embedded inside thin film layer of the flagellin. The change in refractive index due to the binding of the Salmonella bacterium with flagellin layer causes a shift in the output signal wavelength and the variation in through and drop port's intensities, which leads to the detection of Salmonella bacterium in drinking water. The sensitivity of proposed sensor for detecting of Salmonella bacterium in water solution is 149 nm/RIU and the limit of detection is 7 × 10(-4)RIU.

  5. Carbon nanoparticles-assisted mediator-less microbial fuel cells using Proteus vulgaris.

    PubMed

    Yuan, Yong; Ahmed, Jalal; Zhou, Lihua; Zhao, Bo; Kim, Sunghyun

    2011-09-15

    Recently mediator-less microbial fuel cells (MFCs) are attracting great interest among researchers due to their potential applications to electricity generation as well as wastewater treatment. Common mediator-less MFCs employ electroactive bacteria called exoelectrogens to directly transfer electrons to the anode from the bacteria. However, exoelectrogens are rather limited in number and thus may not find general use for practical purposes. Here we showed our results in which mediator-less MFCs could be developed from Gram-negative non-exoelectrogens. By using carbon nanoparticles as a conductive medium to immobilize bacteria, it was possible to generate appreciable electricity from Proteus vulgaris without exogenous mediators. Maximum power density of 269 mW m(-2) and cell voltage of ca. 400 mV were obtained using glucose as a substrate. Power generation was attributed to direct electron transfer and to self-produced mediators, both of which were assisted by carbon nanoparticles. Bacillus subtilis, a Gram-positive bacterium, in the meantime, did not produce appreciable electricity.

  6. Desulfovibrio magneticus RS-1 contains an iron- and phosphorus-rich organelle distinct from its bullet-shaped magnetosomes

    PubMed Central

    Byrne, Meghan E.; Ball, David A.; Guerquin-Kern, Jean-Luc; Rouiller, Isabelle; Wu, Ting-Di; Downing, Kenneth H.; Vali, Hojatollah; Komeili, Arash

    2010-01-01

    Intracellular magnetite crystal formation by magnetotactic bacteria has emerged as a powerful model for investigating the cellular and molecular mechanisms of biomineralization, a process common to all branches of life. Although magnetotactic bacteria are phylogenetically diverse and their crystals morphologically diverse, studies to date have focused on a few, closely related species with similar crystal habits. Here, we investigate the process of magnetite biomineralization in Desulfovibrio magneticus sp. RS-1, the only reported species of cultured magnetotactic bacteria that is outside of the α-Proteobacteria and that forms bullet-shaped crystals. Using a variety of high-resolution imaging and analytical tools, we show that RS-1 cells form amorphous, noncrystalline granules containing iron and phosphorus before forming magnetite crystals. Using NanoSIMS (dynamic secondary ion mass spectroscopy), we show that the iron-phosphorus granules and the magnetite crystals are likely formed through separate cellular processes. Analysis of the cellular ultrastructure of RS-1 using cryo-ultramicrotomy, cryo-electron tomography, and tomography of ultrathin sections reveals that the magnetite crystals are not surrounded by membranes but that the iron-phosphorus granules are surrounded by membranous compartments. The varied cellular paths for the formation of these two minerals lead us to suggest that the iron-phosphorus granules constitute a distinct bacterial organelle. PMID:20566879

  7. Anisotropy of Bullet-Shaped Magnetite Nanoparticles in the Magnetotactic Bacteria Desulfovibrio magneticus sp. Strain RS-1

    PubMed Central

    Chariaou, Michalis; Rahn-Lee, Lilah; Kind, Jessica; García-Rubio, Inés; Komeili, Arash; Gehring, Andreas U.

    2015-01-01

    Magnetotactic bacteria (MTB) build magnetic nanoparticles in chain configuration to generate a permanent dipole in their cells as a tool to sense the Earth’s magnetic field for navigation toward favorable habitats. The majority of known MTB align their nanoparticles along the magnetic easy axes so that the directions of the uniaxial symmetry and of the magnetocrystalline anisotropy coincide. Desulfovibrio magneticus sp. strain RS-1 forms bullet-shaped magnetite nanoparticles aligned along their (100) magnetocrystalline hard axis, a configuration energetically unfavorable for formation of strong dipoles. We used ferromagnetic resonance spectroscopy to quantitatively determine the magnetocrystalline and uniaxial anisotropy fields of the magnetic assemblies as indicators for a cellular dipole with stable direction in strain RS-1. Experimental and simulated ferromagnetic resonance spectral data indicate that the negative effect of the configuration is balanced by the bullet-shaped morphology of the nanoparticles, which generates a pronounced uniaxial anisotropy field in each magnetosome. The quantitative comparison with anisotropy fields of Magnetospirillum gryphiswaldense, a model MTB with equidimensional magnetite particles aligned along their (111) magnetic easy axes in well-organized chain assemblies, shows that the effectiveness of the dipole is similar to that in RS-1. From a physical perspective, this could be a reason for the persistency of bullet-shaped magnetosomes during the evolutionary development of magnetotaxis in MTB. PMID:25762338

  8. Crystal Structure of Dimeric Flavodoxin from Desulfovibrio gigas Suggests a Potential Binding Region for the Electron-Transferring Partner

    PubMed Central

    Hsieh, Yin-Cheng; Chia, Tze Shyang; Fun, Hoong-Kun; Chen, Chun-Jung

    2013-01-01

    Flavodoxins, which exist widely in microorganisms, have been found in various pathways with multiple physiological functions. The flavodoxin (Fld) containing the cofactor flavin mononucleotide (FMN) from sulfur-reducing bacteria Desulfovibrio gigas (D. gigas) is a short-chain enzyme that comprises 146 residues with a molecular mass of 15 kDa and plays important roles in the electron-transfer chain. To investigate its structure, we purified this Fld directly from anaerobically grown D. gigas cells. The crystal structure of Fld, determined at resolution 1.3 Å, is a dimer with two FMN packing in an orientation head to head at a distance of 17 Å, which generates a long and connected negatively charged region. Two loops, Thr59–Asp63 and Asp95–Tyr100, are located in the negatively charged region and between two FMN, and are structurally dynamic. An analysis of each monomer shows that the structure of Fld is in a semiquinone state; the positions of FMN and the surrounding residues in the active site deviate. The crystal structure of Fld from D. gigas agrees with a dimeric form in the solution state. The dimerization area, dynamic characteristics and structure variations between monomers enable us to identify a possible binding area for its functional partners. PMID:23322018

