Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| global detection and characterization of hypothetical proteins in shewanella oneidensis mr-1 using lc-ms based proteomics. | the availability of whole genome sequences has enabled the application of powerful tools for assaying global expression patterns in environmentally relevant bacteria such as shewanella oneidensis mr-1. a large number of genes in prokaryote genomes, including mr-1, have been annotated as hypothetical, indicating that no similar protein has yet been identified in other organisms. using high-sensitivity ms coupled with accurate mass and time (amt) tag methodology, 1078 tryptic peptides were collect ... | 2005 | 16038018 |
| estimating the dual-enzyme kinetic parameters for cr (vi) reduction by shewanella oneidensis mr-1 from soil column experiments. | hexavalent chromium (cr (vi)) contamination of soil and groundwater is considered a major environmental concern. bioreduction of cr (vi) to trivalent chromium (cr (iii)) can be considered an effective technology in remediating cr (vi) contaminated sites. among the cr (vi) reducing bacteria, shewanella oneidensis mr-1 (mr-1) is relatively effective. reduction of cr (vi) by mr-1 is defined by the dual-enzyme kinetic model. the feasibility of bioreduction of cr (vi) is usually evaluated by performi ... | 2005 | 16045962 |
| 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 ... | 2005 | 16053318 |
| shewanella oneidensis mr-1 uses overlapping pathways for iron reduction at a distance and by direct contact under conditions relevant for biofilms. | we developed a new method to measure iron reduction at a distance based on depositing fe(iii) (hydr)oxide within nanoporous glass beads. in this "fe-bead" system, shewanella oneidensis reduces at least 86.5% of the iron in the absence of direct contact. biofilm formation accompanies fe-bead reduction and is observable both macro- and microscopically. fe-bead reduction is catalyzed by live cells adapted to anaerobic conditions, and maximal reduction rates require sustained protein synthesis. the ... | 2005 | 16085832 |
| 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. | 2005 | 16085900 |
| 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 ... | 2006 | 16133656 |
| graphical estimation of the dual-enzyme kinetic parameters for cr(vi) reduction. | chromium(vi) (cr(vi)) contamination of soil and groundwater is a major environmental concern. bioreduction of cr(vi) by shewanella oneidensis mr-1 (mr-1) can be considered a feasible option to reduce the toxic and mobile cr(vi) to the less toxic and less mobile chromium(iii) (cr(iii)). the reaction rate expression for cr(vi) reduction is nonlinear and the rate constants are evaluated by employing nonlinear optimization techniques. the outcome of the optimization techniques, in general, depends o ... | 2006 | 16140357 |
| use of microarrays with different probe sizes for monitoring gene expression. | microarrays with oligonucleotides of different lengths were used to monitor gene expression at a whole-genome level. to determine what length of oligonucleotide is a better alternative to pcr-generated probes, the performance of oligonucleotide probes was systematically compared to that of their pcr-generated counterparts for 96 genes from shewanella oneidensis mr-1 in terms of overall signal intensity, numbers of genes detected, specificity, sensitivity, and differential gene expression under e ... | 2005 | 16151099 |
| 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. | 2005 | 16151159 |
| 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 ... | 2005 | 16199584 |
| a method adapting microarray technology for signature-tagged mutagenesis of desulfovibrio desulfuricans g20 and shewanella oneidensis mr-1 in anaerobic sediment survival experiments. | signature-tagged mutagenesis (stm) is a powerful technique that can be used to identify genes expressed by bacteria during exposure to conditions in their natural environments. to date, there have been no reports of studies in which this approach was used to study organisms of environmental, rather than pathogenic, significance. we used a mini-tn10 transposon-bearing plasmid, pbsl180, that efficiently and randomly mutagenized desulfovibrio desulfuricans g20 in addition to shewanella oneidensis m ... | 2005 | 16269742 |
| 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 ... | 2005 | 16269787 |
| 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 ... | 2006 | 16293111 |
| large-scale mulc-ms/ms for silver- and coomassie blue-stained polyacrylamide gels. | 2-de combined with lc-ms/ms has become a routine, reliable protein separation and identification technology for proteome analysis. the demand for large-scale protein identifications after 2-de separation requires a sensitive and high-throughput lc-ms/ms method. in this report, a simple, splitless, fully automated capillary lc-ms/ms system was described for the large-scale identification of proteins from gels stained with either silver or cbb. the gel samples were digested and peptides were extra ... | 2005 | 16315175 |
| improving solubility of shewanella oneidensis mr-1 and clostridium thermocellum jw-20 proteins expressed into esherichia coli. | low solubility of proteins overexpressed in e. coli is a frequent problem in high-throughput structural genomics. to improve solubility of proteins from mesophilic shewanella oneidensis mr-1 and thermophilic clostridium thermocellum jw20, an approach was attempted that included a fusion of the target protein to a maltose-binding protein (mbp) and a decrease of induction temperature. the mbp was selected as the most efficient solubilizing carrier when compared to a glutathione s-transferase and a ... | 2005 | 16335938 |
| cellular response of shewanella oneidensis to strontium stress. | the physiology and transcriptome dynamics of the metal ion-reducing bacterium shewanella oneidensis strain mr-1 in response to nonradioactive strontium (sr) exposure were investigated. studies indicated that mr-1 was able to grow aerobically in complex medium in the presence of 180 mm srcl2 but showed severe growth inhibition at levels above that concentration. temporal gene expression profiles were generated from aerobically grown, mid-exponential-phase mr-1 cells shocked with 180 mm srcl2 and ... | 2006 | 16391131 |
| differential label-free quantitative proteomic analysis of shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach. | we describe the application of lc-ms without the use of stable isotope labeling for differential quantitative proteomic analysis of whole cell lysates of shewanella oneidensis mr-1 cultured under aerobic and suboxic conditions. lc-ms/ms was used to initially identify peptide sequences, and lc-fticr was used to confirm these identifications as well as measure relative peptide abundances. 2343 peptides covering 668 proteins were identified with high confidence and quantified. among these proteins, ... | 2006 | 16401633 |
| 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 ... | 2006 | 16402222 |
