Publications
| Title | Abstract | Year(sorted descending) Filter | PMID Filter |
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| sequence versus structure for the direct detection of 16s rrna on planar oligonucleotide microarrays. | a two-probe proximal chaperone detection system consisting of a species-specific capture probe for the microarray and a labeled, proximal chaperone probe for detection was recently described for direct detection of intact rrnas from environmental samples on oligonucleotide arrays. in this study, we investigated the physical spacing and nucleotide mismatch tolerance between capture and proximal chaperone detector probes that are required to achieve species-specific 16s rrna detection for the diss ... | 2003 | 12732571 |
| redox-bohr and other cooperativity effects in the nine-heme cytochrome c from desulfovibrio desulfuricans atcc 27774: crystallographic and modeling studies. | the nine-heme cytochrome c is a monomeric multiheme cytochrome found in desulfovibrio desulfuricans atcc 27774. the polypeptide chain comprises 296 residues and wraps around nine hemes of type c. it is believed to take part in the periplasmic assembly of proteins involved in the mechanism of hydrogen cycling, receiving electrons from the tetraheme cytochrome c3. with the purpose of understanding the molecular basis of electron transfer processes in this cytochrome, we have determined the crystal ... | 2003 | 12750363 |
| copper resistance in desulfovibrio strain r2. | a sulfate-reducing bacterium, designated as strain r2, was isolated from wastewater of a ball-bearing manufacturing facility in tomsk, western siberia. this isolate was resistant up to 800 mg cu/l in the growth medium. by comparison, cu-resistance of reference cultures of sulfate-reducing bacteria ranged from 50 to 75 mg cu/l. growth experiments with strain r2 showed that cu was an essential trace element and, on one hand, enhanced growth at concentrations up to 10 mg/l but, on the other hand, t ... | 2003 | 12755486 |
| epr and endor evidence for a 1-his, hydroxo-bridged mixed-valent diiron site in desulfovibrio vulgaris rubrerythrin. | key features differentiating the coordination environment of the two irons in the mixed-valent (fe(2+),fe(3+)) diiron site of desulfovibrio vulgaris rubrerythrin (rbr(mv)) were determined by continuous wave (cw) and pulsed endor spectroscopy at 35ghz. (14)n endor evidence indicates that a nitrogen is bound only to the fe(2+) ion of the mixed-valent site. assuming that this nitrogen is from his131ndelta, the same one that furnishes an iron ligand in the crystal structure of the diferric site, the ... | 2003 | 12755623 |
| cloning and expression of the superoxide dismutase gene from the obligate anaerobic bacterium desulfovibrio vulgaris (miyazaki f). | we identified the sod gene in the obligate anaerobic bacterium desulfovibrio vulgaris (miyazaki f) and constructed a high-level expression system in escherichia coli. a 2.6-kbp dna fragment isolated from d. vulgaris (miyazaki f) by double digestion with ecori and smai contained the sod gene and part of another open reading frame. the amino acid sequence deduced from the sod gene, which was composed of 238 amino acid residues, showed high homogeneity with iron-containing sod (fe-sod) and predicte ... | 2003 | 12761175 |
| docking and electron transfer studies between rubredoxin and rubredoxin:oxygen oxidoreductase. | the interaction and electron transfer (et) between rubredoxin (rd) and rubredoxin:oxygen oxidoreductase (roo) from desulfovibrio gigas is studied by molecular modelling techniques. experimental kinetic assays using recombinant proteins show that the rd reoxidation by roo displays a bell-shaped dependence on ionic strength, suggesting a non-trivial electrostatic dependence of the interaction between these two proteins. rigid docking studies reveal a prevalence for rd to interact, in a very specif ... | 2003 | 12761668 |
| reduced hybrid cluster proteins (hcp) from desulfovibrio desulfuricans atcc 27774 and desulfovibrio vulgaris (hildenborough): x-ray structures at high resolution using synchrotron radiation. | the hybrid cluster proteins from the sulfate reducing bacteria desulfovibrio desulfuricans atcc 27774 ( dd) and desulfovibrio vulgaris strain hildenborough ( dv) have been isolated and crystallized anaerobically. in each case, the protein has been reduced with dithionite and the crystal structure of the reduced form elucidated using x-ray synchrotron radiation techniques at 1.25 a and 1.55 a resolution for dd and dv, respectively. although the overall structures of the proteins are unchanged upo ... | 2003 | 12764602 |
| spectroscopic characterization of the [fe(his)(4)(cys)] site in 2fe-superoxide reductase from desulfovibrio vulgaris. | the electronic and vibrational properties of the [fe(his)(4)(cys)] site (center ii) responsible for catalysis of superoxide reduction in the two-iron superoxide reductase (2fe-sor) from desulfovibrio vulgaris have been investigated using the combination of epr, resonance raman, uv/visible/near-ir absorption, cd, and vtmcd spectroscopies. deconvolution of the spectral contributions of center ii from those of the [fe(cys)(4)] site (center i) has been achieved by parallel investigations of the c13s ... | 2003 | 12764688 |
| inhibition of bacterial u(vi) reduction by calcium. | the rapid kinetics of bacterial u(vi) reduction and low solubility of uraninite (uo2,cr) make this process an attractive option for removing uranium from groundwater. nevertheless, conditions that may promote or inhibit u(vi) reduction are not well-defined. recent descriptions of ca-uo2-co3 complexes indicate that these species may dominate the aqueous speciation of u(vi) in many environments. we monitored the bacterial reduction of u(vi) in bicarbonate-buffered solution in the presence and abse ... | 2003 | 12775057 |
| response of a strict anaerobe to oxygen: survival strategies in desulfovibrio gigas. | the biochemical response to oxygen of the strictly anaerobic sulfate-reducing bacterium desulfovibrio gigas was studied with the goal of elucidating survival strategies in oxic environments. cultures of d. gigas on medium containing lactate and sulfate were exposed to oxygen (concentration 5-120 micro m). growth was fully inhibited by oxygen, but the cultures resumed growth as soon as they were shifted back to anoxic conditions. following 24 h exposure to oxygen the growth rate was as high as 70 ... | 2003 | 12777491 |
| desulfovibrio desulfuricans bacteremia and review of human desulfovibrio infections. | one case of primary desulfovibrio desulfuricans bacteremia in an immunocompetent man is presented, and 15 other reported cases are reviewed. while most isolates have not been identified to the species level, desulfovibrio fairfieldensis and d. desulfuricans have been associated with incidents of bacteremia and d. vulgaris has been associated with intra-abdominal infections. in vitro studies suggest that empirical therapy with either imipenem or metronidazole should be considered. | 2003 | 12791922 |
| a novel membrane-bound ech [nife] hydrogenase in desulfovibrio gigas. | in the present study, we report the identification of an operon with six coding regions for a multisubunit membrane-bound [nife] hydrogenase in the genome of desulfovibrio gigas. sequence analysis of the deduced polypeptides reveals a high similarity to subunits of proteins belonging to the family of ech hydrogenases. the operon is organised similarly to the operon coding for the ech hydrogenase from methanosarcina barkeri, suggesting that both encode very similar hydrogenases. expression of the ... | 2003 | 12804572 |
