Publications

TitleAbstractYear
Filter
PMID
Filter
expression of a tetraheme protein, desulfovibrio vulgaris miyazaki f cytochrome c(3), in shewanella oneidensis mr-1.cytochrome c(3) from desulfovibrio vulgaris miyazaki f was successfully expressed in the facultative aerobe shewanella oneidensis mr-1 under anaerobic, microaerophilic, and aerobic conditions, with yields of 0.3 to 0.5 mg of cytochrome/g of cells. a derivative of the broad-host-range plasmid prk415 containing the cytochrome c(3) gene from d. vulgaris miyazaki f was used for transformation of s. oneidensis mr-1, resulting in the production of protein product that was indistinguishable from that p ...200010966450
a simple, rapid, and highly efficient gene expression system for multiheme cytochromes c.the genes of tetraheme cytochrome c3 and hexadecaheme high-molecular-weight cytochrome c from desulfovibrio vulgaris could be overexpressed as holoproteins in shewanella oneidensis tsp-c using puc-type vectors of e. coli. surprisingly, s. oneidensis was transformed directly by puc-type vectors through electroporation. the yields of the recombinant proteins in this expression system were much higher than the previously reported ones.200111272827
dna/dna hybridization to microarrays reveals gene-specific differences between closely related microbial genomes.dna microarrays constructed with full length orfs from shewanella oneidensis, mr-1, were hybridized with genomic dna from nine other shewanella species and escherichia coli k-12. this approach enabled visualization of relationships between organisms by comparing individual orf hybridizations to 164 genes and is further amenable to high-density high-throughput analyses of complete microbial genomes. conserved genes (arca and atp synthase) were identified among all species investigated. the mtr op ...200111493693
dissimilatory fe(iii) and mn(iv) reduction by shewanella putrefaciens requires fere, a homolog of the pule (gspe) type ii protein secretion gene.shewanella putrefaciens strain 200 respires anaerobically on a wide range of compounds as the sole terminal electron acceptor, including ferric iron [fe(iii)] and manganese oxide [mn(iv)]. previous studies demonstrated that a 23.3-kb s. putrefaciens wild-type dna fragment conferred metal reduction capability to a set of respiratory mutants with impaired fe(iii) and mn(iv) reduction activities (t. dichristina and e. delong, j. bacteriol. 176:1468-1474, 1994). in the present study, the smallest co ...200211741854
transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress.the iron-directed, coordinate regulation of genes depends on the fur (ferric uptake regulator) gene product, which acts as an iron-responsive, transcriptional repressor protein. to investigate the biological function of a fur homolog in the dissimilatory metal-reducing bacterium shewanella oneidensis mr-1, a fur knockout strain (fur1) was generated by suicide plasmid integration into this gene and characterized using phenotype assays, dna microarrays containing 691 arrayed genes, and two-dimensi ...200211823232
reconstitution of the trimethylamine oxide reductase regulatory elements of shewanella oneidensis in escherichia coli.several bacteria can grow by using small organic compounds such as trimethylamine oxide (tmao) as electron acceptors. in shewanella species, the tmao reductase respiratory system is encoded by the torecad operon. we showed that production of the tmao reductase of s. oneidensis was induced by tmao and repressed by oxygen, and we noticed that a three-gene cluster (torstr) encoding a complex two-component regulatory system was present downstream of the torecad operon. we introduced the torstr gene ...200211844754
microbial activity at gigapascal pressures.we observed physiological and metabolic activity of shewanella oneidensis strain mr1 and escherichia coli strain mg1655 at pressures of 68 to 1680 megapascals (mpa) in diamond anvil cells. we measured biological formate oxidation at high pressures (68 to 1060 mpa). at pressures of 1200 to 1600 mpa, living bacteria resided in fluid inclusions in ice-vi crystals and continued to be viable upon subsequent release to ambient pressures (0.1 mpa). evidence of microbial viability and activity at these ...200211859192
protective role of tolc in efflux of the electron shuttle anthraquinone-2,6-disulfonate.extracellular electron transfer can play an important role in microbial respiration on insoluble minerals. the humic acid analog anthraquinone-2,6-disulfonate (aqds) is commonly used as an electron shuttle during studies of extracellular electron transfer. here we provide genetic evidence that aqds enters shewanella oneidensis strain mr-1 and causes cell death if it accumulates past a critical concentration. a tolc homolog protects the cell from toxicity by mediating the efflux of aqds. electron ...200211872737
the inti-like tyrosine recombinase of shewanella oneidensis is active as an integron integrase.we have found an integron-like integrase gene and an atti site in shewanella oneidensis as part of a small chromosomal integron. we have cloned this gene and tested the ability of the integrase to excise cassettes from various integrons. most cassettes flanked by two attc sites are readily excised, while cassettes in the "first" position, with an atti1 or atti3 site on one end, are not excised. an exception is a cassette with atti2 on one end. the atti2 site, from tn7, has greater similarity to ...200211872738
electron energy loss spectroscopy techniques for the study of microbial chromium(vi) reduction.electron energy loss spectroscopy (eels) techniques were used to determine oxidation state, at high spatial resolution, of chromium associated with the metal-reducing bacteria, shewanella oneidensis, in anaerobic cultures containing cr(vi)o4(2-). these techniques were applied to fixed cells examined in thin section by conventional transmission electron microscopy (tem) as well as unfixed, hydrated bacteria examined by environmental cell (ec)-tem. two distinct populations of bacteria were observe ...200211943357
crystal structures at atomic resolution reveal the novel concept of "electron-harvesting" as a role for the small tetraheme cytochrome c.the genus shewanella produces a unique small tetraheme cytochrome c that is implicated in the iron oxide respiration pathway. it is similar in heme content and redox potential to the well known cytochromes c(3) but related in structure to the cytochrome c domain of soluble fumarate reductases from shewanella sp. we report the crystal structure of the small tetraheme cytochrome c from shewanella oneidensis mr-1 in two crystal forms and two redox states. the overall fold and heme core are surprisi ...200212080059
microarray transcription profiling of a shewanella oneidensis etra mutant.dna microarrays were used to examine the effect of an insertional mutation in the shewanella oneidensis etra (electron transport regulator) locus on gene expression under anaerobic conditions. the mrna levels of 69 genes with documented functions in energy and carbon metabolism, regulation, transport, and other cellular processes displayed significant alterations in transcript abundance in an etra-mutant genetic background. this is the first microarray study indicating a possible involvement of ...200212142431