| randomized sequence databases for tandem mass spectrometry peptide and protein identification. | tandem mass spectrometry (ms/ms) combined with database searching is currently the most widely used method for high-throughput peptide and protein identification. many different algorithms, scoring criteria, and statistical models have been used to identify peptides and proteins in complex biological samples, and many studies, including our own, describe the accuracy of these identifications, using at best generic terms such as "high confidence." false positive identification rates for these cri ... | 2005 | 16402894 |
| confirmation of the expression of a large set of conserved hypothetical proteins in shewanella oneidensis mr-1. | high-throughput "omic" technologies have allowed for a relatively rapid, yet comprehensive analysis of the global expression patterns within an organism in response to perturbations. in the current study, 9503 different tryptic peptides were identified with high confidence from capillary liquid chromatography-mass spectrometry analysis of 26 chemostat cultures of shewanella oneidensis mr-1 under various conditions. using at least one distinctive and a total of two total peptide identifications p ... | 2006 | 16417935 |
| 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 ... | 2006 | 16423015 |
| 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 ... | 2006 | 16428429 |
| 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 ... | 2006 | 16452448 |
| design of shewanella-specific 16s rrna primers and application to analysis of shewanella in a minerotrophic wetland. | in this study, an existing probe was used as a polymerase chain reaction (pcr) primer to study iron-reducing members of the genus shewanella in a minerotrophic wetland where iron reduction had previously been implicated. the probe was found to be non-specific and a new set of pcr primers were developed that were specific for shewanella. these primers were used to analyse the wetland iron-reducing communities by characterizing 16s rrna genes amplified from dna extracted from peat. polymerase chai ... | 2006 | 16478449 |
| agga is required for aggregation and increased biofilm formation of a hyper-aggregating mutant of shewanella oneidensis mr-1. | shewanella oneidensis coag, a hyper-aggregating mutant of mr-1, was isolated from a rifampicin-challenged culture. compared to the wild-type, coag exhibited increased biofilm formation on glass carrier material. the role of surface-located proteins in the process of coag auto-aggregation was confirmed by different proteolytic treatments of the aggregates. all of the tested proteolytic enzymes resulted in deflocculation within 3 h of incubation. in order to examine the altered expression of outer ... | 2006 | 16514152 |
| molecular dynamics of the shewanella oneidensis response to chromate stress. | temporal genomic profiling and whole-cell proteomic analyses were performed to characterize the dynamic molecular response of the metal-reducing bacterium shewanella oneidensis mr-1 to an acute chromate shock. the complex dynamics of cellular processes demand the integration of methodologies that describe biological systems at the levels of regulation, gene and protein expression, and metabolite production. genomic microarray analysis of the transcriptome dynamics of midexponential phase cells s ... | 2006 | 16524964 |
| extracellular respiration of dimethyl sulfoxide by shewanella oneidensis strain mr-1. | shewanella species are renowned for their respiratory versatility, including their ability to respire poorly soluble substrates by using enzymatic machinery that is localized to the outside of the cell. the ability to engage in "extracellular respiration" to date has focused primarily on respiration of minerals. here, we identify two gene clusters in shewanella oneidensis strain mr-1 that each contain homologs of genes required for metal reduction and genes that are predicted to encode dimethyl ... | 2006 | 16537430 |
| control of formation and cellular detachment from shewanella oneidensis mr-1 biofilms by cyclic di-gmp. | stability and resilience against environmental perturbations are critical properties of medical and environmental biofilms and pose important targets for their control. biofilm stability is determined by two mutually exclusive processes: attachment of cells to and detachment from the biofilm matrix. using shewanella oneidensis mr-1, an environmentally versatile, fe(iii) and mn(iv) mineral-reducing microorganism, we identified mxdabcd as a new set of genes essential for formation of a three-dimen ... | 2006 | 16547056 |
| reduction of soluble and insoluble iron forms by membrane fractions of shewanella oneidensis grown under aerobic and anaerobic conditions. | the effect of iron substrates and growth conditions on in vitro dissimilatory iron reduction by membrane fractions of shewanella oneidensis mr-1 was characterized. membrane fractions were separated by sucrose density gradients from cultures grown with o(2), fumarate, and aqueous ferric citrate as the terminal electron acceptor. marker enzyme assays and two-dimensional gel electrophoresis demonstrated the high degree of separation between the outer and cytosolic membrane. protein expression patte ... | 2006 | 16597999 |
| knock-out of so1377 gene, which encodes the member of a conserved hypothetical bacterial protein family cog2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in shewanella oneidensis mr-1. | shewanella oneidensis mr-1 is a facultative, gram-negative bacterium capable of coupling the oxidation of organic carbon to a wide range of electron acceptors such as oxygen, nitrate and metals, and has potential for bioremediation of heavy metal contaminated sites. the complete 5-mb genome of s. oneidensis mr-1 was sequenced and standard sequence-comparison methods revealed approximately 42% of the mr-1 genome encodes proteins of unknown function. defining the functions of hypothetical proteins ... | 2006 | 16600046 |
| more sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic lc columns with electrospray ionization-mass spectrometry. | the sensitivity of proteomics measurements using liquid chromatography (lc) separations interfaced with electrospray ionization-mass spectrometry (esi-ms) improves approximately inversely with liquid flow rate (for the columns having the same separation efficiency, linear velocity, and porosity), making attractive the use of smaller inner diameter lc columns. we report the development and initial application of 10 microm i.d. silica-based monolithic lc columns providing more sensitive proteomics ... | 2006 | 16674098 |
| high power density from a miniature microbial fuel cell using shewanella oneidensis dsp10. | a miniature microbial fuel cell (mini-mfc) is described that demonstrates high output power per device cross-section (2.0 cm2) and volume (1.2 cm3). shewanella oneidensis dsp10 in growth medium with lactate and buffered ferricyanide solutions were used as the anolyte and catholyte, respectively. maximum power densities of 24 and 10 mw/m2 were measured using the true surface areas of reticulated vitreous carbon (rvc) and graphite felt (gf) electrodes without the addition of exogenous mediators in ... | 2006 | 16683602 |
