Publications

culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off taketomi island, japan.	microbial communities in a shallow submarine hydrothermal system near taketomi island, japan, were investigated using cultivation-based and molecular techniques. the main hydrothermal activity occurred in a craterlike basin (depth, approximately 23 m) on the coral reef seafloor. the vent fluid (maximum temperature, >52 degrees c) contained 175 microm h2s and gas bubbles mainly composed of ch4 (69%) and n2 (29%). a liquid serial dilution cultivation technique targeting a variety of metabolism typ ...	2007	17921273
response of desulfovibrio vulgaris to alkaline stress.	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) contribut ...	2007	17921288
measuring the ph dependence of hydrogenase activities.	the ph dependences of activities of homogenous hydrogenases of thiocapsa roseopersicina and desulfomicrobium baculatum in the reaction of hydrogen uptake in solution in the presence of benzyl viologen and the ph dependences of catalytic currents of hydrogen oxidation by electrodes on which these hydrogenases were immobilized were compared. maximal activities of the hydrogenases from t. roseopersicina and d. baculatum in the reaction hydrogen uptake in solution were observed at ph 9.5 and 8.5, re ...	2007	17922655
biofilm formation in desulfovibrio vulgaris hildenborough is dependent upon protein filaments.	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 ...	2007	17922767
the [nifese] hydrogenase from desulfovibrio vulgaris hildenborough is a bacterial lipoprotein lacking a typical lipoprotein signal peptide.	desulfovibrio vulgaris hildenborough has a membrane-bound [nifese] hydrogenase whose mode of membrane association was unknown since it is constituted by two hydrophilic subunits. this work shows that this hydrogenase is a bacterial lipoprotein bound to the membrane by lipidic groups found at the n-terminus of the large subunit, which is unusual since it is missing the typical lipoprotein signal peptide. nevertheless, the large subunit has a conserved four residue lipobox and its synthesis is sen ...	2007	17601576
function of periplasmic hydrogenases in the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough.	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 def ...	2007	17601789
advantages of using microbial technology over traditional chemical technology in removal of black crusts from stone surfaces of historical monuments.	this study compares two cleaning methods, one involving an ammonium carbonate-edta mixture and the other involving the sulfate-reducing bacterium desulfovibrio vulgaris subsp. vulgaris atcc 29579, for the removal of black crust (containing gypsum) on marble of the milan cathedral (italy). in contrast to the chemical cleaning method, the biological procedure resulted in more homogeneous removal of the surface deposits and preserved the patina noble under the black crust. whereas both of the treat ...	2007	17601804
a qm/mm investigation of the activation and catalytic mechanism of fe-only hydrogenases.	fe-only hydrogenases are enzymes that catalyze dihydrogen production or oxidation, due to the presence of an unusual fe(6)s(6) cluster (the so-called h-cluster) in their active site, which is composed of a fe(2)s(2) subsite, directly involved in catalysis, and a classical fe(4)s(4) cubane cluster. here, we present a hybrid quantum mechanical and molecular mechanical (qm/mm) investigation of the fe-only hydrogenase from desulfovibrio desulfuricans, in order to unravel key issues regarding the act ...	2007	17602468
proteome analysis of desulfovibrio desulfuricans g20 mutants using the accurate mass and time (amt) tag approach.	abundance values obtained from direct lc-ms analyses were used to compare the proteomes of six transposon-insertion mutants of desulfovibrio desulfuricans g20, the lab strain (g20lab) and a sediment-adapted strain (g20sediment). three mutations were in signal transduction histidine kinases, and three mutations were in other regulatory proteins. the high-throughput accurate mass and time (amt) tag proteomic approach was utilized to analyze the proteomes. a total of 1318 proteins was identified wi ...	2007	17602684
comparison between ultrafast fluorescence dynamics of fmn binding protein from desulfovibrio vulgaris, strain miyazaki, in solution vs crystal phases.	ultrafast fluorescence dynamics of fmn binding protein (fbp) from desulfobivrio vulgaris, strain miyaxaki f, were compared in solution and crystal phases. fluorescence lifetimes of fbp were 167 fs (96%) and 1.5 ps (4%) in solution (tau(av) = 220 fs), and 730 fs (60%) and longer than 10 ps (40%) in crystals (tau(av) = 4.44 ps). the quenching of the fluorescence of flavin in the protein was considered to be due to photoinduced electron transfer (et) from trp or tyr to the excited isoalloxazine (is ...	2007	17608527
analysis of a ferric uptake regulator (fur) mutant of desulfovibrio vulgaris hildenborough.	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 ...	2007	17630305
a pcr marker for detection in surface waters of faecal pollution derived from ducks.	detection of the faecal pollution contribution from wildfowl is an important adjunct in determining the sources of faecal pollution in waterways. this is particularly true, where human waste and other animal faecal sources have been eliminated as the pollution source. a polymerase chain reaction (pcr) marker was developed as a duck-specific marker of faecal pollution. the semi-nested primer system targeted an unknown bacterium (e2) isolated from mallard ducks. e2 had the closest 16s rrna sequenc ...	2007	17631940
characterization of black band disease in red sea stony corals.	microbial communities associated with black band disease (bbd) in massive stony corals from the northern red sea (eilat) were examined for the first time using molecular tools and microscopy. a high microbial diversity was revealed in the affected tissue in comparison with the healthy area of the same colony. microscopy revealed the penetration of cyanobacteria into the coral mesoglea and adjacent tissues. cyanobacterial sequences from red sea bbd-affected corals formed a cluster with sequences ...	2007	17635545
[clinical significance of sulfate-reducing bacteria for ulcerative colitis].	ulcerative colitis(uc) is colon localized disease. broad epithelial cell damage, crypt abscesses and accumulation of neutrophils are recognized for uc. although the cause of uc is indistinct at this time, there is a growing consensus that abnormal intestinal microflora would be related with uc. there have been several evidences that excessive production of hydrogen sulfide by bacteria in colon would be associated with uc. sulfate reducing bacteria are able to utilize sulfate as an electron recep ...	2007	17642254
on the predictability of protein database search complexity and its relevance to optimization of distributed searches.	we discuss several aspects related to load balancing of database search jobs in a distributed computing environment, such as linux cluster. load balancing is a technique for making the most of multiple computational resources, which is particularly relevant in environments in which the usage of such resources is very high. the particular case of the sequest program is considered here, but the general methodology should apply to any similar database search program. we show how the runtimes for se ...	2007	17663575