characterization of the lipopolysaccharides and capsules of shewanella spp.electron microscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis with silver staining and (1)h, (13)c, and (31)p-nuclear magnetic resonance (nmr) were used to detect and characterize the lipopolysaccharides (lpss) of several shewanella species. many expressed only rough lps; however, approximately one-half produced smooth lps (and/or capsular polysaccharides). some lpss were affected by growth temperature with increased chain length observed below 25 degrees c. maximum lps heteroge ...200212200327
genome sequence of the dissimilatory metal ion-reducing bacterium shewanella oneidensis.shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems. here we report the sequencing of the s. oneidensis genome, which consists of a 4,969,803-base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (cds) and a 161,613-base pair plasmid with 173 cdss. we identified the first shewanella lambda-like phage, providing a p ...200212368813
determination of the orientation of the axial ligands and of the magnetic properties of the haems in the tetrahaem ferricytochrome from shewanella frigidimarina.the unambiguous assignment of the nuclear magnetic resonance (nmr) signals of the alpha-substituents of the haems in the tetrahaem cytochrome isolated from shewanella frigidimarina ncimb400, was made using a combination of homonuclear and heteronuclear experiments. the paramagnetic (13)c shifts of the nuclei directly bound to the porphyrin of each haem group were analysed in the framework of a model for the haem electronic structure. the analysis yields g-tensors for each haem, which allowed the ...200212435604
breathing metals as a way of life: geobiology in action.many microbes have the ability to reduce transition metals, coupling this reduction to the oxidation of energy sources in a dissimilatory fashion. because of their abundance, iron and manganese have been extensively studied, and it is well established that reduction of mn and fe account for significant turnover of organic carbon in many environments. in addition, many of the dissimilatory metal reducing bacteria (dmrb) also reduce other metals, including toxic metals like cr(vi), and radioactive ...200212448720
detection of fatty acids from intact microorganisms by molecular beam static secondary ion mass spectrometry.we report the use of a surface analysis approach, static secondary ion mass spectrometry (sims) equipped with a molecular (reo(4)(-)) ion primary beam, to analyze the surface of intact microbial cells. sims spectra of 28 microorganisms were compared to fatty acid profiles determined by gas chromatographic analysis of transesterfied fatty acids extracted from the same organisms. the results indicate that surface bombardment using the molecular primary beam cleaved the ester linkage characteristic ...200312689707
dehydrochlorination of 1,1,1-trichloroethane and pentachloroethane by microbially reduced ferruginous smectite.reduction of structural fe(iii) in smectite clay minerals has been identified as a means to promote dechlorination of polychlorinated ethanes, but its environmental significance has yet to be fully assessed because fe reduction has normally been achieved by agents uncommon in the environment (e.g., dithionite). this study reports the dehydrochlorination of pentachloroethane and 1,1,1-trichloroethane in the presence of ferruginous smectite reduced by two cultures of microorganisms, shewanella one ...200312729213
the ars detoxification system is advantageous but not required for as(v) respiration by the genetically tractable shewanella species strain ana-3.arsenate [as(v); haso(4)(2-)] respiration by bacteria is poorly understood at the molecular level largely due to a paucity of genetically tractable organisms with this metabolic capability. we report here the isolation of a new as(v)-respiring strain (ana-3) that is phylogenetically related to members of the genus shewanella and that also provides a useful model system with which to explore the molecular basis of as(v) respiration. this gram-negative strain stoichiometrically couples the oxidati ...200312732551
overlapping role of the outer membrane cytochromes of shewanella oneidensis mr-1 in the reduction of manganese(iv) oxide.to determine if the outer membrane (om) cytochromes omca and omcb of the metal-reducing bacterium shewanella oneidensis mr-1 have distinct or overlapping roles in the reduction of insoluble manganese(iv) oxide.200312803550
modeling chromate reduction in shewanella oneidensis mr-1: development of a novel dual-enzyme kinetic model.chromate (cr(vi)) reduction tests were performed with nitrate- and fumarate-grown stationary phase cultures of shewanella oneidensis mr-1 (henceforth referred to as mr-1) and disappearance of cr(vi) was monitored over time. a rapid initial decrease in cr(vi) concentration was observed, which was followed by a slower, steady decrease. these observations appear to be consistent with our previous results indicating that cr(vi) reduction in mr-1 involves at least two mechanisms (viamajala et al., 20 ...200312889019
the tetraheme cytochrome cyma is required for anaerobic respiration with dimethyl sulfoxide and nitrite in shewanella oneidensis.the tetraheme c-type cytochrome, cyma, from shewanella oneidensis mr-1 has previously been shown to be required for respiration with fe(iii), nitrate, and fumarate [myers, c. r., and myers, j. m. (1997) j. bacteriol. 179, 1143-1152]. it is located in the cytoplasmic membrane where the bulk of the protein is exposed to the periplasm, enabling it to transfer electrons to a series of redox partners. we have expressed and purified a soluble derivative of cyma (cyma(sol)) that lacks the n-terminal me ...200312899636
cell surface exposure of the outer membrane cytochromes of shewanella oneidensis mr-1.to determine if the outer membrane (om) cytochromes of the metal-reducing bacterium shewanella oneidensis mr-1 are exposed on the cell surface.200312904229
the structure of the rough-type lipopolysaccharide from shewanella oneidensis mr-1, containing 8-amino-8-deoxy-kdo and an open-chain form of 2-acetamido-2-deoxy-d-galactose.the lps from shewanella oneidensis strain mr-1 was analysed by chemical methods and by nmr spectroscopy and mass spectrometry. the lps contained no polysaccharide o-chain, and its carbohydrate backbone had the following structure: (1s)-galnaco-(1-->4,6)-alpha-gal-(1-->6)-alpha-gal-(1-->3)-alpha-gal-(1-p-3)-alpha-ddhep-(1-->5)-alpha-8-aminokdo4r-(2-->6)-beta-glcn4p-(1-->6)-alpha-glcn1p, where r is p or etnpp. there are several novel aspects to this lps. it contains a novel linking unit between th ...200314499575
a computational study of shewanella oneidensis mr-1: structural prediction and functional inference of hypothetical proteins.the genomes of many organisms have been sequenced in the last 5 years. typically about 30% of predicted genes from a newly sequenced genome cannot be given functional assignments using sequence comparison methods. in these situations three-dimensional structural predictions combined with a suite of computational tools can suggest possible functions for these hypothetical proteins. suggesting functions may allow better interpretation of experimental data (e.g., microarray data and mass spectrosco ...200314506847
reannotation of shewanella oneidensis genome.as more and more complete bacterial genome sequences become available, the genome annotation of previously sequenced genomes may become quickly outdated. this is primarily due to the discovery and functional characterization of new genes. we have reannotated the recently published genome of shewanella oneidensis with the following results: 51 new genes have been identified, and functional annotation has been added to the 97 genes, including 15 new and 82 existing ones with previously unassigned ...200314506846