| synthesis and structure-activity correlation studies of metal complexes of alpha-n-heterocyclic carboxaldehyde thiosemicarbazones in shewanella oneidensis. | this investigation involved the synthesis of metal complexes to test the hypothesis that structural changesand metal coordination in pyridine thiosemicarbazones affect cell growth and cell proliferation in vitro. thiosemicarbazones are well known to possess antitumor, antiviral, antibacterial, antimalarial, and other activities. extensive research has been carried out on aliphatic, aromatic, heterocyclic and other types of thiosemicarbazones and their metal complexes. due to the pronounced react ... | 2005 | 16705815 |
| optimization of the biological component of a bioelectrochemical cell. | the efficiency of electron transduction by shewanella oneidensis mr-1 was investigated both in batch culture and in a dual-chambered electrochemical cell. aerobically grown bacteria were inoculated into an insoluble feooh suspension in an anaerobic environment. as the bacteria reduced fe(iii) to fe(ii) there was a visible color change from red to bluish black; this simple color change assay proved to be a robust method for determining the electrochemical activity of s. oneidensis mr-1. in an eff ... | 2007 | 16713750 |
| evaluation of the effects of various culture conditions on cr(vi) reduction by shewanella oneidensis mr-1 in a novel high-throughput mini-bioreactor. | the growth and cr(vi) reduction by shewanella oneidensis mr-1 was examined using a mini-bioreactor system that independently monitors and controls ph, dissolved oxygen (do), and temperature for each of its 24, 10-ml reactors. independent monitoring and control of each reactor in the cassette allows the exploration of a matrix of environmental conditions known to influence s. oneidensis chromium reduction. s. oneidensis mr-1 grew in minimal medium without amino acid or vitamin supplementation und ... | 2006 | 16732598 |
| using size exclusion chromatography-rplc and rplc-cief as two-dimensional separation strategies for protein profiling. | bottom-up proteomics (analyzing peptides that result from protein digestion) has demonstrated capability for broad proteome coverage and good throughput. however, due to incomplete sequence coverage, this approach is not ideally suited to the study of modified proteins. the modification complement of a protein can best be elucidated by analyzing the intact protein. 2-de, typically coupled with the analysis of peptides that result from in-gel digestion, is the most frequently applied protein sepa ... | 2006 | 16732621 |
| a rapid mutant screening technique for detection of technetium [tc(vii)] reduction-deficient mutants of shewanella oneidensis mr-1. | microbial metal reduction forms the basis of alternate bioremediation strategies for reductive precipitation and immobilization of toxic metals such as the radionuclide technetium [tc(vii)]. a rapid mutant screening technique was developed to identify shewanella oneidensis mr-1 respiratory mutants unable to reduce tc(vii) as anaerobic electron acceptor. the tc(vii) reduction-deficient (tcr) mutant screening technique was based on the observation that wild-type s. oneidensis produced a black tc(i ... | 2006 | 16734791 |
| global transcriptome analysis of the cold shock response of shewanella oneidensis mr-1 and mutational analysis of its classical cold shock proteins. | this study presents a global transcriptional analysis of the cold shock response of shewanella oneidensis mr-1 after a temperature downshift from 30 degrees c to 8 or 15 degrees c based on time series microarray experiments. more than 700 genes were found to be significantly affected (p < or = 0.05) upon cold shock challenge, especially at 8 degrees c. the temporal gene expression patterns of the classical cold shock genes varied, and only some of them, most notably so1648 and so2787, were diffe ... | 2006 | 16740962 |
| genomic analysis of carbon source metabolism of shewanella oneidensis mr-1: predictions versus experiments. | genomic sequences have been used to find the genetic foundation for carbon source metabolism in shewanella oneidensis mr-1. annotated s. oneidensis mr-1 gene products were examined for their sequence similarity to enzymes participating in pathways for utilization of carbon and energy as described in the biocyc database (http://www.biocyc.org/) or in the primary literature. a picture emerges that relegates five- and six-carbon sugars to minor roles as carbon sources, whereas multiple pathways for ... | 2006 | 16788168 |
| isolation of a high-affinity functional protein complex between omca and mtrc: two outer membrane decaheme c-type cytochromes of shewanella oneidensis mr-1. | shewanella oneidensis mr-1 is a facultatively anaerobic bacterium capable of using soluble and insoluble forms of manganese [mn(iii/iv)] and iron [fe(iii)] as terminal electron acceptors during anaerobic respiration. to assess the structural association of two outer membrane-associated c-type decaheme cytochromes (i.e., omca [so1779] and mtrc [so1778]) and their ability to reduce soluble fe(iii)-nitrilotriacetic acid (nta), we expressed these proteins with a c-terminal tag in wild-type s. oneide ... | 2006 | 16788180 |
| biocatalytic dechlorination of lindane by nano-scale particles of pd(0) deposited on shewanella oneidensis. | a new approach for the removal of the pesticide lindane (gamma-hexachlorocyclohexane or gamma-hch) makes use of catalytic reduction of hch to benzene over a metal catalyst, namely pd(0). since specific surface area plays an important role in reactivity of catalysts, this study investigated the use of biopd(0), i.e. nano-scale pd(0) particles precipitated on the biomass of shewanella oneidensis, for the removal of lindane. it was demonstrated that biopd(0) has catalytic activity towards dechlorin ... | 2007 | 16797673 |
| electrically conductive bacterial nanowires produced by shewanella oneidensis strain mr-1 and other microorganisms. | shewanella oneidensis mr-1 produced electrically conductive pilus-like appendages called bacterial nanowires in direct response to electron-acceptor limitation. mutants deficient in genes for c-type decaheme cytochromes mtrc and omca, and those that lacked a functional type ii secretion pathway displayed nanowires that were poorly conductive. these mutants were also deficient in their ability to reduce hydrous ferric oxide and in their ability to generate current in a microbial fuel cell. nanowi ... | 2006 | 16849424 |
