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Journal of Bacteriology May 2007Desulfovibrio desulfuricans G20 grows and reduces 20 mM arsenate to arsenite in lactate-sulfate media. Sequence analysis and experimental data show that D. desulfuricans...
Desulfovibrio desulfuricans G20 grows and reduces 20 mM arsenate to arsenite in lactate-sulfate media. Sequence analysis and experimental data show that D. desulfuricans G20 has one copy of arsC and a complete arsRBCC operon in different locations within the genome. Two mutants of strain G20 with defects in arsenate resistance were generated by nitrosoguanidine mutagenesis. The arsRBCC operons were intact in both mutant strains, but each mutant had one point mutation in the single arsC gene. Mutants transformed with either the arsC1 gene or the arsRBCC operon displayed wild-type arsenate resistance, indicating that the two arsC genes were equivalently functional in the sulfate reducer. The arsC1 gene and arsRBCC operon were also cloned into Escherichia coli DH5alpha independently, with either DNA fragment conferring increased arsenate resistance. The recombinant arsRBCC operon allowed growth at up to 50 mM arsenate in LB broth. Quantitative PCR analysis of mRNA products showed that the single arsC1 was constitutively expressed, whereas the operon was under the control of the arsR repressor protein. We suggest a model for arsenate detoxification in which the product of the single arsC1 is first used to reduce arsenate. The arsenite formed is then available to induce the arsRBCC operon for more rapid arsenate detoxification.
Topics: Arsenate Reductases; Arsenates; Arsenites; Bacterial Proteins; Desulfovibrio desulfuricans; Drug Resistance, Bacterial; Escherichia coli; Gene Expression Regulation, Bacterial; Gene Expression Regulation, Enzymologic; Genome, Bacterial; Mutagenesis; Operon; Oxidation-Reduction; Phylogeny
PubMed: 17337573
DOI: 10.1128/JB.01913-06 -
PloS One 2012Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint...
Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.
Topics: Base Sequence; DNA, Bacterial; Databases, Genetic; Desulfovibrio africanus; Desulfovibrio desulfuricans; Genome, Bacterial; Inverted Repeat Sequences; Molecular Sequence Annotation; Molecular Sequence Data; Polymerase Chain Reaction; Sequence Analysis, DNA
PubMed: 22859974
DOI: 10.1371/journal.pone.0041295 -
The Journal of Biological Chemistry Sep 2003The nine-heme cytochrome c is a monomeric multiheme cytochrome found in Desulfovibrio desulfuricans ATCC 27774. The polypeptide chain comprises 296 residues and wraps...
The nine-heme cytochrome c is a monomeric multiheme cytochrome found in Desulfovibrio desulfuricans ATCC 27774. The polypeptide chain comprises 296 residues and wraps around nine hemes of type c. It is believed to take part in the periplasmic assembly of proteins involved in the mechanism of hydrogen cycling, receiving electrons from the tetraheme cytochrome c3. With the purpose of understanding the molecular basis of electron transfer processes in this cytochrome, we have determined the crystal structures of its oxidized and reduced forms at pH 7.5 and performed theoretical calculations of the binding equilibrium of protons and electrons in these structures. This integrated study allowed us to observe that the reduction process induced relevant conformational changes in several residues, as well as protonation changes in some protonatable residues. In particular, the surroundings of hemes I and IV constitute two areas of special interest. In addition, we were able to ascertain the groups involved in the redox-Bohr effect present in this cytochrome and the conformational changes that may underlie the redox-cooperativity effects on different hemes. Furthermore, the thermodynamic simulations provide evidence that the N- and C-terminal domains function in an independent manner, with the hemes belonging to the N-terminal domain showing, in general, a lower redox potential than those found in the C-terminal domain. In this way, electrons captured by the N-terminal domain could easily flow to the C-terminal domain, allowing the former to capture more electrons. A notable exception is heme IX, which has low redox potential and could serve as the exit path for electrons toward other proteins in the electron transfer pathway.