| valid publication of the genus name thermodesulfobacterium and the species names thermodesulfobacterium commune (zeikus et al. 1983) and thermodesulfobacterium thermophilum (ex desulfovibrio thermophilus rozanova and khudyakova 1974). opinion 71. | the judicial commission of the international committee on systematics of prokaryotes decided that the date of valid publication of the genus name thermodesulfobacterium and of the species names thermodesulfobacterium commune and thermodesulfobacterium thermophilum is 1995. thermodesulfobacterium mobile rozanova and pivovarova 1988 is an illegitimate, later synonym of thermophilum. | 2003 | 12807221 |
| nitrite reductase activity of sulphate-reducing bacteria prevents their inhibition by nitrate-reducing, sulphide-oxidizing bacteria. | sulphate-reducing bacteria (srb) can be inhibited by nitrate-reducing, sulphide-oxidizing bacteria (nr-sob), despite the fact that these two groups are interdependent in many anaerobic environments. practical applications of this inhibition include the reduction of sulphide concentrations in oil fields by nitrate injection. the nr-sob thiomicrospira sp. strain cvo was found to oxidize up to 15 mm sulphide, considerably more than three other nr-sob strains that were tested. sulphide oxidation inc ... | 2003 | 12823193 |
| toxicity of al to desulfovibrio desulfuricans. | the toxicity of al to desulfovibrio desulfuricans g20 was assessed over a period of 8 weeks in a modified lactate c medium buffered at four initial phs (5.0, 6.5, 7.2, and 8.3) and treated with five levels of added al (0, 0.01, 0.1, 1.0, and 10 mm). at ph 5, cell population densities decreased significantly and any effect of al was negligible compared to that of the ph. at phs 6.5 and 7.2, the cell population densities increased by 30-fold during the first few days and then remained stable for s ... | 2003 | 12839782 |
| evidence for chimeric sequences formed during random arbitrarily primed pcr. | chimeric sequences were observed to occur abundantly (48% of clones) during random arbitrarily primed polymerase chain reaction (rap-pcr) experiments designed to examine differential expression of genes involved in metal resistance in sulfate-reducing bacteria (srb). some of the chimeric sequences were composed of sequence from a gene differentially expressed under the imposed conditions and a sequence of the 16s or 23s rrna gene. the remainder were composed of two rrna sequences. experiments us ... | 2003 | 12842491 |
| hydrogenases in sulfate-reducing bacteria function as chromium reductase. | the ability of sulfate-reducing bacteria (srb) to reduce chromate vi has been studied for possible application to the decontamination of polluted environments. metal reduction can be achieved both chemically, by h(2)s produced by the bacteria, and enzymatically, by polyhemic cytochromes c(3). we demonstrate that, in addition to low potential polyheme c-type cytochromes, the ability to reduce chromate is widespread among [fe], [nife], and [nifese] hydrogenases isolated from srb of the genera desu ... | 2003 | 12861426 |
| gene expression analysis of energy metabolism mutants of desulfovibrio vulgaris hildenborough indicates an important role for alcohol dehydrogenase. | comparison of the proteomes of the wild-type and fe-only hydrogenase mutant strains of desulfovibrio vulgaris hildenborough, grown in lactate-sulfate (ls) medium, indicated the near absence of open reading frame 2977 (orf2977)-coded alcohol dehydrogenase in the hyd mutant. hybridization of labeled cdna to a macroarray of 145 pcr-amplified d. vulgaris genes encoding proteins active in energy metabolism indicated that the adh gene was among the most highly expressed in wild-type cells grown in ls ... | 2003 | 12867442 |
| density functional theory investigation of the active site of [fe]-hydrogenases: effects of redox state and ligand characteristics on structural, electronic, and reactivity properties of complexes related to the [2fe]h subcluster. | the effects of redox state and ligand characteristics on structural, electronic, and reactivity properties of complexes related to the [2fe](h) subcluster of [fe]-hydrogenases have been investigated by dft calculations and compared with experimental and theoretical data obtained investigating both the enzyme and synthetic model complexes. our results show that fe(ii)fe(ii) species characterized by oh or h(2)o groups terminally coordinated to the iron atom distal to the terminal sulfur ligand (fe ... | 2003 | 12870970 |
| a sulfate-reducing bacterium that can detoxify u(vi) and obtain energy via nitrate reduction. | bacterial strain ufz b 490, which was isolated from a uranium dump and is closely related to desulfovibrio vulgaris oxamicus(t) (dsm 1925(t)), is able to detoxify u(vi) in aqueous media. in experiments reported here, u(vi) was used as an electron acceptor and lactate as electron donor. the reduction of soluble u(vi) to solid u(iv) (uraninite) did not provide energy for growth of strain ufz b 490. however, the isolate is able to grow when supplied with nitrate as sole electron acceptor and nitrog ... | 2003 | 12872316 |
| sulphate-reducing bacteria, palladium and the reductive dehalogenation of chlorinated aromatic compounds. | the surfaces of cells of desulfovibrio desulfuricans, desulfovibrio vulgaris and a new strain, desulfovibrio sp. 'oz-7' were used to manufacture a novel bioinorganic catalyst via the reduction of pd(ii) to pd(0) at the cell surface using hydrogen as the electron donor. the ability of the palladium coated (palladised) cells to reductively dehalogenate chlorophenol and polychlorinated biphenyl species was demonstrated. dried, palladised cells of d. desulfuricans, d. vulgaris and desulfovibrio sp. ... | 2003 | 12877464 |
| the cytochrome c3-[fe]-hydrogenase electron-transfer complex: structural model by nmr restrained docking. | cytochrome c(3) (m(r) 13000) is a low redox potential cytochrome specific of the anaerobic metabolism in sulfate-reducing bacteria. this tetrahemic cytochrome is an intermediate between the [fe]-hydrogenase and the cytochrome hmc in desulfovibrio vulgaris hildenborough strain. the present work describes the structural model of the cytochrome c(3)-[fe]-hydrogenase complex obtained by nuclear magnetic resonance restrained docking. this model connects the distal cluster of the [fe]-hydrogenase to h ... | 2003 | 12885397 |
| kinetic behavior of desulfovibrio gigas aldehyde oxidoreductase encapsulated in reverse micelles. | we report the kinetic behavior of the enzyme aldehyde oxidoreductase (aor) from the sulfate reducing bacterium desulfovibrio gigas (dg) encapsulated in reverse micelles of sodium bis-(2-ethylhexyl) sulfosuccinate in isooctane using benzaldehyde, octaldehyde, and decylaldehyde as substrates. dg aor is a 200-kda homodimeric protein that catalyzes the conversion of aldehydes to carboxylic acids. ultrasedimentation analysis of dg aor-containing micelles showed the presence of 100-kda molecular weigh ... | 2003 | 12890482 |
| anti-oxidant defense of the cell desulfovibrio desulfuricans b-1388. | the extracts of desulfovibrio desulfuricans b-1388 cells, grown in anaerobic condition, display the superoxide dismutase activity. the maximum value of level activity (1.02 e/min/mg) is observed in the stationary phase of growth. essentially the whole enzyme is localized in periplasmic fraction. cells desulfovibrio desulfuricans b-1388 do not show the catalase activity but contain active nadh- and nadph-peroxidases. the activity of involved peroxidases depends on the physiological condition of c ... | 2003 | 16887686 |