a derivative of the menaquinone precursor 1,4-dihydroxy-2-naphthoate is involved in the reductive transformation of carbon tetrachloride by aerobically grown shewanella oneidensis mr-1.transformation of carbon tetrachloride (ct) by shewanella oneidensis mr-1 has been proposed to involve the anaerobic respiratory-chain component menaquinone. to investigate this hypothesis a series of menaquinone mutants were constructed. the menf mutant is blocked at the start of the menaquinone biosynthetic pathway. the menb, mena and meng mutants are all blocked towards the end of the pathway, being unable to produce 1,4-dihydroxy-2-naphthoic acid (dhna), demethyl-menaquinone and menaquinone, ...200412908086
cometabolism of cr(vi) by shewanella oneidensis mr-1 produces cell-associated reduced chromium and inhibits growth.microbial reduction is a promising strategy for chromium remediation, but the effects of competing electron acceptors are still poorly understood. we investigated chromate (cr(vi)) reduction in batch cultures of shewanella oneidensis mr-1 under aerobic and denitrifying conditions and in the absence of an additional electron acceptor. growth and cr(vi) removal patterns suggested a cometabolic reduction; in the absence of nitrate or oxygen, mr-1 reduced cr(vi), but without any increase in viable c ...200312889027
characterizing gene sets with funcassociate.summary: funcassociate is a web-based tool to help researchers use gene ontology attributes to characterize large sets of genes derived from experiment. distinguishing features of funcassociate include the ability to handle ranked input lists, and a monte carlo simulation approach that is more appropriate to determine significance than other methods, such as bonferroni or idák p-value correction. funcassociate currently supports 10 organisms (vibrio cholerae, shewanella oneidensis, saccharomyces ...200314668247
gelbank: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes.gelbank is a publicly available database of two-dimensional gel electrophoresis (2de) gel patterns of proteomes from organisms with known genome information (available at http://gelbank.anl.gov and ftp://bioinformatics.anl.gov/gelbank/). currently it includes 131 completed, mostly microbial proteomes available from the national center for biotechnology information. a web interface allows the upload of 2d gel patterns and their annotation for registered users. the images are organized by species, ...200414681486
chromosome-encoded ambler class d beta-lactamase of shewanella oneidensis as a progenitor of carbapenem-hydrolyzing oxacillinase.a chromosome-encoded beta-lactamase gene from a shewanella oneidensis reference strain was cloned and expressed in escherichia coli. it encoded a carbapenem-hydrolyzing ambler class d beta-lactamase, oxa-54, that shared 92% amino acid identity with the plasmid-encoded carbapenem-hydrolyzing oxacillinase oxa-48 from klebsiella pneumoniae. this work suggests that shewanella spp. may produce the progenitor of oxacillinases compromising the efficacy of imipenem in clinically relevant gram-negative p ...200414693565
the acnd genes of shewenella oneidensis and vibrio cholerae encode a new fe/s-dependent 2-methylcitrate dehydratase enzyme that requires prpf function in vivo.the propionate utilization operons of several bacteria differ from each other in the occurrence of two genes, acnd and prpf, in place of or in addition to the prpd gene encoding an fe/s-independent 2-methylcitrate dehydratase enzyme. we cloned the acnd and prpf genes from two organisms, shewanella oneidensis and vibrio cholerae, and found that, together, the acnd and prpf proteins restored the ability of a prpd mutant strain of salmonella enterica to grow on propionate as a source of carbon and ...200414702315
identification of the gene encoding the sole physiological fumarate reductase in shewanella oneidensis mr-1.shewanella oneidensis mr-1 is a gram-negative, nonfermentative rod with a complex electron transport system which facilitates its ability to use a variety of terminal electron acceptors, including fumarate, for anaerobic respiration. cmtn-3, a mutant isolated by transposon (tnphoa) mutagenesis, can no longer use fumarate as an electron acceptor; it lacks fumarate reductase activity as well as a 65-kda soluble tetraheme flavocytochrome c. the sequence of the tnphoa-flanking genomic dna of cmtn-3 ...200312872312
microbial reduction and precipitation of vanadium by shewanella oneidensis.shewanella oneidensis couples anaerobic oxidation of lactate, formate, and pyruvate to the reduction of vanadium pentoxide (v(v)). the bacterium reduces v(v) (vanadate ion) to v(iv) (vanadyl ion) in an anaerobic atmosphere. the resulting vanadyl ion precipitates as a v(iv)-containing solid.200312788772
vanadium(v) reduction by shewanella oneidensis mr-1 requires menaquinone and cytochromes from the cytoplasmic and outer membranes.the metal-reducing bacterium shewanella oneidensis mr-1 displays remarkable anaerobic respiratory plasticity, which is reflected in the extensive number of electron transport components encoded in its genome. in these studies, several cell components required for the reduction of vanadium(v) were determined. v(v) reduction is mediated by an electron transport chain which includes cytoplasmic membrane components (menaquinone and the tetraheme cytochrome cyma) and the outer membrane (om) cytochrom ...200415006760
involvement of cyclic amp (camp) and camp receptor protein in anaerobic respiration of shewanella oneidensis.shewanella oneidensis is a metal reducer that can use several terminal electron acceptors for anaerobic respiration, including fumarate, nitrate, dimethyl sulfoxide (dmso), trimethylamine n-oxide (tmao), nitrite, and insoluble iron and manganese oxides. two s. oneidensis mutants, sr-558 and sr-559, with tn5 insertions in crp, were isolated and analyzed. both mutants were deficient in fe(iii) and mn(iv) reduction. they were also deficient in anaerobic growth with, and reduction of, nitrate, fumar ...200312775705
identification of a novel steroid inducible gene associated with the beta hsd locus of comamonas testosteroni.comamonas testosteroni is a soil bacterium, which can use a variety of steroids as carbon and energy source. even if it can be estimated that the complete degradation of the steroid nucleus requires more than 20 enzymatic reactions, the complete molecular characterization of the genes encoding these steroid degradative enzymes as well as the genetic organization of them remain to be elucidated. we have previously reported the cloning and nucleotide sequence of two steroid-inducible genes, beta h ...200415026087
identification of 42 possible cytochrome c genes in the shewanella oneidensis genome and characterization of six soluble cytochromes.through pattern matching of the cytochrome c heme-binding site (cxxch) against the genome sequence of shewanella oneidensis mr-1, we identified 42 possible cytochrome c genes (27 of which should be soluble) out of a total of 4758. however, we found only six soluble cytochromes c in extracts of s. oneidensis grown under several different conditions: (1) a small tetraheme cytochrome c, (2) a tetraheme flavocytochrome c-fumarate reductase, (3) a diheme cytochrome c4, (4) a monoheme cytochrome c5, ( ...200415107237