[effect of corrosion inhibitor on the producing of exopolymer complex by sulphate-reducing bacteria].	it is established that the specific productivity of exopolymer complex (epm) synthesized by the cells of sulphate-reducing bacteria in a biofilm was 1.5 times higher than in plankton. a sharp increase of the specific productivity of epm in the biofilm is observed when corrosion inhibitor is introduced in the environment. the inhibitor concentration being 1.0 g/l, the biofilm cells produced almost 18 times more of epm than the bacteria cells in plankton. it is shown that the film exopolymers incl ...	2007	17682530
improving sample treatment for in-solution protein identification by peptide mass fingerprint using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.	three ultrasonic energy sources were studied to speed up the sample treatment for in-solution protein identification by peptide mass fingerprint using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. protein reduction, alkylation, and enzymatic digestion steps were done in 15 min. nine proteins, including zinc resistance-associated protein precursor from desulfovibrio desulfuricans strain g20 and split-soret cytochrome c from d. desulfuricans atcc27774 were successfu ...	2007	17683131
thermodynamic and kinetic characterisation of individual haems in multicentre cytochromes c3.	the characterisation of individual centres in multihaem proteins is difficult due to the similarities in the redox and spectroscopic properties of the centres. nmr has been used successfully to distinguish redox centres and allow the determination of the microscopic thermodynamic parameters in several multihaem cytochromes c(3) isolated from different sulphate-reducing bacteria. in this article we show that it is also possible to discriminate the kinetic properties of individual centres in multi ...	2007	17692816
analyses of the vrl gene cluster in desulfococcus multivorans: homologous to the virulence-associated locus of the ovine footrot pathogen dichelobacter nodosus strain a198.	major parts of the virulence-associated vrl locus known from the gammaproteobacterium dichelobacter nodosus, the causative agent of ovine footrot, were analyzed in the genome of the sulfate-reducing deltaproteobacterium desulfococcus multivorans. in the genome of d. multivorans 13 of the 19 vrl genes described for d. nodosus are present and highly conserved with respect to gene sequence and order. the vrl locus and its flanking regions suggest a bacteriophage-mediated transfer into the genome of ...	2007	17693723
identification of genes that confer sediment fitness to desulfovibrio desulfuricans g20.	signature-tagged mutants of desulfovibrio desulfuricans g20 were screened, and 97 genes crucial for sediment fitness were identified. these genes belong to functional categories including signal transduction, binding and transport, insertion elements, and others. mutants with mutations in genes encoding proteins involved in amino acid biosynthesis, hydrogenase activity, and dna repair were further characterized.	2007	17704273
crystal structures of hydrogenase maturation protein hype in the apo and atp-bound forms.	the hydrogenase maturation protein hype serves an essential function in the biosynthesis of the nitrile group, which is subsequently coordinated to fe as cn(-) ligands in [ni-fe] hydrogenase. here, we present the crystal structures of hype from desulfovibrio vulgaris hildenborough in the presence and in the absence of atp at a resolution of 2.0 a and 2.6 a, respectively. comparison of the apo structure with the atp-bound structure reveals that binding atp causes an induced-fit movement of the n- ...	2007	17706667
molecular determinants for fmn-binding in desulfovibrio gigas flavoredoxin.	flavoredoxin participates in desulfovibrio gigas thiosulfate reduction pathway. its 3-dimensional model was generated allowing the oxidized riboflavin-5'-phosphate (fmn) site to be predicted. residues likely to be involved in fmn-binding were identified (n29, w35, t56, k92, h131 and f164) and mutated to alanine. fluorescence titration with apoprotein showed that fmn is strongly bound in the wild-type protein. comparison of k(d) values for mutants suggests that interactions with the phosphate gro ...	2007	17719581
ultrasonic assisted protein enzymatic digestion for fast protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. sonoreactor versus ultrasonic probe.	two different ultrasonic energy sources, the sonoreactor and the ultrasonic probe, are compared for enzymatic digestion of proteins for protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tof-ms) using the peptide mass fingerprint (pmf) procedure. variables such as (i) trypsin/protein ratio; (ii) sonication time; (iii) ultrasound amplitude; and (iv) protein concentration are studied and compared. as a general rule, the trypsin/protein rat ...	2007	17719595
the electronic structure of the h-cluster in the [fefe]-hydrogenase from desulfovibrio desulfuricans: a q-band 57fe-endor and hyscore study.	the active site of the (57)fe-enriched [fefe]-hydrogenase (i.e., the "h-cluster") from desulfovibrio desulfuricans has been examined using advanced pulse epr methods at x- and q-band frequencies. for both the active oxidized state (h(ox)) and the co inhibited form (h(ox)-co) all six (57)fe hyperfine couplings were detected. the analysis shows that the apparent spin density extends over the whole h-cluster. the investigations revealed different hyperfine couplings of all six (57)fe nuclei in the ...	2007	17722921
force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics.	the increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (md) simulations. to enable this md study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the charmm simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. using the aut ...	2007	17763506
desulfovibrio marinus sp. nov., a moderately halophilic sulfate-reducing bacterium isolated from marine sediments in tunisia.	two novel sulfate-reducing bacterial strains, designated e-2(t) and imp-2, were isolated from geographically distinct locations. strain e-2(t) was recovered from marine sediments near sfax (tunisia), whereas strain imp-2 originated from oilfield production fluids in the gulf of mexico. cells were gram-negative, non-sporulated, motile, vibrio-shaped or sigmoid. they were strictly anaerobic, mesophilic and moderately halophilic. sulfate, sulfite, thiosulfate and elemental sulfur served as electron ...	2007	17766893
a needle in a haystack: the active site of the membrane-bound complex cytochrome c nitrite reductase.	cytochrome c nitrite reductase is a multicenter enzyme that uses a five-coordinated heme to perform the six-electron reduction of nitrite to ammonium. in the sulfate reducing bacterium desulfovibrio desulfuricans atcc 27774, the enzyme is purified as a nrfa2nrfh complex that houses 14 hemes. the number of closely-spaced hemes in this enzyme and the magnetic interactions between them make it very difficult to study the active site by using traditional spectroscopic approaches such as epr or uv-vi ...	2007	17207484
