| purification, crystallization and preliminary x-ray analysis of adenylylsulfate reductase from desulfovibrio vulgaris miyazaki f. | sulfur in its various oxidation states is used for energy conservation in many microorganisms. adenylylsulfate reductase is a key enzyme in the sulfur-reduction pathway of sulfate-reducing bacteria. the adenylylsulfate reductase from desulfovibrio vulgaris miyazaki f has been purified and crystallized at 277 k using the vapour-diffusion method with ammonium sulfate as the precipitating agent. a data set was collected to 1.7 a resolution from a single crystal at 100 k using synchrotron radiation. ... | 2008 | 18997328 |
| spin distribution of the h-cluster in the h(ox)-co state of the [fefe] hydrogenase from desulfovibrio desulfuricans: hyscore and endor study of (14)n and (13)c nuclear interactions. | hydrogenases are enzymes which catalyze the reversible cleavage of molecular hydrogen into protons and electrons. in [fefe] hydrogenases the active center is a 6fe6s cluster, referred to as the "h-cluster." it consists of the redox-active binuclear subcluster ([2fe](h)) coordinated by cn(-) and co ligands and the cubane-like [4fe-4s](h) subcluster which is connected to the protein via cys ligands. one of these cys ligands bridges to the [2fe](h) subcluster. the co-inhibited form of [fefe] hydrog ... | 2009 | 19011912 |
| surface functionalization of cu-ni alloys via grafting of a bactericidal polymer for inhibiting biocorrosion by desulfovibrio desulfuricans in anaerobic seawater. | a novel surface modification technique was developed to provide a copper nickel alloy (m) surface with bactericidal and anticorrosion properties for inhibiting biocorrosion. 4-(chloromethyl)-phenyl tricholorosilane (cts) was first coupled to the hydroxylated alloy surface to form a compact silane layer, as well as to confer the surface with chloromethyl functional groups. the latter allowed the coupling of 4-vinylpyridine (4vp) to generate the m-cts-4vp surface with biocidal functionality. subse ... | 2009 | 19021016 |
| factors affecting the performance of microbial fuel cells for sulfur pollutants removal. | a microbial fuel cell (mfc) has been developed for removal of sulfur-based pollutants and can be used for simultaneous wastewater treatment and electricity generation. this fuel cell uses an activated carbon cloth+carbon fibre veil composite anode, air-breathing dual cathodes and the sulfate-reducing species desulfovibrio desulfuricans. 1.16gdm(-3) sulfite and 0.97gdm(-3) thiosulfate were removed from the wastewater at 22 degrees c, representing sulfite and thiosulfate removal conversions of 91% ... | 2009 | 19022647 |
| sulfate-reducing bacteria are common members of bacterial communities in altamira cave (spain). | the conservation of paleolithic paintings such as those in altamira cave (spain) is a primary objective. recent molecular studies have shown the existence of unknown microbial communities in this cave including anaerobic microorganisms on cave walls. herein, we analyzed an anaerobic microbial group, the sulfate-reducing bacteria (srb), from altamira cave with potential negative effects on painting conservation. in the present work, the communities of bacteria and srb were studied through pcr-dgg ... | 2009 | 19027143 |
| oligosaccharide-mediated inhibition of the adhesion of pathogenic escherichia coli strains to human gut epithelial cells in vitro. | the aim of the study was to investigate the ability of pectic oligosaccharides (pos) to inhibit adhesion of three strains of verotoxigenic escherichia coli, three strains of enteropathogenic e. coli, and one nonclinical strain of desulfovibrio desulfuricans to human intestinal epithelial cell cultures. lactobacillus acidophilus and lactobacillus gasseri were included for comparison. attachment was determined in the human ht29 cell line by viable count of adherent bacteria. pos in buffer at ph 7. ... | 2008 | 19044272 |
| preferential reduction of the thermodynamically less favorable electron acceptor, sulfate, by a nitrate-reducing strain of the sulfate-reducing bacterium desulfovibrio desulfuricans 27774. | desulfovibrio desulfuricans strain 27774 is one of a relative small group of sulfate-reducing bacteria that can also grow with nitrate as an alternative electron acceptor, but how nitrate reduction is regulated in any sulfate-reducing bacterium is controversial. strain 27774 grew more rapidly and to higher yields of biomass with nitrate than with sulfate or nitrite as the only electron acceptor. in the presence of both sulfate and nitrate, sulfate was used preferentially, even when cultures were ... | 2009 | 19047345 |
| quantum mechanical study of photoinduced charge transfer in fmn binding protein. | ct interactions between iso* and nearby aromatic amino acids in fbp were investigated by a semiempirical mo method. atomic coordinates of lumiflavin as iso, 3-methylindole as trp, and 4-methylphenol as tyr, used for mo calculations, were obtained from crystal, 20 nmr structures and 40 md structures (20 ps time intervals). geometries of iso-trp32, iso-trp106 and iso-tyr35 systems were optimized by the pm3 method. the interaction energies (kcal/mol) of crystal structure were -16.9 in the iso-trp32 ... | 2008 | 19053889 |
| characterization by culture and molecular analysis of the microbial diversity of a deep subsurface gas storage aquifer. | the bacterial diversity of a subsurface water sample collected from a gas storage aquifer in an upper jurassic calcareous formation was investigated by culture of microorganisms and construction of a 16s rrna gene library. both culture and molecular techniques showed that members of the phyla firmicutes and class delta-proteobacteria dominated the bacterial community. the presence of hydrogen-utilizing autotrophic bacteria including sulfate reducers (e.g. desulfovibrio aespoeensis) and homoaceto ... | 2009 | 19056488 |
| a genomic island of the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough promotes survival under stress conditions while decreasing the efficiency of anaerobic growth. | a 47 kb genomic island (gei) bracketed by 50 bp direct repeats, containing 52 annotated genes, was found to delete spontaneously from the genome of desulfovibrio vulgaris hildenborough. the island contains genes for site-specific recombinases and transposases, rubredoxin:oxygen oxidoreductase-1 (roo1) and hybrid cluster protein-1 (hcp1), which promote survival in air and nitrite stress. the numbering distinguishes these from the roo2 and hcp2 homologues for which the genes are located elsewhere ... | 2009 | 19077010 |
| small molecule mimics of hydrogenases: hydrides and redox. | this tutorial review is aimed at chemical scientists interested in understanding and exploiting the remarkable catalytic behavior of the hydrogenases. the key structural features are analyzed for the active sites of the two most important hydrogenases. reactivity is emphasized, focusing on mechanism and catalysis. through this analysis, gaps are identified in the synthesis of functional replicas of these fascinating and potentially useful enzymes. | 2009 | 19088969 |
| redox properties and crystal structures of a desulfovibrio vulgaris flavodoxin mutant in the monomeric and homodimeric forms. | the mutant s64c of the short-chain flavodoxin from desulfovibrio vulgaris has been designed to introduce an accessible and reactive group on the protein surface. crystals have been obtained of both the monomeric and homodimeric forms of the protein, with the cofactor fmn in either the oxidized or the one electron-reduced (semiquinone) state, and the structures have been determined to high resolution. the redox properties of the different species have been investigated and the variations observed ... | 2009 | 19118653 |