the outer membrane protein omp35 affects the reduction of fe(iii), nitrate, and fumarate by shewanella oneidensis mr-1.shewanella oneidensis mr-1 uses several electron acceptors to support anaerobic respiration including insoluble species such as iron(iii) and manganese(iv) oxides, and soluble species such as nitrate, fumarate, dimethylsulfoxide and many others. mr-1 has complex branched electron transport chains that include components in the cytoplasmic membrane, periplasm, and outer membrane (om). previous studies have implicated a role for anaerobically upregulated om electron transport components in the use ...200415212692
genes regulated by torr, the trimethylamine oxide response regulator of shewanella oneidensis.the torecad operon encoding the trimethylamine oxide (tmao) respiratory system of shewanella oneidensis is positively controlled by the tors/torr two-component system when tmao is available. activation of the tor operon occurs upon binding of the phosphorylated response regulator torr to a single operator site containing the direct repeat nucleotide sequence ttcatan4ttcata. here we show that the replacement of any nucleotide of one ttcata hexamer prevented torr binding in vitro, meaning that tor ...200415231782
analysis of the shewanella oneidensis proteome by two-dimensional gel electrophoresis under nondenaturing conditions.proteomes are dynamic, i.e., the protein components of living cells change in response to various stimuli. protein changes can involve shifts in the abundance of protein components, in the interactions of protein components, and in the activity of protein components. two-dimensional gel electrophoresis (2-de) coupled with peptide mass spectrometry is useful for the analysis of relative protein abundance, but the denaturing conditions of classical 2-de do not allow analysis of protein interaction ...200312748955
characterization of the shewanella oneidensis mr-1 decaheme cytochrome mtra: expression in escherichia coli confers the ability to reduce soluble fe(iii) chelates.shewanella oneidensis mr-1 has the metabolic capacity to grow anaerobically using fe(iii) as a terminal electron acceptor. growth under these conditions results in the de novo synthesis of a number of periplasmic c-type cytochromes, many of which are multiheme in nature and are thought to be involved in the fe(iii) respiratory process. to begin a biochemical study of these complex cytochromes, the mtra gene that encodes an approximate 32-kda periplasmic decaheme cytochrome has been heterologousl ...200312732647
cloning and overproduction of the rpoz gene encoding an rna polymerase omega subunit from a deep-sea piezophilic shewanella violacea strain dss12.we have cloned the rpoz gene, encoding rna polymerase omega protein, by pcr approach from the deep-sea piezophilic and psychrophilic bacterium, shewanella violacea strain dss12. the cloned gene, 285bp in length, was found to encode a protein consisting of 94 amino acid residues with a molecular mass of 10,327 da. significant homology was evident comparing the rpoz protein of s. violacea with that of shewanella oneidensis (69% identity), vibrio cholerae (65% identity), escherichia coli k-12 (64% ...200415346766
integrating 'top-down" and "bottom-up" mass spectrometric approaches for proteomic analysis of shewanella oneidensis.here we present a comprehensive method for proteome analysis that integrates both intact protein measurement ("top-down") and proteolytic fragment characterization ("bottom-up") mass spectrometric approaches, capitalizing on the unique capabilities of each method. this integrated approach was applied in a preliminary proteomic analysis of shewanella oneidensis, a metal-reducing microbe of potential importance to the field of bioremediation. cellular lysates were examined directly by the "bottom- ...200212645901
accumulation of mn(ii) in deinococcus radiodurans facilitates gamma-radiation resistance.deinococcus radiodurans is extremely resistant to ionizing radiation. how this bacterium can grow under chronic gamma radiation [50 grays (gy) per hour] or recover from acute doses greater than 10 kgy is unknown. we show that d. radiodurans accumulates very high intracellular manganese and low iron levels compared with radiation-sensitive bacteria and that resistance exhibits a concentration-dependent response to manganous chloride [mn(ii)]. among the most radiation-resistant bacterial groups re ...200415459345
the outer membrane cytochromes of shewanella oneidensis mr-1 are lipoproteins.to determine if the outer membrane (om) cytochromes omca and omcb of the metal-reducing bacterium shewanella oneidensis mr-1 are lipoproteins, and to assess cell surface exposure of the cytochromes by radioiodination.200415482439
use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses.the use of artificial neural networks (anns) is described for predicting the reversed-phase liquid chromatography retention times of peptides enzymatically digested from proteome-wide proteins. to enable the accurate comparison of the numerous lc/ms data sets, a genetic algorithm was developed to normalize the peptide retention data into a range (from 0 to 1), improving the peptide elution time reproducibility to approximately 1%. the network developed in this study was based on amino acid resid ...200312641221
global transcriptome analysis of the heat shock response of shewanella oneidensis.shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities. however, the genetic basis and regulatory mechanisms underlying the ability of s. oneidensis to survive and adapt to various environmentally relevant stresses is poorly understood. to define this organism's molecular response to elevated growth temperatures, temporal gene expression profiles were examined in cells subjected to heat stress by using whole-genome dna micr ...200415516594
survival of shewanella oneidensis mr-1 after uv radiation exposure.we systematically investigated the physiological response as well as dna damage repair and damage tolerance in shewanella oneidensis mr-1 following uvc, uvb, uva, and solar light exposure. mr-1 showed the highest uvc sensitivity among shewanella strains examined, with d37 and d10 values of 5.6 and 16.5% of escherichia coli k-12 values. stationary cells did not show an increased uva resistance compared to exponential-phase cells; instead, they were more sensitive at high uva dose. uva-irradiated ...200415528503
shewanella profunda sp. nov., isolated from deep marine sediment of the nankai trough.a novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain lt13a(t)) was isolated from a deep sediment layer in the nankai trough (leg 190, ocean drilling program) off the coast of japan. this organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. max ...200415545415
initial phases of biofilm formation in shewanella oneidensis mr-1.shewanella oneidensis mr-1 is a facultative fe(iii)- and mn(iv)-reducing microorganism and serves as a model for studying microbially induced dissolution of fe or mn oxide minerals as well as biogeochemical cycles. in soil and sediment environments, s. oneidensis biofilms form on mineral surfaces and are critical for mediating the metabolic interaction between this microbe and insoluble metal oxide phases. in order to develop an understanding of the molecular basis of biofilm formation, we inves ...200415547283
