Publications

interaction between uranium and the cytochrome c3 of desulfovibrio desulfuricans strain g20.	cytochrome c(3) of desulfovibrio desulfuricans strain g20 is an electron carrier for uranium (vi) reduction. when d. desulfuricans g20 was grown in medium containing a non-lethal concentration of uranyl acetate (1 mm), the rate at which the cells reduced u(vi) was decreased compared to cells grown in the absence of uranium. western analysis did not detect cytochrome c(3) in periplasmic extracts from cells grown in the presence of uranium. the expression of this predominant tetraheme cytochrome w ...	2004	15114437
carbon monoxide and oxidative stress in desulfovibrio desulfuricans b-1388.	it has been shown that carbon monoxide (co) in low concentration may be an active biochemical and physiological regulator of cell function. the bases of co toxicity and cell protection are not clearly understood. to provide insights into these mechanisms, we measured superoxide production by d. desulfuricans b-1388 incubated anaerobically in postgate medium with or without 5% co. d. desulfuricans b-1388 growing with co in the gas phase produced more superoxide radicals then control cells growing ...	2004	15122650
automated purification and suspension array detection of 16s rrna from soil and sediment extracts by using tunable surface microparticles.	autonomous, field-deployable molecular detection systems require seamless integration of complex biochemical solutions and physical or mechanical processing steps. in an attempt to simplify the fluidic requirements for integrated biodetection systems, we used tunable surface microparticles both as an rrna affinity purification resin in a renewable microcolumn sample preparation system and as the sensor surface in a flow cytometer detector. the tunable surface detection limits in both low- and hi ...	2004	15128511
displacement of iron by zinc at the diiron site of desulfovibrio vulgaris rubrerythrin: x-ray crystal structure and anomalous scattering analysis.	x-ray crystal structures of recombinant desulfovibrio (d.) vulgaris rubrerythrin (rbr) have shown a diiron site, whereas the crystal structure of rbr "as-isolated" from d. vulgaris was reported to contain a mixed zn,fe binuclear site. to investigate the possibility that zinc had displaced iron during isolation or crystallization of the "as-isolated" d. vulgaris rbr, the x-ray crystal structure of recombinant d. vulgaris all-iron rbr that had been incubated with excess zinc sulfate prior to cryst ...	2004	15134924
antagonists mo and cu in a heterometallic cluster present on a novel protein (orange protein) isolated from desulfovibrio gigas.	an orange-coloured protein (orp) isolated from desulfovibrio gigas, a sulphate reducer, has been previously shown by extended x-ray absorption fine structure (exafs) to contain a novel mixed-metal sulphide cluster of the type [s(2)mos(2)cus(2)mos(2)] [j. am. chem. soc. 122 (2000) 8321]. we report here the purification and the biochemical/spectroscopic characterisation of this novel protein. orp is a soluble monomeric protein (11.8 kda). the cluster is non-covalently bound to the polypeptide chai ...	2004	15134929
relativistic dft calculation of the reaction cycle intermediates of [nife] hydrogenase: a contribution to understanding the enzymatic mechanism.	structures and spectroscopic observables of the paramagnetic intermediates of the enzymatic reaction cycle of the metalloenzyme [nife] hydrogenase were calculated using relativistic density functional theory (dft) within the zero-order regular approximation (zora). by comparing experimental and calculated magnetic resonance parameters (g- and hyperfine tensors) for the states ni-a, ni-b, ni-c, ni-l, and ni-co the details of the atomic composition of these paramagnetic intermediates could be eluc ...	2004	15134933
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase: head-to-head with a bifunctional enzyme that controls glycolysis.	fru-2,6-p2 (fructose 2,6-bisphosphate) is a signal molecule that controls glycolysis. since its discovery more than 20 years ago, inroads have been made towards the understanding of the structure-function relationships in pfk-2 (6-phosphofructo-2-kinase)/fbpase-2 (fructose-2,6-bisphosphatase), the homodimeric bifunctional enzyme that catalyses the synthesis and degradation of fru-2,6-p2. the fbpase-2 domain of the enzyme subunit bears sequence, mechanistic and structural similarity to the histid ...	2004	15170386
susceptibility of desulfovibrio desulfuricans intestinal strains to sulfasalazine and its biotransformation products.	desulfovibrio desulfuricans intestinal bacteria may contribute to toxic hydrogen sulfide production in the human gut. our objective was to examine whether the d. desulfuricans strains isolated from the human body are susceptible to sulfasalazine (sas) and the products of its biotransformation, i.e. 5-aminosalicylic acid (5-asa) and sulfapyridine (sp), in order to determine the relationship between the strains' susceptibility to sas and their ability to reduce the azo bond within this drug.	2004	15173665
ftir spectroelectrochemical study of the activation and inactivation processes of [nife] hydrogenases: effects of solvent isotope replacement and site-directed mutagenesis.	the kinetics of the activation and anaerobic inactivation processes of desulfovibrio gigas hydrogenase have been measured in d(2)o by ftir spectroelectrochemistry. a primary kinetic solvent isotope effect was observed for the inactivation process but not for the activation step. the kinetics of these processes have been also measured after replacement of a glutamic residue placed near the active site of an analogous [nife] hydrogenase from desulfovibrio fructosovorans. its replacement by a gluta ...	2004	15175937
characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time pcr and effects of antibiotic treatment on the fecal microbiota.	fecal bacteria were studied in healthy elderly volunteers (age, 63 to 90 years; n = 35) living in the local community, elderly hospitalized patients (age, 66 to 103; n = 38), and elderly hospitalized patients receiving antibiotic treatment (age, 65 to 100; n = 21). group- and species-specific primer sets targeting 16s rrna genes were used to quantitate intestinal bacteria by using dna extracted from feces and real-time pcr. the principal difference between healthy elderly volunteers and both pat ...	2004	15184159
the genome of desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold arctic sediments.	desulfotalea psychrophila is a marine sulfate-reducing delta-proteobacterium that is able to grow at in situ temperatures below 0 degrees c. as abundant members of the microbial community in permanently cold marine sediments, d. psychrophila-like bacteria contribute to the global cycles of carbon and sulfur. here, we describe the genome sequence of d. psychrophila strain lsv54, which consists of a 3 523 383 bp circular chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14 66 ...	2004	15305914
changes in the nitrocellulose molecule induced by sulfate-reducing bacteria desulfovibrio desulfuricans 1,388. the enzymes participating in this process.	the appearance of unsubstituted glucopyranose residues in nitrocellulose (nc) induced by desulfovibrio desulfuricans was established by (13)c-nmr spectroscopy. after contact with bacterial cells, the degree of substitution by nitro groups in nc decreased from 2.59 to 2.40. the bacteria possess intra- and extracellular nitroesterase activities, which are responsible for denitration of the polymer. the presence of nc in the growth medium influences the extracellular nitroesterase activity. it is s ...	2004	15310283