| comparative genomics and experimental characterization of n-acetylglucosamine utilization pathway of shewanella oneidensis. | we used a comparative genomics approach implemented in the seed annotation environment to reconstruct the chitin and glcnac utilization subsystem and regulatory network in most proteobacteria, including 11 species of shewanella with completely sequenced genomes. comparative analysis of candidate regulatory sites allowed us to characterize three different glcnac-specific regulons, nagc, nagr, and nagq, in various proteobacteria and to tentatively assign a number of novel genes with specific funct ... | 2006 | 16857666 |
| ligand-induced conformational changes in the capping subdomain of a bacterial old yellow enzyme homologue and conserved sequence fingerprints provide new insights into substrate binding. | we have recently reported that shewanella oneidensis, a gram-negative gamma-proteobacterium with a rich arsenal of redox proteins, possesses four old yellow enzyme (oye) homologues. here, we report a series of high resolution crystal structures for one of these oyes, shewanella yellow enzyme 1 (sye1), in its oxidized form at 1.4a resolution, which binds a molecule of peg 400 in the active site, and in its nadh-reduced and p-hydroxybenzaldehyde- and p-hydroxyacetophenone-bound forms at 1.7a resol ... | 2006 | 16857682 |
| a kinetic model describing shewanella oneidensis mr-1 growth, substrate consumption, and product secretion. | aerobic growth of shewanella oneidensis mr-1 in minimal lactate medium was studied in batch cultivation. acetate production was observed in the middle of the exponential growth phase and was enhanced when the dissolved oxygen (do) concentration was low. once the lactate was nearly exhausted, s. oneidensis mr-1 used the acetate produced during growth on lactate with a similar biomass yield as lactate. a two-substrate monod model, with competitive and uncompetitive substrate inhibition, was devise ... | 2007 | 16865732 |
| nhad type sodium/proton-antiporter of halomonas elongata: a salt stress response mechanism in marine habitats? | sodium/proton-antiporters (nha) are known to play an important role in ph- and na+-homeostasis. in microorganisms several types with different capacity, affinity and selectivity for na+ and li+ exist. the homeostasis system of e. coli, nhaa and nhab, is well researched, but the function of other types of na+/h+-antiporters like nhad is yet to be fully understood. since several antiporters play an important role at various points in the physiology of higher organisms, one can speculate that the m ... | 2006 | 16872527 |
| c-type cytochrome-dependent formation of u(iv) nanoparticles by shewanella oneidensis. | modern approaches for bioremediation of radionuclide contaminated environments are based on the ability of microorganisms to effectively catalyze changes in the oxidation states of metals that in turn influence their solubility. although microbial metal reduction has been identified as an effective means for immobilizing highly-soluble uranium(vi) complexes in situ, the biomolecular mechanisms of u(vi) reduction are not well understood. here, we show that c-type cytochromes of a dissimilatory me ... | 2006 | 16875436 |
| one-step, non-denaturing isolation of an rna polymerase enzyme complex using an improved multi-use affinity probe resin. | the rapid isolation of protein complexes is critical to the goal of establishing protein interaction networks. high-throughput methods for identifying protein binding partners in a way suitable for mass spectrometric identification and structural analysis are required and small molecule/peptide interactions provide the key. we have now shown that a redesigned resin derivatized with a bisarsenical dye can be used to isolate the shewanella oneidensis rna polymerase core enzyme with a tetracysteine ... | 2005 | 16880963 |
| electronic coupling between heme electron-transfer centers and its decay with distance depends strongly on relative orientation. | a method for calculating the electron-transfer matrix element v(rp) using density functional theory kohn-sham orbitals is presented and applied to heme dimers of varying relative orientation. the electronic coupling decays with increased iron separation according to v(rp) = v(0)(rp)exp(-beta r/2) with a distance dependence parameter beta approximately 2 a(-1) for hemes with parallel porphyrins and either 1.1 or 4.0 a(-1) when the porphyrin planes are perpendicular, depending on the alignment of ... | 2006 | 16884282 |
| tale of two metal reducers: comparative proteome analysis of geobacter sulferreducens pca and shewanella oneidensis mr-1. | geobacter sulfurreducens and s. oneidensis are the subjects of intense research efforts due to their potential applications to bioremediation. the characterization of their proteomes, being done in parallel with the analysis of their genome sequences, transcriptomes, and metabolomes, is providing valuable insights to both their similarities and their differences. a primary target of interest in the proteomes of both of these metal-reducing microbes is the characterization of their c-type cytochr ... | 2006 | 16929676 |
| amt tag approach to proteomic characterization of deinococcus radiodurans and shewanella oneidensis. | 2006 | 16929677 | |
| spatiometabolic stratification of shewanella oneidensis biofilms. | biofilms, or surface-attached microbial communities, are both ubiquitous and resilient in the environment. although much is known about how biofilms form, develop, and detach, very little is understood about how these events are related to metabolism and its dynamics. it is commonly thought that large subpopulations of cells within biofilms are not actively producing proteins or generating energy and are therefore dead. an alternative hypothesis is that within the growth-inactive domains of biof ... | 2006 | 16936048 |
| a biofilm enhanced miniature microbial fuel cell using shewanella oneidensis dsp10 and oxygen reduction cathodes. | a miniature-microbial fuel cell (mini-mfc, chamber volume: 1.2 ml) was used to monitor biofilm development from a pure culture of shewanella oneidensis dsp10 on graphite felt (gf) under minimal nutrient conditions. esem evidence of biofilm formation on gf is supported by substantial power density (per device cross-section) from the mini-mfc when using an acellular minimal media anolyte (1500 mw/m2). these experiments demonstrate that power density per volume for a biofilm flow reactor mfc should ... | 2007 | 16939710 |
| global molecular and morphological effects of 24-hour chromium(vi) exposure on shewanella oneidensis mr-1. | the biological impact of 24-h ("chronic") chromium(vi) [cr(vi) or chromate] exposure on shewanella oneidensis mr-1 was assessed by analyzing cellular morphology as well as genome-wide differential gene and protein expression profiles. cells challenged aerobically with an initial chromate concentration of 0.3 mm in complex growth medium were compared to untreated control cells grown in the absence of chromate. at the 24-h time point at which cells were harvested for transcriptome and proteome ana ... | 2006 | 16957260 |