| development and comparison of sybr green quantitative real-time pcr assays for detection and enumeration of sulfate-reducing bacteria in stored swine manure. | to develop and evaluate primer sets targeted to the dissimilatory sulfite reductase gene (dsra) for use in quantitative real-time pcr detection of sulfate-reducing bacteria (srb) in stored swine manure. | 2008 | 19120660 |
| reduction of molybdate by sulfate-reducing bacteria. | molybdate is an essential trace element required by biological systems including the anaerobic sulfate-reducing bacteria (srb); however, detrimental consequences may occur if molybdate is present in high concentrations in the environment. while molybdate is a structural analog of sulfate and inhibits sulfate respiration of srb, little information is available concerning the effect of molybdate on pure cultures. we followed the growth of desulfovibrio gigas atcc 19364, desulfovibrio vulgaris hild ... | 2009 | 19130259 |
| characterization and activity studies of highly heavy metal resistant sulphate-reducing bacteria to be used in acid mine drainage decontamination. | biological treatment with sulphate-reducing bacteria (srb) has been considered as the most promising alternative for acid mine drainage (amd) decontamination. normally, these wastewaters contain high concentrations of sulphate and heavy metals, so the search for srb highly resistant to metals is extremely important for the development of a bioremediation technology. a srb consortium resistant to high concentrations of heavy metals (fe, cu and zn), similar to those typically present in amd, was o ... | 2009 | 19135795 |
| biological sulphate reduction using food industry wastes as carbon sources. | biological treatment with dissimilatory sulphate-reducing bacteria has been considered the most promising alternative for decontamination of sulphate rich effluents. these wastewaters are usually deficient in electron donors and require their external addition to achieve complete sulphate reduction. the aim of the present study was to investigate the possibility of using food industry wastes (a waste from the wine industry and cheese whey) as carbon sources for dissimilatory sulphate-reducing ba ... | 2009 | 19137404 |
| an autocatalytic mechanism for nife-hydrogenase: reduction to ni(i) followed by oxidative addition. | the mechanism for h(2) cleavage in nife-hydrogenase has been reinvestigated with large models using both hybrid dft by itself, or in a qm/mm scheme following the oniom approach. heterolytic cleavage, with one hydrogen ending up as a bridging hydride and one as a proton on a cysteine ligand, was found to have a barrier slightly too high to be compatible with measured catalytic turnover rates. alternative mechanisms were therefore investigated. in the finally suggested mechanism, heterolytic cleav ... | 2009 | 19138102 |
| molybdenum induces the expression of a protein containing a new heterometallic mo-fe cluster in desulfovibrio alaskensis. | the characterization of a novel mo-fe protein (morp) associated with a system that responds to mo in desulfovibrio alaskensis is reported. biochemical characterization shows that morp is a periplasmic homomultimer of high molecular weight (260 +/- 13 kda) consisting of 16-18 monomers of 15321.1 +/- 0.5 da. the uv/visible absorption spectrum of the as-isolated protein shows absorption peaks around 280, 320, and 570 nm with extinction coefficients of 18700, 12800, and 5000 m(-1) cm(-1), respective ... | 2009 | 19138103 |
| cloning and expression of the mutm gene from obligate anaerobic bacterium desulfovibrio vulgaris (miyazaki f). | the gene encoding a mutm from desulfovibrio vulgaris (miyazaki f) was cloned and expressed in escherichia coli. a 5.9-kb dna fragment, isolated from d. vulgaris (miyazaki f) by xhoi and pvuii, contained a mutm gene and other open reading frames. the nucleotide sequence of the mutm gene indicated that the protein was composed of 336 amino acids. the amino-acid sequence deduced from the mutm gene was highly homologous with the mutm of other bacteria; however an additional insert consisted of 64 am ... | 2009 | 19151100 |
| improvements of reliability for methylmercury determination in environmental samples. | the determination of methylmercury (mehg) in environmental samples by ethylation derivation-gas chromatography-atomic fluorescence spectrometry (ed-gc-afs) is associated with an intimate problem of water moisture accumulation introduced in the ethylation step, which enters the detection system and cause a spectroscopic interference. with a simple modification on the gc-afs system, this problem was eliminated and the analytical quality of the measurements was significantly improved. the presence ... | 2009 | 19166718 |
| macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin. | protein dynamics in cells may be different from those in dilute solutions in vitro, because the environment in cells is highly concentrated with other macromolecules. this volume exclusion because of macromolecular crowding is predicted to affect both equilibrium and kinetic processes involving protein conformational changes. to quantify macromolecular crowding effects on protein folding mechanisms, we investigated the folding energy landscape of an alpha/beta protein, apoflavodoxin, in the pres ... | 2009 | 19167312 |
| grafting of antibacterial polymers on stainless steel via surface-initiated atom transfer radical polymerization for inhibiting biocorrosion by desulfovibrio desulfuricans. | to enhance the biocorrosion resistance of stainless steel (ss) and to impart its surface with bactericidal function for inhibiting bacterial adhesion and biofilm formation, well-defined functional polymer brushes were grafted via surface-initiated atom transfer radical polymerization (atrp) from ss substrates. the trichlorosilane coupling agent, containing the alkyl halide atrp initiator, was first immobilized on the hydroxylated ss (ss-oh) substrates for surface-initiated atrp of (2-dimethylami ... | 2009 | 19170239 |
| candidatus desulfovibrio trichonymphae, a novel intracellular symbiont of the flagellate trichonympha agilis in termite gut. | rs-n31, a 16s rrna phylotype affiliated with the genus desulfovibrio, has frequently been detected from the gut of the wood-feeding termite reticulitermes speratus. in this study, we designed a probe specifically targeting phylotype rs-n31 and performed fluorescence in situ hybridization to identify the corresponding cells. the signals were detected exclusively inside the cells of the flagellate trichonympha agilis, which simultaneously harbours another intracellular bacterium belonging to the c ... | 2009 | 19170725 |
| genome sequence of desulfobacterium autotrophicum hrm2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. | sulfate-reducing bacteria (srb) belonging to the metabolically versatile desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. desulfobacterium autotrophicum hrm2 is the first member of this ecophysiologically important group with a now available genome sequence. with 5.6 megabasepairs (mbp) the genome of db. autotrophicum hrm2 is about 2 mbp larger than the sequenced genomes of other sulfate reducers (srb). a h ... | 2009 | 19187283 |
