Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| characterization of shewanella oneidensis mtrc: a cell-surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors. | mtrc is a decaheme c-type cytochrome associated with the outer cell membrane of fe(iii)-respiring species of the shewanella genus. it is proposed to play a role in anaerobic respiration by mediating electron transfer to extracellular mineral oxides that can serve as terminal electron acceptors. the present work presents the first spectropotentiometric and voltammetric characterization of mtrc, using protein purified from shewanella oneidensis mr-1. potentiometric titrations, monitored by uv-vis ... | 2007 | 17701062 |
| activation of year-yoag operon transcription by the nitrate-responsive regulator narl is independent of oxygen- responsive regulator fnr in escherichia coli k-12. | the facultative aerobe escherichia coli k-12 can use respiratory nitrate ammonification to generate energy during anaerobic growth. the toxic compound nitric oxide is a by-product of this metabolism. previous transcript microarray studies identified the year-yoag operon, encoding proteins of unknown function, among genes whose transcription is induced in response to nitrate, nitrite, or nitric oxide. nitrate and nitrite regulate anaerobic respiratory gene expression through the narx-narl and nar ... | 2007 | 17720788 |
| metal reduction kinetics in shewanella. | metal reduction kinetics have been studied in cultures of dissimilatory metal reducing bacteria which include the shewanella oneidensis strain mr-1. estimation of system parameters from time-series data faces obstructions in the implementation depending on the choice of the mathematical model that captures the observed dynamics. the modeling of metal reduction is often based on michaelis-menten equations. these models are often developed using initial in vitro reaction rates and seldom match wit ... | 2007 | 17720985 |
| identification of a new hemolysin from diarrheal isolate ssu of aeromonas hydrophila. | a clinical strain ssu of aeromonas hydrophila produces a potent cytotoxic enterotoxin (act) with cytotoxic, enterotoxic, and hemolytic activities. a new gene, which encoded a hemolysin of 439-amino acid residues with a molecular mass of 49 kda, was identified. this hemolysin (hlya) was detected based on the observation that the act gene minus mutant of a. hydrophila ssu still had residual hemolytic activity. the new hemolysin gene (hlya) was cloned, sequenced, and overexpressed in escherichia co ... | 2007 | 17725618 |
| orthologous transcription factors in bacteria have different functions and regulate different genes. | transcription factors (tfs) form large paralogous gene families and have complex evolutionary histories. here, we ask whether putative orthologs of tfs, from bidirectional best blast hits (bbhs), are evolutionary orthologs with conserved functions. we show that bbhs of tfs from distantly related bacteria are usually not evolutionary orthologs. furthermore, the false orthologs usually respond to different signals and regulate distinct pathways, while the few bbhs that are evolutionary orthologs d ... | 2007 | 17845071 |
| evolutionary analysis of enzymes using chisel. | motivation: availability of large volumes of genomic and enzymatic data for taxonomically and phenotypically diverse organisms allows for exploration of the adaptive mechanisms that led to diversification of enzymatic functions. we present chisel, a computational framework and a pipeline for an automated, high-resolution analysis of evolutionary variations of enzymes. chisel allows automatic as well as interactive identification, and characterization of enzymatic sequences. such knowledge can be ... | 2007 | 17855417 |
| hydrogenase- and outer membrane c-type cytochrome-facilitated reduction of technetium(vii) by shewanella oneidensis mr-1. | pertechnetate, (99)tc(vii)o(4)(-), is a highly mobile radionuclide contaminant at us department of energy sites that can be enzymatically reduced by a range of anaerobic and facultatively anaerobic microorganisms, including shewanella oneidensis mr-1, to poorly soluble tc(iv)o(2(s)). in other microorganisms, tc(vii)o(4)(-) reduction is generally considered to be catalysed by hydrogenase. here, we provide evidence that although the nife hydrogenase of mr-1 was involved in the h(2)-driven reductio ... | 2008 | 17888007 |
| development of biatech-54 standard mixtures for assessment of protein identification and relative expression. | mixtures of known proteins have been very useful in the assessment and validation of methods for high-throughput (htp) ms (ms/ms) proteomics experiments. however, these test mixtures have generally consisted of few proteins at near equal concentration or of a single protein at varied concentrations. such mixtures are too simple to effectively assess the validity of error rates for protein identification and differential expression in htp ms/ms studies. this work aimed at overcoming these limitat ... | 2007 | 17890649 |
| oxygen exposure promotes fuel diversity for shewanella oneidensis microbial fuel cells. | miniature microbial fuel cells (mini-mfcs) were used to monitor the current generated by shewanella oneidensis dsp10 under both anaerobic and aerobic conditions when exposed to glucose as a potential electron donor. in addition to glucose, other carbon fuels including fructose, sucrose, acetate, and ascorbic acid were also tested. when the anolyte containing s. oneidensis was grown in the presence of oxygen, power densities of 270+/-10, 350+/-20, and 120+/-10 w/m(3) were recorded from the mini-m ... | 2008 | 17931851 |
| many microbe microarrays database: uniformly normalized affymetrix compendia with structured experimental metadata. | many microbe microarrays database (m3d) is designed to facilitate the analysis and visualization of expression data in compendia compiled from multiple laboratories. m3d contains over a thousand affymetrix microarrays for escherichia coli, saccharomyces cerevisiae and shewanella oneidensis. the expression data is uniformly normalized to make the data generated by different laboratories and researchers more comparable. to facilitate computational analyses, m3d provides raw data (cel file) and nor ... | 2008 | 17932051 |
| mechanisms of electron transfer in two decaheme cytochromes from a metal-reducing bacterium. | in this report, we analyze and interpret single-molecule current-voltage (i-v) tunneling spectra collected for two decaheme c-type cytochromes using a scanning tunneling microscope. the cytochromes (omca and mtrc) are outer-membrane proteins from the metal-reducing bacterium shewanella oneidensis and function as metal-reducing enzymes. although the two cytochromes are similar in heme count, charge-carrying amino acid content, and molecular mass, their i-v spectra are significantly different. the ... | 2007 | 17939701 |
| mrna-targeted fluorescent in situ hybridization (fish) of gram-negative bacteria without template amplification or tyramide signal amplification. | technologies are needed to study gene expression at the level of individual cells within a population or microbial community. fluorescent in situ hybridization (fish) supplies high-resolution spatial information and has been widely applied to study microbial communities at the rrna level. while mrna-targeted fish has been popular for studying gene expression in eukaryotic cells, very little success has been achieved with prokaryotes. at present, detection of specific mrnas in individual prokaryo ... | 2007 | 17949838 |