roles of noncoordinated aromatic residues in redox regulation of cytochrome c3 from desulfovibrio vulgaris miyazaki f.	the roles of aromatic residues in redox regulation of cytochrome c(3) were investigated by site-directed mutagenesis at every aromatic residue except for axial ligands (phe20, tyr43, tyr65, tyr66, his67, and phe76). the mutations at phe20 induced large chemical shift changes in the nmr signals for hemes 1 and 3, and large changes in the microscopic redox potentials of hemes 1 and 3. the nmr signals of the axial ligands of hemes 1 and 3 were also affected. analysis of the nature of the mutations ...	2004	15323546
overexpression and purification of treponema pallidum rubredoxin; kinetic evidence for a superoxide-mediated electron transfer with the superoxide reductase neelaredoxin.	superoxide reductases are a class of non-haem iron enzymes which catalyse the monovalent reduction of the superoxide anion o2- into hydrogen peroxide and water. treponema pallidum (tp), the syphilis spirochete, expresses the gene for a superoxide reductase called neelaredoxin, having the iron protein rubredoxin as the putative electron donor necessary to complete the catalytic cycle. in this work, we present the first cloning, overexpression in escherichia coli and purification of the tp rubredo ...	2004	15328557
structure of superoxide reductase bound to ferrocyanide and active site expansion upon x-ray-induced photo-reduction.	some sulfate-reducing and microaerophilic bacteria rely on the enzyme superoxide reductase (sor) to eliminate the toxic superoxide anion radical (o2-). sor catalyses the one-electron reduction of o2- to hydrogen peroxide at a nonheme ferrous iron center. the structures of desulfoarculus baarsii sor (mutant e47a) alone and in complex with ferrocyanide were solved to 1.15 and 1.7 a resolution, respectively. the latter structure, the first ever reported of a complex between ferrocyanide and a pro ...	2004	15341736
a theoretical study of spin states in ni-s4 complexes and models of the [nife] hydrogenase active site.	we have applied density functional theory, using both pure (bp86) and hybrid (b3lyp and b3lyp*) functionals, to investigate structural parameters and reaction energies for nickel(ii)-sulfur coordination compounds, as well as for small cluster models of the ni-si and ni-r redox state of [nife] hydrogenases. results obtained investigating experimentally well-characterized complexes show that bp86 is well suited to describe the structural features of this class of compounds. however, the singlet-tr ...	2004	15365900
roll with the flow: microbial masters of redox chemistry.		2004	15381191
inhibition and aerobic inactivation kinetics of desulfovibrio fructosovorans nife hydrogenase studied by protein film voltammetry.	we have used protein film voltammetry to study the nife hydrogenase from desulfovibrio fructosovorans. we show how measurements of transient activity following the addition in the electrochemical cell of h(2), co, or o(2) allow simple and virtually instantaneous determinations of the michaelis constant, inhibition constant, or rate of inactivation, respectively, thus opening new opportunities to study the active site of nife hydrogenases. the binding and release of co occur within a fraction of ...	2004	15382953
epr spectroscopy of protein microcrystals oriented in a liquid crystalline polymer medium.	correlation of the g-tensor of a paramagnetic active center of a protein with its structure provides a unique experimental information on the electronic structure of the metal site. to address this problem, we made solid films containing metalloprotein (desulfovibrio gigas cytochrome c(3)) microcrystals. the microcrystals in a liquid crystalline polymer medium (water/hydroxypropylcellulose) were partially aligned by a shear flow. a strong orientation effect of the metalloprotein was observed by ...	2004	15388083
desulfovibrio bastinii sp. nov. and desulfovibrio gracilis sp. nov., moderately halophilic, sulfate-reducing bacteria isolated from deep subsurface oilfield water.	two moderately halophilic, mesophilic, sulfate-reducing bacteria were isolated from production-water samples from emeraude oilfield, congo. motile, vibrioid cells of srl4225t grew optimally at a concentration of 4 % nacl, at ph 5.8-6.2, with a minimal ph for growth of 5.2, showing that it is a moderately acidophilic bacterium. cells of srl6146t were motile, curved or vibrioid, long and thin rods. optimal growth was obtained at a concentration of 5-6 % nacl, at ph 6.8-7.2. the nutritional require ...	2004	15388730
desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir.	a novel sulphate-reducing bacterium (al1t) was recovered from a soured oil well in purdu bay, alaska. light and atomic force microscopy observations revealed that cells were gram-negative, vibrio-shaped and motile by means of a single polar flagellum. the carbon and energy sources used by the isolate and the salinity, temperature and ph ranges facilitating its growth proved to be typical of a partial lactate-oxidizing, moderately halophilic, mesophilic, sulphate-reducing bacterium. analysis of t ...	2004	15388739
[stages of biofilm formation by sulfate-reducing bacteria].	taxis to fe3+ ions and adhesion to steel-3 of sulphate-reducing bacteria different by corrosion activity have been investigated. it has been shown that taxis activity of cells from the postgate medium "b" was higher than from the buffer. aggressive strains desulfovibrio indonensis, desulfovibrio sp. possessed higher activity taxis with respect to fe3+ ions. it has been noted that aggressive strains of sulphate-reducing bacteria adhered more actively to the steel surface and formed more powerful ...	2004	15456221
thermal unfolding of apo and holo desulfovibrio desulfuricans flavodoxin: cofactor stabilizes folded and intermediate states.	we here compare thermal unfolding of the apo and holo forms of desulfovibrio desulfuricans flavodoxin, which noncovalently binds a flavin mononucleotide (fmn) cofactor. in the case of the apo form, fluorescence and far-uv circular dichroism (cd) detected transitions are reversible but do not overlap (t(m) of 50 and 60 degrees c, respectively, ph 7). the thermal transitions for the holo form follow the same pattern but occur at higher temperatures (t(m) of 60 and 67 degrees c for fluorescence and ...	2004	15461458
bacterial community associated with black band disease in corals.	black band disease (bbd) is a virulent polymicrobial disease primarily affecting massive-framework-building species of scleractinian corals. while it has been well established that the bbd bacterial mat is dominated by a cyanobacterium, the quantitative composition of the bbd bacterial mat community has not described previously. terminal-restriction fragment length polymorphism (t-rflp) analysis was used to characterize the infectious bacterial community of the bacterial mat causing bbd. these a ...	2004	15466538
isolation of sulfate-reducing bacteria from the terrestrial deep subsurface and description of desulfovibrio cavernae sp. nov.	deep subsurface sandstones in the area of berlin (germany) located 600 to 1060 m below the surface were examined for the presence of viable microorganisms. the in situ temperatures at the sampling sites ranged from 37 to 45 degrees c. investigations focussed on sulfate-reducing bacteria able to grow on methanol and triethylene glycol, which are added as chemicals to facilitate the long-term underground storage of natural gas. seven strains were isolated from porewater brines in the porous sandst ...	2004	15490555
cofactor-apoprotein hydrogen bonding in oxidized and fully reduced flavodoxin monitored by trans-hydrogen-bond scalar couplings.	hydrogen bonding plays a key role in the tight binding of the fmn cofactor and the regulation of its redox properties in flavodoxins. hydrogen bonding interactions can be directly observed in solution by multidimensional heteronuclear nmr spectroscopy through the scalar couplings between donor and acceptor nuclei. here we report on the detection of intermolecular trans-hydrogen-bond couplings ((h)j) between the flavin ring system and the backbone of desulfovibrio vulgaris flavodoxin in the oxidi ...	2004	15515086