| desulfovibrio paquesii sp. nov., a hydrogenotrophic sulfate-reducing bacterium isolated from a synthesis-gas-fed bioreactor treating zinc- and sulfate-rich wastewater. | a hydrogenotrophic, sulfate-reducing bacterium, designated strain sb1(t), was isolated from sulfidogenic sludge of a full-scale synthesis-gas-fed bioreactor used to remediate wastewater from a zinc smelter. strain sb1(t) was found to be an abundant micro-organism in the sludge at the time of isolation. hydrogen, formate, pyruvate, lactate, malate, fumarate, succinate, ethanol and glycerol served as electron donors for sulfate reduction. organic substrates were incompletely oxidized to acetate. 1 ... | 2009 | 19196759 |
| effect of no2(-) on stable isotope fractionation during bacterial sulfate reduction. | the effects of low no2(-) concentrations on stable isotope fractionation during dissimilatory sulfate reduction by strain desulfovibrio desulfuricans were investigated. nitrite, formed as an intermediate during nitrification and denitrification processes in marine and freshwater habitats, inhibits the reduction of the sulfuroxy intermediate so3(2-) to h2s even at low concentrations. to gain an understanding of the inhibition effect of the reduction of the sulfuroxy intermediate on stable isotope ... | 2009 | 19209588 |
| hopanoid production by desulfovibrio bastinii isolated from oilfield formation water. | hopanoids are important lipid components of many bacterial groups and are therefore ubiquitous in soils, sediments, and rocks. until recently, it was believed that the synthesis of hopanoids is restricted to at least microaerophilic bacteria and consequently geological findings of hopanoids were used as an indication for oxygenated settings. recent studies, however, demonstrated the biosynthesis of hopanoids under strictly anoxic conditions by a few bacterial groups, although their relevance is ... | 2009 | 19222571 |
| infection after elective colorectal surgery: bacteriological analysis of failures in a randomized trial of cefotetan vs. ertapenem prophylaxis. | a randomized study comparing single-dose cefotetan and ertapenem prophylaxis for elective colorectal surgery in 1,002 patients found ertapenem to be significantly more effective (p < 0.001). failures of prophylaxis were thought to involve organisms resistant to both antimicrobial agents, isolated most often from deep or superficial incision sites. | 2009 | 19226203 |
| a molybdopterin oxidoreductase is involved in h2 oxidation in desulfovibrio desulfuricans g20. | three mutants deficient in hydrogen/formate uptake were obtained through screening of a transposon mutant library containing 5,760 mutants of desulfovibrio desulfuricans g20. mutations were in the genes encoding the type i tetraheme cytochrome c(3) (cyca), fe hydrogenase (hydb), and molybdopterin oxidoreductase (mopb). mutations did not decrease the ability of cells to produce h(2) or formate during growth. complementation of the cyca and mopb mutants with a plasmid carrying the intact cyca and/ ... | 2009 | 19233927 |
| a thermostable hybrid cluster protein from pyrococcus furiosus: effects of the loss of a three helix bundle subdomain. | pyrococcus furiosus hybrid cluster protein (hcp) was expressed in escherichia coli, purified, and characterized. this is the first archaeal and thermostable hcp to be isolated. compared with the protein sequences of previously characterized hcps from mesophiles, the protein sequence of p. furiosus hcp exhibits a deletion of approximately 13 kda as a single amino acid stretch just after the n-terminal cysteine motif, characteristic for class-iii hcps from (hyper)thermophilic archaea and bacteria. ... | 2009 | 19241093 |
| functional characterization of the early steps of tetrapyrrole biosynthesis and modification in desulfovibrio vulgaris hildenborough. | the biosynthesis of the tetrapyrrole framework has been investigated in the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough by characterization of the enzymes required for the transformation of aminolaevulinic acid into sirohydrochlorin. pbg (porphobilinogen) synthase (hemb) was found to be a zinc-dependent enzyme that exists in its native state as a homohexamer. pbg deaminase (hemc) was shown to contain the dipyrromethane cofactor. uroporphyrinogen iii synthase is found fused wi ... | 2009 | 19267692 |
| anaerobic degradation of landfill leachate using an upflow anaerobic fixed-bed reactor with microbial sulfate reduction. | this study evaluated the anaerobic degradation of landfill leachate and sulfate reduction as a function of cod/(so(4)(2-)) ratio in an upflow anaerobic fixed-bed reactor. the reactor, which was inoculated with a mixed consortium, was operated under a constant hydraulic retention time (hrt) of 5 days. we investigated the effect of cod/(so(4)(2-)) ratio variation on the sulfate reduction efficiency, hydrogen sulfide production, chemical oxygen demand (cod) removal, conductivity, and ph variation. ... | 2009 | 19272702 |
| expression profiling of hypothetical genes in desulfovibrio vulgaris leads to improved functional annotation. | hypothetical (hyp) and conserved hyp genes account for >30% of sequenced bacterial genomes. for the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough, 347 of the 3634 genes were annotated as conserved hyp (9.5%) along with 887 hyp genes (24.4%). given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. the study goals were to determine which genes were expressed and provide a more functionally based annotation. to accomplish thi ... | 2009 | 19293273 |
| population dynamics of a single-stage sulfidogenic bioreactor treating synthetic zinc-containing waste streams. | waste streams from industrial processes such as metal smelting or mining contain high concentrations of sulfate and metals with low ph. dissimilatory sulfate reduction carried out by sulfate-reducing bacteria (srb) at low ph can combine sulfate reduction with metal-sulfide precipitation and thus open possibilities for selective metal recovery. this study investigates the microbial diversity and population changes of a single-stage sulfidogenic gas-lift bioreactor treating synthetic zinc-rich was ... | 2009 | 19322604 |
| dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from desulfovibrio gigas. | rubredoxin:oxygen oxidoreductase (roo) is the terminal oxidase of a soluble electron transfer chain found in desulfovibrio gigas. this protein belongs to the flavodiiron family and was initially described as an oxygen reductase, converting this substrate to water and acting as an oxygen-detoxifying system. however, more recent studies evidenced also the ability for this protein to act as a nitric oxide reductase, suggesting an alternative physiological role. to clarify the apparent bifunctional ... | 2009 | 19337761 |
| characterisation of the electron transfer and complex formation between flavodoxin from d. vulgaris and the haem domain of cytochrome p450 bm3 from b. megaterium. | investigation of the complex formation and electron transfer kinetics between p450 bmp and flavodoxin was carried out following the suggested involvement of flavodoxin in modulating the electron transfer to bmp in artificial redox chains bound to an electrode surface. while electron transfer measurements show the formation of a tightly bound complex, the nmr data indicate the formation of shortly lived complexes. the measured k(obs) ranged from 24.2 s(-1) to 44.1 s(-1) with k(on) ranging from 0. ... | 2009 | 19366612 |
| a professional and personal odyssey. | | 2009 | 19398561 |