  9. The epidemiology of acne vulgaris in late adolescence

    PubMed Central

    Lynn, Darren D; Umari, Tamara; Dunnick, Cory A; Dellavalle, Robert P

    2016-01-01

    Importance Acne vulgaris is the most common skin condition affecting late adolescents across the globe. Although prior studies have evaluated epidemiologic patterns of acne vulgaris in various ethnicities and regions, adequate understanding of the worldwide burden of the disease associated with patients in their late adolescence (15–19-year olds) remains lacking. Objective To assess the global burden of the disease associated with acne vulgaris for late adolescents (15–19-year olds) and provide an overview of the epidemiology, pathophysiology, and treatment options for acne in this population. Design Database summary study. Setting Global Burden of Disease Study 2010 database. Participants Global Burden of Disease regions comprised countries with prevalence of acne vulgaris between the ages of 15 and 19 years. Main outcomes and measures Geographic region-level disability-adjusted life year rates (per 100,000 persons) associated with acne vulgaris in years 1990 through 2010. Median percentage change in disability-adjusted life year rates was estimated for each region across the specified study period. Conclusion and relevance Acne vulgaris-associated disease burden exhibits global distribution and has continued to grow in prevalence over time within this population. This continued growth suggests an unmet dermatologic need worldwide for this disorder and potential opportunities for improved access and delivery of dermatologic care. Our analysis of the literature reveals numerous opportunities for enhanced patient care. To that end, we highlight some of the effective and promising treatments currently available and address important factors, such as sex, nationality, genetics, pathophysiology, and diet, as they relate to acne vulgaris in late adolescence. PMID:26955297

  10. Delayed diagnosis in a case of lupus vulgaris with unusual localization.

    PubMed

    Ceylan, Can; Gerceker, Bengu; Ozdemir, Fezal; Kazandi, Alican

    2004-01-01

    Lupus vulgaris is the most common form of cutaneous tuberculosis, and the usual sites of involvement are the head and neck. We present a forty-six-year-old woman with lupus vulgaris on the external surface of the left leg and foot, an unusual site. Based on histopathological and clinical features, this case was diagnosed as lupus vulgaris with unusual localization.

  11. Draft Genome Sequence of the Suttonella ornithocola Bacterium

    PubMed Central

    Waldman Ben-Asher, Hiba; Yerushalmi, Rebecca; Wachtel, Chaim; Barbiro-Michaely, Efrat

    2017-01-01

    ABSTRACT   We report here the draft genome sequence of the Suttonella ornithocola bacterium. To date, this bacterium, found in birds, passed only phylogenetic and phenotypic analyses. To our knowledge, this is the first publication of the Suttonella ornithocola genome sequence. The genetic profile provides a basis for further analysis of its infection pathways. PMID:28209820

  12. [Lupus vulgaris manifestation as a destructive nose and facial tumor].

    PubMed

    Haller, D; Reisser, C

    2009-04-01

    Lupus vulgaris is the most frequent manifestation of cutaneous tuberculosis, but in Europe it is limited to isolated cases. Mainly immunocompetent individuals are affected by this result of an endogenous reinfection on a lymphogenous-less frequently hematogenous-pathway. Lupus vulgaris has been observed to develop in more than 50% of all patients who already suffer from other manifestations of tuberculosis. The development of a squamous cell carcinoma in the lupus vulgaris is a rare complication; therefore, lupus vulgaris is deemed a facultative precancerosis.A 68-year-old female Serbo-Croatian patient presented with an extensive ulcerative nose and facial tumor. Her anamnesis included a squamous cell carcinoma of the nose that had been excised alio loco 3 years before. Further examinations revealed enlarged cervical lymphoma on both sides, and pulmonary metastases were also suspected. The tumor biopsy revealed a necrotic, granulomatous inflammation. No acid-fast rods were seen on Ziehl-Neelsen stain. The tuberculous origin of this ulcerative skin tumor-the lupus vulgaris-as an endogenous reinfection of pulmonary tuberculosis manifestation was confirmed by the detection of Mycobacterium tuberculosis DNA in polymerase chain reaction and the growth of Mycobacterium tuberculosis colonies in the bacterial culture (skin biopsy and bronchial secretion). The skin tumor as well as the pulmonary manifestation were successfully treated with combined tuberculostatic therapy and showed a dramatic response within 3 months.

  13. Gender-based variability in disease presentation in pemphigus vulgaris.

    PubMed

    Naseer, Sahar Y; Gill, Liza; Shah, Jay; Sinha, Animesh A

    2014-10-01

    Pemphigus vulgaris is a chronic autoimmune blistering disorder of the skin. As with many autoimmune diseases, a female predominance in pemphigus vulgaris is well established. The genetic and physiological basis for this gender bias is not well understood. Moreover, it is unclear whether the affect of gender extends beyond disease susceptibility to influence disease presentation. To address this issue, we performed a comprehensive analysis of 72 male and 125 female pemphigus vulgaris patients across a set of defined demographic (HLA type, ethnicity) and clinical (age at disease onset, anti-desmoglein antibody levels, site of lesions, and history of autoimmune disease) factors. We find that male patients are more likely to present with disease onset before age 40 than females. Additionally, we find that males have increased cutaneous involvement and display greater co-expression of anti-Dsg1 and anti-Dsg3 antibodies, while females tend to have mucosal predominance and stronger personal and family histories of autoimmunity. We do not find any differences in the distribution of HLA type or ethnicity between male and female pemphigus vulgaris patients. Our findings establish that gender does influence disease presentation in pemphigus vulgaris, supporting a role for genetic and hormonal factors in immune dysregulation and perpetuation of the autoimmune phenotype.

  14. Agrobacterium tumefaciens is a diazotrophic bacterium

    SciTech Connect

    Kanvinde, L.; Sastry, G.R.K. )

    1990-07-01

    This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grown on nitrogen-free medium, reduce acetylene to ethylene, and incorporate {sup 15}N supplied as {sup 15}N{sub 2}. As with most other well-characterized diazotrophic bacteria, the presence of NH{sub 4}{sup +} in the medium and aerobic conditions repress nitrogen fixation by A. tumefaciens. The system requires molybdenum. No evidence for nodulation was found with pea, peanut, or soybean plants. Further understanding of the nitrogen-fixing ability of this bacterium, which has always been considered a pathogen, should cast new light on the evolution of a pathogenic versus symbiotic relationship.