| metabolic uncoupling of shewanella oneidensis mr-1, under the influence of excess substrate and 3, 3', 4', 5-tetrachlorosalicylanilide (tcs). | the dissociation between catabolism and anabolism is generally termed as metabolic uncoupling. experimentally, metabolic uncoupling is characterized by a reduction in the observed biomass yield. this condition can be brought about by: (a) excess-substrate (as measured by s(0)/x(0)), and (b) addition of chemical uncouplers such as 3, 3', 4', 5-tetrachlorosalicylanilide (tcs). an empirical model is proposed to quantify the uncoupling effects of both excess-substrate and uncoupler addition on the m ... | 2008 | 17972334 |
| shewanella oneidensis mr-1 h-nox regulation of a histidine kinase by nitric oxide. | nitric oxide (no) signaling in animals controls processes such as smooth muscle relaxation and neurotransmission by activation of soluble guanylate cyclase (sgc). prokaryotic homologues of the sgc heme domain, called h-nox domains, have been identified and are generally found in a predicted operon in conjunction with a histidine kinase. here, we show that an h-nox protein (so2144) from shewanella oneidensis directly interacts with the sensor histidine kinase (so2145), binds no in a 5-coordinate ... | 2007 | 17988156 |
| growth with high planktonic biomass in shewanella oneidensis fuel cells. | shewanella oneidensis mr-1 grew for over 50 days in microbial fuel cells, incompletely oxidizing lactate to acetate with high recovery of the electrons derived from this reaction as electricity. electricity was produced with lactate or hydrogen and current was comparable to that of electricigens which completely oxidize organic substrates. however, unlike fuel cells with previously described electricigens, in which cells are primarily attached to the anode, at least as many of the s. oneidensis ... | 2008 | 17995953 |
| increased catalytic efficiency following gene fusion of bifunctional methionine sulfoxide reductase enzymes from shewanella oneidensis. | methionine sulfoxide reductase enzymes msra and msrb have complementary stereospecificities that reduce the s and r stereoisomers of methionine sulfoxide (metso), respectively, and together function as critical antioxidant enzymes. in some pathogenic and metal-reducing bacteria, these genes are fused to form a bifunctional methionine sulfoxide reductase (i.e., msrba) enzyme. to investigate how gene fusion affects the substrate specificity and catalytic activities of msr, we have cloned and expre ... | 2007 | 17997579 |
| the influence of cultivation methods on shewanella oneidensis physiology and proteome expression. | high-throughput analyses that are central to microbial systems biology and ecophysiology research benefit from highly homogeneous and physiologically well-defined cell cultures. while attention has focused on the technical variation associated with high-throughput technologies, biological variation introduced as a function of cell cultivation methods has been largely overlooked. this study evaluated the impact of cultivation methods, controlled batch or continuous culture in bioreactors versus s ... | 2008 | 18030449 |
| fully automated four-column capillary lc-ms system for maximizing throughput in proteomic analyses. | we describe a four-column, high-pressure capillary liquid chromatography (lc) system for robust, high-throughput liquid chromatography-mass spectrometry (lc-ms(/ms)) analyses. this system performs multiple lc separations in parallel, but staggers each of them such that the data-rich region of each separation is sampled sequentially. by allowing nearly continuous data acquisition, this design maximizes the use of the mass spectrometer. each analytical column is connected to a corresponding esi em ... | 2008 | 18044960 |
| utilization of dna as a sole source of phosphorus, carbon, and energy by shewanella spp.: ecological and physiological implications for dissimilatory metal reduction. | the solubility of orthophosphate (po4(3-)) in iron-rich sediments can be exceedingly low, limiting the bioavailability of this essential nutrient to microbial populations that catalyze critical biogeochemical reactions. here we demonstrate that dissolved extracellular dna can serve as a sole source of phosphorus, as well as carbon and energy, for metal-reducing bacteria of the genus shewanella. shewanella oneidensis mr-1, shewanella putrefaciens cn32, and shewanella sp. strain w3-18-1 all grew w ... | 2008 | 18156329 |
| systematic assessment of the benefits and caveats in mining microbial post-translational modifications from shotgun proteomic data: the response of shewanella oneidensis to chromate exposure. | microbes are known to regulate both gene expression and protein activity through the use of post-translational modifications (ptms). common ptms involved in cellular signaling and gene control include methylations, acetylations, and phosphorylations, whereas oxidations have been implicated as an indicator of stress. shewanella oneidensis mr-1 is a gram-negative bacterium that demonstrates both respiratory versatility and the ability to sense and adapt to diverse environmental conditions. the dat ... | 2008 | 18171020 |
| probing regulon of arca in shewanella oneidensis mr-1 by integrated genomic analyses. | the arc two-component system is a global regulator controlling many genes involved in aerobic/anaerobic respiration and fermentative metabolism in escherichia coli. shewanella oneidensis mr-1 contains a gene encoding a putative arca homolog with ~81% amino acid sequence identity to the e. coli arca protein but not a full-length arcb gene. | 2008 | 18221523 |
| correlated biofilm imaging, transport and metabolism measurements via combined nuclear magnetic resonance and confocal microscopy. | bacterial biofilms are complex, three-dimensional communities found nearly everywhere in nature and are also associated with many human diseases. detailed metabolic information is critical to understand and exploit beneficial biofilms as well as combat antibiotic-resistant, disease-associated forms. however, most current techniques used to measure temporal and spatial metabolite profiles in these delicate structures are invasive or destructive. here, we describe imaging, transport and metabolite ... | 2008 | 18253132 |
| the use of electrochemical impedance spectroscopy (eis) in the evaluation of the electrochemical properties of a microbial fuel cell. | electrochemical impedance spectroscopy (eis) has been used to determine several electrochemical properties of the anode and cathode of a mediator-less microbial fuel cell (mfc) under different operational conditions. these operational conditions included a system with and without the bacterial catalyst and eis measurements at the open-circuit potential of the anode and the cathode or at an applied cell voltage. in all cases the impedance spectra followed a simple one-time-constant model (otcm) i ... | 2008 | 18294928 |
| construction and use of new cloning vectors for the rapid isolation of recombinant proteins from escherichia coli. | we describe the construction and use of two sets of vectors for the over-expression and purification of protein from escherichia coli. the set of ptev plasmids (ptev3, 4, 5) directs the synthesis of a recombinant protein with a n-terminal hexahistidine (his(6)) tag that is removable by the tobacco etch virus (tev) protease. the set of pkld plasmids (pkld66, 116) directs the synthesis of a recombinant protein that contains a n-terminal his(6) and maltose-binding protein tag in tandem, which can a ... | 2008 | 18295882 |