| desulfovibrio marrakechensis sp. nov., a 1,4-tyrosol-oxidizing, sulfate-reducing bacterium isolated from olive mill wastewater. | a novel mesophilic sulfate-reducing bacterium, emssdq(4)(t), was isolated from olive mill wastewater in the semi-arid region of morocco (marrakech). cells were gram-negative, catalase-positive, straight rods that were non-motile and non-spore-forming and contained cytochrome c(3) and desulfoviridin. the dna g+c content was 65.1 mol%. phylogenetic analysis based on 16s rrna gene sequences revealed that the isolate was a member of the genus desulfovibrio with desulfovibrio carbinoliphilus d41(t), ... | 2009 | 19406771 |
| desulfovibrio tunisiensis sp. nov., a novel weakly halotolerant, sulfate-reducing bacterium isolated from exhaust water of a tunisian oil refinery. | a novel weakly halotolerant, sulfate-reducing bacterium, designated strain rb22(t), was isolated from exhaust water of a tunisian oil refinery. cells of strain rb22(t) were gram-negative, motile, vibrio-shaped or sigmoid and non-spore-forming, and occurred singly or in chains. strain rb22(t) grew between 15 and 45 degrees c (optimum, 37 degrees c) and at ph 4.5 to 9 (optimum, ph 7). nacl was not required for growth, but the strain tolerated high nacl concentrations (up to 70 g l(-1)) with an opt ... | 2009 | 19406793 |
| effect of oxidized leachate on degradation of lignin by sulfate-reducing bacteria. | municipal solid waste materials (msws) in landfills need a long period of stabilization because lignin compounds in msws and leachate are not readily biodegraded, but inhibit methanogenic metabolism. recirculation of leachate into the landfill offers the potential advantage of increasing the rate of decomposition of organic matter. however, the degradation of lignin by leachate recirculation alone is quite difficult. several recent studies have demonstrated that sulfate-reducing bacteria (srb) w ... | 2009 | 19423591 |
| biochemistry, physiology and biotechnology of sulfate-reducing bacteria. | chemolithotrophic bacteria that use sulfate as terminal electron acceptor (sulfate-reducing bacteria) constitute a unique physiological group of microorganisms that couple anaerobic electron transport to atp synthesis. these bacteria (220 species of 60 genera) can use a large variety of compounds as electron donors and to mediate electron flow they have a vast array of proteins with redox active metal groups. this chapter deals with the distribution in the environment and the major physiological ... | 2009 | 19426853 |
| diversity of culturable sulfidogenic bacteria in two oil-water separation tanks in the north-eastern oil fields of india. | sulfidogenic communities in the production waters of onshore oil fields in north-eastern india were examined using a culturing approach. production water samples were inoculated into medium selective for sulfate reducing bacteria (srb) and thiosulfate reducing bacteria (trb). the total number of viable sulfidogenic microorganisms in the samples obtained from the two production water tanks was approximately 10(5) mpn ml(-1) (most probable number per ml). most of the isolates were thermo-tolerant ... | 2010 | 19427389 |
| desulfovibrio portus sp. nov., a novel sulfate-reducing bacterium in the class deltaproteobacteria isolated from an estuarine sediment. | a strictly anaerobic, mesophilic, sulfate-reducing bacterial strain (msl79t) isolated from an estuarine sediment in the sea of japan of the japanese islands was characterized phenotypically and phylogenetically. cells were gram-negative, motile with a polar flagellum, non-spore-forming, curved rods. cells had desulfoviridin and c-type cytochrome. catalase and oxidase activities were not detected. the optimum nacl concentration for growth was 2.0% (wt/vol). the optimum temperature was 35 degrees ... | 2009 | 19436129 |
| integrative analysis of transcriptomic and proteomic data of desulfovibrio vulgaris: a non-linear model to predict abundance of undetected proteins. | gene expression profiling technologies can generally produce mrna abundance data for all genes in a genome. a dearth of proteomic data persists because identification range and sensitivity of proteomic measurements lag behind those of transcriptomic measurements. using partial proteomic data, it is likely that integrative transcriptomic and proteomic analysis may introduce significant bias. developing methodologies to accurately estimate missing proteomic data will allow better integration of tr ... | 2009 | 19447782 |
| [nitrate reductase activity of desulfovibrio vulgaris bkm 1388]. | | 2009 | 19449731 |
| kinetic, structural, and epr studies reveal that aldehyde oxidoreductase from desulfovibrio gigas does not need a sulfido ligand for catalysis and give evidence for a direct mo-c interaction in a biological system. | aldehyde oxidoreductase from desulfovibrio gigas (dgaor) is a member of the xanthine oxidase (xo) family of mononuclear mo-enzymes that catalyzes the oxidation of aldehydes to carboxylic acids. the molybdenum site in the enzymes of the xo family shows a distorted square pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. we report here steady-state kinetic studies of dgaor with the inh ... | 2009 | 19459677 |
| pseudosymmetry, high copy number and twinning complicate the structure determination of desulfovibrio desulfuricans (atcc 29577) flavodoxin. | the crystal structure of oxidized flavodoxin from desulfovibrio desulfuricans (atcc 29577) was determined by molecular replacement in two crystal forms, p3(1)21 and p4(3), at 2.5 and 2.0 a resolution, respectively. structure determination in space group p3(1)21 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). initial phasing attempts in space group p3(1)21 by molecular replacement using a poor search model (46% identity) an ... | 2009 | 19465766 |
| interstrain diversity of 2-keto-3-deoxyoctonate content in lipopolysaccharides of desulfovibrio desulfuricans. | bacteria of desulfovibrio desulfuricans species are gram-negative, anaerobic rods selectively reducing sulphates and colonizing oxygen-free ecosystems. they are ubiquitous in the natural environment and have been also found to reside in the human digestive tract. they are suggested to be involved in the pathogenesis ofulcerative colitis and crohn's disease. the d. desulfuricans wild strains were isolated from feces and bioptate of patients suffering from various digestive tract disorders. lpss w ... | 2009 | 19469282 |
| thioredoxin is involved in u(vi) and cr(vi) reduction in desulfovibrio desulfuricans g20. | a transposon insertion mutant has been identified in a desulfovibrio desulfuricans g20 mutant library that does not grow in the presence of 2 mm u(vi) in lactate-sulfate medium. this mutant has also been shown to be deficient in the ability to grow with 100 microm cr(vi) and 20 mm as(v). experiments with washed cells showed that this mutant had lost the ability to reduce u(vi) or cr(vi), providing an explanation for the lower tolerance. a gene encoding a cyclic amp (camp) receptor protein (crp) ... | 2009 | 19482922 |
| density functional theory study of model complexes for the revised nitrate reductase active site in desulfovibrio desulfuricans napa. | [mo(ssch3)(s2c2(ch3)2)2](x) complexes with charges x between -3 and +3 were investigated by density functional theory computations as minimal nitrate reductase active-site models. the strongly reduced species (x = -2, -3) exist preferentially as pentacoordinate sulfo complexes separated from a thiolate anion. the oxidized extremes (x > 0) clearly prefer hexacoordinate complexes with an eta(2)-mess ligand. among the neutral and especially for the singly negatively charged species structures with ... | 2009 | 19484273 |
