-
Scientific Reports Jul 2017Molybdenum and tungsten are taken up by bacteria and archaea as their soluble oxyanions through high affinity transport systems belonging to the ATP-binding cassette...
Molybdenum and tungsten are taken up by bacteria and archaea as their soluble oxyanions through high affinity transport systems belonging to the ATP-binding cassette (ABC) transporters. The component A (ModA/TupA) of these transporters is the first selection gate from which the cell differentiates between MoO, WO and other similar oxyanions. We report the biochemical characterization and the crystal structure of the apo-TupA from Desulfovibrio desulfuricans G20, at 1.4 Å resolution. Small Angle X-ray Scattering data suggests that the protein adopts a closed and more stable conformation upon ion binding. The role of the arginine 118 in the selectivity of the oxyanion was also investigated and three mutants were constructed: R118K, R118E and R118Q. Isothermal titration calorimetry clearly shows the relevance of this residue for metal discrimination and oxyanion binding. In this sense, the three variants lost the ability to coordinate molybdate and the R118K mutant keeps an extremely high affinity for tungstate. These results contribute to an understanding of the metal-protein interaction, making it a suitable candidate for a recognition element of a biosensor for tungsten detection.
Topics: Amino Acid Substitution; Calorimetry; Crystallography, X-Ray; DNA Mutational Analysis; Desulfovibrio desulfuricans; Membrane Transport Proteins; Models, Molecular; Protein Conformation; Substrate Specificity; Tungsten Compounds
PubMed: 28724964
DOI: 10.1038/s41598-017-06133-y -
Microbiology Resource Announcements Aug 2019We report the complete genome sequence of the anaerobic, sulfonate-respiring, sulfate-reducing bacterium IC1. The genome was assembled into a single 3.25-Mb circular...
We report the complete genome sequence of the anaerobic, sulfonate-respiring, sulfate-reducing bacterium IC1. The genome was assembled into a single 3.25-Mb circular chromosome with 2,680 protein-coding genes identified. Sequencing of sulfonate-metabolizing anaerobes is key for understanding sulfonate degradation and its role in the sulfur cycle.
PubMed: 31371536
DOI: 10.1128/MRA.00456-19 -
European Journal of Biochemistry Mar 1994Flavodoxin was isolated and purified from Desulfovibrio desulfuricans ATCC 27774, a sulfate-reducing organism that can also utilize nitrate as an alternative electron...
Flavodoxin was isolated and purified from Desulfovibrio desulfuricans ATCC 27774, a sulfate-reducing organism that can also utilize nitrate as an alternative electron acceptor. Mid-point oxidation-reduction potentials of this flavodoxin were determined by ultraviolet/visible and EPR methods coupled to potentiometric measurements and their pH dependence studied in detail. The redox potential E2, for the couple oxidized/semiquinone forms at pH 6.7 and 25 degrees C is -40 mV, while the value for the semiquinone/hydroquinone forms (E1), at the same pH, -387 mV. E2 varies linearly with pH, while E1 is independent of pH at high values. However, at low pH (< 7.0), this value is less negative, compatible with a redox-linked protonation of the flavodoxin hydroquinone. A comparative study is presented for Desulfovibrio salexigens NCIB 8403 flavodoxin [Moura, I., Moura, J.J.G., Bruschi, M. & LeGall, J. (1980) Biochim. Biophys. Acta 591, 1-8]. The complete primary amino acid sequence was obtained by automated Edman degradation from peptides obtained by chemical and enzymic procedures. The amino acid sequence was confirmed by FAB/MS. Using the previously determined tridimensional structure of Desulfovibrio vulgaris flavodoxin as a model [similarity, 48.6%; Watenpaugh, K.D., Sieker, L.C., Jensen, L.H., LeGall, J. & Dubourdieu M. (1972) Proc. Natl Acad. Sci. USA 69, 3185-3188], the tridimensional structure of D. desulfuricans ATCC 27774 flavodoxin was predicted using AMBER force-field calculations.
Topics: Amino Acid Sequence; Base Sequence; Desulfovibrio; Electron Spin Resonance Spectroscopy; Flavodoxin; Hydrogen-Ion Concentration; Molecular Sequence Data; Oxidation-Reduction; Protein Structure, Tertiary; Sequence Homology, Amino Acid; Spectrophotometry, Ultraviolet; Spectrum Analysis
PubMed: 8143752
DOI: 10.1111/j.1432-1033.1994.tb18703.x -
Antimicrobial Agents and Chemotherapy Dec 2009Antimicrobial susceptibilities of 23 strains of Desulfovibrio spp. were tested by Etest. Generally, Desulfovibrio spp. were highly susceptible to sulbactam-ampicillin,...