the bacterial metallome: composition and stability with specific reference to the anaerobic bacterium desulfovibrio desulfuricans.	in bacteria, the intracellular metal content or metallome reflects the metabolic requirements of the cell. when comparing the composition of metals in phytoplankton and bacteria that make up the macronutrients and the trace elements, we have determined that the content of trace elements in both of these microorganisms is markedly similar. the trace metals consisting of transition metals plus zinc are present in a stoichometric molar formula that we have calculated to be as follows: fe(1)mn(0.3)z ...	2007	17216357
molecular characterisation of the gut microflora of healthy and inflammatory bowel disease cats using fluorescence in situ hybridisation with special reference to desulfovibrio spp.	inflammatory bowel disease (ibd) is a common cause of chronic large bowel diarrhoea in cats. although the aetiology of ibd is unknown, an immune-mediated response to a luminal antigen is thought to be involved. as knowledge concerning the colonic microflora of cats is limited and requires further investigation, the purpose of this study was to determine the presence of specific bacterial groups in normal and ibd cats, and the potential role they play in the health of the host. total bacterial po ...	2007	17217390
preparation, structures and electrochemical property of phosphine substituted diiron azadithiolates relevant to the active site of fe-only hydrogenases.	mono- and di-phosphine diiron azadithiolate complexes [{(mu-sch(2))(2)n(4-no(2)c(6)h(4))}fe(2)(co)(5)(pme(3))] (2), [{(mu-sch(2))(2)n(4-no(2)c(6)h(4))}{fe(co)(2)l}(2)] (3, l=pme(3); 4, pme(2)ph) and the mu-hydride diiron complex [3(fehfe)](+)[pf(6)](-) were prepared as biomimetic models of the active site of fe-only hydrogenases. the complexes 2-4 and [3(fehfe)](+)[pf(6)](-) were characterized by ir, (31)p, (1)h and (13)c nmr spectra and their molecular structures were determined by single cryst ...	2007	17222911
improved pulse sequences for sequence specific assignment of aromatic proton resonances in proteins.	aromatic proton resonances of proteins are notoriously difficult to assign. through-bond correlation experiments are preferable over experiments that rely on through-space interactions because they permit aromatic chemical shift assignments to be established independently of the structure determination process. known experimental schemes involving a magnetization transfer across the cbeta-cgamma bond in aromatic side chains either suffer from low efficiency for the relay beyond the cdelta positi ...	2007	17237975
the anaerobe desulfovibrio desulfuricans atcc 27774 grows at nearly atmospheric oxygen levels.	sulfate reducing bacteria of the desulfovibrio genus are considered anaerobes, in spite of the fact that they are frequently isolated close to oxic habitats. however, until now, growth in the presence of high concentrations of oxygen was not reported for members of this genus. this work shows for the first time that the sulfate reducing bacterium desulfovibrio desulfuricans atcc 27774 is able to grow in the presence of nearly atmospheric oxygen levels. in addition, the activity and expression pr ...	2007	17239374
determination of the role of the carboxyl-terminal leucine-122 in fmn-binding protein by mutational and structural analysis.	mutants of flavin mononucleotide-binding protein (fmn-bp) were made by site-directed mutagenesis to investigate the role of carboxyl-terminal leu122 of the pairing subunit in controlling redox potentials, binding the prosthetic group, and forming the tertiary and quaternary structure. we compared the oxidation-reduction potentials, fmn-binding properties, and higher structures of wild-type fmn-bp and four mutant proteins (l122y, l122e, l122k and l122-deleted). we found that the redox potentials ...	2007	17261542
sonoreactor-based technology for fast high-throughput proteolytic digestion of proteins.	fast (120 s) and high-throughput (more than six samples at once) in-gel trypsin digestion of proteins using sonoreactor technology has been achieved. successful protein identification was done by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, maldi-tof-ms. specific identification of the adenylylsulphate reductase alfa subunit from a complex protein mixture from desulfovibrio desulfuricans atcc 27774 was done as a proof of the methodology. the new sample treatment i ...	2007	17269750
correlating epr and x-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase.	two arsenite-inhibited forms of each of the aldehyde oxidoreductases from desulfovibrio gigas and desulfovibrio desulfuricans have been studied by x-ray crystallography and electron paramagnetic resonance (epr) spectroscopy. the molybdenum site of these enzymes shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. arsenite addition to active as-prepared enzyme or ...	2007	17139522
phytic acid modulates in vitro il-8 and il-6 release from colonic epithelial cells stimulated with lps and il-1beta.	phytic acid (pa), a major fiber-associated component of wheat bran and legumes, is physiologically present in the human large gut. the aim of this study was to examine the role of pa in immunologic function of intestinal epithelial cells by analyzing its effect on interleukin (il)-8 and il-6 secretion by colonocytes and its role in the response of these cells to bacterial lipopolysaccharides (lps) and il-1beta. the human colon cell line caco-2 was exposed to lps isolated from two strains of desu ...	2007	17160716
process of maturation of tetraheme cytochrome c3 in a shewanella expression system.	the process of maturation of multiheme proteins is not yet well known, while that of monoheme ones has been relatively well investigated. two kinds of partly unfolded tetraheme cytochrome c3 were obtained on overexpression in shewanella oneidensis tsp-c. these proteins were characterized by circular dichroism and nuclear magnetic resonance spectroscopy. it turned out that the tetraheme architecture, and the fifth and sixth ligand coordination are almost mature, while some parts of the polypeptid ...	2007	17167041
uranium immobilization by sulfate-reducing biofilms grown on hematite, dolomite, and calcite.	biofilms of sulfate-reducing bacteria desulfovibrio desulfuricans g20 were used to reduce dissolved u(vi) and subsequently immobilize u(iv) in the presence of uranium-complexing carbonates. the biofilms were grown in three identically operated fixed bed reactors, filled with three types of minerals: one noncarbonate-bearing mineral (hematite) and two carbonate-bearing minerals (calcite and dolomite). the source of carbonates in the reactors filled with calcite and dolomite were the minerals, whi ...	2007	18200862
[microbiological analysis of cryopegs from the varandei peninsula, barents sea].	the paper deals with the microbiological characterization of water-saturated horizons in permafrost soils (cryopegs) found on the varandei peninsula (barents sea coast), 4-20 m deep. the total quantity of bacteria in the water of cryopegs was 3.5 x 10(8) cells/ml. the population of cultivated aerobic heterotrophic bacteria was 3-4 x 10(7) cells/ml and the number of anaerobic heterotrophic bacteria varied from 10(2) to 10(5) cells/ml depending on cultivation temperature and salinity. sulfate-redu ...	2007	18069331
