Publications

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comparative analysis of highly homologous shewanella cytochromes c5 for stability and function.homologous cytochromes c(5) from a mesophile, shewanella amazonensis (sa cytc(5)), and a psychrophile, shewanella violacea (sv cytc(5)), were compared to elucidate the molecular mechanisms underlying protein stability and function. cyclic voltammetry revealed that the two proteins had the same redox potential value. differential scanning calorimetry showed that sv cytc(5) was more stable than sa cytc(5) in an enthalpic manner. these results and the structure model of shewanella oneidensis cytoch ...201020460724
characterization of a diguanylate cyclase from shewanella woodyi with cyclase and phosphodiesterase activities.cyclic-di-gmp signaling is used by many bacteria to control biofilm formation. as biofilm formation is an important survival strategy for many bacteria, the synthesis and degradation of cyclic-di-gmp is tightly regulated by enzymes containing domains with conserved ggdef and eal sequence motifs, respectively. in this report we characterize a protein with both cyclase and phosphodiesterase activities and demonstrate that it contributes to secretion of the extracellular polysaccharide matrix, an i ...201020467666
u(vi) reduction to mononuclear u(iv) by desulfitobacterium species.the bioreduction of u(vi) to u(iv) affects uranium mobility and fate in contaminated subsurface environments and is best understood in gram-negative model organisms such as geobacter and shewanella spp. this study demonstrates that u(vi) reduction is a common trait of gram-positive desulfitobacterium spp. five different desulfitobacterium isolates reduced 100 microm u(vi) to u(iv) in <10 days, whereas u(vi) remained soluble in abiotic and heat-killed controls. u(vi) reduction in live cultures wa ...201020469854
effects of oxyanions, natural organic matter, and bacterial cell numbers on the bioreduction of lepidocrocite (gamma-feooh) and the formation of secondary mineralization products.microbial reduction of fe(iii) oxides results in the production of fe(ii) and may lead to the subsequent formation of fe(ii)-bearing secondary mineralization products including magnetite, siderite, vivianite, chukanovite (ferrous hydroxy carbonate (fhc)), and green rust; however, the factors controlling the formation of specific fe(ii) phases are often not well-defined. this study examined effects of (i) a range of inorganic oxyanions (arsenate, borate, molybdate, phosphate, silicate, and tungst ...201020476735
spatiotemporal activity of the msha gene system in shewanella oneidensis mr-1 biofilms.type iv pili and a putative eps biosynthetic gene cluster (mxdabcd) have been implicated previously in biofilm formation in shewanella oneidensis mr-1. here, we report that the mannose-sensitive hemagglutinin (msha) pilus mediates a reversible, d-mannose-sensitive association of cells to the substratum surface or to other cells that is critical within the first 5 microm of the biofilm from the substratum. the presence of the msha pilus alone is insufficient to confer biofilm-forming capacity; it ...201020487019
genome-wide expression links the electron transfer pathway of shewanella oneidensis to chemotaxis.by coupling the oxidation of organic substrates to a broad range of terminal electron acceptors (such as nitrate, metals and radionuclides), shewanella oneidensis mr-1 has the ability to produce current in microbial fuel cells (mfcs). omca, mtra, omcb (also known as mtrc), mtrb, and gspf are some known genes of s. oneidensis mr-1 that participate in the process of electron transfer. how does the cell coordinate the expression of these genes? to shed light on this problem, we obtain the gene expr ...201020492688
effects of oxygen on shewanella decolorationis ntou1 electron transfer to carbon-felt electrodes.to clarify the major factor caused by oxygen-enhancing charge production of shewanella decolorationis ntou1 towards a polarized anode, a series of experimental runs (i.e., with/without ambient air flushing and with/without ammonia addition as nitrogen source) were conducted in this study. within 6-day of operation at +0.4 v vs. ag|agcl and starting with 35 mm of lactate, consistently the electrical charge production under the aerobic condition was higher than that under the anaerobic condition. ...201020494569
a universal tagmodule collection for parallel genetic analysis of microorganisms.systems-level analyses of non-model microorganisms are limited by the existence of numerous uncharacterized genes and a corresponding over-reliance on automated computational annotations. one solution to this challenge is to disrupt gene function using dna tag technology, which has been highly successful in parallelizing reverse genetics in saccharomyces cerevisiae and has led to discoveries in gene function, genetic interactions and drug mechanism of action. to extend the yeast dna tag methodol ...201020494978