| in vivo identification of the outer membrane protein omca-mtrc interaction network in shewanella oneidensis mr-1 cells using novel hydrophobic chemical cross-linkers. | outer membrane (om) cytochromes omca (so1779) and mtrc (so1778) are the integral components of electron transfer used by shewanella oneidensis for anaerobic respiration of metal (hydr)oxides. here the omca-mtrc interaction was identified in vivo using a novel hydrophobic chemical cross-linker (mrn) combined with immunoprecipitation techniques. in addition, identification of other om proteins from the cross-linked complexes allows first visualization of the omca-mtrc interaction network. further ... | 2008 | 18303833 |
| shewanella secretes flavins that mediate extracellular electron transfer. | bacteria able to transfer electrons to metals are key agents in biogeochemical metal cycling, subsurface bioremediation, and corrosion processes. more recently, these bacteria have gained attention as the transfer of electrons from the cell surface to conductive materials can be used in multiple applications. in this work, we adapted electrochemical techniques to probe intact biofilms of shewanella oneidensis mr-1 and shewanella sp. mr-4 grown by using a poised electrode as an electron acceptor. ... | 2008 | 18316736 |
| empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis. | signal-to-noise-ratio (snr) thresholds for microarray data analysis were experimentally determined with an oligonucleotide array that contained perfect-match (pm) and mismatch (mm) probes based upon four genes from shewanella oneidensis mr-1. a new snr calculation, called the signal-to-both-standard-deviations ratio (ssdr), was developed and evaluated, along with other two methods, the signal-to-standard-deviation ratio (ssr) and the signal-to-background ratio (sbr). at a low stringency, the thr ... | 2008 | 18344333 |
| characterization of the shewanella oneidensis fur gene: roles in iron and acid tolerance response. | iron homeostasis is a key metabolism for most organisms. in many bacterial species, coordinate regulation of iron homeostasis depends on the protein product of a fur gene. fur also plays roles in virulence, acid tolerance, redox-stress responses, flagella chemotaxis and metabolic pathways. | 2008 | 18366600 |
| identification of mobile elements and pseudogenes in the shewanella oneidensis mr-1 genome. | shewanella oneidensis mr-1 is the first of 22 different shewanella spp. whose genomes have been or are being sequenced and thus serves as the model organism for studying the functional repertoire of the shewanella genus. the original mr-1 genome annotation revealed a large number of transposase genes and pseudogenes, indicating that many of the genome's functions may be decaying. comparative analyses of the sequenced shewanella strains suggest that 209 genes in mr-1 have in-frame stop codons, fr ... | 2008 | 18378659 |
| dissimilatory iron reduction in escherichia coli: identification of cyma of shewanella oneidensis and napc of e. coli as ferric reductases. | over geological time scales, microbial reduction of chelated fe(iii) or fe(iii) minerals has profoundly affected today's composition of our bio- and geosphere. however, the electron transfer reactions that are specific and defining for dissimilatory iron(iii)-reducing (dir) bacteria are not well understood. using a synthetic biology approach involving the reconstruction of the putative electron transport chain of the dir bacterium shewanella oneidensis mr-1 in escherichia coli, we showed that ex ... | 2008 | 18394146 |
| evaluation of antifouling activity of eight commercially available organic chemicals against the early foulers marine bacteria and ulva spores. | environmental impacts caused by tin and copper based commercial antifouling (af) paints were proved to be detrimental to aquatic ecosystems. therefore, a search of environmental friendly af compounds to be used in marine paint to protect the surface of maritime developmental structures from the unwanted biofouling is a burning issue of the present time. commercially available eight organic chemicals--allyl isothiocyanate, beta-myrecene, cis-3-hexenyl acetate, citral, ethyl heptanoate, eugenol, m ... | 2007 | 18405125 |
| oxygen-dependent autoaggregation in shewanella oneidensis mr-1. | in aerobic chemostat cultures maintained at 50% dissolved o(2) tension (3.5 mg l(-1) dissolved o(2)), shewanella oneidensis strain mr-1 rapidly aggregated upon addition of 0.68 mm cacl(2) and retained this multicellular phenotype at high dilution rates. confocal microscopy analysis of the extracellular matrix material contributing to the stability of the aggregate structures revealed the presence of extracellular dna, protein and glycoconjugates. upon onset of o(2)-limited growth (dissolved o(2) ... | 2008 | 18412550 |
| microbial fuel cell technology for measurement of microbial respiration of lactate as an example of bioremediation amendment. | microbial fuel cell (mfc) based sensing was explored to provide for the development of an in situ bioremediation monitoring approach for substrate concentrations and microbial respiration rates. mfc systems were examined in column systems where shewanella oneidensis mr1 used an external electron acceptor (an electrode) to metabolize lactate (a bioremediation additive) to acetate. column systems were operated with varying influent lactate concentrations (0-41 mm) and monitored for current generat ... | 2008 | 18414805 |
| predicting sigma28 promoters in eleven shewanella genomes. | an iterative position-specific score matrix (pssm)-based approach was used to predict sigma(28) promoters in 11 shewanella genomes. the shewanella correlation browser was used to distinguish true-positive predictions from false-positive predictions in shewanella oneidensis mr-1 by generating a sigma(28)-regulated transcriptional network from transcriptional profiling data. this dual-pronged approach identified several genes that have sigma(28) promoters and that may be involved with motility or ... | 2008 | 18430000 |
| the molecular density of states in bacterial nanowires. | the recent discovery of electrically conductive bacterial appendages has significant physiological, ecological, and biotechnological implications, but the mechanism of electron transport in these nanostructures remains unclear. we here report quantitative measurements of transport across bacterial nanowires produced by the dissimilatory metal-reducing bacterium, shewanella oneidensis mr-1, whose electron transport system is being investigated for renewable energy recovery in microbial fuel cells ... | 2008 | 18441026 |
| investigations of structure and metabolism within shewanella oneidensis mr-1 biofilms. | biofilms possess spatially and temporally varying metabolite concentration profiles at the macroscopic and microscopic scales. this results in varying growth environments that may ultimately drive species diversity, determine biofilm structure and the spatial distribution of the community members. using non-invasive nuclear magnetic resonance (nmr) microscopic imaging/spectroscopy and confocal imaging, we investigated the kinetics and stratification of anaerobic metabolism within live biofilms o ... | 2008 | 18448180 |
| a support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. | the standard approach to identifying peptides based on accurate mass and elution time (amt) compares profiles obtained from a high resolution mass spectrometer to a database of peptides previously identified from tandem mass spectrometry (ms/ms) studies. it would be advantageous, with respect to both accuracy and cost, to only search for those peptides that are detectable by ms (proteotypic). | 2008 | 18453551 |