proton thrusters: overview of the structural and functional features of soluble tetrahaem cytochromes c3.	tetrahaem cytochromes c (3) from sulfate-reducing bacteria have revealed exquisite complexity in their ligand binding properties and they couple the cooperative binding of two electrons with the binding of protons. in this review, the molecular mechanisms for these cooperative effects are described, and the functional consequences of these cooperativities are discussed in the context of the general mechanisms of biological energy transduction and the specific physiological metabolism of desulfov ...	2007	16964504
new findings for in-gel digestion accelerated by high-intensity focused ultrasound for protein identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.	new findings in sample treatment based on high-intensity focused ultrasound (hifu) for protein digestion after polyacrylamide gel electrophoresis separation are presented. the following variables were studied: (i) sample volume; (ii) sonotrode diameter; (iii) previous protein denaturation; (iv) cooling; (v) enzyme concentration; and (vi) protein concentration. results showed that positive protein identification could be done after protein separation by gel electrophoresis through peptide mass fi ...	2007	17034802
superoxide reduction by archaeoglobus fulgidus desulfoferrodoxin: comparison with neelaredoxin.	superoxide reductases (sors) are non-heme iron-containing enzymes that remove superoxide by reducing it to hydrogen peroxide. the active center of sors consists of a ferrous ion coordinated by four histidines and one cysteine in a square-pyramidal geometry. in the 2fe-sor, a distinct family of sors, there is an additional desulforedoxin-like site that does not appear to be involved in sor activity. our previous studies on recombinant archaeoglobus fulgidus neelaredoxin (1fe-sor) have shown that ...	2007	17066300
analysis of diversity and activity of sulfate-reducing bacterial communities in sulfidogenic bioreactors using 16s rrna and dsrb genes as molecular markers.	here we describe the diversity and activity of sulfate-reducing bacteria (srb) in sulfidogenic bioreactors by using the simultaneous analysis of pcr products obtained from dna and rna of the 16s rrna and dissimilatory sulfite reductase (dsrab) genes. we subsequently analyzed the amplified gene fragments by using denaturing gradient gel electrophoresis (dgge). we observed fewer bands in the rna-based dgge profiles than in the dna-based profiles, indicating marked differences in the populations pr ...	2007	17098925
evolution of the syntrophic interaction between desulfovibrio vulgaris and methanosarcina barkeri: involvement of an ancient horizontal gene transfer.	the sulfate reducing bacteria desulfovibrio vulgaris and the methanogenic archaea methanosarcina barkeri can grow syntrophically on lactate. in this study, a set of three closely located genes, dvu2103, dvu2104, and dvu2108 of d. vulgaris, was found to be up-regulated 2- to 4-fold following the lifestyle shift from syntroph to sulfate reducer; moreover, none of the genes in this gene set were differentially regulated when comparing gene expression from various d. vulgaris pure culture experiment ...	2007	17107661
pathway confirmation and flux analysis of central metabolic pathways in desulfovibrio vulgaris hildenborough using gas chromatography-mass spectrometry and fourier transform-ion cyclotron resonance mass spectrometry.	flux distribution in central metabolic pathways of desulfovibrio vulgaris hildenborough was examined using 13c tracer experiments. consistent with the current genome annotation and independent evidence from enzyme activity assays, the isotopomer results from both gas chromatography-mass spectrometry (gc-ms) and fourier transform-ion cyclotron resonance mass spectrometry (ft-icr ms) indicate the lack of an oxidatively functional tricarboxylic acid (tca) cycle and an incomplete pentose phosphate p ...	2007	17114264
from bio-mineralisation to fuel cells: biomanufacture of pt and pd nanocrystals for fuel cell electrode catalyst.	biosynthesis of nano-scale platinum and palladium was achieved via enzymatically-mediated deposition of metal ions from solution. the bio-accumulated pt(0) and pd(0) crystals were dried, applied onto carbon paper and tested as anodes in a polymer electrolyte membrane (pem) fuel cell for power production. up to 100% and 81% of the maximum power generation was achieved by the bio-pt and bio-pd catalysts, respectively, compared to commercial fuel cell grade pt catalyst. hence, biomineralisation cou ...	2007	17295088
analysis of amino acid isotopomers using ft-icr ms.	fluxes through known metabolic pathways and the presence of novel metabolic reactions are often determined by feeding isotopically labeled substrate to an organism and then determining the isotopomer distribution in amino acids in proteins. however, commonly used techniques to measure the isotopomer distributions require derivatization prior to analysis (gas chromatography/mass spectrometry (gc/ms)) or large sample sizes (nuclear magnetic resonance (nmr) spectroscopy). here, we demonstrate the u ...	2007	17305312
oil field souring control by nitrate-reducing sulfurospirillum spp. that outcompete sulfate-reducing bacteria for organic electron donors.	nitrate injection into oil reservoirs can prevent and remediate souring, the production of hydrogen sulfide by sulfate-reducing bacteria (srb). nitrate stimulates nitrate-reducing, sulfide-oxidizing bacteria (nr-sob) and heterotrophic nitrate-reducing bacteria (hnrb) that compete with srb for degradable oil organics. up-flow, packed-bed bioreactors inoculated with water produced from an oil field and injected with lactate, sulfate, and nitrate served as sources for isolating several nrb, includi ...	2007	17308184
functional properties of type i and type ii cytochromes c3 from desulfovibrio africanus.	type i cytochrome c(3) is a key protein in the bioenergetic metabolism of desulfovibrio spp., mediating electron transfer between periplasmic hydrogenase and multihaem cytochromes associated with membrane bound complexes, such as type ii cytochrome c(3). this work presents the nmr assignment of the haem substituents in type i cytochrome c(3) isolated from desulfovibrio africanus and the thermodynamic and kinetic characterisation of type i and type ii cytochromes c(3) belonging to the same organi ...	2007	17316553
force measurements of bacterial adhesion on metals using a cell probe atomic force microscope.	the adhesion of microbial cells to metal surfaces in aqueous media is an important phenomenon in both the natural environment and engineering systems. the adhesion of two anaerobic sulfate-reducing bacteria (desulfovibrio desulfuricans and a local marine isolate) and an aerobe (pseudomonas sp.) to four polished metal surfaces (i.e., stainless steel 316, mild steel, aluminum, and copper) was examined using a force spectroscopy technique with an atomic force microscope (afm). using a modified bact ...	2007	17321534