silver nanocrystallites: biofabrication using shewanella oneidensis, and an evaluation of their comparative toxicity on gram-negative and gram-positive bacteria.microorganisms have long been known to develop resistance to metal ions either by sequestering metals inside the cell or by effluxing them into the extracellular media. here we report the biosynthesis of extracellular silver-based single nanocrystallites of well-defined composition and homogeneous morphology utilizing the gamma-proteobacterium, shewanella oneidensis mr-1, upon incubation with aqueous silver nitrate solution. further characterization of these particles revealed that the crystals ...201020509652
biodegradation and microbial community changes upon shrimp shell wastes amended in mangrove river sediment.chitin, a homopolymer of n-acetyl-d-glucosamine (glcnac) residues linked by beta 1-4 bonds, is the most abundant renewable natural resource after cellulose. it is widely distributed in nature as the integuments of crustaceans and insects and as a component of fungi and algae. this study investigated the effects of a bifunctional chitinase/lysozyme-producing strain, pseudomonas aeruginosa k-187, on degradation of shrimp shells and the survival conditions of bacterial strains in mangrove river sed ...201020512738
ventilator-associated pneumonia due to shewanella putrefaciens.the first reported u.s. case of ventilator-associated pneumonia evidently caused by shewanella putrefaciens is described.201020516471
shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein.the ability of bacterial plasmids to adapt to novel hosts and thereby shift their host range is key to their long-term persistence in bacterial communities. promiscuous plasmids of the incompatibility group p (incp)-1 can colonize a wide range of hosts, but it is not known if and how they can contract, shift or further expand their host range. to understand the evolutionary mechanisms of host range shifts of incp-1 plasmids, an incp-1β mini-replicon was experimentally evolved in four hosts in wh ...201020520653
surface complexation of neptunium(v) onto whole cells and cell components of shewanella alga: modeling and experimental study.we systematically quantified surface complexation of np(v) onto whole cells, cell wall, and extracellular polymeric substances (eps) of shewanella alga strain bry. we first performed acid and base titrations and used the mathematical model fiteql to estimate the concentrations and deprotonation constants of specific surface functional groups. deprotonation constants most likely corresponded to a carboxyl group not associated with amino acids (pk(a) approximately 5), a phosphoryl site (pk(a) appr ...201020521812
epidemiology and clinical features of shewanella infection over an eight-year period.shewanella is a rare human pathogen that can lead to fatal infections. however, clinical information about this bacterium remains scarce. in this study, we retrospectively reviewed all patients with laboratory isolates of shewanella over an 8-y period to assess risk factors, clinical manifestations and outcome. twenty-nine patients were identified. shewanella was most commonly isolated from intra-abdominal specimens (48.2%), followed by skin and soft tissue specimens (27.6%), blood (13.8%) and s ...201020524786
[isolation and characterization of a humic-reducing bacterium shewanella strain w3 from mangrove sediment].a humus-reducing bacterium strain w3 was isolated from the mangrove sediment. based on the analysis of morphology, physiobiochemical characteristics and 16s rdna gene sequence, this strain was identified as shewanella sp. w3. strain w3 was able to reduce humic with lactate, formate and pyruvate as electron donor and the humic reduction rates to 1 mmol/l aqds were 96%, 40% and 10% respectively within 48 hours. in addition, the bacteria can grow coupled with the humic reduction. strain w3 grew to ...201020527189
defensin of the zebra mussel (dreissena polymorpha): molecular structure, in vitro expression, antimicrobial activity, and potential functions.a 409 bp full length defensin gene was cloned and sequenced based on an expressed sequence tag (est) obtained from a normalized zebra mussel (dreissena polymorpha) foot cdna library developed in our laboratory. the d. polymorpha defensin (dpd) gene encoded a peptide with 76 amino acid residues. the mature dpd contains 54 amino acids with a fully functional insect defensin a domain. homologue searching against genbank database suggested that this dpd was phylogenetically close to defensins from a ...201020537393
a versatile miniature bioreactor and its application to bioelectrochemistry studies.often, reproducible investigations on bio-microsystems essentially require a flexible but well-defined experimental setup, which in its features corresponds to a bioreactor. we therefore developed a miniature bioreactor with a volume in the range of a few millilitre that is assembled by alternate stacking of individual polycarbonate elements and silicone gaskets. all the necessary supply pipes are incorporated as bore holes or cavities within the individual elements. their combination allows for ...201020537883