| desulfovibrio capillatus sp. nov., a novel sulfate-reducing bacterium isolated from an oil field separator located in the gulf of mexico. | a new spirilloid sulfate-reducing bacterium designated strain met2(t) (t=type strain), was isolated from a mexican oil field separator. electron microscopy revealed a gram-negative cell wall consisting of a 150nm thick undulating outer membrane. strain met2(t) appeared singly or in long chains and was actively motile with a corkscrew-like motion. the isolate grew optimally at 40 degrees c, ph 7.4 and 3% nacl in a medium containing lactate, thiosulfate and yeast extract. sulfate, sulfite, thiosul ... | 2003 | 16887695 |
| biotechnological potential of sulfate-reducing bacteria for transformation of nitrocellulose. | the biotransformation of nc by desulfovibrio sp. was studied. the mass of nc was decreased by 4.9-9.3%. the rate of nc transformation was between 46 and 73 mg nc per mg of bacterial protein in 10 days. moreover, n content (%n) in the remaining nc was reduced by 2-12%. the inhibitory effect of nc was clearly expressed when the growth of d. desulfuricans 1388 in lactate/sulfate medium was initiated. the growth rate of bacteria was 1.5-fold greater when nc was not added (0.074 and 0.05 h(-1) respec ... | 2002 | 16887675 |
| hydrogen metabolism in desulfovibrio desulfuricans strain new jersey (ncimb 8313)--comparative study with d. vulgaris and d. gigas species. | this article aims to study hydrogen production/consumption in desulfovibrio (d.) desulfuricans strain new jersey, a sulfate reducer isolated from a medium undergoing active biocorrosion and to compare its hydrogen metabolism with two other desulfovibrio species, d. gigas and d. vulgaris hildenborough. hydrogen production was followed during the growth of these three bacterial species under different growth conditions: no limitation of sulfate and lactate, sulfate limitation, lactate limitation, ... | 2002 | 16887677 |
| activity of sulfate-reducing bacteria in human periodontal pocket. | samples of subgingival dental tissues were examined for the presence of sulfate-reducing bacteria (srb). using enrichment cultures, srbs were detected in 9 of 17 individuals. a pure culture of srb was obtained from one sample collected from a patient with type iv periodontal disease. the characterization of this isolate showed that it belongs to the genus desulfovibrio. the isolate used pyruvate, lactate, glucose, fructose, and ethanol as the sole source of carbon. however, the isolate was unabl ... | 2002 | 12619823 |
| new oxovanadium bis(1,2-dithiolate) compounds that mimic the hydrogen-bonding interactions at the active sites of mononuclear molybdenum enzymes. | reaction of vo(acac)(2) with 1,2-dithiols in the presence of triethylamine gives pentacoordinate oxovanadium complexes [hnet(3)](2)[vo(bdt)(2)] (1), [hnet(3)](2)[vo(tdt)(2)] (2), and [hnet(3)](2)[vo(bdtcl(2))(2)] (3) (where h(2)bdt = 1,2-benzenedithiol, h(2)tdt = 3,4-toluenedithiol, and h(2)bdtcl(2) = 3,6-dichloro-1,2-benzenedithiol). compounds 1-3 have been characterized by ir, uv/visible, epr, and mass spectroscopies. the x-ray crystal stuctures of 1 and 2 show hydrogen-bonding interactions be ... | 2002 | 12495349 |
| molecular dynamics study of desulfovibrio africanus cytochrome c3 in oxidized and reduced forms. | a 5-ns molecular dynamics study of a tetraheme cytochrome in fully oxidized and reduced forms was performed using the charmm molecular modeling program, with explicit water molecules, langevin dynamics thermalization, particle mesh ewald long-range electrostatics, and quantum mechanical determination of heme partial charges. the simulations used, as starting points, crystallographic structures of the oxidized and reduced forms of the acidic cytochrome c(3) from desulfovibrio africanus obtained a ... | 2002 | 12496077 |
| identification of the clostridium perfringens genes involved in the adaptive response to oxidative stress. | clostridium perfringens is a ubiquitous gram-positive pathogen that is present in the air, soil, animals, and humans. although c. perfringens is strictly anaerobic, vegetative and stationary cells can survive in a growth-arrested stage in the presence of oxygen and/or low concentrations of superoxide and hydroxyl radicals. indeed, it possesses an adaptive response to oxidative stress, which can be activated in both aerobic and anaerobic conditions. to identify the genes involved in this oxidativ ... | 2002 | 11948145 |
| the nadp-reducing hydrogenase from desulfovibrio fructosovorans: functional interaction between the c-terminal region of hnda and the n-terminal region of hndd subunits. | the hndabcd operon from desulfovibrio fructosovorans encodes an uncommon heterotetrameric nadp-reducing iron hydrogenase. the presence of a [2fe-2s] cluster likely located in the c-terminal region of the hnda subunit has already been revealed. we have cloned and expressed the truncated hnda gene in escherichia coli to isolate the structural [2fe-2s] module. optical and epr spectra are found identical to that of the native hnda subunit and the midpoint redox potential (-385 mv) is similar to that ... | 2002 | 12460679 |
| the crystal structure of the hexadeca-heme cytochrome hmc and a structural model of its complex with cytochrome c(3). | sulfate-reducing bacteria contain a variety of multi-heme c-type cytochromes. the cytochrome of highest molecular weight (hmc) contains 16 heme groups and is part of a transmembrane complex involved in the sulfate respiration pathway. we present the 2.42 a resolution crystal structure of the desulfovibrio vulgaris hildenborough cytochrome hmc and a structural model of the complex with its physiological electron transfer partner, cytochrome c(3), obtained by nmr restrained soft-docking calculatio ... | 2002 | 12467575 |
| a mechano-chemical model for energy transduction in cytochrome c oxidase: the work of a maxwell's god. | cytochrome c3 has a central role in the energetics of desulfovibrio sp., where it performs an electroprotonic energy transduction step. this process uses a network of cooperativities, largely based on anti-coulomb components, resulting from a mechano-chemical energy coupling mechanism. this mechanism provides a model coherent with the data available for the redox chemistry of haem a of cytochrome c oxidase and its link to the activation of protons. a crucial feature of the model is an anti-coulo ... | 2002 | 12482576 |
| the influence of fluid shear on the structure and material properties of sulphate-reducing bacterial biofilms. | biofilms of sulphate-reducing desulfovibrio sp. ex265 were grown in square section glass capillary flow cells under a range of fluid flow velocities from 0.01 to 0.4 m/s (wall shear stress, tau(w), from 0.027 to 1.0 n/m(2)). in situ image analysis and confocal scanning laser microscopy revealed biofilm characteristics similar to those reported for aerobic biofilms. biofilms in both flow cells were patchy and consisted of cell clusters separated by voids. length-to-width ratio measurements (l(c): ... | 2002 | 12483477 |
| reduction of np(v) and precipitation of np(iv) by an anaerobic microbial consortium. | a combination of experimental, analytical, and modeling investigations shows that an anaerobic, sulfate-reducing consortium reduced np(v) to np(iv), with subsequent precipitation of a np(iv) solid. precipitation of np(iv) during growth on pyruvate occurred before sulfate reduction began. h2 stimulated precipitation of np(iv) when added alone to growing cells, but it slowed precipitation when added along with pyruvate. increasing concentrations of pyruvate also retarded precipitation. accumulatio ... | 2002 | 12688585 |