| atr-ftir spectroscopy reveals bond formation during bacterial adhesion to iron oxide. | the contribution of various bacterial surface functional groups to adhesion at hematite and znse surfaces was examined using attenuated total reflectance (atr) fourier transform infrared (ftir) spectroscopy. when live shewanella oneidensis, pseudomonas aeruginosa, and bacillus subtilis cells were introduced to a horizontal hematite (alpha-fe(2)o(3))-coated internal reflection element (ire), ftir peaks emerged corresponding to bacterial phosphate group binding. these ir peaks were not observed wh ... | 2006 | 16981768 |
| physiological changes induced in four bacterial strains following oxidative stress. | in order to study the behaviour and resistance of bacteria under extreme conditions, physiological changes associated with oxidative stress were monitored using flow cytometry. the study was conducted to assess the maintenance of membrane integrity and potential as well as the esterase activity, the intracellular ph and the production of superoxide anions in four bacterial strains (ralstonia metallidurans, escherichia coli, shewanella oneidensis and deinococcus radiodurans). the strains were cho ... | 2006 | 17022450 |
| biological control of the size and reactivity of catalytic pd(0) produced by shewanella oneidensis. | the interaction between shewanella oneidensis mr-1 and the soluble metal pd(ii) during the reductive precipitation of pd(0) determined the size and properties of the precipitated pd(0) nanoparticles. assessment of cell viability indicated that the bioreduction of pd(ii) was a detoxification mechanism depending on the pd(ii) concentration and on the presence and properties of the electron donor. the addition of h(2) in the headspace allowed s. oneidensis to resist the toxic effects of pd(ii). int ... | 2006 | 17033880 |
| predicting gene expression level from codon usage bias. | the "expression measure" of a gene, e(g), is a statistic devised to predict the level of gene expression from codon usage bias. e(g) has been used extensively to analyze prokaryotic genome sequences. we discuss 2 problems with this approach. first, the formulation of e(g) is such that genes with the strongest selected codon usage bias are not likely to have the highest predicted expression levels; indeed the correlation between e(g) and expression level is weak among moderate to highly expressed ... | 2007 | 17038449 |
| high-affinity binding and direct electron transfer to solid metals by the shewanella oneidensis mr-1 outer membrane c-type cytochrome omca. | the purified outer membrane bacterial protein omca binds densely to the surface of hematite (fe2o3), permitting direct electron transfer to this solid mineral to reduce fe (iii) with an electron flux of about 1013 electrons /cm2/s. in the presence of hematite, there is a substantial increase in the amplitude of internal protein motions that correlate with metal reduction. binding is highly favorable, with a partition coefficient of approximately 2 x 105 (deltago' = -28 kj/mol), where approximate ... | 2006 | 17061851 |
| respiratory nitrate ammonification by shewanella oneidensis mr-1. | anaerobic cultures of shewanella oneidensis mr-1 grown with nitrate as the sole electron acceptor exhibited sequential reduction of nitrate to nitrite and then to ammonium. little dinitrogen and nitrous oxide were detected, and no growth occurred on nitrous oxide. a mutant with the napa gene encoding periplasmic nitrate reductase deleted could not respire or assimilate nitrate and did not express nitrate reductase activity, confirming that the napa enzyme is the sole nitrate reductase. hence, s. ... | 2007 | 17098906 |
| microarray-based analysis of microbial community rnas by whole-community rna amplification. | a new approach, termed whole-community rna amplification (wcra), was developed to provide sufficient amounts of mrnas from environmental samples for microarray analysis. this method employs fusion primers (six to nine random nucleotides with an attached t7 promoter) for the first-strand synthesis. the shortest primer (t7n6s) gave the best results in terms of the yield and representativeness of amplification. about 1,200- to 1,800-fold amplification was obtained with amounts of the rna templates ... | 2007 | 17098911 |
| shewanella oneidensis mr-1 fluxome under various oxygen conditions. | the central metabolic fluxes of shewanella oneidensis mr-1 were examined under carbon-limited (aerobic) and oxygen-limited (microaerobic) chemostat conditions, using 13c-labeled lactate as the sole carbon source. the carbon labeling patterns of key amino acids in biomass were probed using both gas chromatography-mass spectrometry (gc-ms) and 13c nuclear magnetic resonance (nmr). based on the genome annotation, a metabolic pathway model was constructed to quantify the central metabolic flux distr ... | 2007 | 17098921 |
| anaerobic central metabolic pathways in shewanella oneidensis mr-1 reinterpreted in the light of isotopic metabolite labeling. | it has been proposed that during growth under anaerobic or oxygen-limited conditions, shewanella oneidensis mr-1 uses the serine-isocitrate lyase pathway common to many methylotrophic anaerobes, in which formaldehyde produced from pyruvate is condensed with glycine to form serine. the serine is then transformed through hydroxypyruvate and glycerate to enter central metabolism at phosphoglycerate. to examine its use of the serine-isocitrate lyase pathway under anaerobic conditions, we grew s. one ... | 2007 | 17114268 |
| genes that enhance the ecological fitness of shewanella oneidensis mr-1 in sediments reveal the value of antibiotic resistance. | environmental bacteria persist in various habitats, yet little is known about the genes that contribute to growth and survival in their respective ecological niches. signature-tagged mutagenesis (stm) of shewanella oneidensis mr-1 coupled with a screen involving incubations of mutant strains in anoxic aquifer sediments allowed us to identify 47 genes that enhance fitness in sediments. gene functions inferred from annotations provide us with insight into physiological and ecological processes tha ... | 2007 | 17114320 |
| kinetics of microbial reduction of solid phase u(vi). | sodium boltwoodite (nauo2sio3oh x 1.5 h2o) was used to assess the kinetics of microbial reduction of solid-phase u(vi) by a dissimilatory metal-reducing bacterium (dmrb), shewanella oneidensis strain mr-1. the bioreduction kinetics was studied with na-boltwoodite in suspension or within alginate beads in a nongrowth medium with lactate as electron donor at ph 6.8 buffered with pipes. concentrations of u(vi)tot and cell number were varied to evaluate the coupling of u(vi) dissolution, diffusion, ... | 2006 | 17120555 |
| enrichment of functional redox reactive proteins and identification by mass spectrometry results in several terminal fe(iii)-reducing candidate proteins in shewanella oneidensis mr-1. | identification of the proteins directly involved in microbial metal-reduction is important to understanding the biochemistry involved in heavy metal-reduction/immobilization and the ultimate cleanup of doe contaminated sites. although previous strategies for the identification of these proteins have traditionally required laborious protein purification/characterization of metal-reducing capability, activity is often lost before the final purification step, thus creating a significant knowledge g ... | 2007 | 17137661 |