recombinant production of omega-3 fatty acids in escherichia coli using a gene cluster isolated from shewanella baltica mac1.to isolate eicosapentaenoic acid (epa) and docosahexaenoic acid (dha) genes from shewanella baltica mac1 and to examine recombinant production of epa and dha in e. coli to investigate cost-effective, sustainable and convenient alternative sources for fish oils.201020666868
phenotypic characterization of shewanella oneidensis mr-1 under aerobic and anaerobic growth conditions by using fourier transform infrared spectroscopy and high-performance liquid chromatography analyses.shewanella oneidensis is able to conserve energy for growth by reducing a wide variety of terminal electron acceptors during anaerobic respiration, including several environmentally hazardous pollutants. this bacterium employs various electron transfer mechanisms for anaerobic respiration, including cell-bound reductases and secreted redox mediators. the aim of this study was to develop rapid tools for profiling the key metabolic changes associated with these different growth regimes and physiol ...201020675447
reservoir of antimicrobial resistance determinants associated with horizontal gene transfer in clinical isolates of the genus shewanella. 201020679508
electrochemical characterization of a single electricity-producing bacterial cell of shewanella by using optical tweezers. 201020680950
biodegradable gelatin-chitosan films incorporated with essential oils as antimicrobial agents for fish preservation.essential oils of clove (syzygium aromaticum l.), fennel (foeniculum vulgare miller), cypress (cupressus sempervirens l.), lavender (lavandula angustifolia), thyme (thymus vulgaris l.), herb-of-the-cross (verbena officinalis l.), pine (pinus sylvestris) and rosemary (rosmarinus officinalis) were tested for their antimicrobial activity on 18 genera of bacteria, which included some important food pathogen and spoilage bacteria. clove essential oil showed the highest inhibitory effect, followed by ...201020688230
mapping the subcellular proteome of shewanella oneidensis mr-1 using sarkosyl-based fractionation and lc-ms/ms protein identification.a simple and effective subcellular proteomic method for fractionation based on osmotic lysis, differential centrifugation, and sarkosyl solubilization was applied to the gram-negative bacterium shewanella oneidensis to gain insight into its subcellular architecture. global differences in bacterial cytoplasm, inner membrane, periplasm, and outer membrane protein fractions were observed by sds page and heme staining, and tryptic peptides were analyzed using high-resolution liquid chromatography-ta ...201020690604
the octahaem sira catalyses dissimilatory sulfite reduction in shewanella oneidensis mr-1.summary shewanella oneidensis mr-1 is a metal reducer that uses a large number of electron acceptors including thiosulfate, polysulfide and sulfite. the enzyme required for thiosulfate and polysulfide respiration has been recently identified, but the mechanisms of sulfite reduction remained unexplored. analysis of mr-1 cultures grown anaerobically with sulfite suggested that the dissimilatory sulfite reductase catalyses six-electron reduction of sulfite to sulfide. reduction of sulfite required ...201020695879
physiology and biochemistry of reduction of azo compounds by shewanella strains relevant to electron transport chain.azo dyes are toxic, highly persistent, and ubiquitously distributed in the environments. the large-scale production and application of azo dyes result in serious environmental pollution of water and sediments. bacterial azo reduction is an important process for removing this group of contaminants. recent advances in this area of research reveal that azo reduction by shewanella strains is coupled to the oxidation of electron donors and linked to the electron transport and energy conservation in t ...201020706834
to boost c-type cytochrome wire efficiency of electrogenic bacteria with fe3o4/au nanocomposites.a significant increase (ca. 22-fold) in the electricity generation due to a shewanella oneidensis mr-1 biofilm was observed in the presence of fe(3)o(4)/au nanocomposites.201020717577
reduction of graphene oxide via bacterial respiration.here we present that graphene oxide (go) can act as a terminal electron acceptor for heterotrophic, metal-reducing, and environmental bacteria. the conductance and physical characteristics of bacterially converted graphene (bcg) are comparable to other forms of chemically converted graphene (ccg). electron transfer to go is mediated by cytochromes mtra, mtrb, and mtrc/omca, while mutants lacking cyma, another cytochrome associated with extracellular electron transfer, retain the ability to reduc ...201020731460