| in search of the microbe/mineral interface: quantitative analysis of bacteria on metal surfaces using vertical scanning interferometry. | to understand the development of biofilms on metal surfaces, analysis of initial bacterial attachment to surfaces is crucial. here we present the results of a study, using shewanella oneidensis mr-1 as a model organism, in which vertical scanning interferometry (vsi) was used to investigate the initial stages of cell attachment to glass, steel and aluminium surfaces. it was found that while vsi gave unambiguous results with opaque surfaces, when reflective surfaces were used, an artifact sometim ... | 2008 | 18459964 |
| comparison of uranium(vi) removal by shewanella oneidensis mr-1 in flow and batch reactors. | to better understand the interactions among metal contaminants, nutrients, and microorganisms in subsurface fracture-flow systems, biofilms of pure culture of shewanella oneidensis mr-1 were grown in six fracture-flow reactors (ffrs) of different geometries. the spatial and temporal distribution of uranium and bacteria were examined using a tracer dye (brilliant blue fcf) and microscopy. the results showed that plugging by bacterial cells was dependent on the geometry of the reactor and that bio ... | 2008 | 18468655 |
| the c-type cytochrome omca localizes to the outer membrane upon heterologous expression in escherichia coli. | we have functionally produced the outer membrane cytochrome omca from shewanella oneidensis in escherichia coli. substrate accessibility experiments indicate that omca is surface exposed in an e. coli b strain but not in a k-12 strain. we show that a functional type ii secretion system is required for surface localization. | 2008 | 18487320 |
| direct involvement of type ii secretion system in extracellular translocation of shewanella oneidensis outer membrane cytochromes mtrc and omca. | mtrc and omca are cell surface-exposed lipoproteins important for reducing solid metal oxides. deletions of type ii secretion system (t2ss) genes reduced their extracellular release and their accessibility to the proteinase k treatment, demonstrating the direct involvement of t2ss in translocation of mtrc and omca to the bacterial cell surface. | 2008 | 18502849 |
| automated gain control ion funnel trap for orthogonal time-of-flight mass spectrometry. | time-of-flight mass spectrometry (tof ms) is increasingly used in proteomics research. herein, we report on the development and characterization of a tof ms instrument with improved sensitivity equipped with an electrodynamic ion funnel trap (ift) that employs an automated gain control (agc) capability. the ift-tof ms was coupled to a reversed-phase capillary liquid chromatography (rplc) separation and evaluated in experiments with complex proteolytic digests. when applied to a global tryptic di ... | 2008 | 18512944 |
| [electricity from microorganisms]. | over the last ten years, the recently discovered process of direct electron transfer from anaerobically grown microorganisms to an electrode of a fuel cell has been the object of intense study. the microorganisms responsible for such electron transport were termed electrogenic; the devices using them to generate electric current, microbial fuel cells (mfcs). the review discussed the molecular mechanisms of electron transfer to the environment in the case of the two best studied microorganisms, s ... | 2008 | 18522314 |
| expression, purification, crystallization and structure determination of two glutathione s-transferase-like proteins from shewanella oneidensis. | genome analysis of shewanella oneidensis, a gram-negative bacterium with an unusual repertoire of respiratory and redox capabilities, revealed the presence of six glutathione s-transferase-like genes (sogst1-sogst6). glutathione s-transferases (gsts; ec 2.5.1.18) are found in all kingdoms of life and are involved in phase ii detoxification processes by catalyzing the nucleophilic attack of reduced glutathione on diverse electrophilic substrates, thereby decreasing their reactivity. structure-fun ... | 2008 | 18540073 |
| identification of diverse carbon utilization pathways in shewanella oneidensis mr-1 via expression profiling. | to identify pathways of carbon utilization in the metal-reducing marine bacterium shewanella oneidensis mr-1, we assayed the expression of cells grown with various carbon sources using a high-density oligonucleotide affymetrix microarray. our expression profiles reveal genes and regulatory mechanisms which govern the sensing, import, and utilization of the nucleoside inosine, the chitin monomer n-acetylglucosamine, and a casein-derived mixture of amino acids. our analysis suggests a prominent ro ... | 2007 | 18546496 |
| in vitro evolution of a peptide with a hematite binding motif that may constitute a natural metal-oxide binding archetype. | phage-display technology was used to evolve peptides that selectively bind to the metal-oxide hematite (fe2o3) from a library of approximately 3 billion different polypeptides. the sequences of these peptides contained the highly conserved amino acid motif, ser/thr-hydrophobic/aromatic-ser/thr-pro-ser/thr. to better understand the nature of the peptide-metal oxide binding demonstrated by these experiments, molecular dynamics simulations were carried out for ser-pro-ser at a hematite surface. the ... | 2008 | 18546729 |
| structure of so2946 orphan from shewanella oneidensis shows "jelly-roll" fold with carbohydrate-binding module. | the crystal structure of the uncharacterized protein so2946 from shewanella oneidensis mr-1 was determined with single-wavelength anomalous diffraction (sad) and refined to 2.0 a resolution. the so2946 protein consists of a short helical n-terminal domain and a large c-terminal domain with the "jelly-roll" topology. the protein assembles into a propeller consisting of three c-terminal blades arranged around a central core formed by the n-terminal domains. the function of so2946 could not be infe ... | 2008 | 18566914 |
| electrochemical interrogations of the mtr cytochromes from shewanella: opening a potential window. | the multi-heme cytochromes from shewanella oneidensis associated with the dissimilatory metal reduction (dmr) pathway have been investigated using the technique of protein film voltammetry (pfv). using pfv, we have interrogated each of the multi-heme cytochromes (mtra, stc, and solubilized versions of the membrane-bound proteins cyma, omca, and mtrc) under identical conditions for the first time. each cytochrome reveals a broad envelope of voltammetric response, indicative of multiple redox cofa ... | 2008 | 18575901 |
| a general system for studying protein-protein interactions in gram-negative bacteria. | one of the most promising methods for large-scale studies of protein interactions is isolation of an affinity-tagged protein with its in vivo interaction partners, followed by mass spectrometric identification of the copurified proteins. previous studies have generated affinity-tagged proteins using genetic tools or cloning systems that are specific to a particular organism. to enable protein-protein interaction studies across a wider range of gram-negative bacteria, we have developed a methodol ... | 2008 | 18590317 |