  15. The complete chloroplast genome sequence of sugar beet (Beta vulgaris ssp. vulgaris).

    PubMed

    Li, Han; Cao, Hua; Cai, Yan-Fei; Wang, Ji-Hua; Qu, Su-Ping; Huang, Xing-Qi

    2014-06-01

    The complete nucleotide sequence of the sugar beet (Beta vulgaris ssp. vulgaris) chloroplast genome (cpDNA) was determined in this study. The cpDNA was 149,637 bp in length, containing a pair of 24,439 bp inverted repeat regions (IR), which were separated by small and large single copy regions (SSC and LSC) of 17,701 and 83,057 bp, respectively. 53.4% of the sugar beet cpDNA consisted of gene coding regions (protein coding and RNA genes). The gene content and relative positions of 113 individual genes (79 protein encoding genes, 30 tRNA genes, 4 rRNA genes) were almost identical to those of tobacco cpDNA. The overall AT contents of the sugar beet cpDNA were 63.6% and in the LSC, SSC and IR regions were 65.9%, 70.8% and 57.8%, respectively. Fifteen genes contained one intron, while three genes had two introns.

  16. ACNE VULGARIS TREATMENT : THE CURRENT SCENARIO

    PubMed Central

    Rathi, Sanjay K

    2011-01-01

    Acne Vulgaris is one of the most common skin disorders which dermatologists have to treat. It mainly affect adolescent, though may present at any age. In recent years, due to better understanding of the pathogenesis of acne, new therapeutic modalities and various permutation and combinations have been designed. In topical agents; benzoyl peroxide, antibiotics, retinoids, etc are the mainstay of treatment; can be given in combinations. While systemic therapy includes oral antibiotics, hormonal therapy, and isotretinoin, depending upon the need of patients it has to be selected. Physical treatment in the form of lesion removal, photo-therapy is also helpful in few of them. Since various old and new topical and systemic agents are available to treat acne, it sometime confuse treating dermatologist. To overcome this, panel of physicians and researchers worked together as a global alliance and task force to improve outcomes in acne treatment. They have tried to give consensus recommendation for the treatment of acne. Successful management of acne needs careful selection of anti-acne agents according to clinical presentation and individual patient needs. PMID:21572783

  17. Treatment of acne vulgaris in pregnant patients.

    PubMed

    Pugashetti, Rupa; Shinkai, Kanade

    2013-01-01

    The management of acne vulgaris in the setting of pregnancy raises important clinical considerations regarding the efficacy and safety of acne treatments in this special patient population. Particular challenges include the absence of safety data, discrepancy in safety data between different safety rating systems, and lack of evidence-based recommendations for the treatment of acne during pregnancy. Nonetheless, many therapeutic options exist, and the treatment of acne in pregnant women can be safely and often effectively accomplished. For mild or moderate disease, patients can be treated with topical antimicrobial agents, anti-inflammatory agents, as well as glycolic and salicylic acid. Several topical agents, notably benzoyl peroxide, previously viewed as potentially dangerous are cited by many sources as being considered safe. When necessary, systemic therapies that can be safely added include penicillins, amoxicillin, cephalosporins, erythromycin, clindamycin, and tetracyclines or sulfonamides, depending on the stage of fetal development. Adjunct therapy may include phototherapy or laser treatments. Physicians should work with this often highly motivated, safety-conscious patient population to tailor an individualized treatment regimen. This treatment regimen will likely shift throughout the different stages of fetal development, as distinct safety considerations are raised prior to conception as well as during each of the trimesters of pregnancy. Important considerations regarding acne management in breast-feeding mothers is also discussed.

  18. How Finsen's light cured lupus vulgaris.

    PubMed

    Møller, Kirsten Iversen; Kongshoj, Brian; Philipsen, Peter Alshede; Thomsen, Vibeke Ostergaard; Wulf, Hans Christian

    2005-06-01

    In 1903, Niels Ryberg Finsen was awarded the Nobel Prize for his invention of light therapy for skin tuberculosis (lupus vulgaris). The mechanism of action has not been shown; thus, we wanted to elucidate the mechanism of Finsen's light therapy. We measured radiation that could be transmitted through his lens systems and absorption of the stain solution filters in the lamps, and related the obtained results to the possible biological effects on Mycobacterium tuberculosis. Judged from transmission characteristics all tested lens systems were glass lenses (absorbing wavelength < 340 nm). The tested filters likewise absorbed wavelengths < 340 nm. The methylene blue solution used to absorb heat, blocked out wavelengths below 340 nm and between 550 and 700 nm. Furthermore, fluorescence of M. tuberculosis indicated the presence of porphyrins and HPLC analysis of sonicated M. marinum showed that coproporphyrin III was present, which highly justified that porphyrins were present in M. tuberculosis. Production of singlet oxygen through radiation of porphyrins with light of e.g. 400 nm seems to be a most plausible explanation why Finsen's therapy worked in spite of the lack of shortwave ultraviolet radiation, which Finsen believed was the most effective radiation for treating skin tuberculosis.

  19. Atypical Histiocytosis in Red Squirrels (Sciurus vulgaris).

    PubMed

    Smith, S H; Stevenson, K; Del-Pozo, J; Moss, S; Meredith, A

    2017-03-17

    Four red squirrels (Sciurus vulgaris) were subjected to necropsy examination over a 3-year period as part of a broader surveillance study. The squirrels presented with cutaneous, subcutaneous and/or internal swellings and nodules that consisted microscopically of sheets of atypical round cells and multinucleated giant cells. There was moderate anisokaryosis with rare mitoses. Nuclei ranged from oval to indented or C-shaped and some were bizarre, twisted or multilobulated. Many giant cells also had a bizarre morphology, with anisokaryosis within individual cells. Giant cell nuclei were often multilobulated, ring-shaped or segmented. Affected internal organs varied depending on the squirrel, but included lymph node, kidney, intestinal tract and lungs. Representative lesions from each of the four squirrels were negative for acid-fast organisms. Formalin-fixed tissues from all four squirrels and ethanol-fixed tissue from one animal were negative for Mycobacterium by polymerase chain reaction. Immunohistochemically, the majority of mononuclear and multinucleated giant cells in all four squirrels strongly expressed vimentin and class II molecules of the major histocompatibility complex. Otherwise, the atypical mononuclear and multinucleated cells were negative for CD3, Pax-5, Mac387, CD18 and E-cadherin. Based on the combination of cellular morphology, arrangement and immunophenotype, a novel form of atypical histiocytosis is considered most likely in these squirrels, although the exact origin and triggering factors remain uncertain.