| novel reduction of mercury (ii) by mercury-sensitive dissimilatory metal reducing bacteria. | the dissimilatory metal reducing bacterium (dmrb) shewanella oneidensis mr-1 reduces ionic mercury (hg[ii]) to elemental mercury (hg[0]) by an activity not related to the mera mercuric reductase. in s. oneidensis, this activity is constitutive and effective at hg(ii) concentrations too low to induce mer operon functions. reduction of hg(ii) by mr-1 required the presence of electron donors and electron acceptors. reduction occurred with oxygen or fumarate, but had the highest rate when ferric oxy ... | 2006 | 17144297 |
| process of maturation of tetraheme cytochrome c3 in a shewanella expression system. | the process of maturation of multiheme proteins is not yet well known, while that of monoheme ones has been relatively well investigated. two kinds of partly unfolded tetraheme cytochrome c3 were obtained on overexpression in shewanella oneidensis tsp-c. these proteins were characterized by circular dichroism and nuclear magnetic resonance spectroscopy. it turned out that the tetraheme architecture, and the fifth and sixth ligand coordination are almost mature, while some parts of the polypeptid ... | 2007 | 17167041 |
| the pio operon is essential for phototrophic fe(ii) oxidation in rhodopseudomonas palustris tie-1. | phototrophic fe(ii)-oxidizing bacteria couple the oxidation of ferrous iron [fe(ii)] to reductive co(2) fixation by using light energy, but until recently, little has been understood about the molecular basis for this process. here we report the discovery, with rhodopseudomonas palustris tie-1 as a model organism, of a three-gene operon, designated the pio operon (for phototrophic iron oxidation), that is necessary for phototrophic fe(ii) oxidation. the first gene in the operon, pioa, encodes a ... | 2007 | 17189359 |
| hydrogen metabolism in shewanella oneidensis mr-1. | shewanella oneidensis mr-1 is a facultative sediment microorganism which uses diverse compounds, such as oxygen and fumarate, as well as insoluble fe(iii) and mn(iv) as electron acceptors. the electron donor spectrum is more limited and includes metabolic end products of primary fermenting bacteria, such as lactate, formate, and hydrogen. while the utilization of hydrogen as an electron donor has been described previously, we report here the formation of hydrogen from pyruvate under anaerobic, s ... | 2007 | 17189435 |
| molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase. | tryptophan 2,3-dioxygenase (tdo) and indoleamine 2,3-dioxygenase (ido) constitute an important, yet relatively poorly understood, family of heme-containing enzymes. here, we report extensive structural and biochemical studies of the xanthomonas campestris tdo and a related protein so4414 from shewanella oneidensis, including the structure at 1.6-a resolution of the catalytically active, ferrous form of tdo in a binary complex with the substrate l-trp. the carboxylate and ammonium moieties of try ... | 2007 | 17197414 |
| terminal electron acceptors influence the quantity and chemical composition of capsular exopolymers produced by anaerobically growing shewanella spp. | bacterial exopolymers perform various roles, including acting as a carbon sink, a protective layer against desiccation or antimicrobial agents, or a structural matrix in biofilms. despite such varied roles, little is known about the heterogeneity of bacterial exopolymer production under varying growth conditions. here we describe experiments designed to characterize the quantity and quality of exopolymers produced by two commonly studied members of the widely distributed genus shewanella. electr ... | 2007 | 17206803 |
| the cyma gene, encoding a tetraheme c-type cytochrome, is required for arsenate respiration in shewanella species. | in shewanella sp. strain ana-3, utilization of arsenate as a terminal electron acceptor is conferred by a two-gene operon, arrab, which lacks a gene encoding a membrane-anchoring subunit for the soluble arrab protein complex. analysis of the genome sequence of shewanella putrefaciens strain cn-32 showed that it also contained the same arrab operon with 100% nucleotide identity. here, we report that cn-32 respires arsenate and that this metabolism is dependent on arra and an additional gene encod ... | 2007 | 17209025 |
| microspe-nanolc-esi-ms/ms using 10-microm-i.d. silica-based monolithic columns for proteomics. | silica-based monolithic capillary columns (25 cm x 10 microm i.d.) with integrated nanoesi emitters have been developed to provide high-quality and robust microspe-nanolc-esi-ms analyses. the integrated nanoesi emitter adds no dead volume to the lc separation, allowing stable electrospray operation at flow rates of approximately 10 nl/min. in an initial application with a linear ion trap ms, we identified 5510 unique peptides that covered 1443 distinct shewanella oneidensis proteins from a 300-n ... | 2007 | 17222018 |
| combined spectroscopic and topographic characterization of nanoscale domains and their distributions of a redox protein on bacterial cell surfaces. | redox protein nanoscale domains on the cell surface of a bacterium, shewanella oneidensis mr1, grown in the absence and presence of electron acceptors, is topographically characterized using combined atomic force microscopy (afm) and confocal surface enhanced raman scattering (sers) spectroscopy. the protruding nanoscale domains on the outer membrane of s. oneidensis were observed, as was their disappearance upon exposure to electron acceptors such as oxygen, nitrate, fumarate, and iron nitrilot ... | 2007 | 17241055 |
| proteomic profiling of intact proteins using wax-rplc 2-d separations and fticr mass spectrometry. | we investigated the combination of weak anion exchange (wax) fractionation and on-line reversed-phase liquid chromatography (rplc) separation using a 12 t fticr mass spectrometer for the detection of intact proteins from a shewanella oneidensis mr-1 cell lysate. this work aimed at optimizing intact protein detection for profiling proteins at a level that incorporates their modification state. a total of 715 intact proteins were detected, and the combined results from the wax fractions and the un ... | 2007 | 17269717 |
| profiling the membrane proteome of shewanella oneidensis mr-1 with new affinity labeling probes. | the membrane proteome plays a critical role in electron transport processes in shewanella oneidensis mr-1, a bacterial organism that has great potential for bioremediation. biotinylation of intact cells with subsequent affinity-enrichment has become a useful tool for characterization of the membrane proteome. as opposed to these commonly used, water-soluble commercial reagents, we here introduce a family of hydrophobic, cell-permeable affinity probes for extensive labeling and detection of membr ... | 2007 | 17269728 |