| simple menaquinones reduce carbon tetrachloride and iron (iii). | cell-free supernatant from shewanella oneidensis mr-1 reduced carbon tetrachloride to chloroform, a suspension of fe(iii) and solid fe(iii) to iron (ii). the putative reducing agent was tentatively identified as menaquinone-1 (mq-1)-a water-soluble menaquinone with a single isoprenoid residue in the side chain. synthetic mq-1 reduced carbon tetrachloride to chloroform and amorphous iron (iii) hydroxide to iron (ii). to test the generality of this result among menaquinones, the reductive activiti ... | 2009 | 18594993 |
| identification and characterization of n-acylhomoserine lactone-acylase from the fish intestinal shewanella sp. strain mib015. | n-acylhomoserine lactones (ahls) are used as quorum-sensing signal molecules by many gram-negative bacteria. we have reported that shewanella sp. strain mib015 degrades ahls. in the present study, we cloned the aac gene from mib015 by pcr with specific primers based on the aac gene in shewanella oneidensis strain mr-1, which showed high homology with the known ahl-acylases. escherichia coli expressing aac showed high degrading activity of ahls with long acyl chains. hplc analysis revealed that a ... | 2008 | 18603799 |
| towards environmental systems biology of shewanella. | bacteria of the genus shewanella are known for their versatile electron-accepting capacities, which allow them to couple the decomposition of organic matter to the reduction of the various terminal electron acceptors that they encounter in their stratified environments. owing to their diverse metabolic capabilities, shewanellae are important for carbon cycling and have considerable potential for the remediation of contaminated environments and use in microbial fuel cells. systems-level analysis ... | 2008 | 18604222 |
| application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: proteomics on the fly. | a new method for rapid proteolytic digestion of proteins under high pressure that uses pressure cycling technology in the range of 5-35 kpsi was demonstrated for proteomic analysis. successful in-solution digestions of single proteins and complex protein mixtures were achieved in 60 s and then analyzed by reversed phase liquid chromatography-electrospray ionization ion trap-mass spectrometry. method performance in terms of the number of shewanella oneidensis peptides and proteins identified in a ... | 2008 | 18605748 |
| use of atomic force microscopy and transmission electron microscopy for correlative studies of bacterial capsules. | bacteria can possess an outermost assembly of polysaccharide molecules, a capsule, which is attached to their cell wall. we have used two complementary, high-resolution microscopy techniques, atomic force microscopy (afm) and transmission electron microscopy (tem), to study bacterial capsules of four different gram-negative bacterial strains: escherichia coli k30, pseudomonas aeruginosa frd1, shewanella oneidensis mr-4, and geobacter sulfurreducens pca. tem analysis of bacterial cells using diff ... | 2008 | 18606791 |
| remarkable stabilization of a psychrotrophic rnase hi by a combination of thermostabilizing mutations identified by the suppressor mutation method. | ribonuclease hi from the psychrotrophic bacterium shewanella oneidensis mr-1 (so-rnase hi) is much less stable than escherichia coli rnase hi (ec-rnase hi) by 22.4 degrees c in t m and 12.5 kj mol (-1) in delta g(h 2o), despite their high degrees of structural and functional similarity. to examine whether the stability of so-rnase hi increases to a level similar to that of ec-rnase hi via introduction of several mutations, the mutations that stabilize so-rnase hi were identified by the suppresso ... | 2008 | 18616283 |
| a high-throughput percentage-of-binding strategy to measure binding energies in dna-protein interactions: application to genome-scale site discovery. | quantifying the binding energy in dna-protein interactions is of critical importance to understand transcriptional regulation. based on a simple computational model, this study describes a high-throughput percentage-of-binding strategy to measure the binding energy in dna-protein interactions between the shewanella oneidensis arca two-component transcription factor protein and a systematic set of mutants in an arca-p (phosphorylated arca) binding site. the binding energies corresponding to each ... | 2008 | 18653527 |
| addressing shewanella oneidensis "cytochromome": the first step towards high-throughput expression of cytochromes c. | integrated studies that address proteins structure and function in the new era of systems biology and genomics often require the application of high-throughput approaches for parallel production of many different purified proteins from the same organism. cytochromes c-electron transfer proteins carrying one or more hemes covalently bound to the polypeptide chain-are essential in most organisms. however, they are one of the most recalcitrant classes of proteins with respect to heterologous expres ... | 2008 | 18657620 |
| enhancement of heterologous production of eicosapentaenoic acid in escherichia coli by substitution of promoter sequences within the biosynthesis gene cluster. | to enhance the heterologous production of eicosapentaenoic acid (epa) in escherichia coli, the epa biosynthesis gene cluster from shewanella oneidensis mr-1 was cloned under the lacz promoter on a high-copy number plasmid, pbluescript sk+. the production of epa was remarkably enhanced yielding levels of up to 7.5% of the total fatty acid content in the recombinant e. coli strain by induction with iptg, whereas the stimulation of epa production was abolished by adding glucose into the culture med ... | 2008 | 18661106 |
| validating annotations for uncharacterized proteins in shewanella oneidensis. | proteins of unknown function are a barrier to our understanding of molecular biology. assigning function to these "uncharacterized" proteins is imperative, but challenging. the usual approach is similarity searches using annotation databases, which are useful for predicting function. however, since the performance of these databases on uncharacterized proteins is basically unknown, the accuracy of their predictions is suspect, making annotation difficult. to address this challenge, we developed ... | 2008 | 18687039 |
| the cis-regulatory map of shewanella genomes. | while hundreds of microbial genomes are sequenced, the challenge remains to define their cis-regulatory maps. here, we present a comparative genomic analysis of the cis-regulatory map of shewanella oneidensis, an important model organism for bioremediation because of its extraordinary abilities to use a wide variety of metals and organic molecules as electron acceptors in respiration. first, from the experimentally verified transcriptional regulatory networks of escherichia coli, we inferred 24 ... | 2008 | 18701645 |
| generation and validation of a shewanella oneidensis mr-1 clone set for protein expression and phage display. | a comprehensive gene collection for s. oneidensis was constructed using the lambda recombinase (gateway) cloning system. a total of 3584 individual orfs (85%) have been successfully cloned into the entry plasmids. to validate the use of the clone set, three sets of orfs were examined within three different destination vectors constructed in this study. success rates for heterologous protein expression of s. oneidensis his- or his/gst-tagged proteins in e. coli were approximately 70%. the arca an ... | 2008 | 18714347 |