| [effect of various anions on the rate of microbe-induced corrosion]. | experimental corroboration of correctness of theoretical thermodynamic calculations of e.m.f. of corrosion reactions induced by soil microorganisms is obtained in the work. a hypothesis is put forward on possible mechanism for stimulation of microbe-induced corrosion by chloride ions. the results obtained permit revealing the reasons of low efficiency conditions of cathode protection in cases of active involvement of soil microorganisms into corrosion processes which are used for maintenance of ... | 2002 | 12664552 |
| [effect of sulfate-reducing bacteria on steel corrosion in the presence of inhibitors]. | steel 08kp corrosion was studied as affected by inhibitors in presence of sulphate-reducing bacteria (srb). organic compounds, containing functional groups with nitrogen, oxygen and sulphur atoms, were investigated as corrosion inhibitors. it is shown that the studied inhibitors may be divided into three groups as to the mechanism of protective action. it has been established that cation-active nitrogen-containing surfactants ([symbol: see text] x, [symbol: see text]-1, [symbol: see text]-1m, ca ... | 2002 | 12664553 |
| molecular lego: design of molecular assemblies of p450 enzymes for nanobiotechnology. | this paper reports on the application of the molecular lego approach to p450 enzymes. protein domains are used as catalytic (p450 bm3 haem domain and human p450 2e1) or electron transfer (flavodoxin and p450 bm3 reductase) modules. the objectives are to build assemblies with improved electrochemical properties, to construct soluble human p450 enzymes, and to generate libraries of new p450 catalytic modules based on p450 bm3. a rationally designed, gene-fused assembly (bmp-fld) was obtained from ... | 2002 | 11742744 |
| phylogenetic identification and substrate uptake patterns of sulfate-reducing bacteria inhabiting an oxic-anoxic sewer biofilm determined by combining microautoradiography and fluorescent in situ hybridization. | we simultaneously determined the phylogenetic identification and substrate uptake patterns of sulfate-reducing bacteria (srb) inhabiting a sewer biofilm with oxygen, nitrate, or sulfate as an electron acceptor by combining microautoradiography and fluorescent in situ hybridization (mar-fish) with family- and genus-specific 16s rrna probes. the mar-fish analysis revealed that desulfobulbus hybridized with probe 660 was a dominant srb subgroup in this sewer biofilm, accounting for 23% of the total ... | 2002 | 11772645 |
| 17o endor detection of a solvent-derived ni-(oh(x))-fe bridge that is lost upon activation of the hydrogenase from desulfovibrio gigas. | crystallographic studies of the hydrogenases (hases) from desulfovibrio gigas (dg) and desulfovibrio vulgaris miyazaki (dvm) have revealed heterodinuclear nickel-iron active centers in both enzymes. the structures, which represent the as-isolated (unready) ni-a (s = (1)/(2)) enzyme state, disclose a nonprotein ligand (labeled as x) bridging the two metals. the bridging atom was suggested to be an oxygenic (o(2)(-) or oh(-)) species in dg hase and an inorganic sulfide in dvm hase. to determine th ... | 2002 | 11782180 |
| a comparison of the urea-induced unfolding of apoflavodoxin and flavodoxin from desulfovibrio vulgaris. | the kinetics and thermodynamics of the urea-induced unfolding of flavodoxin and apoflavodoxin from desulfovibrio vulgaris were investigated by measuring changes in flavin and protein fluorescence. the reaction of urea with flavodoxin is up to 5000 times slower than the reaction with the apoprotein (0.67 s(-1) in 3 m urea in 25 mm sodium phosphate at 25 degrees c), and it results in the dissociation of fmn. the rate of unfolding of apoflavodoxin depends on the urea concentration, while the reacti ... | 2002 | 11784315 |
| effects of deletion of genes encoding fe-only hydrogenase of desulfovibrio vulgaris hildenborough on hydrogen and lactate metabolism. | the physiological properties of a hyd mutant of desulfovibrio vulgaris hildenborough, lacking periplasmic fe-only hydrogenase, have been compared with those of the wild-type strain. fe-only hydrogenase is the main hydrogenase of d. vulgaris hildenborough, which also has periplasmic nife- and nifese-hydrogenases. the hyd mutant grew less well than the wild-type strain in media with sulfate as the electron acceptor and h(2) as the sole electron donor, especially at a high sulfate concentration. al ... | 2002 | 11790737 |
| evidence for a fourth hydrogenase in desulfovibrio fructosovorans. | a strain devoid of the three hydrogenases characterized for desulfovibrio fructosovorans was constructed using marker exchange mutagenesis. as expected, the h(2)-dependent methyl viologen reduction activity of the strain was null, but physiological studies showed no striking differences between the mutated and wild-type strains. the h(+)-d(2) exchange activity measured in the mutated strain indicates the presence of a fourth hydrogenase in d. fructosovorans. | 2002 | 11790758 |
| high-spin ni(ii), a surprisingly good structural model for [nife] hydrogenase. | the first density functional calculations on high-spin (hs) ni(ii) models for the active site of the [nife] hydrogenases predict a ligand arrangement about ni that is in better agreement with the crystal structures than previous predictions for low-spin (ls) ni(ii) models. with the crystal structures' geometry, the hs form is approximately 20 kcal/mol lower in energy than the ls one. | 2002 | 11792207 |
| quinol:fumarate oxidoreductases and succinate:quinone oxidoreductases: phylogenetic relationships, metal centres and membrane attachment. | a comprehensive phylogenetic analysis of the core subunits of succinate:quinone oxidoreductases and quinol:fumarate oxidoreductases is performed, showing that the classification of the enzymes as type a to e based on the type of the membrane anchor fully correlates with the specific characteristics of the two core subunits. a special emphasis is given to the type e enzymes, which have an atypical association to the membrane, possibly involving anchor subunits with amphipathic helices. furthermor ... | 2002 | 11803024 |
| tetrachloroethene dehalorespiration and growth of desulfitobacterium frappieri tce1 in strict dependence on the activity of desulfovibrio fructosivorans. | tetrachloroethene (pce) dehalorespiration was investigated in a continuous coculture of the sulfate-reducing bacterium desulfovibrio fructosivorans and the dehalorespiring desulfitobacterium frappieri tce1 at different sulfate concentrations and in the absence of sulfate. fructose (2.5 mm) was the single electron donor, which could be used only by the sulfate reducer. with 2.5 mm sulfate, the dehalogenating strain was outnumbered by the sulfate-reducing bacterium, sulfate reduction was the domin ... | 2002 | 11823202 |
| identification of a bacterium that specifically catalyzes the reductive dechlorination of polychlorinated biphenyls with doubly flanked chlorines. | a microorganism whose growth is linked to the dechlorination of polychlorinated biphenyls (pcbs) with doubly flanked chlorines was identified. identification was made by reductive analysis of community 16s ribosomal dna (rdna) sequences from a culture enriched in the presence of 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-cb), which was dechlorinated at the para position. denaturing gradient gel electrophoresis (dgge) analysis of total 16s rdna extracted from the culture led to identification of three ... | 2002 | 11823222 |