a gold-sputtered carbon paper as an anode for improved electricity generation from a microbial fuel cell inoculated with shewanella oneidensis mr-1.gold is among the highly conductive and stable materials, which are ideal anodes for microbial fuel cells (mfcs). however, previous studies have shown that bare gold surface is recalcitrant for the colonization of some exoelectrogens, e.g., shewanella putrefacians. in this work, the problem regarding the poor bio-compatibility of gold as an anode material was sorted out through coupling it with carbon paper. a new composite anode material was fabricated through sputtering gold layer homogeneousl ...201020801013
an essential role for usha in processing of extracellular flavin electron shuttles by shewanella oneidensis.the facultative anaerobe shewanella oneidensis can reduce a number of insoluble extracellular metals. direct adsorption of cells to the metal surface is not necessary, and it has been shown that s. oneidensis releases low concentrations flavins, including riboflavin and flavin mononucleotide (fmn), into the surrounding medium to act as extracellular electron shuttles. however, the mechanism of flavin release by shewanella remains unknown. we have conducted a transposon mutagenesis screen to iden ...201020807196
label-free bacterial imaging with deep-uv-laser-induced native fluorescence.we introduce a near-real-time optical imaging method that works via the detection of the intrinsic fluorescence of life forms upon excitation by deep-uv (duv) illumination. a duv (<250-nm) source enables the detection of microbes in their native state on natural materials, avoiding background autofluorescence and without the need for fluorescent dyes or tags. we demonstrate that duv-laser-induced native fluorescence can detect bacteria on opaque surfaces at spatial scales ranging from tens of ce ...201020817797
geochip-based functional gene analysis of anodophilic communities in microbial electrolysis cells under different operational modes.a microbial electrolysis cell (mec) is a bioelectrochemical system that can produce hydrogen from acetate at high hydrogen recoveries, but the composition and structure of the microbial communities in this system have not been extensively studied. we used a high throughput metagenomics technology (geochip) to examine the microbial community functional structure in mecs initially operated under different conditions. we found that startup conditions had little or no effect on reactor performance i ...201020831218
genomic encyclopedia of sugar utilization pathways in the shewanella genus.carbohydrates are a primary source of carbon and energy for many bacteria. accurate projection of known carbohydrate catabolic pathways across diverse bacteria with complete genomes constitutes a substantial challenge due to frequent variations in components of these pathways. to address a practically and fundamentally important challenge of reconstruction of carbohydrate utilization machinery in any microorganism directly from its genomic sequence, we combined a subsystems-based comparative gen ...201020836887
probing electron transfer mechanisms in shewanella oneidensis mr-1 using a nanoelectrode platform and single-cell imaging.microbial fuel cells (mfcs) represent a promising approach for sustainable energy production as they generate electricity directly from metabolism of organic substrates without the need for catalysts. however, the mechanisms of electron transfer between microbes and electrodes, which could ultimately limit power extraction, remain controversial. here we demonstrate optically transparent nanoelectrodes as a platform to investigate extracellular electron transfer in shewanella oneidensis mr-1, whe ...201020837546
total and pathogenic vibrio parahaemolyticus in shrimp: fast and reliable quantification by real-time pcr.vibrio parahaemolyticus is found in aquatic environments and is the leading cause of gastroenteritis due to seafood consumption worldwide. we evaluated a quantitative real-time pcr (q-pcr) assay with hydrolysis probes, to determine whether this method could be used for the efficient counting of total, tdh and trh-positive v. parahaemolyticus in shrimps. we assessed the specificity of this assay, using 62 strains from 12 non target bacterial species of the vibrio, photobacterium, shewanella and a ...201020843573
shewanella indica sp. nov., isolated from the sediment of arabian sea.a gram-negative, facultatively anaerobic, rod shaped, motile by single polar flagellum, catalase- and oxidase-positive bacterium, designated strain kjw27t, was isolated from the marine sediment of karwar jetty, west coast of india. the strain was β-hemolytic, grows at 0-10 % (w/v) nacl, 10-45 °c and ph 6.5-10 with optimum growth at 2 % (w/v) nacl, 37 °c and ph 7.5. the major fatty acids were iso-c15:0 (22.2 %), c17:1 ω8c (21 %), summed feature 3 (comprising c16:1ω7c and/or c16:1 ω6c; 10.2 %), c1 ...201020851908