| transcriptome analysis reveals response regulator so2426-mediated gene expression in shewanella oneidensis mr-1 under chromate challenge. | shewanella oneidensis mr-1 exhibits diverse metal ion-reducing capabilities and thus is of potential utility as a bioremediation agent. knowledge of the molecular components and regulatory mechanisms dictating cellular responses to heavy metal stress, however, remains incomplete. in a previous work, the s. oneidensis so2426 gene, annotated as a dna-binding response regulator, was demonstrated to be specifically responsive at both the transcript and protein levels to acute chromate [cr(vi)] chall ... | 2008 | 18718017 |
| hydrogen production using single-chamber membrane-free microbial electrolysis cells. | microbial electrohydrogenesis provides a new approach for hydrogen generation from renewable biomass. membranes were used in all the reported microbial electrolysis cells (mecs) to separate the anode and cathode chambers. to reduce the potential losses associated with membrane and increase the energy recovery of this process, single-chamber membrane-free mecs were designed and used to investigate hydrogen production by one mixed culture and one pure culture: shewanella oneidensis mr-1. at an app ... | 2008 | 18718624 |
| expression of copa and cusa in shewanella during copper stress. | copper homeostasis is tightly regulated in all living cells as a result of the necessity and toxicity of this metal in free cationic form. in gram-negative bacteria cpx-type atpases (e.g. copa in escherichia coli) and heavy-metal efflux rnd proteins (e.g. cusa in e. coli) play an important role in transport of copper across the cytoplasmic and outer membrane. we investigated the expression of cusa- and copa-like proteins in shewanella oneidensis mr1 and shewanella strain mb4, a mn(iv)-reducing i ... | 2008 | 18757804 |
| characterization of electrochemically active bacteria utilizing a high-throughput voltage-based screening assay. | metal reduction assays are traditionally used to select and characterize electrochemically active bacteria (eab) for use in microbial fuel cells (mfcs). however, correlating the ability of a microbe to generate current from an mfc to the reduction of metal oxides has not been definitively established in the literature. as these metal reduction assays may not be generally reliable, here we describe a four- to nine-well prototype high throughput voltage-based screening assay (vbsa) designed using ... | 2009 | 18767193 |
| the influence of acidity on microbial fuel cells containing shewanella oneidensis. | microbial fuel cells (mfcs) traditionally operate at ph values between 6 and 8. however, the effect of ph on the growth and electron transfer abilities of shewanella oneidensis mr-1 (wild-type) and dsp10 (spontaneous mutant), bacteria commonly used in mfcs, to electrodes has not been examined. miniature mfcs using bare graphite felt electrodes and nanoporous polycarbonate membranes with mr-1 or dsp10 cultures generated >8w/m(3) and approximately 400mua between ph 6-7. the dsp10 strain significan ... | 2008 | 18774288 |
| kinetics of reduction of fe(iii) complexes by outer membrane cytochromes mtrc and omca of shewanella oneidensis mr-1. | because of their cell surface locations, the outer membrane c-type cytochromes mtrc and omca of shewanella oneidensis mr-1 have been suggested to be the terminal reductases for a range of redox-reactive metals that form poorly soluble solids or that do not readily cross the outer membrane. in this work, we determined the kinetics of reduction of a series of fe(iii) complexes with citrate, nitrilotriacetic acid (nta), and edta by mtrc and omca using a stopped-flow technique in combination with th ... | 2008 | 18791025 |
| the role of multihaem cytochromes in the respiration of nitrite in escherichia coli and fe(iii) in shewanella oneidensis. | the periplasmic nitrite reductase system from escherichia coli and the extracellular fe(iii) reductase system from shewanella oneidensis contain multihaem c-type cytochromes as electron carriers and terminal reductases. the position and orientation of the haem cofactors in multihaem cytochromes from different bacteria often show significant conservation despite different arrangements of the polypeptide chain. we propose that the decahaem cytochromes of the iron reductase system mtra, mtrc and om ... | 2008 | 18793179 |
| shewanella oneidensis: a new and efficient system for expression and maturation of heterologous [fe-fe] hydrogenase from chlamydomonas reinhardtii. | the eukaryotic green alga, chlamydomonas reinhardtii, produces h2 under anaerobic conditions, in a reaction catalysed by a [fe-fe] hydrogenase hyda1. for further biochemical and biophysical studies a suitable expression system of this enzyme should be found to overcome its weak expression in the host organism. two heterologous expression systems used up to now have several advantages. however they are not free from some drawbacks. in this work we use bacterium shewanella oneidensis as a new and ... | 2008 | 18801156 |
| assessment of data processing to improve reliability of microarray experiments using genomic dna reference. | using genomic dna as common reference in microarray experiments has recently been tested by different laboratories. conflicting results have been reported with regard to the reliability of microarray results using this method. to explain it, we hypothesize that data processing is a critical element that impacts the data quality. | 2008 | 18831796 |
| mechanism and consequences of anaerobic respiration of cobalt by shewanella oneidensis strain mr-1. | bacteria from the genus shewanella are the most diverse respiratory organisms studied to date and can utilize a variety of metals and metal(loid)s as terminal electron acceptors. these bacteria can potentially be used in bioremediation applications since the redox state of metals often influences both solubility and toxicity. understanding molecular mechanisms by which metal transformations occur and the consequences of by-products that may be toxic to the organism and thus inhibitory to the ove ... | 2008 | 18836009 |
| identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry. | we present results from a novel strategy that enables concurrent identification of protein-protein interactions and topologies in living cells without specific antibodies or genetic manipulations for immuno-/affinity purifications. the strategy consists of (i) a chemical cross-linking reaction: intact cell labeling with a novel class of chemical cross-linkers, protein interaction reporters (pirs); (ii) two-stage mass spectrometric analysis: stage 1 identification of pir-labeled proteins and cons ... | 2009 | 18936057 |
| biocatalytic dechlorination of trichloroethylene with bio-palladium in a pilot-scale membrane reactor. | trichloroethylene (tce) is a toxic and recalcitrant groundwater pollutant. an innovative technology using microbial produced pd(0) nanoparticles for the remediation of tce contaminated groundwater was developed. the nanoscale bio-pd particles were precipitated on the biomass of shewanella oneidensis and hydrogen gas, formate, or formic acid were used as hydrogen donors. ethane turned out to be the only organic degradation product and no intermediate chlorinated reaction products were detected. s ... | 2009 | 18949748 |
| the solution structure of a tetraheme cytochrome from shewanella frigidimarina reveals a novel family structural motif. | the bacteria belonging to the genus shewanella are facultative anaerobes that utilize a variety of terminal electron acceptors which includes soluble and insoluble metal oxides. the tetraheme c-type cytochrome isolated during anaerobic growth of shewanella frigidimarina ncimb400 ( sfc) contains 86 residues and is involved in the fe(iii) reduction pathways. although the functional properties of sfc redox centers are quite well described, no structures are available for this protein. in this work, ... | 2008 | 18950243 |