| effect of 2,4-dinitrotoluene on the anaerobic bacterial community in marine sediment. | to study the impact of added 2,4-dinitrotoluene (dnt) on the anaerobic bacterial community in marine sediment collected from an unexploded ordnance dumping site in halifax harbour. | 2009 | 19486208 |
| culture-independent analysis of desulfovibrios in the human distal colon of healthy, colorectal cancer and polypectomized individuals. | the production of hydrogen sulphide, an end product of metabolism by the sulphate-reducing bacteria (srb) has been cited as a potential aetiological agent in gastrointestinal disease. quantitative pcr (q-pcr) assays to enumerate desulfovibrios from two gastrointestinal disease groups: colorectal cancer (crc) n=27 and polypectomized individuals (pp) n=27, and two healthy control groups, elderly (h1) n=8 and young adults (h2) n=30 was performed. analysis of desulfovibrio sp. diversity using the di ... | 2009 | 19496818 |
| bacteriophage lytic to desulfovibrio aespoeensis isolated from deep groundwater. | viruses were earlier found to be 10-fold more abundant than prokaryotes in deep granitic groundwater at the aspö hard rock laboratory (hrl). using a most probable number (mpn) method, 8-30 000 cells of sulphate-reducing bacteria per ml were found in groundwater from seven boreholes at the aspö hrl. the content of lytic phages infecting the indigenous bacterium desulfovibrio aespoeensis in aspö groundwater was analysed using the mpn technique for phages. in four of 10 boreholes, 0.2-80 phages per ... | 2009 | 19516280 |
| identification and phylogenetic analysis of new sulfate-reducing bacteria isolated from oilfield samples. | microbiologically influenced corrosion (mic) caused by sulfate-reducing bacteria (srb) has been investigated in an oilfield injection water system. strain cw-01 was isolated from an oilfield and strain cw-04 was isolated from biofilm dirt of pipeline walls. the strains were facultative anaerobes, non-motile, gram-positive, pole flagellum, and spore-forming curved rods. the growth was observed over the temperature range 20-70 degrees c. strain cw-01 grew optimally at 37 degrees c. the ph range fo ... | 2009 | 19526722 |
| stable isotope fractionation of gamma-hexachlorocyclohexane (lindane) during reductive dechlorination by two strains of sulfate-reducing bacteria. | carbon isotope fractionation factors were determined with the dichloro elimination of gamma-hexachlorocyclohexane (gamma-hch) by the sulfate-reducing bacteria desulfococcus multivorans dsm 2059 and desulfovibrio gigas dsm 1382. both strains are known for cometabolic hch dechlorination. degradation experiments with gamma-hch in concentrations of 22-25 gammam were carried out using benzoate (for d. multivorans) and lactate (for d. gigas) as electron donors, respectively. gamma-hch was dechlorinate ... | 2009 | 19534128 |
| real-time molecular monitoring of chemical environment in obligate anaerobes during oxygen adaptive response. | determining the transient chemical properties of the intracellular environment can elucidate the paths through which a biological system adapts to changes in its environment, for example, the mechanisms that enable some obligate anaerobic bacteria to survive a sudden exposure to oxygen. here we used high-resolution fourier transform infrared (ftir) spectromicroscopy to continuously follow cellular chemistry within living obligate anaerobes by monitoring hydrogen bond structures in their cellular ... | 2009 | 19541631 |
| crystallization and crystallographic analysis of the apo form of the orange protein (orp) from desulfovibrio gigas. | the orange-coloured protein (orp) from desulfovibrio gigas is a 12 kda protein that contains a novel mixed-metal sulfide cluster of the type [s(2)mos(2)cus(2)mos(2)]. diffracting crystals of the apo form of orp have been obtained. data have been collected for the apo form of orp to 2.25 a resolution in-house and to beyond 2.0 a resolution at esrf, grenoble. the crystals belonged to a trigonal space group, with unit-cell parameters a = 43, b = 43, c = 106 a. | 2009 | 19574652 |
| proteomic analysis of irregular, bullet-shaped magnetosomes in the sulphate-reducing magnetotactic bacterium desulfovibrio magneticus rs-1. | recent molecular studies on magnetotactic bacteria have identified a number of proteins associated with bacterial magnetites (magnetosomes) and elucidated their importance in magnetite biomineralisation. however, these analyses were limited to magnetotactic bacterial strains belonging to the alpha-subclass of proteobacteria. we performed a proteomic analysis of magnetosome membrane proteins in desulfovibrio magneticus strain rs-1, which is phylogenetically classified as a member of the delta-pro ... | 2009 | 19579222 |
| the electron transfer system of syntrophically grown desulfovibrio vulgaris. | interspecies hydrogen transfer between organisms producing and consuming hydrogen promotes the decomposition of organic matter in most anoxic environments. although syntrophic coupling between hydrogen producers and consumers is a major feature of the carbon cycle, mechanisms for energy recovery at the extremely low free energies of reactions typical of these anaerobic communities have not been established. in this study, comparative transcriptional analysis of a model sulfate-reducing microbe, ... | 2009 | 19581361 |
| can microbially-generated hydrogen sulfide account for the rates of u(vi) reduction by a sulfate-reducing bacterium? | in situ remediation of uranium contaminated soil and groundwater is attractive because a diverse range of microbial and abiotic processes reduce soluble and mobile u(vi) to sparingly soluble and immobile u(iv). often these processes are linked. sulfate-reducing bacteria (srb), for example, enzymatically reduce u(vi) to u(iv), but they also produce hydrogen sulfide that can itself reduce u(vi). this study evaluated the relative importance of these processes for desulfovibrio aerotolerans, a srb i ... | 2010 | 19597947 |
| desulfovibrio idahonensis sp. nov., sulfate-reducing bacteria isolated from a metal(loid)-contaminated freshwater sediment. | two novel sulfate-reducing bacteria, strains cy1t and cy2, were isolated from heavy-metal-contaminated sediments of lake coeur d'alene, idaho, usa. strains cy1t and cy2 were found to contain c-type cytochromes and to reduce sulfate, sulfite, thiosulfate, elemental sulfur, dmso, anthraquinone disulfonate and fumarate using lactate as an electron donor. in a comparison of 16s rrna gene sequences, cy1t and cy2 were found to be 100% identical, but only 97 and 92.4% similar, respectively, to the type ... | 2009 | 19605721 |
| probing intermediates in the activation cycle of [nife] hydrogenase by infrared spectroscopy: the ni-sir state and its light sensitivity. | the [nife] hydrogenase from the sulphate-reducing bacterium desulfovibrio vulgaris miyazaki f is reversibly inhibited in the presence of molecular oxygen. a key intermediate in the reactivation process, ni-si(r), provides the link between fully oxidized (ni-a, ni-b) and active (ni-si(a), ni-c and ni-r) forms of hydrogenase. in this work ni-si(r) was found to be light-sensitive (t <or= 110 k), similar to the active ni-c and the co-inhibited states. transition to the final photoproduct state (ni-s ... | 2009 | 19626348 |