experimental evaluation and mathematical modeling of microbially enhanced tetrachloroethene (pce) dissolution.	experiments to assess metabolic reductive dechlorination (chlororespiration) at high concentration levels consistent with the presence of free-phase tetrachloroethene (pce) were performed using three pce-to-cis-1,2-dichloroethene (cis-dce) dechlorinating pure cultures (sulfurospirillum multivorans, desulfuromonas michiganensis strain bb1, and geobacter lovleyi strain sz) and desulfitobacterium sp. strain viet1, a pce-to-trichloroethene (tce) dechlorinating isolate. despite recent evidence sugges ...	2007	17328210
alkane biodegradation and dynamics of phylogenetic subgroups of sulfate-reducing bacteria in an anoxic coastal marine sediment artificially contaminated with oil.	for 503 days, unoiled control and artificially oiled sediments were incubated in situ at 20m water depth in a mediterranean coastal area. degradation of the aliphatic fraction of the oil added was followed by gc-ms. at the same time, terminal restriction fragment length polymorphism (t-rflp) of 16s rrna encoding genes was used to detect dynamics in the sulfate-reducing bacteria (srb) community in response to the oil contamination. specific polymerase chain reaction (pcr) primer sets for five gen ...	2007	17337033
influence of vitamin b12 and cocultures on the growth of dehalococcoides isolates in defined medium.	bacteria belonging to the genus dehalococcoides play a key role in the complete detoxification of chloroethenes as these organisms are the only microbes known to be capable of dechlorination beyond dichloroethenes to vinyl chloride (vc) and ethene. however, dehalococcoides strains usually grow slowly with a doubling time of 1 to 2 days and have complex nutritional requirements. here we describe the growth of dehalococcoides ethenogenes 195 in a defined mineral salts medium, improved growth of st ...	2007	17337553
regulation of arsenate resistance in desulfovibrio desulfuricans g20 by an arsrbcc operon and an arsc gene.	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. mut ...	2007	17337573
molecular characterization of sheep ruminal enrichments that detoxify pyrrolizidine alkaloids by denaturing gradient gel electrophoresis and cloning.	an enrichment of strictly anaerobic bacteria from ovine rumen fluid, which has previously been named l4m2, is known to detoxify animal hepatotoxins from the pyrrolizidine alkaloid family. these toxins are present in the tansy ragwort plant (senecio jacobaea). these plants have been described in livestock animals' range forages in regions of the world such as the northwest united states and south africa. the bacterial enrichment was characterized by molecular cloning techniques and by the molecul ...	2007	17345134
detection of structural changes in a cofactor binding protein by using a wheat germ cell-free protein synthesis system coupled with unnatural amino acid probing.	a cell-free protein synthesis system is a powerful tool with which unnatural amino acids can be introduced into polypeptide chains. here, the authors describe unnatural amino acid probing in a wheat germ cell-free translation system as a method for detecting the structural changes that occur in a cofactor binding protein on a conversion of the protein from an apo-form to a holo-form. the authors selected the fmn-binding protein from desulfovibrio vulgaris as a model protein. the apo-form of the ...	2007	17348022
quantification of sulfate-reducing bacteria in industrial wastewater, by real-time polymerase chain reaction (pcr) using dsra and apsa genes.	real-time polymerase chain reaction (pcr) is considered a highly sensitive method for the quantification of microbial organisms in environmental samples. this study was conducted to evaluate real-time pcr with sybrgreen detection as a quantification method for sulfate-reducing bacteria (srb) in industrial wastewater produced by several chemical industries. we designed four sets of primers and developed standard curves based on genomic dna of desulfovibrio vulgaris from pure culture and on plasmi ...	2007	17351812
metabolic modeling of a mutualistic microbial community.	the rate of production of methane in many environments depends upon mutualistic interactions between sulfate-reducing bacteria and methanogens. to enhance our understanding of these relationships, we took advantage of the fully sequenced genomes of desulfovibrio vulgaris and methanococcus maripaludis to produce and analyze the first multispecies stoichiometric metabolic model. model results were compared to data on growth of the co-culture on lactate in the absence of sulfate. the model accurate ...	2007	17353934
nitrogen fixation by reductively dechlorinating bacteria.	significant advances in the ecology, physiology and genetics of reductively dechlorinating bacteria have revealed their important environmental roles in bioremediation and in the global chlorine cycle. n2 fixation has been widely observed in symbiotic, associative and free-living bacteria. here we show physiological and molecular evidence that reductively dechlorinating bacteria are capable of fixing atmospheric nitrogen. furthermore, n2 fixation in some of these dechlorinating bacteria stimulat ...	2007	17359278
functional roles of the heme architecture and its environment in tetraheme cytochrome c.	cytochromes are involved in a wide variety of redox reactions in living systems. some of them contain multiple hemes such as desulfovibrio cytochrome c3 and shewanella small tetraheme cytochrome c. the significance of c-type tetraheme architectures was discussed. a cyclic heme architecture and its environment regulate the extremely low redox potentials of cytochrome c3 in addition to bis-imidazole coordination and heme exposure. each heme in cytochrome c3 plays a different role in the electron t ...	2007	17370988
abundance and diversity of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (hmx)-metabolizing bacteria in uxo-contaminated marine sediments.	octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (hmx) is a toxic explosive known to be resistant to biodegradation. in this study, we found that sediment collected from two unexploded ordnance (uxo) disposal sites (uxo-3, uxo-5) and one nearby reference site (midref) in hawaii contained anaerobic bacteria capable of removing hmx. two groups of hmx-removing bacteria were found in uxo-5: group i contained aerotolerant anaerobes and microaerophiles, and group ii contained facultative anaerobes. in ...	2007	17381523
octomeric pyruvate-ferredoxin oxidoreductase from desulfovibrio vulgaris.	pyruvate-ferredoxin oxidoreductatse (pfor) carries out the central step in oxidative decarboxylation of pyruvate to acetyl-coa. we have purified this enzyme from desulfovibrio vulgaris hildenborough (dvh) as part of a systematic characterization of as many multiprotein complexes as possible for this organism, and the three-dimensional structure of this enzyme has been determined by a combination of electron microscopy (em), single particle image analysis, homology modeling and computational mole ...	2007	17400475