Antimicrobial susceptibilities of 23 strains of Desulfovibrio spp. were tested by Etest. Generally, Desulfovibrio spp. were highly susceptible to sulbactam-ampicillin, meropenem, clindamycin, metronidazole, and chloramphenicol: MIC(90)s of 6, 4, 0.19, 0.25, and 8 microg/ml, respectively. In addition, these strains generally showed high MICs to piperacillin and piperacillin-tazobactam. Desulfovibrio fairfieldensis (eight strains) was the species least susceptible to most agents, especially beta-lactams, and was the only species resistant to fluoroquinolones. Desulfovibrio desulfuricans strain Essex 6 isolates were less susceptible to beta-lactams than D. desulfuricans strain MB isolates.
Topics: Ampicillin; Anti-Bacterial Agents; Chloramphenicol; Clindamycin; Desulfovibrio; Fluoroquinolones; Humans; Metronidazole; Microbial Sensitivity Tests; Penicillanic Acid; Piperacillin; Piperacillin, Tazobactam Drug Combination; Sulbactam
PubMed: 19786606
DOI: 10.1128/AAC.00630-09 -
Applied and Environmental Microbiology Jun 2002Previous in vitro experiments with Desulfovibrio vulgaris strain Hildenborough demonstrated that extracts containing hydrogenase and cytochrome c3 could reduce...
Previous in vitro experiments with Desulfovibrio vulgaris strain Hildenborough demonstrated that extracts containing hydrogenase and cytochrome c3 could reduce uranium(VI) to uranium(IV) with hydrogen as the electron donor. To test the involvement of these proteins in vivo, a cytochrome c3 mutant of D. desulfuricans strain G20 was assayed and found to be able to reduce U(VI) with lactate or pyruvate as the electron donor at rates about one-half of those of the wild type. With electrons from hydrogen, the rate was more severely impaired. Cytochrome c3 appears to be a part of the in vivo electron pathway to U(VI), but additional pathways from organic donors can apparently bypass this protein.
Topics: Cytochrome c Group; Desulfovibrio; Mutation; Oxidation-Reduction; Uranium
PubMed: 12039777
DOI: 10.1128/AEM.68.6.3129-3132.2002 -
Applied and Environmental Microbiology Feb 1981When grown in the absence of added sulfate, cocultures of Desulfovibrio desulfuricans or Desulfovibrio vulgaris with Methanobrevibacter smithii (Methanobacterium...
When grown in the absence of added sulfate, cocultures of Desulfovibrio desulfuricans or Desulfovibrio vulgaris with Methanobrevibacter smithii (Methanobacterium ruminantium), which uses H(2) and CO(2) for methanogenesis, degraded lactate, with the production of acetate and CH(4). When D. desulfuricans or D. vulgaris was grown in the absence of added sulfate in coculture with Methanosarcina barkeri (type strain), which uses both H(2)-CO(2) and acetate for methanogenesis, lactate was stoichiometrically degraded to CH(4) and presumably to CO(2). 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 CH(4). Later, acetate was degraded to CH(4) and presumably to CO(2). 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 H(2) was detected in cocultures which contained D. desulfuricans and M. barkeri until after all lactate was degraded. The addition of H(2), but not of lactate, to the growth medium inhibited acetate degradation by pure cultures of M. barkeri. Pure cultures of M. barkeri produced CH(4) from acetate at a rate equivalent to that observed for cocultures containing M. barkeri. Inocula of M. barkeri grown with H(2)-CO(2) as the methanogenic substrate produced CH(4) 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 H(2) produced by the Desulfovibrio species during growth with lactate inhibited acetate degradation by M. barkeri.
PubMed: 16345708
DOI: 10.1128/aem.41.2.346-354.1981 -
Journal of Clinical Microbiology Oct 2010The advancement in culture identification methods has made possible the culture and identification of slow-growing anaerobic bacteria in clinical samples. Here, we...
The advancement in culture identification methods has made possible the culture and identification of slow-growing anaerobic bacteria in clinical samples. Here, we describe a case of polymicrobial bloodstream infection (BSI) caused by Eggerthella lenta and Desulfovibrio desulfuricans, identified by API 20A and Vitek 2 systems and by 16S rRNA sequencing.
Topics: Actinobacteria; Aged, 80 and over; Anti-Bacterial Agents; Bacteremia; Bacterial Typing Techniques; DNA, Bacterial; DNA, Ribosomal; Desulfovibrio desulfuricans; Desulfovibrionaceae Infections; Female; Gram-Positive Bacterial Infections; Humans; Microbial Sensitivity Tests; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 20720029
DOI: 10.1128/JCM.02481-09 -
Journal of Bacteriology Oct 1969The cytochrome c(3) of Desulfovibrio desulfuricans and that of D. vulgaris were purified to homogeneity as judged by disc gel electrophoresis and by ultracentrifugation....