  20. An update on the management of acne vulgaris

    PubMed Central

    Keri, Jonette; Shiman, Michael

    2009-01-01

    Acne vulgaris is a common skin disorder that can affect individuals from childhood to adulthood, most often occurring in the teenage years. Acne can have a significant physical, emotional, and social impact on an individual. Many different treatment options are available for the treatment of acne vulgaris. Commonly used topical treatments include benzoyl peroxide, antibiotics, sulfur and sodium sulfacetamide, azelaic acid, and retinoids. Systemic treatment is frequently used and includes the use of systemic antibiotics, oral contraceptives, antiandrogens, and retinoids. Other treatment modalities exist such as the use of superficial chemical peels as well as using laser and light devices for the treatment of acne. With the multitude of treatment options and the rapidly expanding newer technologies available to clinicians, it is important to review and be aware of the current literature and studies regarding the treatment of acne vulgaris. PMID:21436973

  1. Lupus vulgaris in a pediatric patient: a clinicohistopathological diagnosis.

    PubMed

    Afsar, F Sule; Afsar, Ilhan; Diniz, Gulden; Asilsoy, Suna; Sorguc, Yelda

    2008-04-01

    Lupus vulgaris is the most common form of cutaneous tuberculosis which usually occurs in patients previously sensitized to Mycobacterium tuberculosis. We present a case of a 10-year-old boy who was diagnosed as lupus vulgaris clinically and histopathologically. He had well demarcated, irregularly bordered, pink, infiltrated plaques on his left cheek showing apple-jelly appearance on diascopy. The histopathological examination showed tuberculoid granulomas with Langhans type giant cells. The Mantoux reactivity was in normal limits, and no acid-fast bacilli was found in the lesion, either by direct stained smears or by culture. The lesions showed marked improvement on anti-tuberculosis treatment. We want to emphasize that histopathological examination has diagnostic value in lupus vulgaris in correlation with clinical appearance, when direct analysis or culture is negative.

  2. Gingival pemphigus vulgaris preceding cutaneous lesion: A rare case report.

    PubMed

    Rath, Saroj K; Reenesh, M

    2012-10-01

    Pemphigus is a group of autoimmune diseases characterized by formation of intraepithelial bullae in skin and the mucous membrane. Pemphigus vulgaris affects the oral mucosa in nearly all cases. Pemphigus vulgaris is characterized by auto antibodies directed against desmosome-associated protein antigens (desmoglein-3) found in epithelial and epidermal intercellular substance. We report here a case of pemphigus vulgaris of gingiva in an adult female patient at an early stage followed by dermatologic involvement. Perilesional incision was taken and histopathological and direct immunofluorescence was done for identification of specific antibodies. The oral lesions were treated with 0.1% Triamcinolone acetonide ointment and Prednisolone 20 mg twice daily with multivitamins was administered systemically for skin lesion.

  3. Autoreactive T cells in the immune pathogenesis of pemphigus vulgaris.

    PubMed

    Amber, Kyle T; Staropoli, Patrick; Shiman, Michael I; Elgart, George W; Hertl, Michael

    2013-11-01

    Pemphigus vulgaris is a life-threatening autoimmune blistering disease caused by anti-desmoglein IgG autoantibodies that finally lead to acantholysis presenting clinically as progressive blistering. Whilst the production of pathogenic antibodies is key to the development of pemphigus vulgaris, many immunological steps are required prior to autoantibody induction. We review advances in the understanding of these immunologic processes with a focus on human leucocyte antigen polymorphisms and antigen recognition, epitope spreading, central and peripheral tolerance, T helper differentiation, induction of pro- and anti-inflammatory cytokines and T-cell regulation of B cells. Targeting autoaggressive T cells as regulators and stimulators of B-cell antibody production should allow for more specific therapeutic immune interventions, avoiding the global immunosuppression seen with many commonly used immunosuppressants in pemphigus vulgaris.

  4. Timely recognition of pemphigus vulgaris by dental professionals.

    PubMed

    Fatahzadeh, Mahnaz

    2013-07-01

    Pemphigus vulgaris is a potentially fatal mucocutaneous, vesiculobullous disorder of autoimmune etiology. Regrettably, affected patients frequently experience considerable discomfort and diagnostic delay for months in spite of multiple clinician contacts. The high likelihood of disease manifestations in the oral cavity and serious nature of potential oral and systemic complications mandates dental professionals to recognize early oral signs and symptoms of pemphigus vulgaris and contribute to timely diagnosis and medical intervention to prevent disease progression. This case report presents a young man with pemphigus vulgaris whose oral disease caused him significant suffering and spread to the skin before he was finally diagnosed 3 months after the onset. The signs and symptoms of the disease are reviewed and the potential role of dental providers in timely recognition and management is emphasized.

  5. Recycling of food waste as nutrients in Chlorella vulgaris cultivation.

    PubMed

    Lau, Kin Yan; Pleissner, Daniel; Lin, Carol Sze Ki

    2014-10-01

    Heterotrophic cultivation of Chlorella vulgaris was investigated in food waste hydrolysate. The highest exponential growth rate in terms of biomass of 0.8day(-1) was obtained in a hydrolysate consisting of 17.9gL(-1) glucose, 0.1gL(-1) free amino nitrogen, 0.3gL(-1) phosphate and 4.8mgL(-1) nitrate, while the growth rate was reduced in higher concentrated hydrolysates. C. vulgaris utilized the nutrients recovered from food waste for the formation of biomass and 0.9g biomass was produced per gram glucose consumed. The microalgal biomass produced in nutrient sufficient batch cultures consisted of around 400mgg(-1) carbohydrates, 200mgg(-1) proteins and 200mgg(-1) lipids. The conversion of nutrients derived from food waste and the balanced biomass composition make C. vulgaris a promising strain for the recycling of food waste in food, feed and fuel productions.

  6. Effects of cellular sorption on mercury bioavailability and methylmercury production by Desulfovibrio desulfuricans ND132

    SciTech Connect

    Liu, Yu-Rong; Lu, Xia; Zhao, Linduo; An, Jing; He, Ji-Zheng; Pierce, Eric M.; Johs, Alexander; Gu, Baohua

    2016-11-14

    Microbial conversion of inorganic mercury (IHg) to methylmercury (MeHg) is a significant environmental concern because of the bioaccumulation and biomagnification of toxic MeHg in the food web. Laboratory incubation studies have shown that, despite the presence of large quantities of IHg in cell cultures, MeHg biosynthesis often reaches a plateau or a maximum within hours or a day by an as yet unexplained mechanism. In this paper, we report that mercuric Hg(II) can be taken up rapidly by cells of Desulfovibrio desulfuricans ND132, but a large fraction of the Hg(II) is unavailable for methylation because of strong cellular sorption. Thiols, such as cysteine, glutathione, and penicillamine, added either simultaneously with Hg(II) or after cells have been exposed to Hg(II), effectively desorb or mobilize the bound Hg(II), leading to a substantial increase in MeHg production. The amount of thiol-desorbed Hg(II) is strongly correlated to the amount of MeHg produced (r = 0.98). Furthermore, cells do not preferentially take up Hg(II)–thiol complexes, but Hg(II)–ligand exchange between these complexes and the cell-associated proteins likely constrains Hg(II) uptake and methylation. Finally, we suggest that, aside from aqueous chemical speciation of Hg(II), binding and exchange of Hg(II) between cells and complexing ligands such as thiols and naturally dissolved organics in solution is an important controlling mechanism of Hg(II) bioavailability, which should be considered when predicting MeHg production in the environment.