| epr studies of the mo-enzyme aldehyde oxidoreductase from desulfovibrio gigas: an application of the bloch-wangsness-redfield theory to a system containing weakly-coupled paramagnetic redox centers with different relaxation rates. | electron transfer proteins and redox enzymes containing paramagnetic redox centers with different relaxation rates are widespread in nature. despite both the long distances and chemical paths connecting these centers, they can present weak magnetic couplings produced by spin-spin interactions such as dipolar and isotropic exchange. we present here a theoretical model based on the bloch-wangsness-redfield theory to analyze the dependence with temperature of epr spectra of interacting pairs of spi ... | 2009 | 19628281 |
| immobilization of the hyperthermophilic hydrogenase from aquifex aeolicus bacterium onto gold and carbon nanotube electrodes for efficient h2 oxidation. | the electrochemistry of membrane-bound [nife] hydrogenase i ([nife]-hase i) from the hyperthermophilic bacterium aquifex aeolicus was investigated at gold and graphite electrodes. direct and mediated h(2) oxidation were proved to be efficient in a temperature range of 25-70 degrees c, describing a potential window for h(2) oxidation similar to that of o(2)-tolerant hydrogenases. search for enhancement of current densities and enzyme stability was achieved by the use of carbon nanotube coatings. ... | 2009 | 19629542 |
| characterization of pnc1, a small and mobilizable plasmid for use in genetic manipulation of desulfovibrio africanus. | to develop a vector system that facilitates genetic manipulation in desulfovibrio species, we screened native sulfate-reducing bacteria for small plasmids. a self-replicating plasmid was discovered in desulfovibrio africanus sr-1. sequence analysis of this 8568-bp plasmid (pnc1) revealed a g+c content of 47.2% and nine open reading frames. this plasmid has a copy number of six. compatible hosts include d. africanus and pseudomonas aeruginosa pa14. genetic characterization of pnc1 revealed that 5 ... | 2009 | 19631701 |
| nmr assignment of the apo-form of a desulfovibrio gigas protein containing a novel mo-cu cluster. | we report the 98% assignment of the apo-form of an orange protein, containing a novel mo-cu cluster isolated from desulfovibrio gigas. this protein presents a region where backbone amide protons exchange fast with bulk solvent becoming undetectable. these residues were assigned using 13c-detection experiments. | 2007 | 19636833 |
| (14)n hyscore investigation of the h-cluster of [fefe] hydrogenase: evidence for a nitrogen in the dithiol bridge. | hydrogenases are enzymes catalyzing the reversible heterolytic splitting of molecular hydrogen. despite extensive investigations of this class of enzymes its catalytic mechanism is not yet well understood. in this paper spectroscopic investigations of the active site of [fefe] hydrogenase are presented. the so-called h-cluster consists of a bi-nuclear catalytically active subcluster connected to a [4fe4s] ferredoxin-like unit via a cys-thiol bridge. an important feature of the h-cluster is that ... | 2009 | 19639134 |
| desulfocurvus vexinensis gen. nov., sp. nov., a sulfate-reducing bacterium isolated from a deep subsurface aquifer. | a novel anaerobic, chemo-organotrophic bacterium, designated vns36(t), was isolated from a well that collected water from a deep saline aquifer used for underground gas storage at a depth of 830 m in the paris basin, france. cells were curved motile rods or vibrios (3.0-5.0x0.5 microm). strain vns36(t) grew at temperatures between 20 and 50 degrees c (optimum 37 degrees c) and at ph values between 5.0 and 9.0 (optimum 6.9). it did not require salt for growth, but tolerated up to 20 g nacl l(-1) ... | 2009 | 19643880 |
| thermodesulfatator atlanticus sp. nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a mid-atlantic ridge hydrothermal vent. | a novel, strictly anaerobic, thermophilic, sulfate-reducing bacterium, designated strain at1325(t), was isolated from a deep-sea hydrothermal vent at the rainbow site on the mid-atlantic ridge. this strain was subjected to a polyphasic taxonomic analysis. cells were gram-negative motile rods (approximately 2.4 x 0.6 microm) with a single polar flagellum. strain at1325(t) grew at 55-75 degrees c (optimum, 65-70 degrees c), at ph 5.5-8.0 (optimum, 6.5-7.5) and in the presence of 1.5-4.5 % (w/v) na ... | 2010 | 19648352 |
| uranium reduction and resistance to reoxidation under iron-reducing and sulfate-reducing conditions. | oxidation and mobilization of microbially-generated u(iv) is of great concern for in situ uranium bioremediation. this study investigated the reoxidation of uranium by oxygen and nitrate in a sulfate-reducing enrichment and an iron-reducing enrichment derived from sediment and groundwater from the field research center in oak ridge, tennessee. both enrichments were capable of reducing u(vi) rapidly. 16s rrna gene clone libraries of the two enrichments revealed that desulfovibrio spp. are dominan ... | 2009 | 19651424 |
| rubredoxin as a paramagnetic relaxation-inducing probe. | the paramagnetic effect due to the presence of a metal center with unpaired electrons is no longer considered a hindrance in protein nmr spectroscopy. in the present work, the paramagnetic effect due to the presence of a metal center with unpaired electrons was used to map the interface of an electron transfer complex. desulfovibrio gigas cytochrome c(3) was chosen as target to study the effect of the paramagnetic probe, fe-rubredoxin, which produced specific line broadening in the heme iv methy ... | 2009 | 19651443 |
| desulfovibrio butyratiphilus sp. nov., a gram-negative, butyrate-oxidizing, sulfate-reducing bacterium isolated from an anaerobic municipal sewage sludge digester. | strictly anaerobic, mesophilic, sulfate-reducing bacterial strains were isolated from two anaerobic municipal sewage sludge digesters. one representative strain (bsy(t)) was characterized phenotypically and phylogenetically. cells were gram-negative, motile by means of a single polar flagellum, non-spore-forming, curved rods. cells had desulfoviridin and cytochrome type c. catalase and oxidase activities were not detected. the optimum nacl concentration for growth was 0.5 % (w/v). the optimum te ... | 2010 | 19654341 |
| desulfovibrio africanus subsp. uniflagellum subsp. nov., a sulfate-reducing bacterium from a uranium-contaminated subsurface aquifer. | the bacterial strain sr-1(t) was isolated from subsurface sediments of a uranium-contaminated site in shiprock, new mexico, usa. cells are vibrioid and motile by means of a single polar flagellum. strain sr-1(t) grows on sulfate, oxidizing formate, lactate and h2, but not malate, and ferments pyruvate. the dna sequences of the 16s rrna gene and the 16s-23s internal transcribed spacer of strain sr-1(t) showed 99.9 and 99.4 % similarity, respectively, to those of the type strain desulfovibrio afri ... | 2010 | 19661495 |
| hydrogenase cluster biosynthesis: organometallic chemistry nature's way. | it has been over a decade now since it was revealed that the metal containing active sites of hydrogenases possess carbonyl and cyanide ligands bound to iron. the presence of these ligands in hydrogenases came as a surprise and to-date these ligands have not been observed to be associated with any other enzymatic metallocenter. the elucidation of the structures of these unique metalloenzymes and their associated metal clusters created opportunity for a number of different lines of research. for ... | 2009 | 19662302 |