Topics: Binding Sites; Crystallography, X-Ray; Cytochromes c; Desulfovibrio; Electron Transport; Electrons; Heme; Hydrogen-Ion Concentration; Models, Molecular; Monte Carlo Method; Oxidation-Reduction; Oxygen; Protein Conformation; Protein Structure, Tertiary; Protons
PubMed: 12750363
DOI: 10.1074/jbc.M301745200 -
Applied and Environmental Microbiology Mar 1998The kinetics of oxygen reduction by Desulfovibrio salexigens Mast1 and the role of polyglucose in this activity were examined and compared with those of strains of D....
The kinetics of oxygen reduction by Desulfovibrio salexigens Mast1 and the role of polyglucose in this activity were examined and compared with those of strains of D. desulfuricans and D. gigas. Oxidation rates were highest at air saturation (up to 40 nmol of O(2) min mg of protein) and declined with decreasing oxygen concentrations. Studies with cell extracts (CE) indicated that NADH oxidase was entirely responsible for the oxygen reduction in strain Mast1. In D. desulfuricans CSN, at least three independent systems appeared to reduce oxygen. Two were active at all oxygen concentrations (NADH oxidase and NADPH oxidase), and one was maximally active at less than 10 muM oxygen. In contrast to D. gigas and D. salexigens strains, the D. desulfuricans strains also contained NADH peroxidase and NADPH peroxidase activities and did not accumulate polyglucose under nonlimiting growth conditions. At air saturation, initial activities of the oxidases and peroxidases of cells harvested at the end of the log phase were on the order of 20 to 140 nmol of O(2) min mg of protein. In all strains, these enzymes were relatively stable but were susceptible to inactivation as soon as substrates were added to the assay mixture. Under those conditions, all oxidation activity disappeared after ca. 1 h of incubation. The same finding was observed with whole cells of D. desulfuricans CSN and D. desulfuricans ATCC 27774, but inactivation was less pronounced with cells of D. salexigens Mast1. It appeared that the presence of polyglucose in the whole cells retarded the process of inactivation of NADH oxidase, but this property was lost in crude CE. In spite of the effect of polyglucose on the oxidative potential, oxygen-dependent growth of D. salexigens Mast1 could be demonstrated neither in batch nor in continuous culture.
PubMed: 16349510
DOI: 10.1128/AEM.64.3.1034-1039.1998 -
European Journal of Biochemistry Dec 1993Plasmid pRC41, containing the cyf gene encoding cytochrome c533 from Desulfovibrio vulgaris Hildenborough, was transferred by conjugation from Escherichia coli to...
Overexpression of Desulfovibrio vulgaris Hildenborough cytochrome c553 in Desulfovibrio desulfuricans G200. Evidence of conformational heterogeneity in the oxidized protein by NMR.
Plasmid pRC41, containing the cyf gene encoding cytochrome c533 from Desulfovibrio vulgaris Hildenborough, was transferred by conjugation from Escherichia coli to Desulfovibrio desulfuricans G200. The structural properties of the purified protein were studied by one-dimensional and two-dimensional NMR. A heterogeneity in the folding of the cytochrome isolated from D. vulgaris Hildenborough and from D. desulfuricans G200 was observed for the oxidized from. Temperature, pH and salt-dependence studies indicated that the heterogeneity does not result from an intermediate in the protein unfolding process, but derives from two conformations which are not in dynamic equilibrium.
Topics: Amino Acid Sequence; Base Sequence; Cloning, Molecular; Cytochrome c Group; DNA, Bacterial; Desulfovibrio; Desulfovibrio vulgaris; Hydrogen-Ion Concentration; Magnetic Resonance Spectroscopy; Molecular Sequence Data; Oxidation-Reduction; Protein Conformation; Recombinant Proteins; Salts; Sequence Homology, Amino Acid; Temperature
PubMed: 8269917
DOI: 10.1111/j.1432-1033.1993.tb18377.x -
Applied and Environmental Microbiology May 2020Microbial production of the neurotoxin methylmercury (MeHg) is a significant health and environmental concern, as it can bioaccumulate and biomagnify in the food web. A...