| scaling up microbial fuel cells. | the goal of this study was to quantify the relation between the surface area of the current-limiting electrode of a microbial fuel cell (mfc) and the power density generated by the mfc. shewanella oneidensis (mr-1) was grown anaerobically in the anodic compartment of an mfc utilizing lactate as the electron donor. graphite plate electrodes of various sizes were used as anodes. commercially available air electrodes, composed of manganese-based catalyzed carbon bonded to a current-collecting scree ... | 2008 | 18983087 |
| high-throughput protein concentration and buffer exchange: comparison of ultrafiltration and ammonium sulfate precipitation. | high-throughput protein purification is a complex, multi-step process. there are several technical challenges in the course of this process that are not experienced when purifying a single protein. among the most challenging are the high-throughput protein concentration and buffer exchange, which are not only labor-intensive but can also result in significant losses of purified proteins. we describe two methods of high-throughput protein concentration and buffer exchange: one using ammonium sulf ... | 2009 | 18988034 |
| structure of biogenic uraninite produced by shewanella oneidensis strain mr-1. | the stability of biogenic uraninite with respect to oxidation is seminal to the success of in situ bioreduction strategies for remediation of subsurface u(vi) contamination. the properties and hence stability of uraninite are dependent on its size, structure, and composition. in this study, the local-, intermediate-, and long-range molecular-scale structure of nanoscale uraninite produced by shewanella oneidensis strain mr-1 was investigated using exafs, sr-based powder diffraction and tem. the ... | 2008 | 19031878 |
| investigation of the structure and function of a shewanella oneidensis arsenical-resistance family transporter. | the toxic metalloid arsenic is an abundant element and most organisms possess transport systems involved in its detoxification. one such family of arsenite transporters, the acr3 family, is widespread in fungi and bacteria. to gain a better understanding of the molecular mechanism of arsenic transport, we report here the expression and characterization of a family member, so_acr3, from the bacterium shewanella oneidensis mr-1. surprisingly, expression of this transporter in the arsenic-hypersens ... | 2008 | 19039703 |
| the tetraheme cytochrome from shewanella oneidensis mr-1 shows thermodynamic bias for functional specificity of the hemes. | bacteria of the genus shewanella contain an abundant small tetraheme cytochrome in their periplasm when growing anaerobically. data collected for the protein isolated from s. oneidensis mr-1 and s. frigidimarina indicate differences in the order of oxidation of the hemes. a detailed thermodynamic characterization of the cytochrome from s. oneidensis mr-1 in the physiological ph range was performed, with data collected in the ph range 5.5-9.0 from nmr experiments using partially oxidized samples ... | 2009 | 19048308 |
| catabolite repression control of napf (periplasmic nitrate reductase) operon expression in escherichia coli k-12. | escherichia coli, a facultative aerobe, expresses two distinct respiratory nitrate reductases. the periplasmic napabc enzyme likely functions during growth in nitrate-limited environments, whereas the membrane-bound narghi enzyme functions during growth in nitrate-rich environments. maximal expression of the napfdaghbc operon encoding periplasmic nitrate reductase results from synergistic transcription activation by the fnr and phospho-narp proteins, acting in response to anaerobiosis and nitrat ... | 2009 | 19060147 |
| experimental approach for deep proteome measurements from small-scale microbial biomass samples. | many methods of microbial proteome characterizations require large quantities of cellular biomass (>1-2 g) for sample preparation and protein identification. our experimental approach differs from traditional techniques by providing the ability to identify the proteomic state of a microbe from a few milligrams of starting cellular material. the small-scale, guanidine lysis method minimizes sample loss by achieving cellular lysis and protein digestion in a single-tube experiment. for this experim ... | 2008 | 19072265 |
| in vivo assembly and single-molecule characterization of the transcription machinery from shewanella oneidensis mr-1. | harnessing the new bioremediation and biotechnology applications offered by the dissimilatory metal-reducing bacteria, shewanella oneidensis mr-1, requires a clear understanding of its transcription machinery, a pivotal component in maintaining vitality and in responding to various conditions, including starvation and environmental stress. here, we have reconstituted the s. oneidensis rna polymerase (rnap) core in vivo by generating a co-overexpression construct that produces a long polycistroni ... | 2009 | 19111618 |
| comparative temporal proteomics of a response regulator (so2426)-deficient strain and wild-type shewanella oneidensis mr-1 during chromate transformation. | predicted orphan response regulators encoded in the shewanella oneidensis mr-1 genome are poorly understood from a cellular function perspective. our previous transcriptomic and proteomic analyses demonstrated that an annotated dna-binding response regulator, so2426, was significantly up-regulated in wild-type s. oneidensis cells at both the mrna and protein levels in response to acute chromate [cr(vi)] challenge, suggesting a potential regulatory role for this protein in metal stress pathways. ... | 2009 | 19118451 |
| destabilization of psychrotrophic rnase hi in a localized fashion as revealed by mutational and x-ray crystallographic analyses. | the arg97 --> gly and asp136 --> his mutations stabilized so-rnase hi from the psychrotrophic bacterium shewanella oneidensis mr-1 by 5.4 and 9.7 degrees c, respectively, in t(m), and 3.5 and 6.1 kj x mol(-1), respectively, in deltag(h2o). these mutations also stabilized the so-rnase hi derivative (4x-rnase hi) with quadruple thermostabilizing mutations in an additive manner. as a result, the resultant sextuple mutant protein (6x-rnase hi) was more stable than the wild-type protein by 28.8 degre ... | 2009 | 19120449 |
| involvement of shewanella oneidensis mr-1 luxs in biofilm development and sulfur metabolism. | the role of luxs in shewanella oneidensis mr-1 has been examined by transcriptomic profiling, biochemical, and physiological experiments. the results indicate that a mutation in luxs alters biofilm development, not by altering quorum-sensing abilities but by disrupting the activated methyl cycle (amc). the s. oneidensis wild type can produce a luminescence response in the ai-2 reporter strain vibrio harveyi mm32. this luminescence response is abolished upon the deletion of luxs. the deletion of ... | 2009 | 19124589 |
| crystal structure of the fic (filamentation induced by camp) family protein so4266 (gi|24375750) from shewanella oneidensis mr-1 at 1.6 a resolution. | 2009 | 19127588 | |
| early detection of oxidized surfaces using shewanella oneidensis mr-1 as a tool. | corrosion is a natural global problem of immense importance. oxidation of iron and steel not only compromises the structural stability of a widely used and versatile material but it also creates an abrasive compound (iron oxide) that can score the surfaces of metals, rendering them useless for the purpose for which they were designed. clearly, the identification of corrosion in its nascent stages is a high priority for reasons that range from aesthetics to economics. many bacteria in the faculta ... | 2009 | 19165644 |