transcriptomic and proteomic characterization of the fur modulon in the metal-reducing bacterium shewanella oneidensis.the availability of the complete genome sequence for shewanella oneidensis mr-1 has permitted a comprehensive characterization of the ferric uptake regulator (fur) modulon in this dissimilatory metal-reducing bacterium. we have employed targeted gene mutagenesis, dna microarrays, proteomic analysis using liquid chromatography-mass spectrometry, and computational motif discovery tools to define the s. oneidensis fur regulon. using this integrated approach, we identified nine probable operons (con ...200415576789
effects of isso2 insertions in structural and regulatory genes of the trimethylamine oxide reductase of shewanella oneidensis.we have isolated three shewanella oneidensis mutants specifically impaired in trimethylamine oxide (tmao) respiration. the mutations arose from insertions of an isso2 element into tora, torr, and tors, encoding, respectively, the tmao reductase tora, the response regulator torr, and the sensor tors. although tora is not the sole enzyme reducing tmao in s. oneidensis, growth analysis showed that it is the main respiratory tmao reductase. use of a plasmid-borne tore'-lacz fusion confirmed that the ...200312618472
in situ environmental cell-transmission electron microscopy study of microbial reduction of chromium(vi) using electron energy loss spectroscopy.reduction of cr(vi) by the bacterium, shewanella oneidensis (previously classified shewanella putrefaciens strain mr-1), was studied by absorption spectrophotometry and in situ, environmental cell-transmission electron microscopy (ec-tem) coupled with electron energy loss spectroscopy (eels). bacteria from rinsed cultures were placed directly in the environmental cell of the transmission electron microscope and examined under 100 torr pressure. bright field ec-tem images show two distinct popula ...200112597792
a directional electron transfer regulator based on heme-chain architecture in the small tetraheme cytochrome c from shewanella oneidensis.the macroscopic and microscopic redox potentials of the four hemes of the small tetraheme cytochrome c from shewanella oneidensis were determined. the microscopic redox potentials show that the order of reduction is from hemes in the c-terminal domain (hemes 3 and 4) to the n-terminal domain (heme 1), demonstrating the polarization of the tetraheme chain during reduction. this makes heme 4 the most efficient electron delivery site. furthermore, multi-step reduction of other redox centers through ...200212482588
growth of iron(iii)-reducing bacteria on clay minerals as the sole electron acceptor and comparison of growth yields on a variety of oxidized iron forms.smectite clay minerals are abundant in soils and sediments worldwide and are typically rich in fe. while recent investigations have shown that the structural fe(iii) bound in clay minerals is reduced by microorganisms, previous studies have not tested growth with clay minerals as the sole electron acceptor. here we have demonstrated that a pure culture of shewanella oneidensis strain mr-1 as well as enrichment cultures of fe(iii)-reducing bacteria from rice paddy soil and subsurface sediments ar ...200212450850
primegens: robust and efficient design of gene-specific probes for microarray analysis.motivation: dna microarray is a powerful high-throughput tool for studying gene function and regulatory networks. due to the problem of potential cross hybridization, using full-length genes for microarray construction is not appropriate in some situations. a bioinformatic tool, primegens, has recently been developed for the automatic design of pcr primers using dna fragments that are specific to individual open reading frames (orfs). results: primegens first carries out a blast search for each ...200212424113
low-temperature growth of shewanella oneidensis mr-1.shewanella oneidensis mr-1 is a mesophilic bacterium with a maximum growth temperature of approximately 35 degrees c but the ability to grow over a wide range of temperatures, including temperatures near zero. at room temperature ( approximately 22 degrees c) mr-1 grows with a doubling time of about 40 min, but when moved from 22 degrees c to 3 degrees c, mr-1 cells display a very long lag phase of more than 100 h followed by very slow growth, with a doubling time of approximately 67 h. in compa ...200515691935
reduction kinetics of fe(iii), co(iii), u(vi), cr(vi), and tc(vii) in cultures of dissimilatory metal-reducing bacteria.the reduction kinetics of fe(iii)citrate, fe(iii)nta, co(iii)edta-, u(vi)o(2) (2+), cr(vi)o(4) (2-), and tc(vii)o(4) (-) were studied in cultures of dissimilatory metal reducing bacteria (dmrb): shewanella alga strain bry, shewanella putrefaciens strain cn32, shewanella oneidensis strain mr-1, and geobacter metallireducens strain gs-15. reduction rates were metal specific with the following rate trend: fe(iii)citrate > or = fe(iii)nta > co(iii)edta- >> uo(2)(2+) > cro(4)(2-) > tco(4)(-), except ...200212378605
the membrane-bound tetrahaem c-type cytochrome cyma interacts directly with the soluble fumarate reductase in shewanella.shewanella spp. demonstrate great variability in the use of terminal electron acceptors in anaerobic respiration; these include nitrate, fumarate, dmso, trimethylamine oxide, sulphur compounds and metal oxides. these pathways open up possible applications in bioremediation. the wide variety of respiratory substrates for shewanella is correlated with the evolution of several multi-haem membrane-bound, periplasmic and outer-membrane c-type cytochromes. the 21 kda c-type cytochrome cyma of the fres ...200212196158
application of flow field flow fractionation-icpms for the study of uranium binding in bacterial cell suspensions.field flow fractionation (fff) is a size-based separation technique applicable to biomolecules, colloids, and bacteria in solution. when interfaced with icpms on-line, elemental data can be collected concurrent with size distribution. we employed hyperlayer flow fff (fl fff) methodology to separate cells of shewanella oneidensis strain mr-1 from exopolymers present in washed cell suspensions. with a channel flow of 4 ml min-1 and a cross-flow of 0.4 ml min-1 cells eluted with a retention time of ...200515732923
chromate/nitrite interactions in shewanella oneidensis mr-1: evidence for multiple hexavalent chromium [cr(vi)] reduction mechanisms dependent on physiological growth conditions.inhibition of hexavalent chromium [cr(vi)] reduction due to nitrate and nitrite was observed during tests with shewanella oneidensis mr-1 (previously named shewanella putrefaciens mr-1 and henceforth referred to as mr-1). initial cr(vi) reduction rates were measured at various nitrite concentrations, and a mixed inhibition kinetic model was used to determine the kinetic parameters-maximum cr(vi) reduction rate and inhibition constant [v(max,cr(vi)) and k(i,cr(vi))]. values of v(max,cr(vi)) and k ...200212001169
chromate reduction in shewanella oneidensis mr-1 is an inducible process associated with anaerobic growth.cr(vi) reduction was observed during tests with shewanella oneidensis mr-1 (previously named s. putrefaciens mr-1) while being grown with nitrate or fumarate as electron acceptor and lactate as electron donor. from the onset of anoxic growth on fumarate, we measured a gradual and progressive increase in the specific cr(vi) reduction rate with incubation time until a maximum was reached at late exponential/early stationary phase. under denitrifying conditions, the specific cr(vi) reduction rate w ...200211934298