The cytochrome c(3) of Desulfovibrio desulfuricans and that of D. vulgaris were purified to homogeneity as judged by disc gel electrophoresis and by ultracentrifugation. Both cytochromes had an oxidation-reduction potential of -205 +/- 5 mv at pH 7.0 and showed characteristic absorption bands at 525 and 553 nm in the reduced state. The molecular weights of the two cytochromes (calculated from sedimentation and diffusion data) were similar, with values of 13,500 to 14,300 for D. desulfuricans and 13,800 to 14,700 for D. vulgaris. The two cytochromes differed in their electrophoretic properties on Geon and polyacrylamide gel electrophoresis and did not share a common precipitating antigenic determinant as judged by immunodiffusion data.
Topics: Bacteria; Cytochromes; Electrophoresis; Immunodiffusion; Molecular Weight
PubMed: 4981060
DOI: 10.1128/jb.100.1.358-364.1969 -
Journal of Bacteriology Oct 1985Comparisons among 16S rRNA sequences from various eubacteria reveal a natural relationship between the bacteroides (represented by the Bacteroides fragilis sequence) and...
Comparisons among 16S rRNA sequences from various eubacteria reveal a natural relationship between the bacteroides (represented by the Bacteroides fragilis sequence) and a phylogenetic unit that comprises the flavobacteria, cytophagae, flexibacteria, and others (represented by the Flavobacterium heparinum sequence). Although the relationship is not a close one, it is, nevertheless, specific. rRNAs from these two organisms are not only closer to one another in overall sequence than they are to outgroup species (such as Bacillus subtilis, Escherichia coli, Desulfovibrio desulfuricans, and Agrobacterium tumefaciens), but they show common idiosyncrasies (i.e., derived characteristics) in both rRNA sequences and higher-order structures.
Topics: Bacteroides; Base Composition; Base Sequence; Flavobacterium; Phenotype; Phylogeny; RNA, Bacterial; RNA, Ribosomal
PubMed: 2413007
DOI: 10.1128/jb.164.1.230-236.1985 -
European Journal of Biochemistry Oct 2003The cytochrome c nitrite reductase is isolated from the membranes of the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 as a heterooligomeric complex...
The isolation and characterization of cytochrome c nitrite reductase subunits (NrfA and NrfH) from Desulfovibrio desulfuricans ATCC 27774. Re-evaluation of the spectroscopic data and redox properties.
The cytochrome c nitrite reductase is isolated from the membranes of the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 as a heterooligomeric complex composed by two subunits (61 kDa and 19 kDa) containing c-type hemes, encoded by the genes nrfA and nrfH, respectively. The extracted complex has in average a 2NrfA:1NrfH composition. The separation of ccNiR subunits from one another is accomplished by gel filtration chromatography in the presence of SDS. The amino-acid sequence and biochemical subunits characterization show that NrfA contains five hemes and NrfH four hemes. These considerations enabled the revision of a vast amount of existing spectroscopic data on the NrfHA complex that was not originally well interpreted due to the lack of knowledge on the heme content and the oligomeric enzyme status. Based on EPR and Mössbauer parameters and their correlation to structural information recently obtained from X-ray crystallography on the NrfA structure [Cunha, C.A., Macieira, S., Dias, J.M., Almeida, M.G., Gonçalves, L.M.L., Costa, C., Lampreia, J., Huber, R., Moura, J.J.G., Moura, I. & Romão, M. (2003) J. Biol. Chem. 278, 17455-17465], we propose the full assignment of midpoint reduction potentials values to the individual hemes. NrfA contains the high-spin catalytic site (-80 mV) as well as a quite unusual high reduction potential (+150 mV)/low-spin bis-His coordinated heme, considered to be the site where electrons enter. In addition, the reassessment of the spectroscopic data allowed the first partial spectroscopic characterization of the NrfH subunit. The four NrfH hemes are all in a low-spin state (S = 1/2). One of them has a gmax at 3.55, characteristic of bis-histidinyl iron ligands in a noncoplanar arrangement, and has a positive reduction potential.
Topics: Amino Acid Sequence; Bacterial Proteins; Cytochromes a1; Cytochromes c1; Desulfovibrio; Electron Spin Resonance Spectroscopy; Electrophoresis, Polyacrylamide Gel; Heme; Molecular Sequence Data; Nitrate Reductases; Oxidation-Reduction; Protein Conformation; Protein Subunits; RNA-Binding Proteins; Sequence Homology, Amino Acid; Solubility; Spectroscopy, Mossbauer; Transcription Factors
PubMed: 14511372
DOI: 10.1046/j.1432-1033.2003.03772.x