  7. Impact of different environmental conditions on the aggregation of biogenic U(IV) nanoparticles synthesized by Desulfovibrio alaskensis G20

    SciTech Connect

    Şengör, S. Sevinç; Singh, Gursharan; Dohnalkova, Alice; Spycher, Nicolas; Ginn, Timothy R.; Peyton, Brent M.; Sani, Rajesh K.

    2016-09-13

    This study investigates the impact of specific environmental conditions on the formation of colloidal U(IV) nanoparticles by the sulfate reducing bacteria (SRB, Desulfovibrio alaskensis G20). The reduction of soluble U(VI) to less soluble U(IV) was quantitatively investigated under growth and non-growth conditions in bicarbonate or 1,4-piperazinediethanesulfonic acid (PIPES) buffered environments. The results showed that under non-growth conditions, the majority of the reduced U nanoparticles aggregated and precipitated out of solution. High resolution transmission electron microscopy revealed that only a very small fraction of cells had reduced U precipitates in the periplasmic spaces in the presence of PIPES buffer, whereas in the presence of bicarbonate buffer, reduced U was also observed in the cytoplasm with greater aggregation of biogenic U(IV) particles at higher initial U(VI) concentrations. The same experiments were repeated under growth conditions using two different electron donors (lactate and pyruvate) and three electron acceptors (sulfate, fumarate, and thiosulfate). In contrast to the results of the non-growth experiments, even after 0.2 m filtration, the majority of biogenic U(IV) remained in the aqueous phase resulting in potentially mobile biogenic U(IV) nanoparticles. Size fractionation results showed that U(IV) aggregates were between 18 and 200 nm in diameter, and thus could be very mobile. The findings of this study are helpful to assess the size and potential mobility of reduced U nanoparticles under different environmental conditions, and would provide insights on their potential impact affecting U(VI) bioremediation efforts at subsurface contaminated sites.

  8. EPR characterization of the molybdenum(V) forms of formate dehydrogenase from Desulfovibrio desulfuricans ATCC 27774 upon formate reduction.

    PubMed

    Rivas, María G; González, Pablo J; Brondino, Carlos D; Moura, José J G; Moura, Isabel

    2007-11-01

    The EPR characterization of the molybdenum(V) forms obtained on formate reduction of both as-prepared and inhibited formate dehydrogenase from Desulfovibrio desulfuricans ATCC 27774, an enzyme that catalyzes the oxidation of formate to CO(2), is reported. The Mo(V) EPR signal of the as-prepared formate-reduced enzyme is rhombic (g(max)=2.012, g(mid)=1.996, g(min)=1.985) and shows hyperfine coupling with two nuclear species with I=1/2. One of them gives an anisotropic splitting and is not solvent exchangeable (A(max)=11.7, A(mid)=A(min)=non-detectable, A-values in cm(-1)x10(-4)). The second species is exchangeable with solvent and produces a splitting at the three principal g-values (A(max)=7.7, A(mid)=10.0, A(min)=9.3). The hyperfine couplings of the non-solvent and solvent exchangeable nuclei are assigned to the hydrogen atoms of the beta-methylene carbon of a selenocysteine and to a Mo ligand whose nature, sulfydryl or hydroxyl, is still in debate. The Mo(V) species obtained in the presence of inhibitors (azide or cyanide) yields a nearly axial EPR signal showing only one detectable splitting given by nuclear species with I=1/2 (g(max)=2.092, g(mid)=2.000, g(min)=1.989, A(max)=non-detectable, A(mid)=A(min)=7.0), which is originated from the alpha-proton donated by the formate to a proximal ligand of the molybdenum. The possible structures of both paramagnetic molybdenum species (observed upon formate reduction in presence and absence of inhibitors) are discussed in comparison with the available structural information of this enzyme and the structural and EPR properties of the closely related formate dehydrogenase-H from Escherichia coli.

  9. Impact of different environmental conditions on the aggregation of biogenic U(IV) nanoparticles synthesized by Desulfovibrio alaskensis G20.

    PubMed

    Şengör, S Sevinç; Singh, Gursharan; Dohnalkova, Alice; Spycher, Nicolas; Ginn, Timothy R; Peyton, Brent M; Sani, Rajesh K

    2016-12-01

    This study investigates the impact of specific environmental conditions on the formation of colloidal U(IV) nanoparticles by the sulfate reducing bacteria (SRB, Desulfovibrio alaskensis G20). The reduction of soluble U(VI) to less soluble U(IV) was quantitatively investigated under growth and non-growth conditions in bicarbonate or 1,4-piperazinediethanesulfonic acid (PIPES) buffered environments. The results showed that under non-growth conditions, the majority of the reduced U nanoparticles aggregated and precipitated out of solution. High resolution transmission electron microscopy revealed that only a very small fraction of cells had reduced U precipitates in the periplasmic spaces in the presence of PIPES buffer, whereas in the presence of bicarbonate buffer, reduced U was also observed in the cytoplasm with greater aggregation of biogenic U(IV) particles at higher initial U(VI) concentrations. The same experiments were repeated under growth conditions using two different electron donors (lactate and pyruvate) and three electron acceptors (sulfate, fumarate, and thiosulfate). In contrast to the results of the non-growth experiments, even after 0.2 μm filtration, the majority of biogenic U(IV) remained in the aqueous phase resulting in potentially mobile biogenic U(IV) nanoparticles. Size fractionation results showed that U(IV) aggregates were between 18 and 200 nm in diameter, and thus could be very mobile. The findings of this study are helpful to assess the size and potential mobility of reduced U nanoparticles under different environmental conditions, and would provide insights on their potential impact affecting U(VI) bioremediation efforts at subsurface contaminated sites.