| critical aspects of [nife]hydrogenase ligand composition. | structural analysis of the resting state of [nife]hydrogenase ([nife]h(2)ase) shows that the active site has a characteristic bis(mu-thiolato)nife unit, where the ni atom and the fe atom are bridged by an undetermined oxygen-bearing ligand. this ligand probably derives from the aqueous solvent and is therefore most likely to be h(2)o, oh(-) or o(2-). here, we compare the reactivities of a nife and a niru complex when bearing either acetonitrile or aqueous ligands and demonstrate the critical rol ... | 2009 | 19662307 |
| [effect of nickel ions on physiological and corrosion activity of bacteria of sulfur cycle]. | the paper deals with the effect of nickel ions concentration in nutrient medium on sulfate-reducing bacteria desulfovibrio desulfuricans 10-v (srb) and their artificial corrosion-active associations which included thionic bacteria and their satellite stenotrophomonas maltophilia. it is shown that the concentration of nickel in the nutrient medium being increased, the duration of lag-phase of srb growth became 2-2.5 times less, and that of artificial associations--3-3.5 times less. the specific g ... | 2009 | 19663327 |
| conformational selection or induced fit: a flux description of reaction mechanism. | the mechanism of ligand binding coupled to conformational changes in macromolecules has recently attracted considerable interest. the 2 limiting cases are the "induced fit" mechanism (binding first) or "conformational selection" (conformational change first). described here are the criteria by which the sequence of events can be determined quantitatively. the relative importance of the 2 pathways is determined not by comparing rate constants (a common misconception) but instead by comparing the ... | 2009 | 19666553 |
| whole genome sequence of desulfovibrio magneticus strain rs-1 revealed common gene clusters in magnetotactic bacteria. | magnetotactic bacteria are ubiquitous microorganisms that synthesize intracellular magnetite particles (magnetosomes) by accumulating fe ions from aquatic environments. recent molecular studies, including comprehensive proteomic, transcriptomic, and genomic analyses, have considerably improved our hypotheses of the magnetosome-formation mechanism. however, most of these studies have been conducted using pure-cultured bacterial strains of alpha-proteobacteria. here, we report the whole-genome seq ... | 2009 | 19675025 |
| molecular dynamics at constant ph and reduction potential: application to cytochrome c(3). | here we present a new implementation and extension of the stochastic titration method which makes it possible to perform md simulations at constant ph and reduction potential. the method was applied to the redox titration of cytochrome c(3) from desulfovibrio vulgaris hildenborough, and a major finding of this study was that the method showed a better performance when the protein region is assigned a high dielectric constant. this dependence on the value of the protein dielectric constant was no ... | 2009 | 19685871 |
| isolation and characterization of a new cu-fe protein from desulfovibrio aminophilus dsm12254. | the isolation and characterization of a new metalloprotein containing cu and fe atoms is reported. the as-isolated cu-fe protein shows an uv-visible spectrum with absorption bands at 320 nm, 409 nm and 615 nm. molecular mass of the native protein along with denaturating electrophoresis and mass spectrometry data show that this protein is a multimer consisting of 14+/-1 subunits of 15254.3+/-7.6 da. mössbauer spectroscopy data of the as-isolated cu-fe protein is consistent with the presence of [2 ... | 2009 | 19699535 |
| versatility of a new bioinorganic catalyst: palladized cells of desulfovibrio desulfuricans and application to dehalogenation of flame retardant materials. | the versatility and reaction specificity of a novel bioinorganic catalyst is demonstrated in various reactions. palladized cells (biopd) of the sulphate-reducing bacterium desulfovibrio desulfuricans showed an increased product selectivity and a catalytic activity comparable to a commercial pd catalyst in several industrially relevant hydrogenations and hydrogenolyses (reductive dehalogenations). the ability of palladized cells to promote the reductive debromination of a polybrominated diphenyl ... | 2009 | 19705605 |
| structure analysis of the flavoredoxin from desulfovibrio vulgaris miyazaki f reveals key residues that discriminate the functions and properties of the flavin reductase family. | the crystal structure of flavoredoxin from desulfovibrio vulgaris miyazaki f was determined at 1.05 a resolution and its ferric reductase activity was examined. the aim was to elucidate whether flavoredoxin has structural similarity to ferric reductase and ferric reductase activity, based on the sequence similarity to ferric reductase from archaeoglobus fulgidus. as expected, flavoredoxin shared a common overall structure with a. fulgidus ferric reductase and displayed weak ferric reductase and ... | 2009 | 19708087 |
| growth and chemosensory behavior of sulfate-reducing bacteria in oxygen-sulfide gradients. | growth and chemotactic behavior in oxic-anoxic gradients were studied with two freshwater and four marine strains of sulfate-reducing bacteria related to the genera desulfovibrio, desulfomicrobium or desulfobulbus. cells were grown in oxygen-sulfide counter-gradients within tubes filled with agar-solidified medium. the immobilized cells grew mainly in the anoxic zone, revealing a peak below the oxic-anoxic interface. all tested strains survived exposure to air for 8 h and all were capable of oxy ... | 2002 | 19709210 |
| sulfate-reducing bacteria in human feces and their association with inflammatory bowel diseases. | we have searched for sulfate-reducing bacteria in the feces of 41 healthy individuals and 110 patients from a hepato-gastro-enterology unit using a specific liquid medium (test-kit labège, compagnie française de géothermie, orléans, france). the 110 patients were separated in 22 patients presenting with inflammatory bowel diseases and 88 patients hospitalized for other lower (n=30) or upper (n=58) digestive tract diseases. sulfate-reducing bacteria were isolated from 10 healthy individuals (24%) ... | 2002 | 19709217 |
| sulfate-reducing bacterial community response to carbon source amendments in contaminated aquifer microcosms. | abstract microbial sulfate reduction is an important metabolic activity in many reduced habitats. however, little is known about the sulfate-reducing communities inhabiting petroleum hydrocarbon (phc)-contaminated freshwater aquifer sediments. the purpose of this study was to identify the groups of sulfate-reducing bacteria (srb) selectively stimulated when sediment from a phc-contaminated freshwater aquifer was incubated in sulfate-reducing aquifer microcosms that were amended with specific car ... | 2002 | 19709270 |
| 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 |
| phylogenetic and metabolic diversity of hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx)-transforming bacteria in strictly anaerobic mixed cultures enriched on rdx as nitrogen source. | five obligate anaerobes that were most closely related to clostridium bifermentans, clostridium celerecrescens, clostridium saccharolyticum, clostridium butyricum and desulfovibrio desulfuricans by their 16s rrna genes sequences were isolated from enrichment cultures using hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx) as a nitrogen source. the above isolates transformed rdx at rates of 24.0, 5.4, 6.2, 2.5, 5.5 mumol h(-1) g (dry weight) of cells(-1), respectively, to nitrite, formaldehyde, metha ... | 2003 | 19719572 |