how radiation kills cells: survival of deinococcus radiodurans and shewanella oneidensis under oxidative stress.we have recently shown that deinococcus radiodurans and other radiation resistant bacteria accumulate exceptionally high intracellular manganese and low iron levels. in comparison, the dissimilatory metal-reducing bacterium shewanella oneidensis accumulates fe but not mn and is extremely sensitive to radiation. we have proposed that for fe-rich, mn-poor cells killed at radiation doses which cause very little dna damage, cell death might be induced by the release of fe(ii) from proteins during ir ...200515808748
gene and protein expression profiles of shewanella oneidensis during anaerobic growth with different electron acceptors.changes in mrna and protein expression profiles of shewanella oneidenesis mr-1 during switch from aerobic to fumarate-, fe(iii)-, or nitrate-reducing conditions were examined using dna microarrays and two-dimensional polyacrylamide gel electrophoresis (2-d page). in response to changes in growth conditions, 121 of the 691 arrayed genes displayed at least a two-fold difference in transcript abundance as determined by microarray analysis. genes involved in aerobic respiration encoding cytochrome c ...200211881834
comparative analysis of differentially expressed genes in shewanella oneidensis mr-1 following exposure to uvc, uvb, and uva radiation.we previously reported that shewanella oneidensis mr-1 is highly sensitive to uvc (254 nm), uvb (290 to 320 nm), and uva (320 to 400 nm). here we delineated the cellular response of mr-1 to uv radiation damage by analyzing the transcriptional profile during a 1-h recovering period after uvc, uvb, and uva exposure at a dose that yields about a 20% survival rate. although the sos response was observed with all three treatments, the induction was more robust in response to short-wavelength uv radia ...200515866945
anaerobic regulation by an atypical arc system in shewanella oneidensis.shewanella oneidensis strain mr-1 is well known for its respiratory versatility, yet little is understood about how it regulates genes involved in anaerobic respiration. the arc two-component system plays an important role in this process in escherichia coli; therefore, we determined its function in s. oneidensis. arca from s. oneidensis complements an e. coli arca mutant, but the arc regulon in s. oneidensis constitutes a different suite of genes. for example, one of the strongest arca-regulate ...200515882425
microbial iron respiration can protect steel from corrosion.microbiologically influenced corrosion (mc) of steel has been attributed to the activity of biofilms that include anaerobic microorganisms such as iron-respiring bacteria, yet the mechanisms by which these organisms influence corrosion have been unclear. to study this process, we generated mutants of the iron-respiring bacterium shewanella oneidensis strain mr-1 that were defective in biofilm formation and/or iron reduction. electrochemical impedance spectroscopy was used to determine changes in ...200211872499
the structure of the capsular polysaccharide of shewanella oneidensis strain mr-4.capsular polysaccharides were extracted from shewanella oneidensis strain mr-4, grown on two different culture media. the polysaccharides were analyzed using 1h and 13c nmr spectroscopy, and the following structure of the repeating unit was established: [structure: see text] where the residue of 4-amino-4,6-dideoxy-d-glucose (qui4n) was substituted with different n-acyl groups depending on the growth media. all monosaccharides are present in the pyranose form. in the ps from cells grown on enric ...200515936738
identification of a small tetraheme cytochrome c and a flavocytochrome c as two of the principal soluble cytochromes c in shewanella oneidensis strain mr1.two abundant, low-redox-potential cytochromes c were purified from the facultative anaerobe shewanella oneidensis strain mr1 grown anaerobically with fumarate. the small cytochrome was completely sequenced, and the genes coding for both proteins were cloned and sequenced. the small cytochrome c contains 91 residues and four heme binding sites. it is most similar to the cytochromes c from shewanella frigidimarina (formerly shewanella putrefaciens) ncimb400 and the unclassified bacterial strain h1 ...200111425747
bacterial recognition of mineral surfaces: nanoscale interactions between shewanella and alpha-feooh.force microscopy has been used to quantitatively measure the infinitesimal forces that characterize interactions between shewanella oneidensis (a dissimilatory metal-reducing bacterium) and goethite (alpha-feooh), both commonly found in earth near-surface environments. force measurements with subnanonewton resolution were made in real time with living cells under aerobic and anaerobic solutions as a function of the distance, in nanometers, between a cell and the mineral surface. energy values [i ...200111359008
polyphasic taxonomy of the genus shewanella and description of shewanella oneidensis sp. nov.the genus shewanella has been studied since 1931 with regard to a variety of topics of relevance to both applied and environmental microbiology. recent years have seen the introduction of a large number of new shewanella-like isolates, necessitating a coordinated review of the genus. in this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. this polyphasic taxonomy takes into ...199910319494
proteomics of the dissimilatory iron-reducing bacterium shewanella oneidensis mr-1, using a matrix-assisted laser desorption/ionization-tandem-time of flight mass spectrometer.shewanella oneidensis mr-1 is a gram-negative facultative aerobic bacterium living at oxic-anoxic interfaces in nature. the plasticity of terminal electron-acceptors used under anaerobic conditions is huge, but the adaptation to these different environmental conditions remains unclear. in this work, we used a proteomic approach to study the protein content when the organism is grown under anaerobic respiration conditions on insoluble ferric oxide. by analysis of two-dimensional gel patterns of s ...200314595823
chemotactic responses to metals and anaerobic electron acceptors in shewanella oneidensis mr-1.although a previous study indicated that the dissimilatory metal-reducing bacterium shewanella oneidensis mr-1 lacks chemotactic responses to metals that can be used as anaerobic electron acceptors, new results show that this bacterium responds to both mn(iii) and fe(iii). cells were also shown to respond to another unusual electron acceptor, the humic acid analog anthraquinone-2,6-disulfonate. these results indicate that s. oneidensis is capable of moving towards a number of unusual anaerobic e ...200515995227
genome-wide examination of the natural solar radiation response in shewanella oneidensis mr-1.we previously reported that shewanella oneidensis mr-1 is extremely sensitive to natural solar radiation (nsr). here we analyzed the global transcriptional profile of mr-1 during a 1-h recovering period after exposure to ambient solar light at a dose that yields about 20% survival rate on a luria-bertani (lb) plate. we observed the induction of dna damage-repair genes, the sos response as well as detoxification strategies that we previously observed in mr-1 following artificial uv-a irradiation. ...200516022560