| desulfovibrio magneticus sp. nov., a novel sulfate-reducing bacterium that produces intracellular single-domain-sized magnetite particles. | a novel type of dissimilatory sulfate-reducing bacterium, designated strain rs-1t, capable of producing intracellular magnetite particles (magnetosomes) was isolated from freshwater sulfide-rich sediments. phylogenetic analysis based on 16s rdna sequences revealed that rs-1t is a member of the genus desulfovibrio. its closest known relative is desulfovibrio burkinensis (sequence similarity of 98.7%). strain rs-1t contains desulfoviridin, c-type cytochromes and, unlike other desulfovibrio spp., i ... | 2002 | 11837306 |
| functional control of the binuclear metal site in the metallo-beta-lactamase-like fold by subtle amino acid replacements. | at present there are three protein families that share a common structural domain, the alphabeta/betaalpha fold of class b beta-lactamases: zinc beta-lactamases, glyoxalases ii, and a-type flavoproteins. a detailed inspection of their superimposed structures was undertaken and showed that although these proteins contain binuclear metal sites in spatially equivalent positions, there are some subtle differences within the first ligand sphere that determine a distinct composition of metals. althoug ... | 2002 | 11847294 |
| the quinol:fumarate oxidoreductase from the sulphate reducing bacterium desulfovibrio gigas: spectroscopic and redox studies. | the membrane bound fumarate reductase (frd) from the sulphate-reducer desulfovibrio gigas was purified from cells grown on a fumarate/sulphate medium and extensively characterized. the frd is isolated with three subunits of apparent molecular masses of 71, 31, and 22 kda. the enzyme is capable of both fumarate reduction and succinate oxidation, exhibiting a higher specificity toward fumarate (km for fumarate is 0.42 and for succinate 2 mm) and a reduction rate 30 times faster than that for oxida ... | 2002 | 11860177 |
| hydrogenases in the "active" state: determination of g-matrix axes and electron spin distribution at the active site by 1h endor spectroscopy. | hydrons and electrons are substrates for the enzyme hydrogenase, but cannot be observed in x-ray crystal structures. high-resolution 1h electron nuclear double resonance (endor) spectroscopy offers a means to detect the distribution of protons and unpaired electrons. endor spectra were recorded from frozen solutions of the nickel-iron hydrogenases of desulfovibrio gigas and desulfomicrobium baculatum, in the "active" state ("ni-c" epr signal) and analyzed by orientationally selective simulation ... | 2002 | 11862554 |
| studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail. | a comparative study of tetraheme cytochrome c3 molecules from several species was carried out using recently developed theoretical methods based on continuum electrostatics. the binding joint equilibrium of electrons and protons was simulated, revealing the complete thermodynamic aspects of electron-proton coupling in these molecules. the method yields excellent accuracy in terms of midpoint potentials, giving the correct reduction orders in all molecules examined, except for one heme site. the ... | 2002 | 11862556 |
| successional development of sulfate-reducing bacterial populations and their activities in an activated sludge immobilized agar gel film. | a combination of fluorescence in situ hybridization (fish), microprofiles, and denaturing gradient gel electrophoresis (dgge) analysis of pcr-amplified 16s rdna fragments followed by hybridization analysis with specific probes was applied to investigate successional development of sulfate-reducing bacteria (srb) community structure and in situ sulfide production activity within an activated sludge immobilized agar gel film. in this model biofilm system, since biases arising from biofilm heteroge ... | 2002 | 11870602 |
| successional development of sulfate-reducing bacterial populations and their activities in a wastewater biofilm growing under microaerophilic conditions. | a combination of fluorescence in situ hybridization, microprofiles, denaturing gradient gel electrophoresis of pcr-amplified 16s ribosomal dna fragments, and 16s rrna gene cloning analysis was applied to investigate successional development of sulfate-reducing bacteria (srb) community structure and in situ sulfide production activity within a biofilm growing under microaerophilic conditions (dissolved oxygen concentration in the bulk liquid was in the range of 0 to 100 microm) and in the presenc ... | 2002 | 11872492 |
| a hydrogenosomal [fe]-hydrogenase from the anaerobic chytrid neocallimastix sp. l2. | the presence of a [fe]-hydrogenase in the hydrogenosomes of the anaerobic chytridiomycete fungus neocallimastix sp. l2 has been demonstrated by immunocytochemistry, subcellular fractionation, western-blotting and measurements of hydrogenase activity in the presence of various concentrations of carbon monoxide (co). since the hydrogenosomal hydrogenase activity can be inhibited nearly completely by low concentrations of co, it is likely that the [fe]-hydrogenase is responsible for at least 90% of ... | 2002 | 11891051 |
| dft investigation of structural, electronic, and catalytic properties of diiron complexes related to the [2fe](h) subcluster of fe-only hydrogenases. | hydrogenases catalyze the reversible oxidation of dihydrogen to protons and electrons. the structures of two fe-only hydrogenases have been recently reported [peters, j. w.; lanzilotta, w. n.; lemon, b. j.; seefeldt, l. c. science 1998, 282, 1853-1858. nicolet, y.; piras, c.; legrand, p.; hatchikian, e. c.; fontecilla-camps, j. c. structure 1999, 7, 13-23], showing that the likely site of dihydrogen activation is the so-called [2fe](h) cluster, where each fe ion is coordinated by co and cn(-) li ... | 2002 | 11896710 |
| characterization of a novel insertion sequence, is bp1, in burkholderia pseudomallei. | during screening for antigenic proteins in burkholderia pseudomallei, a novel insertion sequence, is bp1, was found by sequence similarity searches. is bp1 contains two overlapping orfs of 261 bp ( orfa) and 852 bp ( orfb), encoding 87 and 284 amino acid residues, respectively, and an imperfect inverted repeat. the putative protein encoded by orfa (orfa) is similar to the orfa in insertion sequences of the is 3 family in other bacteria, showing 49% and 76% amino acid identity and similarity, res ... | 2002 | 11907683 |
| superoxide reductase activities of neelaredoxin and desulfoferrodoxin metalloproteins. | superoxide reductases have now been well characterized from several organisms. unique biochemical features include the ability of the reduced enzyme to react with o2- but not dioxygen (reduced sors are stable in an aerobic atmosphere for hours). future biochemical assays that measure the reaction of sor with o2- should take into account the difficulties of assaying o2- directly and the myriad of redox reactions that can take place between components in the assay, for example, direct electron tra ... | 2002 | 11912914 |
| kinetics and mechanism of superoxide reduction by two-iron superoxide reductase from desulfovibrio vulgaris. | superoxide reductases (sors) contain a novel square pyramidal ferrous [fe(nhis)(4)(scys)] site that rapidly reduces superoxide to hydrogen peroxide. here we report extensive pulse radiolysis studies on recombinant two-iron sor (2fe-sor) from desulfovibrio vulgaris. the results support and elaborate on our originally proposed scheme for reaction of the [fe(nhis)(4)(scys)] site with superoxide [coulter, e. d., emerson, j. e., kurtz, d. m., jr., and cabelli, d. e. (2000) j. am. chem. soc. 122, 1155 ... | 2002 | 11914081 |