| two different stator systems drive a single polar flagellum in shewanella oneidensis mr-1. | the gram-negative metal ion-reducing bacterium shewanella oneidensis mr-1 is motile by means of a single polar flagellum. we identified two potential stator systems, pomab and motab, each individually sufficient as a force generator to drive flagellar rotation. physiological studies indicate that pomab is sodium-dependent while motab is powered by the proton motive force. flagellar function mainly depends on the pomab stator; however, the presence of both stator systems under low-sodium conditio ... | 2009 | 19170881 |
| mercury stable isotope fractionation during reduction of hg(ii) by different microbial pathways. | mercury (hg) stable isotope fractionation has recently been developed as a tool in biogeochemistry. in this study, the extent of hg stable isotope fractionation during reduction of ionic mercury [hg(ii)] by two hg(ii)-resistant strains, bacillus cereus 5 and the thermophile anoxybacillus sp. fb9 [which actively detoxify hg(ii) by the mer system] and a hg(ii)-sensitive metal-reducing anaerobe, shewanella oneidensis mr-1 [which reduces hg(ii) at low concentrations], was investigated. in all cases, ... | 2008 | 19174888 |
| simultaneous analysis of physiological and electrical output changes in an operating microbial fuel cell with shewanella oneidensis. | changes in metabolism and cellular physiology of facultative anaerobes during oxygen exposure can be substantial, but little is known about how these changes connect with electrical current output from an operating microbial fuel cell (mfc). a high-throughput voltage based screening assay (vbsa) was used to correlate current output from a mfc containing shewanella oneidensis mr-1 to carbon source (glucose or lactate) utilization, culture conditions, and biofilm coverage over 250 h. lactate induc ... | 2009 | 19189395 |
| genomic reconstruction of shewanella oneidensis mr-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. | the ability to use lactate as a sole source of carbon and energy is one of the key metabolic signatures of shewanellae, a diverse group of dissimilatory metal-reducing bacteria commonly found in aquatic and sedimentary environments. nonetheless, homology searches failed to recognize orthologs of previously described bacterial d- or l-lactate oxidizing enzymes (escherichia coli genes dld and lldd) in any of the 13 analyzed genomes of shewanella spp. by using comparative genomic techniques, we ide ... | 2009 | 19196979 |
| a putative azoreductase gene is involved in the shewanella oneidensis response to heavy metal stress. | the shewanella oneidensis mr-1 gene so3585, which is annotated as a putative flavin mononucleotide-dependent azoreductase, shares 28% sequence identity with bacillus subtilis azoreductase and pseudomonas putida chrr, a soluble flavoprotein exhibiting chromate reductase activity. reverse transcription polymerase chain reaction demonstrated that the so3585 gene is co-transcribed with two downstream open reading frames: so3586 (a glyoxalase family protein) and so3587 (a predicted membrane-associate ... | 2009 | 19238379 |
| isolation and characterization of shewanella oneidensis wl-7 capable of decolorizing azo dye reactive black 5. | 2009 | 19282633 | |
| antibody recognition force microscopy shows that outer membrane cytochromes omca and mtrc are expressed on the exterior surface of shewanella oneidensis mr-1. | antibody recognition force microscopy showed that omca and mtrc are expressed on the exterior surface of living shewanella oneidensis mr-1 cells when fe(iii), including solid-phase hematite (fe(2)o(3)), was the terminal electron acceptor. omca was localized to the interface between the cell and mineral. mtrc displayed a more uniform distribution across the cell surface. both cytochromes were associated with an extracellular polymeric substance. | 2009 | 19286784 |
| snapshot of iron response in shewanella oneidensis by gene network reconstruction. | iron homeostasis of shewanella oneidensis, a gamma-proteobacterium possessing high iron content, is regulated by a global transcription factor fur. however, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. in this work, we integrate physiological, transcriptomics and genetic approaches to delineate the iron response of s. oneidensis. | 2009 | 19321007 |
| integron mobilization unit as a source of mobility of antibiotic resistance genes. | antibiotic resistance genes are spread mostly through plasmids, integrons (as a form of gene cassettes), and transposons in gram-negative bacteria. we describe here a novel genetic structure, named the integron mobilization unit (imu), that has characteristics similar to those of miniature inverted transposable elements (mites). two imus (288 bp each) were identified from a carbapenem-resistant enterobacter cloacae isolate that formed a composite structure encompassing a defective class 1 integr ... | 2009 | 19332679 |
| mitigation of the effect of catholyte contamination in microbial fuel cells using a wicking air cathode. | cathode design greatly affects microbial fuel cell (mfc) performance. cathode contamination is inevitable in a single-chamber mfc yet it is impossible to study the magnitude of this effect in the single-chambered format. therefore to study the effect of contamination at the cathode two-chamber mfcs must be used. the advantages of the two-chamber mfc design used in this study include: the assembled and filled fuel cell is autoclavable and the cathode can easily be moved from the submerged to air ... | 2009 | 19359159 |
| plutonium(v/vi) reduction by the metal-reducing bacteria geobacter metallireducens gs-15 and shewanella oneidensis mr-1. | we examined the ability of the metal-reducing bacteria geobacter metallireducens gs-15 and shewanella oneidensis mr-1 to reduce pu(vi) and pu(v). cell suspensions of both bacteria reduced oxidized pu [a mixture of pu(vi) and pu(v)] to pu(iv). the rate of plutonium reduction was similar to the rate of u(vi) reduction obtained under similar conditions for each bacteria. the rates of pu(vi) and u(vi) reduction by cell suspensions of s. oneidensis were slightly higher than the rates observed with g. ... | 2009 | 19363069 |
| c-terminal sequence analysis of 2de-separated proteins. | 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 n- or c-terminus are by far the most common types of ptms. nevertheless, little attention has been paid to the development of approaches that allow a systematic analysis of these proteolytic processing events. here we present a protocol that allows the identification of the c-terminal sequence of protein ... | 2009 | 19381603 |
| reduction of nitrate in shewanella oneidensis depends on atypical nap and nrf systems with napb as a preferred electron transport protein from cyma to napa. | in the genome of shewanella oneidensis, a napdaghb gene cluster encoding periplasmic nitrate reductase (napa) and accessory proteins and an nrfa gene encoding periplasmic nitrite reductase (nrfa) have been identified. these two systems seem to be atypical because the genome lacks genes encoding cytoplasmic membrane electron transport proteins, napc for nap and nrfbcd/nrfh for nrf, respectively. here, we present evidence that reduction of nitrate to ammonium in s. oneidensis is carried out by the ... | 2009 | 19387485 |