| influence of calcium on microbial reduction of solid phase uranium(vi). | the effect of calcium on the dissolution and microbial reduction of a representative solid phase uranyl [u(vi)], sodium boltwoodite (nauo(2)sio(3)oh . 1.5h(2)o), was investigated to evaluate the rate-limiting step of microbial reduction of the solid phase u(vi). microbial reduction experiments were performed in a culture of a dissimilatory metal-reducing bacterium (dmrb), shewanella oneidensis strain mr-1, in a bicarbonate medium with lactate as electron donor at ph 6.8 buffered with pipes. calc ... | 2007 | 17274063 |
| charge-associated effects of fullerene derivatives on microbial structural integrity and central metabolism. | the effects of four types of fullerene compounds (c60, c60-oh, c60-cooh, c60-nh2) were examined on two model microorganisms (escherichia coli w3110 and shewanella oneidensis mr-1). positively charged c60-nh2 at concentrations as low as 10 mg/l inhibited growth and reduced substrate uptake for both microorganisms. scanning electron microscopy (sem) revealed damage to cellular structures. neutrally charged c60 and c60-oh had mild negative effects on s. oneidensis mr-1, whereas the negatively charg ... | 2007 | 17288489 |
| remodeling of the bacterial rna polymerase supramolecular complex in response to environmental conditions. | directed binding of rna polymerase to distinct promoter elements controls transcription and promotes adaptive responses to changing environmental conditions. to identify proteins that modulate transcription, we have expressed a tagged alpha-subunit of rna polymerase in shewanella oneidensis under controlled growth conditions, isolated the protein complex using newly developed multiuse affinity probes, and used lc-ms/ms to identify proteins in the complex. complementary fluorescence correlation s ... | 2007 | 17319694 |
| dosage-dependent proteome response of shewanella oneidensis mr-1 to acute chromate challenge. | proteome alterations in the metal-reducing bacterium shewanella oneidensis mr-1 in response to different acute dose challenges (0.3, 0.5, or 1 mm) of the toxic metal chromate [cr(vi)] were characterized with multidimensional hplc-ms/ms. proteome measurements were performed and compared on both quadrupole ion traps as well as linear trapping quadrupole mass spectrometers. we have found that the implementation of multidimensional liquid chromatography on-line with the rapid scanning, high throughp ... | 2007 | 17385904 |
| specific bonds between an iron oxide surface and outer membrane cytochromes mtrc and omca from shewanella oneidensis mr-1. | shewanella oneidensis mr-1 is purported to express outer membrane cytochromes (e.g., mtrc and omca) that transfer electrons directly to fe(iii) in a mineral during anaerobic respiration. a prerequisite for this type of reaction would be the formation of a stable bond between a cytochrome and an iron oxide surface. atomic force microscopy (afm) was used to detect whether a specific bond forms between a hematite (fe(2)o(3)) thin film, created with oxygen plasma-assisted molecular beam epitaxy, and ... | 2007 | 17468239 |
| immunoaffinity purification and characterization of rna polymerase from shewanella oneidensis. | shewanella oneidensis is of particular interest for research because of its unique ability to use a variety of metals as final respiratory electron acceptors and reduce them into insoluble oxides. a collection of monoclonal antibodies (mabs) that were prepared towards escherichia coli rna polymerase (rnap) was tested for reactivity with proteins extracted from s. oneidensis. two polyol-responsive monoclonal antibodies (pr-mabs) were used to purify rna polymerase from s. oneidensis using immunoaf ... | 2007 | 17507238 |
| targeted tandem mass spectrometry for high-throughput comparative proteomics employing nanolc-fticr ms with external ion dissociation. | targeted tandem mass spectrometry (ms/ms) is an attractive proteomic approach that allows selective identification of peptides exhibiting abundance differences, e.g., between culture conditions and/or diseased states. herein, we report on a targeted lc-ms/ms capability realized with a hybrid quadrupole-7 tesla fourier transform ion cyclotron resonance (fticr) mass spectrometer that provides data-dependent ion selection, accumulation, and dissociation external to the icr trap, and a control softw ... | 2007 | 17531500 |
| biological reduction of np(v) and np(v) citrate by metal-reducing bacteria. | oxidized actinide species are often more mobile than reduced forms. bioremediation strategies have been developed to exploit this chemistry and stabilize actinides in subsurface environments. we investigated the ability of metal-reducing bacteria geobacter metallireducens and shewanella oneidensis to enzymatically reduce np(v) and np(v) citrate, as well as the toxicity of np(v) to these organisms. a toxic effect was observed for both bacteria at concentrations of > or = 4.0 mm np(v) citrate. bel ... | 2007 | 17533836 |
| structural, thermodynamic, and mutational analyses of a psychrotrophic rnase hi. | ribonuclease (rnase) hi from the psychrotrophic bacterium shewanella oneidensis mr-1 was overproduced in escherichia coli, purified, and structurally and biochemically characterized. the amino acid sequence of mr-1 rnase hi is 67% identical to that of e. coli rnase hi. the crystal structure of mr-1 rnase hi determined at 2.0 a resolution was highly similar to that of e. coli rnase hi, except that the number of intramolecular ion pairs and the fraction of polar surface area of mr-1 rnase hi were ... | 2007 | 17536836 |
| cell-free synthesis and maturation of [fefe] hydrogenases. | [fefe] hydrogenases catalyze the reversible reduction of protons to molecular hydrogen (adams (1990); biochim biophys acta 1020(2): 115-145) and are of significant interest for the biological production of hydrogen fuel. they are complex proteins with active sites containing iron, sulfur, and carbon monoxide and cyanide ligands (peters et al. (1998); science 282(5395): 1853-1858). maturation enzymes for [fefe] hydrogenases have been identified (posewitz et al. (2004); j biol chem 279(24): 25711- ... | 2008 | 17546685 |
| the three-dimensional crystal structure of the prpf protein of shewanella oneidensis complexed with trans-aconitate: insights into its biological function. | in bacteria, the dehydration of 2-methylcitrate to yield 2-methylaconitate in the 2-methylcitric acid cycle is catalyzed by a cofactor-less (prpd) enzyme or by an aconitase-like (acnd) enzyme. bacteria that use acnd also require the function of the prpf protein, whose function was previously unknown. to gain insights into the function of prpf, the three-dimensional crystal structure of the prpf protein from the bacterium shewanella oneidensis was solved at 2.0 a resolution. the protein fold of p ... | 2007 | 17567742 |