| desulfovibrio sp. genes involved in the respiration of sulfate during metabolism of hydrogen and lactate. | to develop a better understanding of respiration by sulfate-reducing bacteria, we examined transcriptional control of respiratory genes during growth with lactate or hydrogen as an electron donor. rna extracts of desulfovibrio desulfuricans subsp. aestuarii were analyzed by using random arbitrarily primed pcr. rna was reverse transcribed under low-stringency conditions with a set of random primers, and candidate cdnas were cloned, sequenced, and characterized by blast analysis. putative differen ... | 2002 | 11916715 |
| hydrogenases: hydrogen-activating enzymes. | 2002 | 11921392 | |
| evolution of nitrate reductase: molecular and structural variations on a common function. | the biological transformation of nitrogen oxyanions is widespread in nature and gives rise to a robust biogeochemical cycle. the first step in nitrate reduction is carried out by the enzyme nitrate reductase (nr). although nr always catalyzes the same chemical reaction (conversion of nitrate into nitrite), its location in the cell, structure, and function are organism-dependent. we use protein sequence data to determine phylogenetic relationships and to examine similarities in structure and func ... | 2002 | 11921398 |
| ir spectroelectrochemical study of the binding of carbon monoxide to the active site of desulfovibrio fructosovorans ni-fe hydrogenase. | the binding of carbon monoxide, a competitive inhibitor of many hydrogenases, to the active site of desulfovibrio fructosovorans hydrogenase has been studied by infrared spectroscopy in a spectroelectrochemical cell. direct evidence has been obtained of which redox states of the enzyme can bind extrinsic co. redox states a, b and su do not bind extrinsic co; only after reductive activation of the hydrogenase can co bind to the active site. two states with bound extrinsic co can be distinguished ... | 2002 | 11935356 |
| the 1.25 a resolution structure of the diheme napb subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement. | the diheme cytochrome napb constitutes the small subunit of a periplasmic nitrate reductase found in a wide variety of bacterial species, including pathogens. the napb protein is essential in transferring electrons to the large catalytic subunit napa, which subsequently reduces nitrate to nitrite. here we present the crystal structure of a proteolyzed form of recombinant napb from haemophilus influenzae, which was determined by the multiple-wavelength anomalous dispersion (mad) method at 1.25 a ... | 2002 | 11939777 |
| hybrid cluster proteins (hcps) from desulfovibrio desulfuricans atcc 27774 and desulfovibrio vulgaris (hildenborough): x-ray structures at 1.25 a resolution using synchrotron radiation. | the structures of the hybrid cluster proteins (hcps) from the sulfate-reducing bacteria desulfovibrio desulfuricans (atcc 27774) and desulfovibrio vulgaris (hildenborough) have been elucidated at a resolution of 1.25 a using x-ray synchrotron radiation techniques. in the case of the d. desulfuricans protein, protein isolation, purification, crystallization and x-ray data collection were carried out under strict anaerobic conditions, whereas for the d. vulgaris protein the conditions were aerobic ... | 2002 | 11941509 |
| anabaena sp. pcc 7119 flavodoxin as electron carrier from photosystem i to ferredoxin-nadp+ reductase. role of trp(57) and tyr(94). | the influence of the amino acid residues sandwiching the flavin ring in flavodoxin (fld) from the cyanobacterium anabaena sp. pcc 7119 in complex formation and electron transfer (et) with its natural partners, photosystem i (psi) and ferredoxin-nadp(+) reductase (fnr), was examined in mutants of the key residues trp(57) and tyr(94). the mutants' ability to form complexes with either fnr or psi is similar to that of wild-type fld. however, some of the mutants exhibit altered kinetic properties in ... | 2002 | 11950835 |
| purification and characterization of a membrane-bound enzyme complex from the sulfate-reducing archaeon archaeoglobus fulgidus related to heterodisulfide reductase from methanogenic archaea. | heterodisulfide reductase (hdr) is a unique disulfide reductase that plays a key role in the energy metabolism of methanogenic archaea. the genome of the sulfate-reducing archaeon archaeoglobus fulgidus encodes several proteins of unknown function with high sequence similarity to the catalytic subunit of hdr. here we report on the purification of a multisubunit membrane-bound enzyme complex from a. fulgidus that contains a subunit related to the catalytic subunit of hdr. the purified enzyme is a ... | 2002 | 11952791 |
| growth of sulfate-reducing bacteria with solid-phase electron acceptors. | hannebachite (caso3 x 0.5h2o), gypsum (caso4 x 2h2o), anglesite (pbso4), and barite (baso4) were tested as electron acceptors for sulfate-reducing bacteria with lactate as the electron donor. hannebachite and gypsum are commonly associated with flue gas desulfurization products, and anglesite is a weathering product found in lead mines. barite was included as the most insoluble sulfate. growth of sulfate-reducing bacteria was monitored by protein and sulfide (dissolved h2s and hs-) measurements. ... | 2002 | 11954795 |
| reduction of humic substances by halorespiring, sulphate-reducing and methanogenic microorganisms. | physiologically distinct anaerobic microorganisms were explored for their ability to oxidize different substrates with humic acids or the humic analogue, anthraquinone-2,6-disulphonate (aqds), as a terminal electron acceptor. most of the microorganisms evaluated including, for example, the halorespiring bacterium, desulfitobacterium pce1, the sulphate-reducing bacterium, desulfovibrio g11 and the methanogenic archaeon, methanospirillum hungatei jf1, could oxidize hydrogen linked to the reduction ... | 2002 | 11966825 |
| presence of the cofactor speeds up folding of desulfovibrio desulfuricans flavodoxin. | flavodoxin is an alpha/beta protein with a noncovalently bound flavin-mononucleotide (fmn) cofactor. the apo-protein adopts a structure identical to that of the holo-form, although there is more dynamics in the fmn-binding loops. the equilibrium unfolding processes of azotobacter vinelandii apo-flavodoxin, and desulfovibrio desulfuricans atcc strain 27774 apo- and holo-flavodoxins involve rather stable intermediates. in contrast, we here show that both holo- and apo-forms of flavodoxin from d. d ... | 2002 | 11967369 |
| anaerobic reduction of a sulfonated azo dye, congo red, by sulfate-reducing bacteria. | the capacity for anaerobic decolorization of a sulfonated azo dye, congo red, by a strain of a sulfate-reducing bacterium was evaluated. after optimizing the growth rate of the bacteria on a simple carbon source and terminal electron acceptor pair, lactate and sulfate, respectively, the effect of the dye concentration on their growth rate was analyzed. the decolorization rate was affected by the dye concentration in the growth medium. the azo-bond cleavage mechanism of reductive decolorization w ... | 2002 | 11998840 |
| methanogenesis from furfural by defined mixed cultures. | methanogenesis from furfural by defined mixed cultures was studied. under sulfate-reducing conditions, a desulfovibrio strain was used as the furfural-degrading species producing acetic acid. this sulfate-reducing bacterium (srb) desulfovibrio strain b is an incomplete oxidizer, unable to carry out the terminal oxidation of organic substrates, leaving acetic acid as the end product. introduction of acetate-utilizing methanogenic archaeon methanosarcina barkeri 227 converted acetic acid to methan ... | 2002 | 12000990 |