[effect of corrosion inhibitor on adhesion of sulfate-reducing bacteria to steel and their production of exopolymer complex].	it was shown in the laboratory investigations that the cells of sulphate-reducing bacteria of both aggressive desulfovibrio sp. strain kiev-10 and nonaggressive desulfovibrio desulfuricans strain kiev-45 strains can produce exopolysaccharides (eps). plankton (freely floating) cells of sulphate-reducing bacteria produce greater quantity of eps than the cells of the biofilm formed on steel. the inducing effect of metal on eps synthesis by sulphate-reducing bacteria has been established. the conten ...	2004	15515905
direct monitoring of the electron pool effect of cytochrome c3 by highly sensitive eqcm measurements.	cytochrome c(3) from desulfovibrio vulgaris has four hemes per molecule, and a redox change at the hemes alters the conformation of the protein, leading to a redox-dependent change in the interaction of cytochrome c(3) with redox partners (an electron acceptor or an electron donor). the redox-dependent change in this interaction was directly monitored by the high-performance electrochemical quartz crystal microbalance (eqcm) technique that has been improved to give high sensitivity in solution. ...	2004	15517437
reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria.	relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. the recent availability of complete finished or draft-quality genome sequences for seven representatives allowed us to investigate the genetic and regulatory factors in a number of key pathways involved in the biosynthesis of building blocks and cofactors, metal-ion homeostasis, stress response, and energy metabolism using a combination of regulatory ...	2004	15535866
physiological and gene expression analysis of inhibition of desulfovibrio vulgaris hildenborough by nitrite.	a desulfovibrio vulgaris hildenborough mutant lacking the nrfa gene for the catalytic subunit of periplasmic cytochrome c nitrite reductase (nrfha) was constructed. in mid-log phase, growth of the wild type in medium containing lactate and sulfate was inhibited by 10 mm nitrite, whereas 0.6 mm nitrite inhibited the nrfa mutant. lower concentrations (0.04 mm) inhibited the growth of both mutant and wild-type cells on plates. macroarray hybridization indicated that nitrite upregulates the nrfha ge ...	2004	15547266
sulfate-reducing bacteria in tubes constructed by the marine infaunal polychaete diopatra cuprea.	marine infaunal burrows and tubes greatly enhance solute transport between sediments and the overlying water column and are sites of elevated microbial activity. biotic and abiotic controls of the compositions and activities of burrow and tube microbial communities are poorly understood. the microbial communities in tubes of the marine infaunal polychaete diopatria cuprea collected from two different sediment habitats were examined. the bacterial communities in the tubes from a sandy sediment di ...	2004	15574900
multiple orientations in a physiological complex: the pyruvate-ferredoxin oxidoreductase-ferredoxin system.	ferredoxin i from desulfovibrio africanus (da fdi) is a small acidic [4fe-4s] cluster protein that exchanges electrons with pyruvate-ferredoxin oxidoreductase (pfor), a key enzyme in the energy metabolism of anaerobes. the thermodynamic properties and the electron transfer between pfor and either native or mutated fdi have been investigated by microcalorimetry and steady-state kinetics, respectively. the association constant of the pfor-fdi complex is 3.85 x 10(5) m(-1), and the binding affinity ...	2004	15581360
continuous removal of cr(vi) from aqueous solution catalysed by palladised biomass of desulfovibrio vulgaris.	growth-decoupled cells of desulfovibrio vulgaris ncimb 8303 can be used to reduce pd(ii) to cell-bound pd(0) (bio-pd(0)), a bioinorganic catalyst capable of reducing hexavalent chromium to less toxic cr(iii), using formate as the electron donor. magnetic resonance imaging showed that bio-pd(0), immobilized in chitosan and agar beads, is distinguishable from the surrounding gel and is evenly dispersed within the immobilization matrix. agar-immobilized bio-pd(0) and 'chemical pd(0)' were packed in ...	2004	15604792
an orientation-selected endor and hyscore study of the ni-c active state of desulfovibrio vulgaris miyazaki f hydrogenase.	electron nuclear double resonance (endor) and hyperfine sublevel correlation spectroscopy (hyscore) are applied to study the active site of catalytic [nife]-hydrogenase from desulfovibrio vulgaris miyazaki f in the reduced ni-c state. these techniques offer a powerful tool for detecting nearby magnetic nuclei, including a metal-bound substrate hydrogen, and for mapping the spin density distribution of the unpaired electron at the active site. the observed hyperfine couplings are assigned via com ...	2004	15611882
superoxide reductase from desulfoarculus baarsii: identification of protonation steps in the enzymatic mechanism.	superoxide reductase (sor) is a metalloenzyme that catalyzes the reduction of o2*- to h2o2 and provides an antioxidant mechanism in some anaerobic and microaerophilic bacteria. its active site contains an unusual mononuclear ferrous center (center ii). protonation processes are essential for the reaction catalyzed by sor, since two protons are required for the formation of h2o2. we have investigated the acido-basic and ph dependence of the redox properties of the active site of sor from desulfoa ...	2004	14730986
thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the central indian ridge.	a thermophilic, marine, anaerobic, chemolithoautotrophic, sulfate-reducing bacterium, strain cir29812t, was isolated from a deep-sea hydrothermal vent site at the kairei vent field on the central indian ridge. cells were gram-negative motile rods that did not form spores. the temperature range for growth was 55-80 degrees c, with an optimum at 70 degrees c. the nacl concentration range for growth was 10-35 g l(-1), with an optimum at 25 g l(-1). the ph range for growth was 6-6.7, with an optimum ...	2004	14742485
cloning and expression of the enolase gene from desulfovibrio vulgaris (miyazaki f).	the gene encoding an enolase from desulfovibrio vulgaris (miyazaki f) was cloned and overexpressed in escherichia coli. a 2.1-kb dna fragment, isolated from d. vulgaris (miyazaki f) by double digestion with psti and bamhi, contained an enolase gene (eno) and part of the methylenetetrahydrofolate dehydrogenase gene (fold). the nucleotide sequence of eno indicates that the protein monomer is composed of 434 amino acids. an expression system for eno under control of the t7 promoter was constructed ...	2004	14746912
enzymatic mechanism of fe-only hydrogenase: density functional study on h-h making/breaking at the diiron cluster with concerted proton and electron transfers.	the mechanism of the enzymatic hydrogen bond forming/breaking (2h(+) + 2e<==>h(2)) and the plausible charge and spin states of the catalytic diiron subcluster [fefe](h) of the h cluster in fe-only hydrogenases are probed computationally by the density functional theory. it is found that the active center [fefe](h) can be rationally simulated as [[h](ch(3)s)(co)(cn(-))fe(p)(co(b))(mu-srs)fe(d)(co)(cn(-))l], where the monovalence [h] stands for the [4fe4s](h)(2+) subcluster bridged to the [fefe](h ...	2004	14753812