  10. Coincident systemic lupus erythematosus and psoriasis vulgaris: a case report.

    PubMed

    Wang, Y; Da, G; Yu, Y; Han, J; Li, H

    2015-12-01

    Psoriasis vulgaris is an autoimmune chronic inflammatory skin disease, but its association with other typical autoimmune disease such as systemic lupus erythematosus has only occasionally been reported. We presented a 25-year-old female who developed systemic lupus erythematosus associated with psoriasis vulgaris. Her conditions were in good control after she got administration of prednisolone (5 mg/day) and Tripterygium Wilfordii Hook (20 mg/day). It is necessary to integrate past history and physical examination to diagnose coincident SLE and psoriasis, and combined treatment with prednisolone and Tripterygium Wilfordii Hook proves effective.

  11. The dual nature of Interleukin-10 in pemphigus vulgaris

    PubMed Central

    Cho, Michael Jeffrey; Ellebrecht, Christoph T.; Payne, Aimee S.

    2014-01-01

    The immunomodulatory cytokine interleukin-10 (IL-10) plays beneficial but also potentially detrimental roles in inflammation, infection, and autoimmunity. Recent studies suggest a regulatory role for IL-10-expressing B cells in the autoimmune blistering disease pemphigus vulgaris. Here we review the studies on IL-10 in pemphigus vulgaris and discuss the potential pathophysiological significance of these findings in comparison to prior studies of IL-10 in other human conditions. A better understanding of the complex roles of IL-10 in immune regulation may improve our understanding of pemphigus pathogenesis and treatment. PMID:25464924

  12. The dual nature of interleukin-10 in pemphigus vulgaris.

    PubMed

    Cho, Michael Jeffrey; Ellebrecht, Christoph T; Payne, Aimee S

    2015-06-01

    The immunomodulatory cytokine interleukin-10 (IL-10) plays beneficial but also potentially detrimental roles in inflammation, infection, and autoimmunity. Recent studies suggest a regulatory role for IL-10-expressing B cells in the autoimmune blistering disease pemphigus vulgaris. Here we review the studies on IL-10 in pemphigus vulgaris and discuss the potential pathophysiological significance of these findings in comparison to prior studies of IL-10 in other human conditions. A better understanding of the complex roles of IL-10 in immune regulation may improve our understanding of pemphigus pathogenesis and treatment.

  13. Production of superoxide dismutases from Proteus mirabilis and Proteus vulgaris.

    PubMed

    Dayton, T M; Diefenbach, K A; Fuller, M L; Valtos, J; Niederhoffer, E C

    1996-04-01

    Proteus mirabilis and Proteus vulgaris expressed a combination of superoxide dismutase (Sod) activities, which was assigned to FeSod1, FeSod2 and MnSod for P. mirabilis, and FeSod, MnSod and CuZnSod for P. vulgaris. Production of the Sod proteins was dependent on the availability of iron, whether cells were grown under anaerobiosis or aerobiosis and growth phase. Nalidixic acid and chloramphenicol inhibited cell growth and the iron- and dioxygen-dependent production of Sod. These results support the involvement of metal ions and redox status in the production of Proteus Sods.

  14. Characterizations of intracellular arsenic in a bacterium

    NASA Astrophysics Data System (ADS)

    Wolfe-Simon, F.; Yannone, S. M.; Tainer, J. A.

    2011-12-01

    Life requires a key set of chemical elements to sustain growth. Yet, a growing body of literature suggests that microbes can alter their nutritional requirements based on the availability of these chemical elements. Under limiting conditions for one element microbes have been shown to utilize a variety of other elements to serve similar functions often (but not always) in similar molecular structures. Well-characterized elemental exchanges include manganese for iron, tungsten for molybdenum and sulfur for phosphorus or oxygen. These exchanges can be found in a wide variety of biomolecules ranging from protein to lipids and DNA. Recent evidence suggested that arsenic, as arsenate or As(V), was taken up and incorporated into the cellular material of the bacterium GFAJ-1. The evidence was interpreted to support As(V) acting in an analogous role to phosphate. We will therefore discuss our ongoing efforts to characterize intracellular arsenate and how it may partition among the cellular fractions of the microbial isolate GFAJ-1 when exposed to As(V) in the presence of various levels of phosphate. Under high As(V) conditions, cells express a dramatically different proteome than when grown given only phosphate. Ongoing studies on the diversity and potential role of proteins and metabolites produced in the presence of As(V) will be reported. These investigations promise to inform the role and additional metabolic potential for As in biology. Arsenic assimilation into biomolecules contributes to the expanding set of chemical elements utilized by microbes in unusual environmental niches.

  15. Differential expression patterns of non-symbiotic hemoglobins in sugar beet (Beta vulgaris ssp. vulgaris).

    PubMed

    Leiva-Eriksson, Nélida; Pin, Pierre A; Kraft, Thomas; Dohm, Juliane C; Minoche, André E; Himmelbauer, Heinz; Bülow, Leif

    2014-04-01

    Biennial sugar beet (Beta vulgaris spp. vulgaris) is a Caryophyllidae that has adapted its growth cycle to the seasonal temperature and daylength variation of temperate regions. This is the first time a holistic study of the expression pattern of non-symbiotic hemoglobins (nsHbs) is being carried out in a member of this group and under two essential environmental conditions for flowering, namely vernalization and length of photoperiod. BvHb genes were identified by sequence homology searches against the latest draft of the sugar beet genome. Three nsHb genes (BvHb1.1, BvHb1.2 and BvHb2) and one truncated Hb gene (BvHb3) were found in the genome of sugar beet. Gene expression profiling of the nsHb genes was carried out by quantitative PCR in different organs and developmental stages, as well as during vernalization and under different photoperiods. BvHb1.1 and BvHb2 showed differential expression during vernalization as well as during long and short days. The high expression of BvHb2 indicates that it has an active role in the cell, maybe even taking over some BvHb1.2 functions, except during germination where BvHb1.2 together with BvHb1.1-both Class 1 nsHbs-are highly expressed. The unprecedented finding of a leader peptide at the N-terminus of BvHb1.1, for the first time in an nsHb from higher plants, together with its observed expression indicate that it may have a very specific role due to its suggested location in chloroplasts. Our findings open up new possibilities for research, breeding and engineering since Hbs could be more involved in plant development than previously was anticipated.

  16. Variation in Breeding Systems in Hypericum Perforatum and Prunella Vulgaris

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effective conservation of new crop germplasm and its efficient use in new-crop development both rely on a clear understanding of the crop's reproductive biology. Hypericum perforatum (St. John's wort) and Prunella vulgaris (Common selfheal) are two medicinal plant species with potential for crop...