dehalogenation of polychlorinated biphenyls and polybrominated diphenyl ethers using a hybrid bioinorganic catalyst.	the environmentally prevalent polybrominated diphenyl ether (pbde) #47 and polychlorinated biphenyls (pcbs) #28 and #118 were challenged for 24 hours with a novel biomass-supported pd catalyst (bio-pd(0)). analysis of the products via gc-ms revealed the bio-pd(0) to cause the challenged compounds to undergo stepwise dehalogenation with preferential loss of the least sterically hindered halogen atom. a mass balance for pcb #28 showed that it is degraded to three dichlorobiphenyls (33.9%), two mon ...	2007	17410306
hydrogen sulfide production from elemental sulfur by desulfovibrio desulfuricans in an anaerobic bioreactor.	feasibility of elemental sulfur reduction by desulfovibrio desulfuricans in anaerobic conditions in a stirred reactor was studied. hydrogen was used as energy source, whereas the carbonated species were bicarbonate and yeast extract. attention was paid to reactor engineering aspects, biofilm formation on the sulfur surface, hydrogen sulfide formation rate and kinetics limitations of the sulfur reduction. d. desulfuricans formed stable biofilms on the sulfur surface. it was found that active sulf ...	2007	17421040
co-existence of physiologically similar sulfate-reducing bacteria in a full-scale sulfidogenic bioreactor fed with a single organic electron donor.	a combination of culture-dependent and independent methods was used to study the co-existence of different sulfate-reducing bacteria (srb) in an upflow anaerobic sludge bed reactor treating sulfate-rich wastewater. the wastewater was fed with ethanol as an external electron donor. twenty six strains of srb were randomly picked and isolated from the highest serial dilution that showed growth (i.e. 10(8)). repetitive enterobacterial palindromic polymerase chain reaction and whole cell protein prof ...	2007	17440719
development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress.	the application of dna microarray technology to investigate multiple-species microbial communities presents great challenges. in this study, we reported the design and quality assessment of four whole genome oligonucleotide microarrays for two syntroph bacteria, desulfovibrio vulgaris and syntrophobacter fumaroxidans, and two archaeal methanogens, methanosarcina barkeri, and methanospirillum hungatei, and their application to analyze global gene expression in a four-species microbial community i ...	2007	17498652
superoxide radical sensing using a cytochrome c3 immobilized conducting polymer electrode.	a biosensor based on cytochrome c3 (cyt c3) has been introduced to detect and quantify superoxide radical (o2*-). cyt c3, isolated from the sulfate-reducing bacterium (desulfovibrio vulgaris miyazaki f. strain), and its mutant were immobilized onto a conducting polymer coated electrodes by the covalent bonding with carbodiimide chemistry. the immobilization of cyt c3 was investigated with quartz crystal microbalance, electrochemical impedance spectroscopy, and cyclic voltammetric studies. the cv ...	2007	17507210
prophage-like gene transfer agents-novel mechanisms of gene exchange for methanococcus, desulfovibrio, brachyspira, and rhodobacter species.	gene transfer agents (gtas) are novel mechanisms for bacterial gene transfer. they resemble small, tailed bacteriophages in ultrastructure and act like generalized transducing prophages. in contrast to functional prophages, gtas package random fragments of bacterial genomes and incomplete copies of their own genomes. the packaged dna content is characteristic of the gta and ranges in size from 4.4 to 13.6kb. gtas have been reported in species of brachyspira, methanococcus, desulfovibrio, and rho ...	2007	17513139
crystal structure of the 16 heme cytochrome from desulfovibrio gigas: a glycosylated protein in a sulphate-reducing bacterium.	sulphate-reducing bacteria have a wide variety of periplasmic cytochromes involved in electron transfer from the periplasm to the cytoplasm. hmca is a high molecular mass cytochrome of 550 amino acid residues that harbours 16 c-type heme groups. we report the crystal structure of hmca isolated from the periplasm of desulfovibrio gigas. crystals were grown using polyethylene glycol 8k and zinc acetate, and diffracted beyond 2.1 a resolution. a multiple-wavelength anomalous dispersion experiment a ...	2007	17531266
cell-wide responses to low-oxygen exposure in desulfovibrio vulgaris hildenborough.	the responses of the anaerobic, sulfate-reducing organism desulfovibrio vulgaris hildenborough to low-oxygen exposure (0.1% o(2)) were monitored via transcriptomics and proteomics. exposure to 0.1% o(2) 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% o(2) exposure. several of the candidates also showed increases in protein abundance. among the remaining sma ...	2007	17545284
assessing the role of the active-site cysteine ligand in the superoxide reductase from desulfoarculus baarsii.	superoxide reductase is a novel class of non-heme iron proteins that catalyzes the one-electron reduction of o(2)(.) to h(2)o(2), providing an antioxidant defense in some bacteria. its active site consists of an unusual non-heme fe(2+) center in a [his(4) cys(1)] square pyramidal pentacoordination. in this class of enzyme, the cysteine axial ligand has been hypothesized to be an essential feature in the reactivity of the enzyme. previous fourier transform infrared spectroscopy studies on the enz ...	2007	17545670
a dual-electrochemical cell to study the biocorrosion of stainless steel.	the presence of microorganisms on metal surfaces can alter the local physical/chemical conditions and lead to microbiologically influenced corrosion (mic). the goal of the present work was to study the effect of a mixed aerobic-anaerobic biofilm on the behaviour of stainless steel (316 l) in underground conditions. rather than testing different bacteria or consortia, investigations were based on the mechanisms of mic. mixed biofilms were simulated by the addition of glucose oxidase to reproduce ...	2007	17547022
desulfovibrio fairfieldensis bacteremia associated with choledocholithiasis and endoscopic retrograde cholangiopancreatography.	desulfovibrio fairfieldensis is a gram-negative, curved, motile, anaerobic bacillus. d. fairfieldensis has been isolated only from human specimens and is considered a normal resident of the human gastrointestinal tract. we report the second case of desulfovibrio bacteremia associated with choledocholithiasis and review the other reported cases of d. fairfieldensis bacteremia.	2007	17567792
comparative transcriptome analysis of desulfovibrio vulgaris grown in planktonic culture and mature biofilm on a steel surface.	biofilm build-up of sulphate-reducing bacteria (srb) on metal 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 desulfovibrio vulgaris on a steel surface. statistical analysis revealed that 472 genes were differentially expressed (1.5-fold or more with a q value less than 0.025) by comparing ...	2007	17571259
epr characterization of the molybdenum(v) forms of formate dehydrogenase from desulfovibrio desulfuricans atcc 27774 upon formate reduction.	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 ...	2007	17574676