a novel approach to investigate biofilm accumulation and bacterial transport in porous matrices.	knowledge of bacterial transport through, and biofilm growth in, porous media is vitally important in numerous natural and engineered environments. despite this, porous media systems are generally oversimplified and the local complexity of cell transport, biofilm formation and the effect of biofilm accumulation on flow patterns is lost. in this study, cells of the sulphate-reducing bacterium, desulfovibrio sp. ex265, accumulated primarily on the leading faces of obstructions and developed into b ...	2004	14756882
stable carbon isotope ratios of lipid biomarkers of sulfate-reducing bacteria.	we examined the potential use of natural-abundance stable carbon isotope ratios of lipids for determining substrate usage by sulfate-reducing bacteria (srb). four srb were grown under autotrophic, mixotrophic, or heterotrophic growth conditions, and the delta13c values of their individual fatty acids (fa) were determined. the fa were usually 13c depleted in relation to biomass, with deltadelta13c(fa - biomass) of -4 to -17 per thousand; the greatest depletion occurred during heterotrophic growth ...	2004	14766550
detection and characterization of a dehalogenating microorganism by terminal restriction fragment length polymorphism fingerprinting of 16s rrna in a sulfidogenic, 2-bromophenol-utilizing enrichment.	terminal restriction fragment length polymorphism analysis of reverse-transcribed 16s rrna during periods of community flux was used as a tool to delineate the roles of the members of a 2-bromophenol-degrading, sulfate-reducing consortium. starved, washed cultures were amended with 2-bromophenol plus sulfate, 2-bromophenol plus hydrogen, phenol plus sulfate, or phenol with no electron acceptor and were monitored for substrate use. in the presence of sulfate, 2-bromophenol and phenol were complet ...	2004	14766602
incorporation of either molybdenum or tungsten into formate dehydrogenase from desulfovibrio alaskensis ncimb 13491; epr assignment of the proximal iron-sulfur cluster to the pterin cofactor in formate dehydrogenases from sulfate-reducing bacteria.	we report the characterization of the molecular properties and epr studies of a new formate dehydrogenase (fdh) from the sulfate-reducing organism desulfovibrio alaskensis ncimb 13491. fdhs are enzymes that catalyze the two-electron oxidation of formate to carbon dioxide in several aerobic and anaerobic organisms. d. alaskensis fdh is a heterodimeric protein with a molecular weight of 126+/-2 kda composed of two subunits, alpha=93+/-3 kda and beta=32+/-2 kda, which contains 6+/-1 fe/molecule, 0. ...	2004	14669076
a glutamate is the essential proton transfer gate during the catalytic cycle of the [nife] hydrogenase.	kinetic, epr, and fourier transform infrared spectroscopic analysis of desulfovibrio fructosovorans [nife] hydrogenase mutants targeted to glu-25 indicated that this amino acid participates in proton transfer between the active site and the protein surface during the catalytic cycle. replacement of that glutamic residue by a glutamine did not modify the spectroscopic properties of the enzyme but cancelled the catalytic activity except the para-h(2)/ortho-h(2) conversion. this mutation impaired t ...	2004	14688251
improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraints.	protein comparative modeling has useful applications in large-scale structural initiatives and in rational design of drug targets in medicinal chemistry. the reliability of a homology model is dependent on the sequence identity between the query and the structural homologue used as a template for modeling. here, we present a method for the utilization and conservation of important structural features of template structures by providing additional spatial restraints in comparative modeling progra ...	2004	14691673
molecular basis for redox-bohr and cooperative effects in cytochrome c3 from desulfovibrio desulfuricans atcc 27774: crystallographic and modeling studies of oxidized and reduced high-resolution structures at ph 7.6.	the tetraheme cytochrome c3 is a small metalloprotein with ca. 13,000 da found in sulfate-reducing bacteria, which is believed to act as a partner of hydrogenase. the three-dimensional structure of the oxidized and reduced forms of cytochrome c3 from desulfovibrio desulfuricans atcc 27774 at ph 7.6 were determined using high-resolution x-ray crystallography and were compared with the previously determined oxidized form at ph 4.0. theoretical calculations were performed with both structures, usin ...	2004	14705030
periplasmic cytochrome c3 of desulfovibrio vulgaris is directly involved in h2-mediated metal but not sulfate reduction.	kinetic parameters and the role of cytochrome c(3) in sulfate, fe(iii), and u(vi) reduction were investigated in desulfovibrio vulgaris hildenborough. while sulfate reduction followed michaelis-menten kinetics (k(m) = 220 micro m), loss of fe(iii) and u(vi) was first-order at all concentrations tested. initial reduction rates of all electron acceptors were similar for cells grown with h(2) and sulfate, while cultures grown using lactate and sulfate had similar rates of metal loss but lower sulfa ...	2004	14711670
a new function of the desulfovibrio vulgaris hildenborough [fe] hydrogenase in the protection against oxidative stress.	sulfate-reducing bacteria, like desulfovibrio vulgaris hildenborough, have developed a set of reactions allowing them to survive in oxic environments and even to reduce molecular oxygen to water. d. vulgaris contains a cytoplasmic superoxide reductase (sor) and a periplasmic superoxide dismutase (sod) involved in the elimination of superoxide anions. to assign the function of sod, the periplasmic [fe] hydrogenase activity was followed in both wild-type and sod deletant strains. this activity was ...	2004	14594815
x-ray induced reduction of the crystal of high-molecular-weight cytochrome c revealed by microspectrophotometry.	the crystal structures of high-molecular-weight cytochrome c (hmc) from desulfovibrio vulgaris hildenborough in the transient and reduced states have been determined at 2.8 a resolution. an absorption spectrum measured with microspectrophotometer indicated that about 86% of the hemes were reduced after 45 min irradiation of the x-ray beam. further exposure for 90 min did not significantly change the spectrum. these results suggest that hmc in the crystalline state is easily reduced by illuminati ...	2004	14646149
inhibiting mild steel corrosion from sulfate-reducing bacteria using antimicrobial-producing biofilms in three-mile-island process water.	biofilms were used to produce gramicidin s (a cyclic decapeptide) to inhibit corrosion-causing, sulfate-reducing bacteria (srb). in laboratory studies these biofilms protected mild steel 1010 continuously from corrosion in the aggressive, cooling service water of the amergen three-mile-island (tmi) nuclear plant, which was augmented with reference srb. the growth of both reference srb (gram-positive desulfosporosinus orientis and gram-negative desulfovibrio vulgaris) was shown to be inhibited by ...	2004	12898064
application of cell-free translation systems to studies of cofactor binding proteins.	to develop applications of in vitro cell-free translation systems for production and characterization of cofactor binding proteins, we investigate the production of apo- or holo-forms of flavin mono nucleotide (fmn)-binding protein from desulfovibrio vulgaris (miyazaki f) and purified them. the redox potential analysis and measurements of uv-, visible, and fluorescent spectra of reconstructed holo-protein showed that the fmn correctly bound to the fmn binding site. on the other hand, contrary to ...	2004	17150519