cell density related h2 consumption in relation to anoxic fe(0) corrosion and precipitation of corrosion products by shewanella oneidensis mr-1.in the absence of oxygen, a protective h2 film is formed around an fe(0) surface, inhibiting the electron flow from this surface. our study of anoxic corrosion of fe(0) beads revealed that, in the presence of shewanella oneidensis mr-1, h2 removal and precipitation of fe mineral particles on the cell surface are determining processes for corrosion. these two biologically mediated processes were governed by cell density. h2 removal by shewanella oneidensis was detected at cell concentrations of 1 ...200314641597
toxic effects of chromium(vi) on anaerobic and aerobic growth of shewanella oneidensis mr-1.cr(vi) was added to early- and mid-log-phase shewanella oneidensis (s. oneidensis) mr-1 cultures to study the physiological state-dependent toxicity of cr(vi). cr(vi) reduction and culture growth were measured during and after cr(vi) reduction. inhibition of growth was observed when cr(vi) was added to cultures of mr-1 growing aerobically or anaerobically with fumarate as the terminal electron acceptor. under anaerobic conditions, there was immediate cessation of growth upon addition of cr(vi) i ...200414763828
shewanella oneidensis mr-1 restores menaquinone synthesis to a menaquinone-negative mutant.the mechanisms underlying the use of insoluble electron acceptors by metal-reducing bacteria, such as shewanella oneidensis mr-1, are currently under intensive study. current models for shuttling electrons across the outer membrane (om) of mr-1 include roles for om cytochromes and the possible excretion of a redox shuttle. while mr-1 is able to release a substance that restores the ability of a menaquinone (mk)-negative mutant, cma-1, to reduce the humic acid analog anthraquinone-2,6-disulfonate ...200415345428
preparation of 20-microm-i.d. silica-based monolithic columns and their performance for proteomics analyses.we describe the preparation and performance of high-efficiency 70 cm x 20 microm i.d. silica-based monolithic capillary lc columns. the monolithic columns at a mobile-phase pressure of 5000 psi provide flow rates of approximately 40 nl/min at a linear velocity of approximately 0.24 cm/s. the columns provide a separation peak capacity of approximately 420 in conjunction with both on-line coupling with microsolid-phase extraction and nanoelectrospray ionization-mass spectrometry. performance was e ...200516053318
effects of a strong static magnetic field on bacterium shewanella oneidensis: an assessment by using whole genome microarray.the effect of a strong static 14.1 t magnetic field on log phase cells of bacterial strain shewanella oneidensis mr-1 was evaluated by using whole genome microarray of this bacterium. although differences were not observed between the treatment and control by measuring the optical density (od), colony forming unit (cfu), as well as post-exposure growth of cells, transcriptional expression levels of 65 genes were altered according to our microarray data. among these genes, 21 were upregulated whi ...200516037957
identification of genes involved in cytochrome c biogenesis in shewanella oneidensis, using a modified mariner transposon.a modified mariner transposon, minihimar rb1, was generated to mutagenize cells of the metal-reducing bacterium shewanella oneidensis. the use of this transposon led to the isolation of stable mutants and allowed rapid identification of disrupted genes. fifty-eight mutants, including bg104 and bg148 with transposon insertions in the cytochrome c maturation genes ccmc and ccmf1, respectively, were analyzed. both mutants were deficient in anaerobic respiration and cytochrome c production.200516085900
identification of genes regulated by changing salinity in the deep-sea bacterium shewanella sp. wp3 using rna arbitrarily primed pcr.the differential gene transcription of a deep-sea bacterium shewanella sp. wp3 in response to changing salinity was analyzed by rna fingerprinting using arbitrarily primed pcr (rap-pcr). ninety primer sets were used to scan two different rna pools derived from cultures of 1% and 7% nacl concentrations. forty-three putative differential-expressed fragments were identified, cloned, and sequenced. six out of the 43 fragments were confirmed to be truly differentially transcribed in terms of changing ...200616133656
integration of electrokinetic-based multidimensional separation/concentration platform with electrospray ionization-fourier transform ion cyclotron resonance-mass spectrometry for proteome analysis of shewanella oneidensis.this work focuses on the development of a multidimensional electrokinetic-based separation/concentration platform coupled with electrospray ionization-fourier transform ion cyclotron resonance mass spectrometry (esi-fticr-ms) for achieving the high resolution and ultrasensitive analysis of complex protein/peptide mixtures. a microdialysis junction is employed as the interface for on-line combination of capillary isoelectric focusing (cief) with transient capillary isotachophoresis/zone electroph ...200314632047
direct observation of microbial inhibition of calcite dissolution.vertical scanning interferometry (vsi) provides a method for quantification of surface topography at the angstrom to nanometer level. time-dependent vsi measurements can be used to study the surface-normal retreat across crystal and other solid surfaces during dissolution or corrosion processes. therefore, vsi can be used to directly and nondestructively measure mineral dissolution rates with high precision. we have used this method to compare the abiotic dissolution behavior of a representative ...200415006787
selenite and tellurite reduction by shewanella oneidensis.shewanella oneidensis mr-1 reduces selenite and tellurite preferentially under anaerobic conditions. the se(0) and te(0) deposits are located extracellularly and intracellularly, respectively. this difference in localization and the distinct effect of some inhibitors and electron acceptors on these reduction processes are taken as evidence of two independent pathways.200516151159
global transcriptome analysis of shewanella oneidensis mr-1 exposed to different terminal electron acceptors.to gain insight into the complex structure of the energy-generating networks in the dissimilatory metal reducer shewanella oneidensis mr-1, global mrna patterns were examined in cells exposed to a wide range of metal and non-metal electron acceptors. gene expression patterns were similar irrespective of which metal ion was used as electron acceptor, with 60% of the differentially expressed genes showing similar induction or repression relative to fumarate-respiring conditions. several groups of ...200516199584
octaheme tetrathionate reductase is a respiratory enzyme with novel heme ligation.we have isolated a soluble cytochrome from shewanella oneidensis that contains eight covalently attached heme groups and determined its crystal structure. one of these hemes exhibits novel ligation of the iron atom by the epsilon-amino group of a lysine residue, despite its attachment via a typical cxxch motif. this heme is most likely the active site for tetrathionate reduction, a reaction catalyzed efficiently by this enzyme.200415361860
global transcriptional profiling of shewanella oneidensis mr-1 during cr(vi) and u(vi) reduction.whole-genome dna microarrays were used to examine the gene expression profile of shewanella oneidensis mr-1 during u(vi) and cr(vi) reduction. the same control, cells pregrown with nitrate and incubated with no electron acceptor, was used for the two time points considered and for both metals. u(vi)-reducing conditions resulted in the upregulation (> or = 3-fold) of 121 genes, while 83 genes were upregulated under cr(vi)-reducing conditions. a large fraction of the genes upregulated [34% for u(v ...200516269787