Microbial production of the neurotoxin methylmercury (MeHg) is a significant health and environmental concern, as it can bioaccumulate and biomagnify in the food web. A chalkophore or a copper-binding compound, termed methanobactin (MB), has been shown to form strong complexes with mercury [as Hg(II)] and also enables some methanotrophs to degrade MeHg. It is unknown, however, if Hg(II) binding with MB can also impede Hg(II) methylation by other microbes. Contrary to expectations, MB produced by the methanotroph OB3b (OB3b-MB) enhanced the rate and efficiency of Hg(II) methylation more than that observed with thiol compounds (such as cysteine) by the mercury-methylating bacteria ND132 and PCA. Compared to no-MB controls, OB3b-MB decreased the rates of Hg(II) sorption and internalization, but increased methylation by 5- to 7-fold, suggesting that Hg(II) complexation with OB3b-MB facilitated exchange and internal transfer of Hg(II) to the HgcAB proteins required for methylation. Conversely, addition of excess amounts of OB3b-MB or a different form of MB from strain SB2 (SB2-MB) inhibited Hg(II) methylation, likely due to greater binding of Hg(II). Collectively, our results underscore the complex roles of microbial exogenous metal-scavenging compounds in controlling net production and bioaccumulation of MeHg in the environment. Some anaerobic microorganisms convert inorganic mercury (Hg) into the neurotoxin methylmercury, which can bioaccumulate and biomagnify in the food web. While the genetic basis of microbial mercury methylation is known, factors that control net methylmercury production in the environment are still poorly understood. Here, it is shown that mercury methylation can be substantially enhanced by one form of an exogenous copper-binding compound (methanobactin) produced by some methanotrophs, but not by another. This novel finding illustrates that complex interactions exist between microbes and that these interactions can potentially affect the net production of methylmercury .
Topics: Desulfovibrio desulfuricans; Environmental Pollutants; Geobacter; Imidazoles; Mercury; Methylation; Methylosinus trichosporium; Oligopeptides
PubMed: 32220843
DOI: 10.1128/AEM.00122-20 -
The Journal of Biological Chemistry Jan 2012The active center (H-cluster) of [FeFe]-hydrogenases is embedded into a hydrophobic pocket within the protein. We analyzed several amino acids, located in the vicinity...
The active center (H-cluster) of [FeFe]-hydrogenases is embedded into a hydrophobic pocket within the protein. We analyzed several amino acids, located in the vicinity of this niche, by site-directed mutagenesis of the [FeFe]-hydrogenases from Clostridium pasteurianum (CpI) and Chlamydomonas reinhardtii (CrHydA1). These amino acids are highly conserved and predicted to be involved in H-cluster coordination. Characterization of two hydrogenase variants confirmed this hypothesis. The exchange of residues CrHydA1Met(415) and CrHydA1Lys(228) resulted in inactive proteins, which, according to EPR and FTIR analyses, contain no intact H-cluster. However, [FeFe]-hydrogenases in which CpIMet(353) (CrHydA1Met(223)) and CpICys(299) (CrHydA1Cys(169)) were exchanged to leucine and serine, respectively, showed a structurally intact H-cluster with catalytic activity either absent (CpIC299S) or strongly diminished (CpIM353L). In the case of CrHydA1C169S, the H-cluster was trapped in an inactive state exhibiting g values and vibrational frequencies that resembled the H(trans) state of DdH from Desulfovibrio desulfuricans. This cysteine residue, interacting with the bridge head nitrogen of the di(methyl)amine ligand, seems therefore to represent an essential contribution of the immediate protein environment to the reaction mechanism. Exchanging methionine CpIM(353) (CrHydA1M(223)) to leucine led to a strong decrease in turnover without affecting the K(m) value of the electron donor. We suggest that this methionine constitutes a "fine-tuning" element of hydrogenase activity.