simple organic electron donors support diverse sulfate-reducing communities in fluidized-bed reactors treating acidic metal- and sulfate-containing wastewater.	bacterial diversity of lactate- and ethanol-utilizing sulfate-reducing fluidized-bed reactor (fbr) communities was investigated with culture-independent methods. the fbrs were fed for 500 days with synthetic mineral processing wastewater containing sulfate, zinc and iron with hydraulic retention time of 16-24 h. sodium lactate or ethanol was used as electron donor for microbial sulfate reduction. for microbial characterization, 16s rrna gene clone libraries and denaturing gradient gel electropho ...	2004	19712316
molecular quantification of sulfate-reducing microorganisms (carrying dsrab genes) by competitive pcr in estuarine sediments.	in this study, we describe a competitive polymerase chain reaction (pcr) for the quantification of the sequences of dsrab in sulfate-reducing microorganisms. we used the dsr1f/dsr4r set of primers, previously designed by wagner et al. (1998), and a competitor sequence was constructed from the dsrab genes of desulfovibrio vulgaris. the detection limit of competitive pcr corresponded to 45 copies of the dsrab genes per ng of extracted dna, and most of the dsrab sequences amplified and cloned from ...	2004	19712335
purification and preliminary characterization of tetraheme cytochrome c3 and adenylylsulfate reductase from the peptidolytic sulfate-reducing bacterium desulfovibrio aminophilus dsm 12254.	two proteins were purified and preliminarily characterized from the soluble extract of cells (310 g, wet weight) of the aminolytic and peptidolytic sulfate-reducing bacterium desulfovibrio (d.) aminophilus dsm 12254. the iron-sulfur flavoenzyme adenylylsulfate (adenosine 5'-phosphosulfate, aps) reductase, a key enzyme in the microbial dissimilatory sulfate reduction, has been purified in three chromatographic steps (deae-biogel a, source 15, and superdex 200 columns). it contains two different s ...	2005	18365091
ftir-spectroscopic studies of the fine structure of nitrocellulose treated by desulfovibrio desulfuricans.	most studies have concluded that nitrocellulose (nc) with high degree of nitrogen content is resistant to biodegradation. our results demonstrated that nc (>11%n) does undergo biotransformation in the presence of sulfate-reducing bacteria desulfovibrio desulfuricans 1388. ftir analyses indicated that the substitution of nitro groups for oh(-) groups took place. the spectrum of precipitate obtained after acetone extraction of nc resembled mainly the spectrum of native cellulose. thus the syntheti ...	2005	16701591
carbon monoxide inhibits superoxide dismutase and stimulates reactive oxygen species production by desulfovibrio desulfuricans 1388.	the hypothesis that oxidative stress characterized by enhanced superoxide generation underlies the toxicity of some factors to living organisms has been investigated. it is shown that co (5-6% in gas phase) changed some growth parameters (mu, t(d)) of the sulfate-reducing bacterium desulfovibrio desulfuricans 1388. enhanced o(2)(-) generation registered by epr spectroscopy and adrenochrome method was observed when cells were incubated under co. the sod activity in cells from the exponential grow ...	2005	16701596
desulfovibrio aerotolerans sp. nov., an oxygen tolerant sulphate-reducing bacterium isolated from activated sludge.	a new mesophilic sulphate-reducing bacterium, designated strain dvo5(t) (t=type strain), was isolated from the outermost sulphate reduction-positive most-probable-number tube (10(-6) dilution) of an activated sludge sample, which had been oxygenated at 100% air saturation for 120 h. the motile, gram-negative, curved 1 by 2-5 microm and non-spore-forming cells of strain dvo5(t) existed singly or in chains. strain dvo5(t) grew optimally at 29 degrees c, ph 6.9 and 0.05% (w/v) nacl in a medium cont ...	2005	16701597
chemical activity of iron in [2fe-2s]-protein centers and fes2(100) surfaces.	iron atoms bonded to sulfur play an important role in proteins, heterogeneous catalysts, and gas sensors. first-principles density functional calculations were used to investigate the structure and chemical activity of a unique [2fe-2s] center in the split-soret cytochrome c (ssc) from desulfovibrio desulfuricans. in agreement with a previously proposed structural model [abreu et al., j. biol. inorg. chem. 2003, 8, 360], it is found that the [2fe-2s] cluster is located in a surface pocket of the ...	2005	16851284
[sulfate-reducing bacteria in gypsum karst lakes of northern lithuania].	microbiological studies were performed in three small gypsum karst lakes in northern lithuania, most typical of the region. samples were taken in different seasons of 2001. the conditions for microbial growth in the lakes are determined by elevated content of salts (from 0.5 to 2.0 g/l), dominated by so(2-)4 and ca2+ ions (up to 1.4 and 0.6 g/l, respectively). the elevated sulfate concentration is favorable for sulfate-reducing bacteria (srbs). summer and winter stratification gives rise to anae ...	2005	16400994
electrochemical definitions of o2 sensitivity and oxidative inactivation in hydrogenases.	a new strategy is described for comparing, quantitatively, the ability of hydrogenases to tolerate exposure to o2 and anoxic oxidizing conditions. using protein film voltammetry, the inherent sensitivities to these challenges (thermodynamic potentials and rates of reactions) have been measured for enzymes from a range of mesophilic microorganisms. in the absence of o2, all the hydrogenases undergo reversible inactivation at various potentials above that of the h+/h2 redox couple, and h2 oxidatio ...	2005	16366571
desulfovibrio putealis sp. nov., a novel sulfate-reducing bacterium isolated from a deep subsurface aquifer.	a novel sulfate-reducing bacterium was isolated from a well that collected water from a deep aquifer at a depth of 430 m in the paris basin, france. the strain, designated b7-43t, was made up of vibrioid cells that were motile by means of a single polar flagellum. cells contained desulfoviridin. in the presence of sulfate, the following substrates were used as energy and carbon sources: lactate, pyruvate, malate, fumarate, ethanol, butanol, acetate/h2 and glycine. sulfite and thiosulfate were al ...	2005	15653861
epr experiments to elucidate the structure of the ready and unready states of the [nife] hydrogenase of desulfovibrio vulgaris miyazaki f.	isolation and purification of the [nife] hydrogenase of desulfovibrio vulgaris miyazaki f under aerobic conditions leads to a mixture of two states, ni-a (unready) and ni-b (ready). the two states are distinguished by different activation times and different epr spectra. hyscore and endor data and dft calculations show that both states have an exchangeable proton, albeit with a different (1)h hyperfine coupling. this proton is assigned to the bridging ligand between ni and fe. for ni-b, a hydrox ...	2005	15667250
on the relationship between affinity for molecular hydrogen and the physiological directionality of hydrogenases.	the physiological significance of the generic reaction h(2)<-->2[h] is not always clear because hydrogenases may function in the breakdown of molecular hydrogen or in its synthesis or in both directions. fe-hydrogenases have nevertheless been most often associated with proton reduction and nife-hydrogenases with hydrogen oxidation. a re-determination of the k(m) of h(2) oxidation by pyrococcus furiosus nife-hydrogenase-i and by desulfovibrio vulgaris fe-hydrogenase suggests that affinity for hyd ...	2005	15667251
construction of a [nife]-hydrogenase deletion mutant of desulfovibrio vulgaris hildenborough.	a mutant of desulfovibrio vulgaris hildenborough lacking a gene for [nife] hydrogenase was generated. growth studies, performed for the mutant in comparison with the wild-type, showed no strong differences during the exponential growth phase. however, the mutant cells died more rapidly in the stationary growth phase.	2005	15667264