diversity of substrate utilization and growth characteristics of sulfate-reducing bacteria isolated from estuarine sediment in japan.	two different isolation methods, the dilution colony-counting method (colony-isolation) and enrichment culture, were used to isolate sulfate-reducing bacteria (srbs) from estuarine sediment in japan. lactate was used as an electron donor for colony-isolation, and lactate or propionate was used for enrichment culture. all isolates were classified into six different phylogenetic groups according to the 16s rrna gene-based analysis. the closest relatives of the colony-isolates (12 strains) were spe ...	2007	17575452
redox-linked conformational changes of a multiheme cytochrome from geobacter sulfurreducens.	multiheme c-type cytochromes from members of the desulfovibrionacea and geobactereacea families play crucial roles in the bioenergetics of these microorganisms. thermodynamic studies using nmr and visible spectroscopic techniques on tetraheme cytochromes c(3) isolated from desulfovibrio spp. and more recently on a triheme cytochrome from geobacter sulfurreducens showed that the properties of each redox centre are modulated by the neighbouring redox centres enabling these proteins to perform ener ...	2007	17583674
[sulfate-reducing bacteria in reservoirs of the yavoriv sulfur field].	fifteen cultures of bacteria which perform dissimilation sulfate reduction have been isolated from the reservoirs of the yavoriv sulfur deposit. electron-microscopic investigations have shown that the cells of all cultures are of vibroid, spiral and bacillary form. they form no spores. they grow in the medium with sulfates and lactates and do not use propionate and acetate. in the medium with lactate all the cultures accumulated acetate in the medium. cells of all the studied bacteria contain de ...	2006	17388124
x-ray structure of the membrane-bound cytochrome c quinol dehydrogenase nrfh reveals novel haem coordination.	oxidation of membrane-bound quinol molecules is a central step in the respiratory electron transport chains used by biological cells to generate atp by oxidative phosphorylation. a novel family of cytochrome c quinol dehydrogenases that play an important role in bacterial respiratory chains was recognised in recent years. here, we describe the first structure of a cytochrome from this family, nrfh from desulfovibrio vulgaris, which forms a stable complex with its electron partner, the cytochrome ...	2006	17139260
spectroelectrochemistry of type ii cytochrome c3 on a glycosylated self-assembled monolayer.	a modified silver electrode was prepared by the self-assembly of a thiol-derivatized neoglycoconjugate, forming a 2d surface with maltose functionality. this self-assembled-monolayer-modified electrode was utilized for adsorption and spectroelectrochemical studies of tetraheme-containing type ii cytochrome c3. the glycosylated surface allowed for the determination of the hemes' redox potentials and demonstrated enhanced spectroelectrochemical performance, in comparison to the widely used self-as ...	2006	17106964
redox chemistry of low-ph forms of tetrahemic cytochrome c3.	desulfovibrio vulgaris hildenborough cytochrome c(3) contains four hemes in a low-spin state with bis-histidinyl coordination. high-spin forms of cytochrome c(3) can be generated by protonation of the axial ligands in order to probe spin equilibrium (low-spin/high-spin). the spin alterations occurring at acid ph, the associated changes in redox potentials, as well as the reactivity towards external ligands were followed by the conjunction of square wave voltammetry and uv-visible, cd, nmr and ep ...	2006	17084898
interaction of desulfovibrio desulfuricans biofilms with stainless steel surface and its impact on bacterial metabolism.	to study the influence of some metallic elements of stainless steel 304 (ss 304) on the development and activity of a sulfate-reducing bacterial biofilm, using as comparison a reference nonmetallic material polymethylmethacrylate (pmma).	2006	17040232
a 1,1,1-trichloroethane-degrading anaerobic mixed microbial culture enhances biotransformation of mixtures of chlorinated ethenes and ethanes.	1,1,1-trichloroethane (1,1,1-tca) is a common groundwater pollutant as a result of improper disposal and accidental spills. it is often found as a cocontaminant with trichloroethene (tce) and inhibits some tce-degrading microorganisms. 1,1,1-tca removal is therefore required for effective bioremediation of sites contaminated with mixed chlorinated organics. this study characterized ms, a 1,1,1-tca-degrading, anaerobic, mixed microbial culture derived from a 1,1,1-tca-contaminated site in the nor ...	2006	17056695
lc-ms/ms based proteomic analysis and functional inference of hypothetical proteins in desulfovibrio vulgaris.	high efficiency capillary liquid chromatography-tandem mass spectrometry (lc-ms/ms) was used to examine the proteins extracted from desulfovibrio vulgaris cells across six treatment conditions. while our previous study provided a proteomic overview of the cellular metabolism based on proteins with known functions [w. zhang, m.a. gritsenko, r.j. moore, d.e. culley, l. nie, k. petritis, e.f. strittmatter, d.g. camp ii, r.d. smith, f.j. brockman, a proteomic view of the metabolism in desulfovibrio ...	2006	16982031
human inflammatory bowel disease does not associate with lawsonia intracellularis infection.	there is increasing evidence that bacterial infection of the intestinal mucosa may contribute to the pathogenesis of inflammatory bowel diseases (ibd). in pigs, an obligate intracellular bacterium, lawsonia intracellularis (li), was shown to cause proliferative enteropathy (pe) of which some forms display histological and clinical similarities to human ibd. since li-similar desulfovibrio spp. may infect human cells, we hypothesized that li might be associated with the development of human ibd.	2006	16984651
the effect of decreasing alkalinity on microbial community dynamics in a sulfate-reducing bioreactor as analyzed by pcr-sscp.	pcr-single-strand conformation polymorphism (sscp) and southern blotting techniques were adopted to investigate microbial community dynamics in a sulfate-reducing bioreactor caused by decreasing influent alkalinity. experimental results indicated that the sulfate-removal rate approached 87% in 25 d under the conditions of influent alkalinity of 4000 mg/l (as caco3) and sulfate-loading rate of 4.8 g/(l*d), which indicated that the bioreactor started up successfully. the analysis of microbial comm ...	2006	16989283
synergistic inhibition of microbial sulfide production by combinations of the metabolic inhibitor nitrite and biocides.	mics of six broad-spectrum biocides and two specific metabolic inhibitors and fractional inhibitory concentration indexes (ficis) for controlling a sulfide-producing consortium were determined. nitrite was synergistic (fici<1) with all but one biocide due to its specific inhibition of dissimilatory sulfite reductase. hence, combining nitrite with biocides allows more efficient and cost-effective control of sulfate-reducing bacteria.	2006	16997976
recovery of temperate desulfovibrio vulgaris bacteriophage using a novel host strain.	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 tha ...	2006	17014494