| expression of nifh genes by diazotrophic bacteria in the rhizosphere of short form spartina alterniflora. | abstract a diverse assemblage of diazotrophic bacteria exists in the rhizosphere of the smooth cordgrass, spartina alterniflora, but the taxa actively involved in nitrogen fixation have not been determined. in order to identify the diazotrophs that were actively expressing nifh, the gene encoding the nitrogenase iron protein, mrna was extracted from spartina rhizosphere samples and nifh-specific seminested reverse transcriptase-pcr performed. expressed nifh sequences were recovered from organism ... | 2003 | 19719672 |
| purification, crystallization and preliminary crystallographic analysis of the [nifese] hydrogenase from desulfovibrio vulgaris hildenborough. | the [nifese] hydrogenases belong to a subgroup of the [nife] proteins in which a selenocysteine is a ligand of the ni. these enzymes demonstrate interesting catalytic properties, showing a very high h(2)-producing activity that is sustained in the presence of low o(2) concentrations. the purification, crystallization and preliminary x-ray diffraction analysis of the [nifese] hydrogenase isolated from desulfovibrio vulgaris hildenborough are reported. crystals of the soluble form of this hydrogen ... | 2009 | 19724133 |
| cobalt-, zinc- and iron-bound forms of adenylate kinase (ak) from the sulfate-reducing bacterium desulfovibrio gigas: purification, crystallization and preliminary x-ray diffraction analysis. | adenylate kinase (ak; atp:amp phosphotransferase; ec 2.7.4.3) is involved in the reversible transfer of the terminal phosphate group from atp to amp. aks contribute to the maintenance of a constant level of cellular adenine nucleotides, which is necessary for the energetic metabolism of the cell. three metal ions, cobalt, zinc and iron(ii), have been reported to be present in aks from some gram-negative bacteria. native zinc-containing ak from desulfovibrio gigas was purified to homogeneity and ... | 2009 | 19724135 |
| lactate has the potential to promote hydrogen sulphide formation in the human colon. | high concentrations of sulphide are toxic for the gut epithelium and may contribute to bowel disease. lactate is a favoured cosubstrate for the sulphate-reducing colonic bacterium desulfovibrio piger, as shown here by the stimulation of sulphide formation by d. piger dsm749 by lactate in the presence of sulphate. sulphide formation by d. piger was also stimulated in cocultures with the lactate-producing bacterium bifidobacterium adolescentis l2-32. other lactate-utilizing bacteria such as the bu ... | 2009 | 19732152 |
| effect of sulfate absence and nitrate addition on bacterial community in a sulfidogenic bioreactor. | the characteristics and behavior of sulfate-reducing bacteria (srb), methane-producing bacteria (mpb) and denitrifying bacteria (db) were investigated by polymerase chain reaction (pcr) based methods under the transitory sulfate absence or nitrate addition conditions in a sulfidogenic continuously stirred tank reactor. the bioreactor started-up feeding with 4000 mg l(-1) cod (lactate) and 2000 mg l(-1) sulfate (so(4)(2-)). the sulfate removal efficiency reached 3.84 g l(-1)d(-1) when the activat ... | 2009 | 19735978 |
| contribution of mobile genetic elements to desulfovibrio vulgaris genome plasticity. | the genome of desulfovibrio vulgaris strain depue, a sulfate-reducing deltaproteobacterium isolated from heavy metal-impacted lake sediment, was completely sequenced and compared with the type strain d. vulgaris hildenborough. the two genomes share a high degree of relatedness and synteny, but harbour distinct prophage and signatures of past phage encounters. in addition to a highly variable phage contribution, the genome of strain depue contains a cluster of open-reading frames not found in str ... | 2009 | 19737303 |
| horizontal transfer of the nitrogen fixation gene cluster in the cyanobacterium microcoleus chthonoplastes. | the filamentous, non-heterocystous cyanobacterium microcoleus chthonoplastes is a cosmopolitan organism, known to build microbial mats in a variety of different environments. although most of these cyanobacterial mats are known for their capacity to fix dinitrogen, m. chthonoplastes has not been assigned as a diazotrophic organism. none of the strains that were correctly identified as m. chthonoplastes has been shown to fix dinitrogen and it has repeatedly been reported that these organisms lack ... | 2010 | 19741736 |
| [nife] hydrogenases: structural and spectroscopic studies of the reaction mechanism. | [nife] hydrogenases catalyze the reversible oxidation of dihydrogen. for this simple reaction the molecule has developed a complex catalytic mechanism, during which the enzyme passes through various redox states. the [nife] hydrogenase contains several metal centres, including the bimetallic ni-fe active site, iron-sulfur clusters and a mg(2+) ion. the ni-fe active site is located in the inner part of the protein molecule, therefore a number of pathways are involved in the catalytic reaction rou ... | 2009 | 19759926 |
| monitoring microbial populations of sulfate-reducing bacteria using an impedimetric immunosensor based on agglutination assay. | an impedimetric immunosensor was fabricated for rapid and non-labeled detection of sulfate-reducing bacteria, desulforibrio caledoiensis (srb) by immobilizing lectin-concanavalin a using an agglutination assay. the immobilization of lectin was conducted using amine coupling on the surface of a gold (au) electrode assembled with 11-mercaptoundecanoic acid. electrochemical impedance spectroscopy (eis) was used to verify the stepwise assembly of the sensor system. the work conditions of the impedim ... | 2009 | 19782217 |
| do quantum mechanical energies calculated for small models of protein-active sites converge? | a common approach for the computational modeling of enzyme reactions is to study a rather small model of the active site (20-200 atoms) with quantum mechanical (qm) methods, modeling the rest of the surroundings by a featureless continuum with a dielectric constant of approximately 4. in this paper, we discuss how the residues included in the qm model should be selected and how many residues need to be included before reaction energies converge. as a test case, we use a proton-transfer reaction ... | 2009 | 19785474 |
| zinc-, cobalt- and iron-chelated forms of adenylate kinase from the gram-negative bacterium desulfovibrio gigas. | adenylate kinase (ak) from the sulphate-reducing bacterium desulfovibrio gigas (ak) has been characterized earlier as a co(2+)/zn(2+)-containing enzyme, which is an unusual characteristic for adenylate kinases from gram-negative bacteria, in which these enzymes are normally devoid of metal ions. ak was overexpressed in e. coli and homogeneous co(2+)-, zn(2+)- and fe(2+)-forms of the enzyme were obtained under in vivo conditions. their structural stability and spectroscopic and kinetic properties ... | 2009 | 19786047 |
| susceptibilities of 23 desulfovibrio isolates from humans. | antimicrobial susceptibilities of 23 strains of desulfovibrio spp. were tested by etest. generally, desulfovibrio spp. were highly susceptible to sulbactam-ampicillin, meropenem, clindamycin, metronidazole, and chloramphenicol: mic(90)s of 6, 4, 0.19, 0.25, and 8 microg/ml, respectively. in addition, these strains generally showed high mics to piperacillin and piperacillin-tazobactam. desulfovibrio fairfieldensis (eight strains) was the species least susceptible to most agents, especially beta-l ... | 2009 | 19786606 |