applications of bacterial hydrogenases in waste decontamination, manufacture of novel bionanocatalysts and in sustainable energy.	bacterial hydrogenases have been harnessed to the removal of heavy metals from solution by reduction to less soluble metal species. for pd(ii), its bioreduction results in the deposition of cell-bound pd(0)-nanoparticles that are ferromagnetic and have a high catalytic activity. hydrogenases can also be used synthetically in the production of hydrogen from sugary wastes through breakdown of formate produced by fermentation. the bio-h(2) produced can be used to power an electrical device using a ...	2005	15667270
transcriptional regulation of a hybrid cluster (prismane) protein.	hcp (hybrid-cluster protein) contains two fe/s clusters, one of which is a hybrid [4fe-2s-2o] cluster. despite intensive study, its physiological function has not been reported. the escherichia coli hcp gene is located in a two-gene operon with hcr, which encodes an nadh-dependent hcp reductase. e. coli hcp is detected after anaerobic growth with nitrate or nitrite: possible roles for it in hydroxylamine or nitric oxide reduction have been proposed. to study the regulation and role of hcp, an hc ...	2005	15667305
structural determinants of protein stabilization by solutes. the important of the hairpin loop in rubredoxins.	despite their high sequence homology, rubredoxins from desulfovibrio gigas and d. desulfuricans are stabilized to very different extents by compatible solutes such as diglycerol phosphate, the major osmolyte in the hyperthermophilic archaeon archaeoglobus fulgidus[lamosa p, burke a, peist r, huber r, liu m y, silva g, rodrigues-pousada c, legall j, maycock c and santos h (2000) appl environ microbiol66, 1974-1979]. the principal structural difference between these two proteins is the absence of ...	2005	15691333
structure-function relationships in mitochondrial complex i of the strictly aerobic yeast yarrowia lipolytica.	the obligate aerobic yeast yarrowia lipolytica has been established as a powerful model system for the analysis of mitochondrial complex i. using a combination of genomic and proteomic approaches, a total of 37 subunits was identified. several of the accessory subunits are predicted to be stmd (single transmembrane domain) proteins. site-directed mutagenesis of y. lipolytica complex i has provided strong evidence that a significant part of the ubiquinone reducing catalytic core resides in the 49 ...	2005	16042611
biochemical differentiation and comparison of desulfovibrio species and other phenotypically similar genera.	seventeen human clinical isolates representing four species of desulfovibrio were characterized using 16s rrna gene sequences and tests for catalase, indole, nitrate, bile, urease, formate-fumarate stimulation, desulfoviridin, motility, and hydrogen sulfide production, plus susceptibility to antimicrobial agents. eighty additional strains representing 10 phenotypically similar genera (bilophila, selenomonas, capnocytophaga, campylobacter, bacteroides, sutterella, anaerobiospirillum, dialister, v ...	2005	16081948
structure and topology of microbial communities in the major gut compartments of melolontha melolontha larvae (coleoptera: scarabaeidae).	physicochemical gut conditions and the composition and topology of the intestinal microbiota in the major gut compartments of the root-feeding larva of the european cockchafer (melolontha melolontha) were studied. axial and radial profiles of ph, o2, h2, and redox potential were measured with microsensors. terminal restriction fragment length polymorphism (t-rflp) analysis of bacterial 16s rrna genes in midgut samples of individual larvae revealed a simple but variable and probably nonspecific c ...	2005	16085849
cadmium accumulation and dna homology with metal resistance genes in sulfate-reducing bacteria.	cadmium resistance (0.1 to 1.0 mm) was studied in four pure and one mixed culture of sulfate-reducing bacteria (srb). the growth of the bacteria was monitored with respect to carbon source (lactate) oxidation and sulfate reduction in the presence of various concentrations of cadmium chloride. two strains desulfovibrio desulfuricans dsm 1926 and desulfococcus multivorans dsm 2059 showed the highest resistance to cadmium (0.5 mm). transmission electron microscopy of the two strains showed intracel ...	2005	16085855
deletion of flavoredoxin gene in desulfovibrio gigas reveals its participation in thiosulfate reduction.	the gene encoding desulfovibrio gigas flavoredoxin was deleted to elucidate its physiological role in the sulfate metabolism. disruption of flr gene strongly inhibited the reduction of thiosulfate and exhibited a reduced growth in the presence of sulfite with lactate as electron donor. the growth with sulfate was not however affected by the lack of this protein. additionally, flr mutant cells revealed a decrease of about 50% in the h2 consumption rate using thiosulfate as electron acceptor. alto ...	2005	16099456
gene expression analysis of the mechanism of inhibition of desulfovibrio vulgaris hildenborough by nitrate-reducing, sulfide-oxidizing bacteria.	sulfate-reducing bacteria (srb) are inhibited by nitrate-reducing, sulfide-oxidizing bacteria (nr-sob) in the presence of nitrate. this inhibition has been attributed either to an increase in redox potential or to production of nitrite by the nr-sob. nitrite specifically inhibits the final step in the sulfate reduction pathway. when the nr-sob thiomicrospira sp. strain cvo was added to mid-log phase cultures of the srb desulfovibrio vulgaris hildenborough in the presence of nitrate, sulfate redu ...	2005	16104868
study of the spin-spin interactions between the metal centers of desulfovibrio gigas aldehyde oxidoreductase: identification of the reducible sites of the [2fe-2s]1+,2+ clusters.	the aldehyde oxidoreductase from desulfovibrio gigas belongs to the family of molybdenum hydroxylases. besides a molybdenum cofactor which constitutes their active site, these enzymes contain two [2fe-2s](2+,1+) clusters which are believed to transfer the electrons provided by the substrate to an acceptor which is either a fad group or an electron-transferring protein. when the three metal centers of d. gigas aor are simultaneously paramagnetic, splittings due to intercenter spin-spin interactio ...	2005	16114900
characterisation of the 11 kb dna region adjacent to the gene encoding desulfovibrio gigas flavoredoxin.	flavoredoxin is an fmn binding protein that functions as an electron carrier in the sulphate metabolism of desulfovibrio gigas. the neighbouring dna regions of the gene encoding flavoredoxin were sequenced and characterised. transcript analysis of the flavoredoxin gene resulted in a positive band corresponding to the size of the coding region, suggesting that flavoredoxin is encoded by a monocystronic unit, as previously suggested by sequence analysis. analysis of the adjacent dna regions reveal ...	2005	16147877
identification of variant molecules of bacillus thermoproteolyticus ferredoxin: crystal structure reveals bound coenzyme a and an unexpected [3fe-4s] cluster associated with a canonical [4fe-4s] ligand motif.	during the purification of recombinant bacillus thermoproteolyticus ferredoxin (btfd) from escherichia coli, we have noted that some fe-s proteins were produced in relatively small amounts compared to the originally identified btfd carrying a [4fe-4s] cluster. these variants could be purified into three fe-s protein components (designated as v-i, v-ii, and v-iii) by standard chromatography procedures. uv-vis and epr spectroscopic analyses indicated that each of these variants accommodates a [3fe ...	2005	16156653