identification of in vivo hsp90-interacting proteins reveals modularity of hsp90 complexes is dependent on the environment in psychrophilic bacteria.heat shock protein 90 (hsp90) is a conserved molecular chaperone that functions as part of complexes in which different client proteins target it to diverse sets of substrates. in this paper, hsp90 complexes were investigated in γ-proteobacteria from mild (shewanella oneidensis) and cold environments (shewanella frigidimarina and psychrobacter frigidicola), to determine changes in hsp90 interactions with client proteins in response to the adaptation to cold environments. hsp90 participation in c ...201020890740
evidence for the horizontal transfer of an unusual capsular polysaccharide biosynthesis locus in marine bacteria.the most intensely studied of the vibrio vulnificus virulence factors is the capsular polysaccharide (cps). all virulent strains produce copious amounts of cps. acapsular strains are avirulent. the structure of the cps from the clinical isolate atcc 27562 is unusual. it is serine modified and contains, surprisingly, n-acetylmuramic acid. we identified the complete 25-kb cps biosynthesis locus from atcc 27562. it contained 21 open reading frames and was allelic to o-antigen biosynthesis loci. two ...201020921143
redox-responsive switching in bacterial respiratory pathways involving extracellular electron transfer. 201020936647
electrical transport along bacterial nanowires from shewanella oneidensis mr-1.bacterial nanowires are extracellular appendages that have been suggested as pathways for electron transport in phylogenetically diverse microorganisms, including dissimilatory metal-reducing bacteria and photosynthetic cyanobacteria. however, there has been no evidence presented to demonstrate electron transport along the length of bacterial nanowires. here we report electron transport measurements along individually addressed bacterial nanowires derived from electron-acceptor-limited cultures ...201020937892
solar-driven microbial photoelectrochemical cells with a nanowire photocathode.we report a self-biased, solar-driven microbial photoelectrochemical cell (solar mpc) that can produce sustainable energy through coupling the microbial catalysis of biodegradable organic matter with solar energy conversion. the solar mpc consists of a p-type cuprous oxide nanowire-arrayed photocathode and an electricigen (shewanella oneidensis mr-1)-colonizing anode, which can harvest solar energy and bioenergy, respectively. the photocathode and bioanode are interfaced by matching the redox po ...201020939571
structures of the first representatives of pfam family pf06938 (duf1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction.the crystal structures of spo0140 and sbal_2486 were determined using the semiautomated high-throughput pipeline of the joint center for structural genomics (jcsg) as part of the nigms protein structure initiative (psi). the structures revealed a conserved core with domain duplication and a superficial similarity of the c-terminal domain to pleckstrin homology-like folds. the conservation of the domain interface indicates a potential binding site that is likely to involve a nucleotide-based liga ...201020944214
open and closed conformations of two spoiiaa-like proteins (yp_749275.1 and yp_001095227.1) provide insights into membrane association and ligand binding.the crystal structures of the proteins encoded by the yp_749275.1 and yp_001095227.1 genes from shewanella frigidimarina and s. loihica, respectively, have been determined at 1.8 and 2.25 å resolution, respectively. these proteins are members of a novel family of bacterial proteins that adopt the α/β spoiiaa-like fold found in stas and cral-trio domains. despite sharing 54% sequence identity, these two proteins adopt distinct conformations arising from different dispositions of their α2 and α3 h ...201020944218
the tricarboxylic acid cycle in shewanella oneidensis is independent of fur and ryhb control.it is well established in e. coli and vibrio cholerae that strains harboring mutations in the ferric uptake regulator gene (fur) are unable to utilize tricarboxylic acid (tca) compounds, due to the down-regulation of key tca cycle enzymes, such as acna and sdhabcd. this down-regulation is mediated by a fur-regulated small regulatory rna named ryhb. it is unclear in the γ-proteobacterium s. oneidensis whether tca is also regulated by fur and ryhb.201020950482
effects of engineered cerium oxide nanoparticles on bacterial growth and viability.interest in engineered nanostructures has risen in recent years due to their use in energy conservation strategies and biomedicine. to ensure prudent development and use of nanomaterials, the fate and effects of such engineered structures on the environment should be understood. interactions of nanomaterials with environmental microorganisms are inevitable, but the general consequences of such interactions remain unclear, due to a lack of standard methods for assessing such interactions. therefo ...201020952651