| respiration of metal (hydr)oxides by shewanella and geobacter: a key role for multihaem c-type cytochromes. | dissimilatory reduction of metal (e.g. fe, mn) (hydr)oxides represents a challenge for microorganisms, as their cell envelopes are impermeable to metal (hydr)oxides that are poorly soluble in water. to overcome this physical barrier, the gram-negative bacteria shewanella oneidensis mr-1 and geobacter sulfurreducens have developed electron transfer (et) strategies that require multihaem c-type cytochromes (c-cyts). in s. oneidensis mr-1, multihaem c-cyts cyma and mtra are believed to transfer ele ... | 2007 | 17581116 |
| a kinetic approach to the dependence of dissimilatory metal reduction by shewanella oneidensis mr-1 on the outer membrane cytochromes c omca and omcb. | the gram-negative bacterium shewanella oneidensis mr-1 shows a remarkably versatile anaerobic respiratory metabolism. one of its hallmarks is its ability to grow and survive through the reduction of metallic compounds. among other proteins, outer membrane decaheme cytochromes c omca and omcb have been identified as key players in metal reduction. in fact, both of these cytochromes have been proposed to be terminal fe(iii) and mn(iv) reductases, although their role in the reduction of other metal ... | 2007 | 17608722 |
| pathway of phytate dephosphorylation by beta-propeller phytases of different origins. | using a combination of high-performance ion chromatography analysis and kinetic studies, the pathway of myo-inositol hexakisphosphate dephosphorylation by the beta-propeller phytase of shewanella oneidensis was established, which was then compared with that of bacillus subtilis 168, bacillus amyloliquefaciens atcc 15841, and b. amyloliquefaciens 45 beta-propeller phytases. the data demonstrate that all of these beta-propeller phytases dephosphorylate myo-inositol hexakisphosphate in a stereospec ... | 2007 | 17612603 |
| current production and metal oxide reduction by shewanella oneidensis mr-1 wild type and mutants. | shewanella oneidensis mr-1 is a gram-negative facultative anaerobe capable of utilizing a broad range of electron acceptors, including several solid substrates. s. oneidensis mr-1 can reduce mn(iv) and fe(iii) oxides and can produce current in microbial fuel cells. the mechanisms that are employed by s. oneidensis mr-1 to execute these processes have not yet been fully elucidated. several different s. oneidensis mr-1 deletion mutants were generated and tested for current production and metal oxi ... | 2007 | 17644630 |
| plutonium(iv) reduction by the metal-reducing bacteria geobacter metallireducens gs15 and shewanella oneidensis mr1. | the bacterial reduction of actinides has been suggested as a possible remedial strategy for actinide-contaminated environments, and the bacterial reduction of pu(vi/v) has the potential to produce highly insoluble pu(iv) solid phases. however, the behavior of plutonium with regard to bacterial reduction is more complex than for other actinides because it is possible for pu(iv) to be further reduced to pu(iii), which is relatively more soluble than pu(iv). this work investigates the ability of th ... | 2007 | 17644643 |
| crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif. | btdyp from bacteroides thetaiotaomicron (strain vpi-5482) and tyra from shewanella oneidensis are dye-decolorizing peroxidases (dyps), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. here, we report the crystal structures of btdyp and tyra at 1.6 and 2.7 a, respectively. btdyp assembles into a hexamer, while tyra assembles into a dimer; the dimerization interface is conserved between the two proteins. each monomer exhibits a two-domain, alpha+beta ... | 2007 | 17654545 |
| an octaheme c-type cytochrome from shewanella oneidensis can reduce nitrite and hydroxylamine. | a c-type cytochrome from shewanella oneidensis mr-1, containing eight hemes, has been previously designated as an octaheme tetrathionate reductase (otr). the structure of otr revealed that the active site contains an unusual lysine-ligated heme, despite the presence of a cxxch motif in the sequence that would predict histidine ligation. this lysine ligation has been previously observed only in the pentaheme nitrite reductases, suggesting that otr may have a possible role in nitrite reduction. we ... | 2007 | 17659281 |
| characterization of protein-protein interactions involved in iron reduction by shewanella oneidensis mr-1. | the interaction of proteins implicated in dissimilatory metal reduction by shewanella oneidensis mr-1 (outer membrane [om] proteins omca, mtrb, and mtrc; om-associated protein mtra; periplasmic protein ccta; and cytoplasmic membrane protein cyma) were characterized by protein purification, analytical ultracentrifugation, and cross-linking methods. five of these proteins are heme proteins, omca (83 kda), mtrc (75 kda), mtra (32 kda), ccta (19 kda), and cyma (21 kda), and can be visualized after s ... | 2007 | 17675441 |
| informatics strategies for large-scale novel cross-linking analysis. | the detection of protein interactions in biological systems represents a significant challenge for today's technology. chemical cross-linking provides the potential to impart new chemical bonds in a complex system that result in mass changes in a set of tryptic peptides detected by mass spectrometry. however, system complexity and cross-linking product heterogeneity have precluded widespread chemical cross-linking use for large-scale identification of protein-protein interactions. the developmen ... | 2007 | 17676784 |
| a general computational model for predicting ribosomal frameshifts in genome sequences. | programmed ribosomal frameshifts are frequently used by rna viruses to synthesize a single fusion protein from two or more overlapping open reading frames. we previously developed a program called fsfinder for predicting -1 and +1 frameshifts for windows systems. with our new web application and web service called fsfinder2, users can predict frameshifts of any type from any web browser and operating system. we tested it on shewanella oneidensis mr-1, for which exact frameshift sites are not kno ... | 2007 | 17678640 |
| expression in periplasmic space of shewanella oneidensis. | a shewanella expression system has been used for an overproduction of c-type multiheme proteins. the proteins were exported to the periplasmic space for the maturation. since the periplasmic expression system is attractive, especially for protease-sensitive proteins, an expression vector containing a signal peptide was constructed for expressions in the periplasmic space of shewanella oneidensis. to evaluate the system, two eukaryotic proteins which originally do not have signal sequences and ar ... | 2007 | 17689099 |
| whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. | while bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. at the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. in this study, we use tandem mass spectrometry (ms/ms) to annotate the p ... | 2007 | 17690205 |