  17. Anaphylaxis to pine nut: cross-reactivity to Artemisia vulgaris?

    PubMed

    Rodrigues-Alves, R; Pregal, A; Pereira-Santos, M C; Branco-Ferreira, M; Lundberg, M; Oman, H; Pereira-Barbosa, M

    2008-01-01

    The use of pine nuts, the seeds of Pinus pinea, is on the increasing in the modern Mediterranean diet. Little more than 20 cases of allergy to this tree nut have been published, and cross-reactivity with pine pollen, peanut and almond has already been reported. We describe the case of a young boy with several episodes of anaphylaxis after pine nut ingestion. Specific IgE to pine nut and Artemisia vulgaris was demonstrated by skin prick tests and in vitro determination of specific IgE, although no IgE to pine pollen or other nuts was detected. Immunoblotting of Artemisia vulgaris and pine nut revealed two matching diffuse bands, just below 14 kDa and 30 kDa. The ImmunoCAP inhibition assays showed complete inhibition of pine nut specific IgE after serum incubation with Artemisia vulgaris extract. As far as we know, this is the first reported case of documented cross-reactivity between pine nut and Artemisia vulgaris.

  18. Isotretinoin therapy for acne vulgaris: results in an Irish population.

    PubMed

    Buckley, D; Rogers, S; Daly, P

    1990-01-01

    The results of treatment of cystic and antibiotic-resistant acne vulgaris in 96 consecutive patients with the oral retinoid isotretinoin (13-cis-retinoic acid; Roacentane) are reported retrospectively. The results show that the drug, while toxic in the short term, is highly effective in clearing acne.

  19. Lupus vulgaris over a tattoo mark--inoculation tuberculosis.

    PubMed

    Ghorpade, A

    2003-09-01

    Lupus vulgaris developing after tattooing and remaining exclusively confined to it, in a 40-year-old-lady is reported. The tattooing was done one year earlier by a roadside tattoo artist. Diagnosis was suggested by the clinical features and confirmed by histopathology.

  20. Lupus vulgaris in a child following BCG immunization.

    PubMed

    Kokcam, I; Kose, A; Yekeler, H; Doymaz, M Z

    2001-11-01

    A three year old girl presented with lupus vulgaris of the upper arm, which appeared 1 month after BCG immunization. The diagnosis was confirmed by polymerase chain reaction after histology and culture were negative for mycobacteria. Complete healing followed 6 months of oral isoniazid.

  1. Gallium-67-citrate uptake in a case of acne vulgaris

    SciTech Connect

    Kipper, M.S.; Taylor, A.; Ashburn, W.L.

    1981-09-01

    A case of increased Ga-67 uptake in a patient with active acne vulgaris is reported. The scan was requested in a search for metastatic testicular carcinoma or bleomycin pulmonary toxicity. Careful clinical evaluation including physical examination was necessary in order to avoid an erroneous scan interpretation.

  2. A Phaseolus vulgaris diversity panel for Andean bean improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dry beans (Phaseolus vulgaris L.) of the Andean gene pool, including red mottled, kidney, cranberry, and yellow seed types are important in Africa and in the Americas. Andean dry bean breeding gains have lagged behind those of Mesoamerican beans. These differences may be due to a narrower genetic b...

  3. Pemphigus vulgaris activity score and assessment of convergent validity.

    PubMed

    Chams-Davatchi, Cheyda; Rahbar, Ziba; Daneshpazhooh, Maryam; Mortazavizadeh, Seyed Mohammad Ali; Akhyani, Maryam; Esmaili, Nafiseh; Balighi, Kamran

    2013-05-07

    Pemphigus is a rare autoimmune blistering disease with different phenotypes. The evaluation of therapeutic interventions requires a reliable, valid and feasible to use measurement. However, there is no gold standard to measure the disease activity in clinical trials. In this study we aimed to introduce the pemphigus vulgaris activity score (PVAS) measurement and to assess the convergent validity with the experts' opinion of disease activity. In PVAS scoring, the distribution of pemphigus vulgaris antigen expression in different anatomical regions is taking in to account with special consideration of the healing process. PVAS is a 0-18 scale, based on the extent of mucocutaneous involvement, type of lesion and the presence of Nikolsky's sign. The sum of the scores of total number of lesions, number of different anatomic regions involvement and Nikolsky's sign is weighted by the type of lesion. In the present study, PVAS was assessed in 50 patients diagnosed with pemphigus vulgaris by one dermatologist. Independently, five blinded experts scored all the patients through physician's global assessment (PGA). The convergent validity with experts' opinion was assessed. The Spearman coefficient of correlation showed the acceptable value of 0.751 (95%CI: 0.534- 0.876). PVAS is a valid, objective and simple-to-use scoring measurement. It showed a good correlation with PGA of pemphigus disease activity in Iranian patients with pemphigus vulgaris.

  4. [Molecular genetic investigation of sugar beet (Beta vulgaris L.)].

    PubMed

    Butorina, A K; Kornienko, A V

    2011-10-01

    Molecular genetic studies of sugar beet (Beta vulgaris L.) are reviewed as a basis for the development of genomics of this species. The methods used to study structural and functional genomics are considered. The results and their application to increase the efficiency of sugar beet breeding are discussed.

  5. Dapsone 7.5% Gel: A Review in Acne Vulgaris.

    PubMed

    Al-Salama, Zaina T; Deeks, Emma D

    2017-02-01

    Dapsone 7.5% gel (Aczone(®)) is indicated for the once-daily topical treatment of acne vulgaris in patients aged ≥12 years. Dapsone is a sulfone antibacterial with anti-inflammatory actions, which are thought to be largely responsible for its efficacy in treating acne vulgaris. In two phase III trials of 12 weeks' duration in patients aged ≥12 years with moderate acne vulgaris, once-daily dapsone 7.5% gel reduced acne severity (as per the Global Acne Assessment Score) and lesion counts versus vehicle. The benefits of dapsone 7.5% gel over vehicle were seen as early as week 2 for inflammatory lesion counts, and from week 4 or 8 for other outcomes. Dapsone 7.5% gel was well tolerated, with a low incidence of treatment-related adverse events, with the majority of adverse events being administration-site related and mild or moderate in severity. Thus, dapsone 7.5% gel is an effective and well tolerated option for the topical treatment of acne vulgaris in patients aged ≥12 years, with the convenience of once-daily application.

  6. POD DEVELOPMENT INCREASES THE OZONE SENSITIVITY OF PHASEOLUS VULGARIS

    EPA Science Inventory

    The objective of this study was to determine if the O3 sensitivity of Phaseolus vulgaris L. changed with plant development. Plants exposed to charcoal-filtered air or elevated O3 throughout the study were compared to those exposed only during the vegetative or reproductive s...