engineering of a synthetic electron conduit in living cells.engineering efficient, directional electronic communication between living and nonliving systems has the potential to combine the unique characteristics of both materials for advanced biotechnological applications. however, the cell membrane is designed by nature to be an insulator, restricting the flow of charged species; therefore, introducing a biocompatible pathway for transferring electrons across the membrane without disrupting the cell is a significant challenge. here we describe a geneti ...201020956333
phage-induced lysis enhances biofilm formation in shewanella oneidensis mr-1.shewanella oneidensis mr-1 is capable of forming highly structured surface-attached communities. by dnase i treatment, we demonstrated that extracellular dna (edna) serves as a structural component in all stages of biofilm formation under static and hydrodynamic conditions. we determined whether edna is released through cell lysis mediated by the three prophages lambdaso, muso1 and muso2 that are harbored in the genome of s. oneidensis mr-1. mutant analyses and infection studies revealed that al ...201020962878
culturable rhodobacter and shewanella species are abundant in estuarine turbidity maxima of the columbia river.measurements of dissolved, ascorbate-reducible and total mn by icp-oes revealed significantly higher concentrations during estuarine turbidity maxima (etm) events, compared with non-events in the columbia river. most probable number (mpn) counts of mn-oxidizing or mn-reducing heterotrophs were not statistically different from that of other heterotrophs (10³ -10⁴ cells ml⁻¹) when grown in defined media, but counts of mn oxidizers were significantly lower in nutrient-rich medium (13 cells ml⁻¹). m ...201020977571
biogenic formation and growth of uraninite (uo₂).biogenic uo₂ (uraninite) nanocrystals may be formed as a product of a microbial reduction process in uranium-enriched environments near the earth's surface. we investigated the size, nanometer-scale structure, and aggregation state of uo₂ formed by iron-reducing bacterium, shewanella putrefaciens cn32, from a uranium-rich solution. characterization of biogenic uo₂ precipitates by high-resolution transmission electron microscopy (hrtem) revealed that the uo₂ nanoparticles formed were highly aggre ...201020979351
shewanella oneidensis in a lactate-fed pure-culture and a glucose-fed co-culture with lactococcus lactis with an electrode as electron acceptor.bioelectrochemical systems (bess) employing mixed microbial communities as biocatalysts are gaining importance as potential renewable energy, bioremediation, or biosensing devices. while we are beginning to understand how individual microbial species interact with an electrode as electron donor, little is known about the interactions between different microbial species in a community: sugar fermenting bacteria can interact with current producing microbes in a fashion that is either neutral, posi ...201021036604
biological characteristics and pathogenicity of a highly pathogenic shewanella marisflavi infecting sea cucumber, apostichopus japonicus.shewanella marisflavi isolate ap629 is described as a novel pathogen of sea cucumber. the ld(50) values (14 days) in sea cucumber, mice and swordtail fish were 3.89 × 10(6) , 6.80 × 10(4) and 4.85 × 10(4) cfu g(-1) body weight, respectively. studies on s. marisflavi were conducted, including morphology, physiological and biochemical characteristics, haemolysis, whole-cell protein and 16s rdna gene sequence. colonies of s. marisflavi appeared faint red on marine agar and green on thiosulphate-cit ...201021039606
cloning, expression, purification and crystallization of dihydrodipicolinate synthase from the psychrophile shewanella benthica.dihydrodipicolinate synthase (dhdps) is an oligomeric enzyme that catalyzes the first committed step of the lysine-biosynthesis pathway in plants and bacteria, which yields essential building blocks for cell-wall and protein synthesis. dhdps is therefore of interest to drug-discovery research as well as to studies that probe the importance of quaternary structure to protein function, stability and dynamics. accordingly, dhdps from the psychrophilic (cold-dwelling) organism shewanella benthica (s ...201021045309
viability and metal reduction of shewanella oneidensis mr-1 under co2 stress: implications for ecological effects of co2 leakage from geologic co2 sequestration.to study potential ecological impacts of co(2) leakage to shallow groundwater and soil/sediments from geologic co(2) sequestration (gcs) sites, this work investigated the viability and metal reduction of shewanella oneidensis mr-1 under co(2) stress. while mr-1 could grow under high-pressure nitrogen gas (500 psi), the mix of 1% co(2) with n(2) at total pressures of 15 or 150 psi significantly suppressed the growth of mr-1, compared to the n(2) control. when co(2) partial pressures were over 15 ...201021058700