Topics: Bacterial Proteins; Catalysis; Chlamydomonas reinhardtii; Clostridium; Desulfovibrio desulfuricans; Electron Spin Resonance Spectroscopy; Hydrogenase; Kinetics; Mutagenesis, Site-Directed; Plant Proteins; Spectroscopy, Fourier Transform Infrared
PubMed: 22110126
DOI: 10.1074/jbc.M111.305797 -
Journal of Bacteriology Dec 1974The phospholipids of Desulfovibrio desulfuricans, Norway strain, D. vulgaris, and D. gigas were examined in relationship to their qualitative and quantitative... (Comparative Study)
Comparative Study
The phospholipids of Desulfovibrio desulfuricans, Norway strain, D. vulgaris, and D. gigas were examined in relationship to their qualitative and quantitative composition. D. desulfuricans and D. vulgaris exhibited an essentially identical phospholipid composition consisting of phosphatidylethanolamine, phosphatidylglycerol, cardiolipin, and lysophosphatidylserine. Phosphatidylserine (10.9%) was present in D. desulfuricans but was not detected in D. vulgaris. D. gigas was found to contain only two phospholipids, phosphatidylethanolamine (30%) and phosphatidylglycerol (70%). An ornithine-containing lipid was detected in D. gigas which was not present in the other two Desulfovibrio species.
Topics: Cardiolipins; Chromatography, DEAE-Cellulose; Chromatography, Paper; Chromatography, Thin Layer; Desulfovibrio; Phosphatidylethanolamines; Phosphatidylserines; Phospholipids; Phosphorus; Serine; Species Specificity; Tritium
PubMed: 4436257
DOI: 10.1128/jb.120.3.1279-1283.1974 -
Journal of Bacteriology Sep 1963Akagi, J. M. (University of Illinois, Urbana) and L. Leon Campbell. Inorganic pyrophosphatase of Desulfovibrio desulfuricans. J. Bacteriol. 86:563-568. 1963.-The...
Akagi, J. M. (University of Illinois, Urbana) and L. Leon Campbell. Inorganic pyrophosphatase of Desulfovibrio desulfuricans. J. Bacteriol. 86:563-568. 1963.-The inorganic pyrophosphatase of Desulfovibrio desulfuricans was purified 136-fold by (NH(4))(2)SO(4) and ethanol fractionation and diethylaminoethyl cellulose chromatography. Mg(++) or Mn(++) was required for optimal activity; Co(++) was only 65% as effective as Mg(++). The optimal ratio of Mg(++) to pyrophosphate was 1.0 at pH 8.0. The K(s) for the pyrophosphatase was found to be in the region of 1.9 x 10(-3)m. Sulfhydryl inhibitors and sodium fluoride had no effect on enzyme activity at a concentration of 10(-3)m. The purified enzyme did not hydrolyze adenosine triphosphate, glycerol phosphate, diphenyl phosphate, or p-nitrophenyl phosphate. Thermal stability studies showed that the enzyme is rapidly inactivated at temperatures above 40 C.
Topics: Adenosine Triphosphate; Desulfovibrio; Desulfovibrio desulfuricans; Diphosphates; Inorganic Pyrophosphatase; Nitrophenols; Organophosphorus Compounds; Phosphates; Pyrophosphatases; Research; Temperature
PubMed: 14066437
DOI: 10.1128/jb.86.3.563-568.1963 -
Journal of Clinical Microbiology Jan 2012Desulfovibrio spp. are anaerobic, sulfate-reducing, nonfermenting, Gram-negative bacteria found in the digestive tract of humans. Identification of these species with...
Desulfovibrio spp. are anaerobic, sulfate-reducing, nonfermenting, Gram-negative bacteria found in the digestive tract of humans. Identification of these species with conventional methods is difficult. The reported case of a Desulfovibrio desulfuricans bacteremia occurring in an immunocompromised host with ulcerative colitis confirms that this organism may be a possible opportunistic human pathogen.
Topics: Aged; Bacteremia; Colitis, Ulcerative; Desulfovibrio desulfuricans; Desulfovibrionaceae Infections; Female; Humans; Immunocompromised Host; Liver Transplantation
PubMed: 22075582
DOI: 10.1128/JCM.00987-11