| substrate recognition by 2-oxoacid:ferredoxin oxidoreductase from sulfolobus sp. strain 7. | 2-oxoacid:ferredoxin oxidoreductase (ofor) catalyzes the coenzyme a-dependent oxidative decarboxylation of 2-oxoacids, at an analogous metabolic position to 2-oxoacid dehydrogenase multienzyme complex. the enzyme from sulfolobus sp. strain 7, a thermoacidophilic crenarchaeon, is a heterodimer comprising two subunits, a (632 amino acids) and b (305 amino acids). in contrast to other ofors, the sulfolobus enzyme shows a broad specificity for 2-oxoacids such as pyruvate and 2-oxoglutarate. based on ... | 2002 | 12009405 |
| active site structure and dynamics of cytochrome c3 from desulfovibrio gigas immobilized on electrodes. | cytochrome c3 from desulfovibrio gigas is electrostatically adsorbed on ag electrodes coated with self-assembled monolayers (sams) of 11-mercaptoundecanoic acid. the redox equilibria and electron transfer dynamics of the adsorbed four-heme protein are studied by surface enhanced resonance raman spectroscopy. immobilization on the coated electrodes does not cause any structural changes in the redox sites. the potential-dependent stationary experiments distinguish the redox potential of heme iv (- ... | 2002 | 12012460 |
| cadmium recovery by a sulfate-reducing magnetotactic bacterium, desulfovibrio magneticus rs-1, using magnetic separation. | cadmium recovery by a sulfate-reducing magnetotactic bacterium, desulfovibrio magneticus strain rs-1, was investigated. d. magneticus precipitated >95% of cadmium at an initial concentration of 1.3 ppm in the growth medium. electron microscopic analysis revealed that d. magneticus formed electron-dense particles on its surface when cultivated in the presence of cadmium ions (cd2+). sulfide was also found in the precipitate, and the composition ratio of sulfide/cadmium was 0.7. sixty percent of v ... | 2002 | 12018305 |
| uranium reduction by desulfovibrio desulfuricans strain g20 and a cytochrome c3 mutant. | previous in vitro experiments with desulfovibrio vulgaris strain hildenborough demonstrated that extracts containing hydrogenase and cytochrome c3 could reduce uranium(vi) to uranium(iv) with hydrogen as the electron donor. to test the involvement of these proteins in vivo, a cytochrome c3 mutant of d. desulfuricans strain g20 was assayed and found to be able to reduce u(vi) with lactate or pyruvate as the electron donor at rates about one-half of those of the wild type. with electrons from hydr ... | 2002 | 12039777 |
| characterization of microbial community in granular sludge treating brewery wastewater. | the diversity and distribution of microbes within brewery-degrading anaerobic sludge granules were studied using various molecular techniques. molecular cloning of small-subunit rrna gene sequences indicated that all archaeal clones were affiliated with methanosaeta concillii (>99% sequence similarity), and the bacterial clones were mostly affiliated with a not-yet-cultured clostridium cluster (48 out of 99 clones) in the low g + c gram-positive group, xanthomonas spp. in the gamma-subclass of p ... | 2002 | 12044076 |
| redox-coupled conformational alternations in cytochrome c(3) from d. vulgaris miyazaki f on the basis of its reduced solution structure. | heteronuclear nmr spectroscopy was performed to determine the solution structure of (15)n-labeled ferrocytochrome c(3) from desulfovibrio vulgaris miyazaki f (dvmf). although the folding of the reduced cytochrome c(3) in solution was similar to that of the oxidized one in the crystal structure, the region involving hemes 1 and 2 was different. the redox-coupled conformational change is consistent with the reported solution structure of d. vulgaris hildenborough ferrocytochrome c(3), but is diffe ... | 2002 | 12054869 |
| sequential nmr assignment of the ferri-cytochrome c3 from desulfovibrio vulgaris hildenborough. | 2002 | 12061720 | |
| what is the ultimate fate of superoxide anion in vivo? | for three decades, oxidative stress and the role of reactive oxygen species in biology have been extensively studied. recently, a new interest in these areas has emerged with the discovery of superoxide reductases, a family of familiar bacterial metalloenzymes whose heretofore unknown function has now been apparently revealed. in a series of experiments utilizing genetic, molecular biological, and biochemical methods, these enzymes have been shown to be physiologically competent at removing supe ... | 2002 | 12072975 |
| superoxide scavenging by neelaredoxin: dismutation and reduction activities in anaerobes. | a superfamily of mononuclear iron proteins, originally named desulfoferrodoxin and neelaredoxin, has been identified by in vivo and in vitro studies as scavengers of the superoxide anion radical. these proteins, whose genes are present in all the so-far known genomes from anaerobes and in the microaerophilic pathogen treponema pallidum, show not only a considerable amino acid sequence identity but, most importantly, a common active iron site, fe[his(4)cysglu], in the oxidized state which loses t ... | 2002 | 12072976 |
| contribution of neelaredoxin to oxygen tolerance by treponema pallidum. | 2002 | 12078490 | |
| tuning the reduction potential of engineered cytochrome c-553. | cytochrome c-553 from desulfovibrio vulgaris exhibits a highly exposed heme and an unusually low reduction potential with respect to other c-type cytochromes. solvent heme exposure has been indicated as one of the most important factors in modulating the midpoint potential of the redox center. to test this hypothesis, a unique surface-exposed cysteine has been substituted for either m23 or g51 to produce the corresponding mutants and allow the formation of homodimers through a specific disulfide ... | 2002 | 12093290 |
| phylogenetic characterization of microbial communities that reductively dechlorinate tce based upon a combination of molecular techniques. | an anaerobic microbial consortium (referred to as anas) that reductively dechlorinates trichloroethene (tce) completely to ethene with the transient production of cisdichloroethene (cdce) and vinyl chloride was enriched from contaminated soil obtained from alameda naval air station. anas uses lactate as its electron donor and has been functionally stable for over 2 years. following a brief exposure to oxygen, a subculture (designated vcc) derived from anas could dechlorinate tce only to vinyl ch ... | 2002 | 12099461 |
| effect of complexing agents on reduction of cr(vi) by desulfovibrio vulgaris atcc 29579. | the reduction of cr(vi) at the expense of molecular hydrogen was studied using resting cells of desulfovibrio vulgaris atcc 29579 in anaerobic resting cell suspensions in mops buffer. bioreduction occurred only in the presence of ligands or chelating agents (co32-, citrate, nta, edta, dtpa). the stimulatory effect of these ligands on the rate of cr(vi) reduction was correlated (r = 0.988) with the strength of the ligand/chelate complex of cr(iii). the data are examined with respect to likely sol ... | 2002 | 12115402 |
| characterization of the bacterial consortium associated with black band disease in coral using molecular microbiological techniques. | the bacterial community associated with black band disease (bbd) of the scleractinian corals diploria strigosa, montastrea annularis and colpophyllia natans was examined using culture-independent techniques. two complementary molecular screening techniques of 16s rdna genes [amplified 16s ribosomal dna restriction analysis (ardra) of clone libraries and denaturing gradient gel electrophoresis (dgge)] were used to give a comprehensive characterization of the community. findings support previous s ... | 2002 | 12123476 |