enabling unbalanced fermentations by using engineered electrode-interfaced bacteria.cellular metabolism is a series of tightly linked oxidations and reductions that must be balanced. recycling of intracellular electron carriers during fermentation often requires substrate conversion to undesired products, while respiration demands constant addition of electron acceptors. the use of electrode-based electron acceptors to balance biotransformations may overcome these constraints. to test this hypothesis, the metal-reducing bacterium shewanella oneidensis was engineered to stoichio ...201021060736
non-uraninite products of microbial u(vi) reduction.a promising remediation approach to mitigate subsurface uranium contamination is the stimulation of indigenous bacteria to reduce mobile u(vi) to sparingly soluble u(iv). the product of microbial uranium reduction is often reported as the mineral uraninite. here, we show that the end products of uranium reduction by several environmentally relevant bacteria (gram-positive and gram-negative) and their spores include a variety of u(iv) species other than uraninite. u(iv) products were prepared in ...201021069950
the quorum-quenching n-acyl homoserine lactone acylase pvdq is an ntn-hydrolase with an unusual substrate-binding pocket.in many gram-negative pathogens, their virulent behavior is regulated by quorum sensing, in which diffusible signals such as n-acyl homoserine lactones (ahls) act as chemical messaging compounds. enzymatic degradation of these diffusible signals by, e.g., lactonases or amidohydrolases abolishes ahl regulated virulence, a process known as quorum quenching. here we report the first crystal structure of an ahl amidohydrolase, the ahl acylase pvdq from pseudomonas aeruginosa. pvdq has a typical alph ...201020080736
shewanella oneidensis mr-1 mutants selected for their inability to produce soluble organic-fe(iii) complexes are unable to respire fe(iii) as anaerobic electron acceptor.recent voltammetric analyses indicate that shewanella putrefaciens strain 200 produces soluble organic-fe(iii) complexes during anaerobic respiration of sparingly soluble fe(iii) oxides. results of the present study expand the range of shewanella species capable of producing soluble organic-fe(iii) complexes to include shewanella oneidensis mr-1. soluble organic-fe(iii) was produced by s. oneidensis cultures incubated anaerobically with fe(iii) oxides, or with fe(iii) oxides and the alternate el ...201020089045
molecular basis for directional electron transfer.biological macromolecules involved in electron transfer reactions display chains of closely packed redox cofactors when long distances must be bridged. this is a consequence of the need to maintain a rate of transfer compatible with metabolic activity in the framework of the exponential decay of electron tunneling with distance. in this work intermolecular electron transfer was studied in kinetic experiments performed with the small tetraheme cytochrome from shewanella oneidensis mr-1 and from s ...201020089857
comparative eco-toxicities of nano-zno particles under aquatic and aerosol exposure modes.the antimicrobial activity of zno nanoparticles (nps) was investigated under aquatic and aerosol exposure modes. zno nps in aquatic media aggregated to micrometer-sized particles and did not interact with microorganisms effectively. hence, the inhibition of microbial growth by nano-zno nps (e.g., mycobacterium smegmatis and cyanothece 51142) in aquatic media was mainly attributable to dissolved zinc species. shewanella oneidensis mr-1 and escherichia coli were able to produce large amounts of ex ...201020102184
bio-electro-fenton process driven by microbial fuel cell for wastewater treatment.in this study, we proposed a new concept of utilizing the biological electrons produced from a microbial fuel cell (mfc) to power an e-fenton process to treat wastewater at neutral ph as a bioelectro-fenton (bio-e-fenton) process. this process can be achieved in a dual-chamber mfc from which electrons were generated via the catalyzation of shewanella decolorationis s12 in its anaerobic anode chamber and transferred to its aerated cathode chamber equipped with a carbon nanotube (cnt)/gamma-feooh ...201020108963
membrane vesicles: a common feature in the extracellular matter of cold-adapted antarctic bacteria.many gram-negative, cold-adapted bacteria from the antarctic environment produce large amounts of extracellular matter, which has potential biotechnology applications. we examined the ultrastructure of extracellular matter from five antarctic bacteria (shewanella livingstonensis nf22(t), shewanella vesiculosa m7(t), pseudoalteromonas sp. m4.2, psychrobacter fozii nf23(t), and marinobacter guineae m3b(t)) by transmission electron microscopy after high-pressure freezing and freeze substitution. al ...201020127086