comparative characterization and expression analysis of the four old yellow enzyme homologues from shewanella oneidensis indicate differences in physiological function.shewanella oneidensis contains four genes that encode proteins that have high sequence identity with yeast oye (old yellow enzyme, an nadph oxidoreductase), the well-studied archetype of the oye protein family. the present paper describes the first comparative study of oyes that are present in a single bacterial species, performed to gain insight into their biochemical properties and physiological importance. the four proteins [named sye1-sye4 (shewanella yellow enzyme 1-4)] were expressed as gl ...200616293111
structure of 2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase from shewanella oneidensis at 1.6 a: identification of farnesyl pyrophosphate trapped in a hydrophobic cavity.isopentenyl pyrophosphate (ipp) is a universal building block for the ubiquitous isoprenoids that are essential to all organisms. the enzymes of the non-mevalonate pathway for ipp synthesis, which is unique to many pathogenic bacteria, have recently been explored as targets for antibiotic development. several crystal structures of 2c-methyl-d-erythritol-2,4-cyclophosphate (mecdp) synthase, the fifth of seven enzymes involved in the non-mevalonate pathway for synthesis of ipp, have been reported; ...200415502301
validation of shewanella oneidensis mr-1 small proteins by amt tag-based proteome analysis.using stringent criteria for protein identification by accurate mass and time (amt) tag mass spectrometric methodology, we detected 36 proteins of <101 amino acids in length, including 10 that were annotated as hypothetical proteins, in 172 global tryptic digests of shewanella oneidensis mr-1 proteins. peptides that map to the conserved, but functionally uncharacterized proteins so4134 and so2787, were the most frequently detected peptides in these samples, while those that map to hypotheticals ...200415669716
proteomics of shewanella oneidensis mr-1 biofilm reveals differentially expressed proteins, including agga and ribb.shewanella oneidensis mr-1 is a gram-negative, facultative aerobic bacterium, able to respire a variety of electron acceptors. due to its capability to reduce solid ferric iron, s. oneidensis plays an important role in microbially induced corrosion of metal surfaces. since this requires cellular adhesion to the metal surface, biofilm growth is an essential feature of this process. the goal of this work was to compare the global protein expression patterns of sessile and planktonic grown s. oneid ...200515712242
a new method for c-terminal sequence analysis in the proteomic era.the overall study of post-translational modifications (ptms) of proteins is gaining strong interest. beside phosphorylation and glycosylation, truncations of the nascent polypeptide chain at the amino or carboxy terminus are by far the most common types of ptms in proteins. in contrast to the analysis of phosphorylation and glycosylation sites, relatively little attention has been paid to the development of approaches for the systematic analysis of proteolytic processing events. here we present ...200515782188
beta-propeller phytases in the aquatic environment.phytate, which is one of the dominant organic phosphorus compounds in nature, is very stable in soils. although a substantial amount of phytate is carried from terrestrial to aquatic systems, it is a minor component of organic phosphorus in coastal sediments. the ephemeral nature of phytate implies the rapid hydrolysis of phytate under aquatic conditions. among the four classes of known phytases that have been identified in terrestrial organisms, only beta-propeller phytase-like sequences have b ...200616402222
respiration and growth of shewanella oneidensis mr-1 using vanadate as the sole electron acceptor.shewanella oneidensis mr-1 is a free-living gram-negative gamma-proteobacterium that is able to use a large number of oxidizing molecules, including fumarate, nitrate, dimethyl sulfoxide, trimethylamine n-oxide, nitrite, and insoluble iron and manganese oxides, to drive anaerobic respiration. here we show that s. oneidensis mr-1 is able to grow on vanadate as the sole electron acceptor. oxidant pulse experiments demonstrated that proton translocation across the cytoplasmic membrane occurs during ...200515866913
automated 20 kpsi rplc-ms and ms/ms with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics.proteomics analysis based-on reversed-phase liquid chromatography (rplc) is widely practiced; however, variations providing cutting-edge rplc performance have generally not been adopted even though their benefits are well established. here, we describe an automated format 20 kpsi rplc system for proteomics and metabolomics that includes on-line coupling of micro-solid phase extraction for sample loading and allows electrospray ionization emitters to be readily replaced. the system uses 50 microm ...200515889897
genomic comparisons among gamma-proteobacteria.predicted highly expressed (phx) genes are compared for 16 gamma-proteobacteria and their similarities and differences are interpreted with respect to known or predicted physiological characteristics of the organisms. predicted highly expressed genes often reflect the organism's predominant lifestyle, habitat, nutrition sources and metabolic propensities. this technique allows to predict principal metabolic activities of the microorganisms operating in their natural habitats. among our findings ...200616423015
transcriptome analysis applied to survival of shewanella oneidensis mr-1 exposed to ionizing radiation.the ionizing radiation (ir) dose that yields 20% survival (d20) of shewanella oneidensis mr-1 is lower by factors of 20 and 200 than those for escherichia coli and deinococcus radiodurans, respectively. transcriptome analysis was used to identify the genes of mr-1 responding to 40 gy (d20). we observed the induction of 170 genes and repression of 87 genes in mr-1 during a 1-h recovery period after irradiation. the genomic response of mr-1 to ir is very similar to its response to uv radiation (25 ...200616428429
transcriptome profiling of shewanella oneidensis gene expression following exposure to acidic and alkaline ph.the molecular response of shewanella oneidensis mr-1 to variations in extracellular ph was investigated based on genomewide gene expression profiling. microarray analysis revealed that cells elicited both general and specific transcriptome responses when challenged with environmental acid (ph 4) or base (ph 10) conditions over a 60-min period. global responses included the differential expression of genes functionally linked to amino acid metabolism, transcriptional regulation and signal transdu ...200616452448
de novo sequence analysis of n-terminal sulfonated peptides after in-gel guanidination.here we report a novel approach in which gel-separated proteins are guanidinated in-gel prior to enzymatic cleavage. in contrast to previously described techniques, this procedure allows the extracted tryptic peptides to be n-terminal sulfonated without any further sample purification. the derivatized peptides were subsequently fragmented using a matrix-assisted laser desorption/ionization time of flight/time of flight instrument. the approach facilitates the de novo sequence analysis and allows ...200515937995
Displaying items 1 - 100 of 968