| [transformation of cellulose nitro ester by the sulfate-reducing bacterium desulfovibrio desulfuricans]. | 2002 | 12138769 | |
| antioxidative enzymes of sulfate-reducing bacterium desulfovibrio desulfuricans: superoxide dismutase and peroxidases. | extracts of desulfovibrio desulfuricans b-1388 cells grown under anaerobic conditions displayed superoxide dismutase activity. the maximal activity was found during the stationary growth phase. the enzyme was virtually completely located in the periplasm fraction. d. desulfuricans b-1388 lacked catalase activity but contained active nadh- and nadph-peroxidases. the activity of nadh-peroxidase depended on the physiological state of the culture. on changing the growth conditions (the presence of 5 ... | 2002 | 12139483 |
| reclassification of the only species of the genus desulfomonas, desulfomonas pigra, as desulfovibrio piger comb. nov. | the growth characteristics, dna g+c content and sequences of 16s rdna and the transcribed 16s-23s rdna internal spacer were determined for desulfomonas pigra atcc 29098t, desulfovibrio desulfuricans subsp. desulfuricans strains essex 6t (= atcc 29577t) and mb (= atcc 27774) and 'desulfovibrio fairfieldensis' atcc 700045. despite phenotypic differences (shape and motility) between desulfomonas pigra and desulfovibrio strains, the molecular analysis suggests that desulfomonas pigra should be recla ... | 2002 | 12148644 |
| redox-dependent structural changes in the superoxide reductase from desulfoarculus baarsii and treponema pallidum: a ftir study. | the redox-induced structural changes at the active site of the superoxide reductase (sor) from desulfoarculus baarsii and treponema pallidum have been monitored by means of ftir difference spectroscopy coupled to electrochemistry. with this technique, the structure and interactions formed by individual amino acids at a redox site can be detected. the infrared data on wild-type, glu47ala, and lys48ile mutants of the sor from d. baarsii provide experimental support for the conclusion that the two ... | 2002 | 12162752 |
| x-ray crystal structures of reduced rubrerythrin and its azide adduct: a structure-based mechanism for a non-heme diiron peroxidase. | rubrerythrin (rbr) is a 44-kda homodimeric protein, found in many air-sensitive bacteria and archaea, which contains a unique combination of a rubredoxin-like [fe(scys)(4)] site and a non-sulfur, oxo/dicarboxylato-bridged diiron site. the diiron site structure resembles those found in o2-activating diiron enzymes. however, rbr instead appears to function as a hydrogen peroxide reductase (peroxidase). the diferrous site in all-ferrous rbr (rbr(red)) shows a much greater reactivity with h2o2 than ... | 2002 | 12175244 |
| a highly selective direct method of detecting sulphate-reducing bacteria in crude oil. | the aim of this work was to develop a highly selective method of detecting sulphate-reducing bacteria (srb) in crude oil. | 2002 | 12180949 |
| density functional calculations for modeling the active site of nickel-iron hydrogenases. 2. predictions for the unready and ready states and the corresponding activation processes. | zora relativistic dft calculations are presented which aim to model the geometric and electronic structure of the active site of nife hydrogenases in its epr-active oxidized states ni-a (unready state) and ni-b (ready state). starting coordinates are taken from the x-ray structure of a mutant of desulfovibrio fructosovorans hydrogenase refined at 1.81 a resolution. nine possible candidates for ni-a and ni-b are analyzed in terms of their geometric and electronic structure. comparison of calculat ... | 2002 | 12184759 |
| diversity and abundance of bacteria in an underground oil-storage cavity. | microorganisms inhabiting subterranean oil fields have recently attracted much attention. since intact groundwater can easily be obtained from the bottom of underground oil-storage cavities without contamination by surface water, studies on such oil-storage cavities are expected to provide valuable information to understand microbial ecology of subterranean oil fields. | 2002 | 12197947 |
| structure-function relationship in type ii cytochrome c(3) from desulfovibrio africanus: a novel function in a familiar heme core. | nmr and visible spectroscopy were used to characterize the type ii tetraheme cytochrome c(3) isolated from the periplasmic space of desulfovibrio africanus, a sulfate-reducing bacterium. although structurally similar to other cytochromes c(3), this protein displays distinct functional properties. proton nmr signals from the four hemes were assigned to the structure in the ferri- and ferrocytochromes using two-dimensional nmr experiments. the thermodynamic parameters of the hemes and of an acid-b ... | 2002 | 12203018 |
| construction and physiological studies of hydrogenase depleted mutants of desulfovibrio fructosovorans. | desulfovibrio fructosovorans possesses two periplasmic hydrogenases (a nickel-iron and an iron hydrogenase) and a cytoplasmic nadp-dependent hydrogenase. the hydab genes encoding the periplasmic iron hydrogenase were replaced, in the wild-type strain as well as in single mutants depleted of one of the other two hydrogenases, by the acc1 gene encoding resistance to gentamycin. molecular characterization and remaining activity measurements of the resulting single and double mutants were performed. ... | 2002 | 12204380 |
| crystallographic investigation of the role of aspartate 95 in the modulation of the redox potentials of desulfovibrio vulgaris flavodoxin. | the side chain of aspartate 95 in flavodoxin from desulfovibrio vulgaris provides the closest negative charge to n(1) of the bound fmn in the protein. site-directed mutagenesis was used to substitute alanine, asparagine, or glutamate for this amino acid to assess the effect of this charge on the semiquinone/hydroquinone redox potential (e(1)) of the fmn cofactor. the d95a mutation shifts the e(1) redox potential positively by 16 mv, while a negative shift of 23 mv occurs in the oxidized/semiquin ... | 2002 | 12206666 |
| gene sequence and the 1.8 a crystal structure of the tungsten-containing formate dehydrogenase from desulfovibrio gigas. | desulfovibrio gigas formate dehydrogenase is the first representative of a tungsten-containing enzyme from a mesophile that has been structurally characterized. it is a heterodimer of 110 and 24 kda subunits. the large subunit, homologous to e. coli fdh-h and to d. desulfuricans nitrate reductase, harbors the w site and one [4fe-4s] center. no small subunit ortholog containing three [4fe-4s] clusters has been reported. the structural homology with e. coli fdh-h shows that the essential residues ... | 2002 | 12220497 |
| biochemical-genetic analysis and distribution of des-1, an ambler class a extended-spectrum beta-lactamase from desulfovibrio desulfuricans. | desulfovibrio spp. are gram-negative anaerobes phylogenetically related to bacteroides spp., which are rarely isolated and which are mostly isolated from intra-abdominal abscesses. desulfovibrio desulfuricans clinical isolate d3 had a clavulanic acid-inhibited beta-lactam resistance profile and was resistant to some expanded-spectrum cephalosporins. a beta-lactamase gene, bla(des-1), was cloned from whole-cell dna of isolate d3 and expressed in escherichia coli. purified beta-lactamase des-1, wi ... | 2002 | 12234847 |