caseinoglycomacropeptide inhibits adhesion of pathogenic escherichia coli strains to human cells in culture.	caseinoglycomacropeptide (cgmp) derived from kappa-casein was investigated for its ability to inhibit the adhesion of 3 strains of verotoxigenic escherichia coli (vtec) and 3 strains of enteropathogenic escherichia coli (epec) to human ht29 tissue cell cultures. effects on adhesion of desulfovibrio desulfuricans, lactobacillus pentosus, lactobacillus casei, lactobacillus acidophilus, and lactobacillus gasseri were also investigated. generally, cgmp exerted effective anti-adhesive properties at a ...	2005	16162518
hydrogenases in desulfovibrio vulgaris hildenborough: structural and physiologic characterisation of the membrane-bound [nifese] hydrogenase.	the genome of desulfovibrio vulgaris hildenborough (dvh) encodes for six hydrogenases (hases), making it an interesting organism to study the role of these proteins in sulphate respiration. in this work we address the role of the [nifese] hase, found to be the major hase associated with the cytoplasmic membrane. the purified enzyme displays interesting catalytic properties, such as a very high h(2) production activity, which is dependent on the presence of phospholipids or detergent, and resista ...	2005	16187073
triple-resonance methods for complete resonance assignment of aromatic protons and directly bound heteronuclei in histidine and tryptophan residues.	a set of three experiments is described which correlate aromatic resonances of histidine and tryptophan residues with amide resonances in 13c/15n-labelled proteins. provided that backbone 1h and 15n positions of the sequentially following residues are known, this results in sequence-specific assignment of histidine 1h(delta2)/13c(delta2) and 1h(epsilon1)/13c(epsilon1) as well as tryptophan 1h(delta1)/13c(delta1), 1h(zeta2)/13c(zeta2), 1h(eta2)/13c(eta2), 1h(epsilon3)/13c(epsilon3), 1h(zeta3)/13c ...	2005	16211484
[determination of minimal concentrations of biocorrosion inhibitors by a bioluminescence method in relation to bacteria, participating in biocorrosion].	by using a bioluminescence atp assay, we have determined the minimal concentrations of some biocorrosion inhibitors (katon, khazar, vfiks-82, nitro-1, kaspii-2, and kaspii-4) suppressing most common microbial corrosion agents: desulfovibrio desulfuricans, desulfovibrio vulgaris, pseudomonas putida, pseudomonas fluorescens, and acidithiobacillus ferrooxidans. the cell titers determined by the bioluminescence method, including not only dividing cells but also their dormant living counterparts, are ...	2005	16212040
[microbial community structure analyzed by single-strand conformation polymorphism technique in sulfate-reducing reactor].	analyses of microbial community structure and the relationships between sulfate-reducing bacteria (srbs) and acidogenic bacteria (abs) in a completely stirred sulfate-reducing reactor were carried out by modified polymerase chain reaction-single-stranded conformation polymorphism (pcr-sscp) targeted eubacterial 16s ribosomal rna gene. a total of 13 bands were obtained and 6 of them (a1, a3, a4, a5, a9, a10) were sequenced. the sequences are similar to leuconostoc mesenteroides (genbank access no ...	2005	16212191
the type i/type ii cytochrome c3 complex: an electron transfer link in the hydrogen-sulfate reduction pathway.	in desulfovibrio metabolism, periplasmic hydrogen oxidation is coupled to cytoplasmic sulfate reduction via transmembrane electron transfer complexes. type ii tetraheme cytochrome c3 (tpii-c3), nine-heme cytochrome c (9hca) and 16-heme cytochrome c (hmca) are periplasmic proteins associated to these membrane-bound redox complexes and exhibit analogous physiological function. type i tetraheme cytochrome c3 (tpi-c3) is thought to act as a mediator for electron transfer from hydrogenase to these mu ...	2005	16226767
multi-heme cytochromes--new structures, new chemistry.	heme is one of the most pervasive cofactors in nature and the c-type cytochromes represent one of the largest families of heme-containing proteins. recent progress in bacterial genomic analysis has revealed a vast range of genes encoding novel c-type cytochromes that contain multiple numbers of heme cofactors. the genome sequence of geobacter sulfurreducens, for example, includes some one hundred genes encoding c-type cytochromes, with around seventy of these containing two, or more, heme groups ...	2005	16234915
geophysical imaging of stimulated microbial biomineralization.	understanding how microorganisms influence the physical and chemical properties of the subsurface is hindered by our inability to observe microbial dynamics in real time and with high spatial resolution. here, we investigate the use of noninvasive geophysical methods to monitor biomineralization at the laboratory scale during stimulated sulfate reduction under dynamic flow conditions. alterations in sediment characteristics resulting from microbe-mediated sulfide mineral precipitation were conco ...	2005	16245832
a method adapting microarray technology for signature-tagged mutagenesis of desulfovibrio desulfuricans g20 and shewanella oneidensis mr-1 in anaerobic sediment survival experiments.	signature-tagged mutagenesis (stm) is a powerful technique that can be used to identify genes expressed by bacteria during exposure to conditions in their natural environments. to date, there have been no reports of studies in which this approach was used to study organisms of environmental, rather than pathogenic, significance. we used a mini-tn10 transposon-bearing plasmid, pbsl180, that efficiently and randomly mutagenized desulfovibrio desulfuricans g20 in addition to shewanella oneidensis m ...	2005	16269742
activation process of [nife] hydrogenase elucidated by high-resolution x-ray analyses: conversion of the ready to the unready state.	hydrogenases catalyze oxidoreduction of molecular hydrogen and have potential applications for utilizing dihydrogen as an energy source. [nife] hydrogenase has two different oxidized states, ni-a (unready, exhibits a lag phase in reductive activation) and ni-b (ready). we have succeeded in converting ni-b to ni-a with the use of na2s and o2 and determining the high-resolution crystal structures of both states. ni-b possesses a monatomic nonprotein bridging ligand at the ni-fe active site, wherea ...	2005	16271886
role of the tetrahemic subunit in desulfovibrio vulgaris hildenborough formate dehydrogenase.	in the anaerobic sulfate-reducing bacterium desulfovibrio vulgaris hildenborough (dvh), the genome sequencing revealed the presence of three operons encoding formate dehydrogenases. fdh1 encodes an alphabetagamma trimeric enzyme containing 11 heme binding sites; fdh2 corresponds to an alphabetagamma trimeric enzyme with a tetrahemic subunit; fdh3 encodes an alphabeta dimeric enzyme. in the present work, spectroscopic measurements demonstrated that the reduction of cytochrome c(553) was obtained ...	2005	16274230
biophysical properties of a c-type heme in chemotaxis signal transducer protein dcra.	chemotaxis signal transducer protein dcra from a sulfate-reducing bacterium desulfovibrio vulgaris hildenborough was previously shown to contain a c-type heme in its periplasmic domain (dcra-n) for sensing redox and/or oxygen [fu et al. (1994) j. bacteriol. 176, 344-350], which is the first example of a heme-based sensor protein containing a c-type heme as a prosthetic group. optical absorption and resonance raman spectroscopies indicates that heme c in dcra-n shows a redox-dependent ligand exch ...	2005	16285745