heme biosynthesis in methanosarcina barkeri via a pathway involving two methylation reactions.	the methanogenic archaeon methanosarcina barkeri synthesizes protoheme via precorrin-2, which is formed from uroporphyrinogen iii in two consecutive methylation reactions utilizing s-adenosyl-l-methionine. the existence of this pathway, previously exclusively found in the sulfate-reducing delta-proteobacterium desulfovibrio vulgaris, was demonstrated for m. barkeri via the incorporation of two methyl groups from methionine into protoheme.	2006	17028275
correlation of mrna expression and protein abundance affected by multiple sequence features related to translational efficiency in desulfovibrio vulgaris: a quantitative analysis.	the modest correlation between mrna expression and protein abundance in large-scale data sets 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 f ...	2006	17028312
spectroelectrochemical characterization of the [nife] hydrogenase of desulfovibrio vulgaris miyazaki f.	the active site in the [nife] hydrogenase of desulfovibrio vulgaris miyazaki f has been investigated by fourier transform infrared (ftir) spectroscopy. analysis of the spectra allowed the three diatomic inorganic ligands to fe in this enzyme to be identified as one co molecule and two cn(-) molecules. furthermore, ph-dependent redox titrations were performed to determine the midpoint potentials as well as the pk value of the respective reactions and revealed that each single-electron redox trans ...	2006	16893172
cr(vi) detoxification by desulfovibrio vulgaris strain hildenborough: microbe-metal interactions studies.	toxic heavy metals constitute a worldwide environmental pollution problem. bioremediation technologies represent efficient alternatives to the classic cleaning-up of contaminated soil and ground water. most toxic heavy metals such as chromium are less soluble and toxic when reduced than when oxidized. sulfate-reducing bacteria (srb) are able to reduce heavy metals by a chemical reduction via the production of h2s and by a direct enzymatic process involving hydrogenases and c3 cytochromes. we hav ...	2006	16896506
sequential and structural analysis of [nife]-hydrogenase-maturation proteins from desulfovibrio vulgaris miyazaki f.	the complete primary structure of the hyn-region in the genome of desulfovibrio vulgaris miyazaki f (dvmf), encoding the [nife]-hydrogenase and two maturation proteins has been identified. besides the formerly reported genes for the large and small subunits, this region comprises genes encoding an endopeptidase (hync) and a putative chaperone (hynd). the complete genomic region covers 4086 nucleotides including the previously published upstream located promoter region and the sequences of the st ...	2006	16902753
palladium and gold removal and recovery from precious metal solutions and electronic scrap leachates by desulfovibrio desulfuricans.	biomass of desulfovibrio desulfuricans was used to recover au(iii) as au(0) from test solutions and from waste electronic scrap leachate. au(0) was precipitated extracellularly by a different mechanism from the biodeposition of pd(0). the presence of cu(2+) ( approximately 2000 mg/l) in the leachate inhibited the hydrogenase-mediated removal of pd(ii) but pre-palladisation of the cells in the absence of added cu(2+) facilitated removal of pd(ii) from the leachate and more than 95% of the pd(ii) ...	2006	16909331
a variant system i for cytochrome c biogenesis in archaea and some bacteria has a novel ccme and no ccmh.	c-type cytochromes are characterized by post-translational covalent attachment of heme to thiols that occur in a cys-xxx-xxx-cys-his motif. three distinct biogenesis systems are known for this heme attachment. archaea are now shown to contain a significantly modified form of cytochrome c maturation system i (the ccm system). the most notable adaptation relative to the well-studied apparatus from proteobacteria and plants is a novel form of the heme chaperone ccme, lacking the highly conserved hi ...	2006	16920107
the tmc complex from desulfovibrio vulgaris hildenborough is involved in transmembrane electron transfer from periplasmic hydrogen oxidation.	three membrane-bound redox complexes have been reported in desulfovibrio spp., whose genes are not found in the genomes of other sulfate reducers such as desulfotalea psycrophila and archaeoglobus fulgidus. these complexes contain a periplasmic cytochrome c subunit of the cytochrome c(3) family, and their presence in these organisms probably correlates with the presence of a pool of periplasmic cytochromes c(3), also absent in the two other sulfate reducers. in this work we report the isolation ...	2006	16922512
rubredoxin:oxygen oxidoreductase enhances survival of desulfovibrio vulgaris hildenborough under microaerophilic conditions.	genes for superoxide reductase (sor), rubredoxin (rub), and rubredoxin:oxygen oxidoreductase (roo) are located in close proximity in the chromosome of desulfovibrio vulgaris hildenborough. protein blots confirmed the absence of roo from roo mutant and sor-rub-roo (srr) mutant cells and its presence in sor mutant and wild-type cells grown under anaerobic conditions. oxygen reduction rates of the roo and srr mutants were 20 to 40% lower than those of the wild type and the sor mutant, indicating th ...	2006	16923892
the role of the hybrid cluster protein in oxidative stress defense.	hybrid cluster proteins (hcp) contain two types of fe/s clusters, namely a [4fe-4s](2+/1+) or [2fe-2s](2+/1+) cluster and a novel type of hybrid cluster, [4fe-2s-2o], in the as-isolated state. although first isolated from anaerobic sulfate-reducing bacteria, the analysis of the genomic sequences reveals that genes encoding putative hybrid cluster proteins are present in a wide range of organisms, aerobic, anaerobic, or facultative, from the bacteria, archaea, and eukarya domains. despite a detai ...	2006	16928682
crystal structure of rubredoxin from desulfovibrio gigas to ultra-high 0.68 a resolution.	rubredoxin (d.g. rd) is a small non-heme iron-sulfur protein shown to function as a redox coupling protein from the sulfate reducing bacteria desulfovibrio gigas. the protein is generally purified from anaerobic bacteria in which it is thought to be involved in electron transfer or exchange processes. rd transfers an electron to oxygen to form water as part of a unique electron transfer chain, composed by nadh:rubredoxin oxidoreductase (nro), rubredoxin and rubredoxin:oxygen oxidoreductase (roo) ...	2006	16930541
a versatile and sensitive tritium-based radioassay for measuring hydrogenase activity in aquatic sediments.	we present a method for the measurement of hydrogenase (h(2)ase) activity in aquatic sediments. the assay is based on the h(2)ase-mediated isotopic exchange between dissolved molecular hydrogen (h(2)) and water. a slurry of sediment material is incubated with a tritiated hydrogen (ht) headspace in a glass syringe on a rotary shaker. the method includes a procedure for preparing ht from radiolabeled sodium borohydride, which is a useful alternative to purchasing ht directly. a method for measurin ...	2006	16356571