  7. Staphylococcus epidermidis in the human skin microbiome mediates fermentation to inhibit the growth of Propionibacterium acnes: implications of probiotics in acne vulgaris.

    PubMed

    Wang, Yanhan; Kuo, Sherwin; Shu, Muya; Yu, Jinghua; Huang, Stephen; Dai, Ashley; Two, Aimee; Gallo, Richard L; Huang, Chun-Ming

    2014-01-01

    Increasing evidence demonstrates that commensal microorganisms in the human skin microbiome help fight pathogens and maintain homeostasis of the microbiome. However, it is unclear how these microorganisms maintain biological balance when one of them overgrows. The overgrowth of Propionibacterium acnes (P. acnes), a commensal skin bacterium, has been associated with the progression of acne vulgaris. Our results demonstrate that skin microorganisms can mediate fermentation of glycerol, which is naturally produced in skin, to enhance their inhibitory effects on P. acnes growth. The skin microorganisms, most of which have been identified as Staphylococcus epidermidis (S. epidermidis), in the microbiome of human fingerprints can ferment glycerol and create inhibition zones to repel a colony of overgrown P. acnes. Succinic acid, one of four short-chain fatty acids (SCFAs) detected in fermented media by nuclear magnetic resonance (NMR) analysis, effectively inhibits the growth of P. acnes in vitro and in vivo. Both intralesional injection and topical application of succinic acid to P. acnes-induced lesions markedly suppress the P. acnes-induced inflammation in mice. We demonstrate for the first time that bacterial members in the skin microbiome can undergo fermentation to rein in the overgrowth of P. acnes. The concept of bacterial interference between P. acnes and S. epidermidis via fermentation can be applied to develop probiotics against acne vulgaris and other skin diseases. In addition, it will open up an entirely new area of study for the biological function of the skin microbiome in promoting human health.

  8. Efficiency assessment and pH effect in removing nitrogen and phosphorus by algae-bacteria combined system of Chlorella vulgaris and Bacillus licheniformis.

    PubMed

    Liang, Zhijie; Liu, Yan; Ge, Fei; Xu, Yin; Tao, Nengguo; Peng, Fang; Wong, Minghung

    2013-08-01

    To achieve better removal of NH4(+) and TP in wastewater, a new algae-bacteria combined system of Chlorella vulgaris and Bacillus licheniformis was investigated in a 6-d experiment. The results showed that 78% of NH4(+) could be removed in the combined system, while 29% in single algae system and only 1% in single bacteria system. Approximately 92% of TP was removed in the combined system, compared with 55% and 78% in single algae and bacteria system, respectively. B. licheniformis was proven to be a growth-promoting bacterium for C. vulgaris by comparing Chl a concentrations in the single and combined systems. In the removal process, pH of the combined system was observed to reduce significantly from 7.0 to 3.5. Whereas with pH regulated to 7.0, higher removal efficiencies of NH4(+) (86%) and TP (93%) were achieved along with the recovery of algal cells and the increase of Chl a. These results suggest that nutrients in wastewater can be removed efficiently by the algae-bacteria combined system and pH control is crucial in the process.

  9. Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

    SciTech Connect

    Dees, C.; Ringleberg, D.; Scott, T.C.; Phelps, T.

    1994-06-01

    The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

  10. Pemphigus vulgaris autoantibody profiling by proteomic technique.

    PubMed

    Kalantari-Dehaghi, Mina; Anhalt, Grant J; Camilleri, Michael J; Chernyavsky, Alex I; Chun, Sookhee; Felgner, Philip L; Jasinskas, Algis; Leiferman, Kristin M; Liang, Li; Marchenko, Steve; Nakajima-Sasaki, Rie; Pittelkow, Mark R; Zone, John J; Grando, Sergei A

    2013-01-01

    Pemphigus vulgaris (PV) is a mucocutaneous blistering disease characterized by IgG autoantibodies against the stratified squamous epithelium. Current understanding of PV pathophysiology does not explain the mechanism of acantholysis in patients lacking desmoglein antibodies, which justifies a search for novel targets of pemphigus autoimmunity. We tested 264 pemphigus and 138 normal control sera on the multiplexed protein array platform containing 701 human genes encompassing many known keratinocyte cell-surface molecules and members of protein families targeted by organ-non-specific PV antibodies. The top 10 antigens recognized by the majority of test patients' sera were proteins encoded by the DSC1, DSC3, ATP2C1, PKP3, CHRM3, COL21A1, ANXA8L1, CD88 and CHRNE genes. The most common combinations of target antigens included at least one of the adhesion molecules DSC1, DSC3 or PKP3 and/or the acetylcholine receptor CHRM3 or CHRNE with or without the MHC class II antigen DRA. To identify the PV antibodies most specific to the disease process, we sorted the data based on the ratio of patient to control frequencies of antigen recognition. The frequency of antigen recognition by patients that exceeded that of control by 10 and more times were the molecules encoded by the CD33, GP1BA, CHRND, SLC36A4, CD1B, CD32, CDH8, CDH9, PMP22 and HLA-E genes as well as mitochondrial proteins encoded by the NDUFS1, CYB5B, SOD2, PDHA1 and FH genes. The highest specificity to PV showed combinations of autoantibodies to the calcium pump encoded by ATP2C1 with C5a receptor plus DSC1 or DSC3 or HLA-DRA. The results identified new targets of pemphigus autoimmunity. Novel autoantibody signatures may help explain individual variations in disease severity and treatment response, and serve as sensitive and specific biomarkers for new diagnostic assays in PV patients.

  11. ICG laser therapy of acne vulgaris

    NASA Astrophysics Data System (ADS)

    Tuchin, Valery V.; Altshuler, Gregory B.; Genina, Elina A.; Bashkatov, Alexey N.; Simonenko, Georgy V.; Odoevskaya, Olga D.; Yaroslavsky, Ilya V.

    2004-07-01

    The near-infrared (NIR) laser radiation due to its high penetration depth is widely used in phototherapy. In application to skin appendages a high selectivity of laser treatment is needed to prevent light action on surrounding tissues. Indocyanine Green (ICG) dye may provide a high selectivity of treatment due to effective ICG uploading by a target and its narrow band of considerable absorption just at the wavelength of the NIR diode laser. The goal of this study is to demonstrate the efficacy of the NIR diode laser phototherapy in combination with topical application of ICG suggested for soft and thermal treatment of acne vulgaris. 28 volunteers with facile or back-located acne were enrolled. Skin sites of subjects were stained by ICG and irradiated by NIR laser-diode light (803 or 809 nm). Untreated, only stained and only light irradiated skin areas served as controls. For soft acne treatment, the low-in