oriented immobilization of desulfovibrio gigas hydrogenase onto carbon electrodes by covalent bonds for nonmediated oxidation of h2.	the orientation of hydrogenase bound covalently to a pyrolytic graphite edge electrode modified with a 4-aminophenyl monolayer can be modulated via electrostatic interactions during the immobilization step. at low ionic strength and when the amino groups of the electrode surface are mostly protonated, the hydrogenase is immobilized with the negatively charged region that surrounds its 4fe4s cluster nearer to the protein surface facing the electrode. this allows direct electron transfer between t ...	2005	16287271
phylogenetic analysis of tce-dechlorinating consortia enriched on a variety of electron donors.	two rapidly fermented electron donors, lactate and methanol, and two slowly fermented electron donors, propionate and butyrate, were selected for enrichment studies to evaluate the characteristics of anaerobic microbial consortia that reductively dechlorinate tce to ethene. each electron donor enrichment subculture demonstrated the ability to dechlorinate tce to ethene through several serial transfers. microbial community analyses based upon 16s rdna, including terminal restriction fragment leng ...	2005	16294874
the influence of nickel on the adhesion ability of desulfovibrio desulfuricans.	the build-up of biofilms on metals surfaces may lead to severe corrosion, especially in the presence of sulphate-reducing bacteria (srb). to prevent the deterioration of material caused by biofilms it is necessary to understand the processes governing biofilm development including mechanisms of cell adhesion. additionally, corrosion of metallic surfaces due to bacteria may lead to the dissolution of metallic elements that may further affect adhesion and biofilm development. a study was carried o ...	2005	16290113
effects of oxygen exposure on respiratory activities of desulfovibrio desulfuricans strain dvo1 isolated from activated sludge.	the present study addresses the effects of oxygen exposure on the aerobic and anaerobic respiratory activity of desulfovibrio desulfuricans strain dvo1. this strain was isolated from the highest sulfate-reduction positive most-probable-number dilution (10(6)) of an activated sludge sample, which had been subjected to 120 h of continuous aeration. washed cell suspensions of strain dvo1 were aerated at 50% atmospheric oxygen saturation in sulfide-free media for a period of 33 h in the presence or ...	2005	16329947
characterisation of intestinal bacteria in infant stools using real-time pcr and northern hybridisation analyses.	real-time pcr and northern hybridisations were used to quantify bacterial populations in the large gut of infants. pcr primers for rapid, sensitive, high throughput detection of bifidobacteria, bacteroides, sulphate-reducing bacteria and enterococcus faecalis, based on analysis of 16s rrna genes were used. bacterial populations were analysed in faeces from 40 infants aged 0-6, 7-12 and 13-24 months. the effects of breast versus bottle feeding was also investigated. real-time pcr indicated that b ...	2005	16329974
interaction and electron transfer between the high molecular weight cytochrome and cytochrome c3 from desulfovibrio vulgaris hildenborough: kinetic, microcalorimetric, epr and electrochemical studies.	the complex formation between the tetraheme cytochrome c3 and hexadecaheme high molecular weight cytochrome c (hmc), the structure of which has recently been resolved, has been characterized by cross-linking experiments, epr, electrochemistry and kinetic analysis, and some key parameters of the interaction were determined. the analysis of electron transfer between [fe] hydrogenase, cytochrome c3 and hmc demonstrates a redox-shuttling role of cytochrome c3 in the pathway from hydrogenase to hmc, ...	2005	15780995
structural differences between the ready and unready oxidized states of [nife] hydrogenases.	[nife] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. so far, the structural basis for this difference has not been understood because of lack of relevant crystallographic data. here, we present the crystal structure of the ready ni-b state of desulfovibrio fructosovorans [nife] hydrogenase and show it to have a putative mu-hydroxo ...	2005	15803334
structure of s35c flavodoxin mutant from desulfovibrio vulgaris in the semiquinone state.	the crystallographic structure of an engineered flavodoxin mutant from desulfovibrio vulgaris has been analysed. site-directed mutagenesis was used to substitute serine 35 with a cysteine to provide a possible covalent linkage. the crystal structure of the semiquinone form of this mutant is similar to the corresponding oxidation state of the wild-type flavodoxin. analysis of the structural changes reveals the interaction between n(5)h of the flavin and the carbonyl o atom of gly61 to be critical ...	2005	15805604
bioinformatics, genomics and evolution of non-flagellar type-iii secretion systems: a darwinian perspective.	we review the biology of non-flagellar type-iii secretion systems from a darwinian perspective, highlighting the themes of evolution, conservation, variation and decay. the presence of these systems in environmental organisms such as myxococcus, desulfovibrio and verrucomicrobium hints at roles beyond virulence. we review newly discovered sequence homologies (e.g., yopn/tyea and sepl). we discuss synapomorphies that might be useful in formulating a taxonomy of type-iii secretion. the problem of ...	2005	15808742
the hydrogenases of geobacter sulfurreducens: a comparative genomic perspective.	the hydrogenase content of the genome of geobacter sulfurreducens, a member of the family geobacteraceae within the delta-subdivision of the proteobacteria, was examined and found to be distinct from that of desulfovibrio species, another family of delta-proteobacteria on which extensive research concerning hydrogen metabolism has been conducted. four [nife]-hydrogenases are encoded in the g. sulfurreducens genome: two periplasmically oriented, membrane-bound hydrogenases, hya and hyb, and two c ...	2005	15817791
analysis of bacterial diversity in acidic pond water and compost after treatment of artificial acid mine drainage for metal removal.	the microbial population of a sludge amended leaf compost material utilized for treatment of artificial acid mine drainage was studied by culture-independent molecular methods. iron-rich and sulfurous wastewater (artificial acid mine drainage) was circulated through a column bioreactor for 16 months. after 12 months the column was inoculated with a mixed culture from an acidic pond receiving acid mine drainage from a tailings impoundment at a decommissioned site in kristineberg, north sweden. hy ...	2005	15818559
reduction of cr(vi) by immobilized cells of desulfovibrio vulgaris ncimb 8303 and microbacterium sp. ncimb 13776.	hexavalent chromium, a carcinogen and mutagen, can be reduced to cr(iii) by desulfovibrio vulgaris ncimb 8303 and microbacterium sp. ncimb 13776. this study examined cr(vi) reduction by immobilized cells of the two strains in a common solution matrix using various entrapment matrices. chitosan and pva-borate beads did not retain integrity and supported low or no reduction of cr(vi) by the cells. a commercial preparation (lentikats) was stable but also did not support cr(vi) reduction. k-carragee ...	2005	15818565
oxygen tolerance of the h2-sensing [nife] hydrogenase from ralstonia eutropha h16 is based on limited access of oxygen to the active site.	hydrogenases, abundant proteins in the microbial world, catalyze cleavage of h2 into protons and electrons or the evolution of h2 by proton reduction. hydrogen metabolism predominantly occurs in anoxic environments mediated by hydrogenases, which are sensitive to inhibition by oxygen. those microorganisms, which thrive in oxic habitats, contain hydrogenases that operate in the presence of oxygen. we have selected the h2-sensing regulatory [nife] hydrogenase of ralstonia eutropha h16 to investiga ...	2005	15849358