microbial population dynamics during startup of a full-scale anaerobic digester treating industrial food waste in kyoto eco-energy project.the microbial community in a full-scale anaerobic digester (2300m3) treating industrial food waste in the kyoto eco-energy project was analyzed using terminal restriction fragment length polymorphism for eubacterial and archaeal 16s rrna genes. both thermophilic and mesophilic sludge of treated swine waste were seeded to the digestion tank. during the 150-day startup period, coffee grounds as a main food waste, along with potato, kelp and boiled beans, tofu, bean curd lees, and deep-fried bean c ...201020129780
adhesion of shewanella oneidensis mr-1 to iron (oxy)(hydr)oxides: microcolony formation and isotherm.the adhesion of dissimilatory metal reducing bacteria (dmrb) to iron (oxy)(hydr)oxides may play an important role in their respiration on ferric iron-containing minerals, but few quantitative surface cell density measurements have been made thus far. we used confocal microscopy to examine the adhesion of a common dmrb species, shewanella oneidensis mr-1, onto iron (oxy)(hydr)oxide particulate-coated glass slides across a broad range of bulk (i.e., solution phase) cell densities from 10(5) cells/ ...201020131792
biological iron-monosulfide production for efficient electricity harvesting from a deep-sea metal-reducing bacterium. 201020146276
xafs investigation of the interactions of u(vi) with secondary mineralization products from the bioreduction of fe(iii) oxides.biogenic fe(ii) phases (magnetite, green rust, siderite, vivianite, etc.) provide a reservoir of reducing capacity in many subsurface environments that may contribute to the reduction of contaminants such as u(vi). we have examined the uptake and reduction of u(vi) in the presence of biogenic green rust (biogr), magnetite (biomag), and siderite (biosid) formed during the reduction of fe(iii) oxides by shewanella putrefaciens cn32. within 48 h, total solution-phase u(vi) concentrations decreased ...201020146462
phylogenetic diversity and antimicrobial activities of bryozoan-associated bacteria isolated from mediterranean and baltic sea habitats.to date, only a small number of investigations covering microbe-bryozoa associations have been carried out. most of them have focused on a few bryozoan species and none have covered the antibacterial activities of associated bacteria. in the current study, the proportion and phylogenetic classification of bryozoan-associated bacteria with antimicrobial properties were investigated. twenty-one specimens of 14 different bryozoan species were collected from several sites in the baltic and the medit ...201020153592
the impact of bacterial strain on the products of dissimilatory iron reduction.three bacterial strains from the genus shewanella were used to examine the influence of specific bacteria on the products of dissimilatory iron reduction. strains cn32, mr-4 and w3-18-1 were incubated with hfo (hydrous ferric oxide) as the terminal electron acceptor and lactate as the organic carbon and energy source. mineral products of iron reduction were analyzed using x-ray powder diffraction, electron microscopy, coulometry and susceptometry. under identical nutrient loadings, iron reductio ...201020161499
colour removal from aqueous solutions of metal-complex azo dyes using bacterial cells of shewanella strain j18 143.the decoloration treatment of textile dye effluents through biodegradation, using bacterial cells, has been studied as a possible means of solving some of the problems that are associated with the pollution of water sources by colorants. in this paper, the use of whole bacterial cells of shewanella j18 143 for the reduction of aqueous solutions of selected mono-azo, metal-complex dyes, namely irgalan grey gln, irgalan black rbln and irgalan blue 3gl, was investigated. the effects of temperature, ...201020167478
first case of human spondylodiscitis due to shewanella algae.we present the first case of human spondylodiscitis due to shewanella algae. our patient did not have any predisposing factors. the portal of entry was probably a cutaneous lesion on the leg, exposed to seawater. bacteria were isolated in pure culture from a needle biopsy specimen of the vertebral disk. automated identification systems identified the organism as shewanella putrefaciens. however, molecular biology identified it as s. algae. treatment with ceftriaxone and amikacin, then ciprofloxa ...201020171131
shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation.shewanella halifaxensis and shewanella sediminis were among a few aquatic gamma-proteobacteria that were psychrophiles and the first anaerobic bacteria that degraded hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx). although many mesophilic or psychrophilic strains of shewanella and gamma-proteobacteria were sequenced for their genomes, the genomic evolution pathways for temperature adaptation were poorly understood. on the other hand, the genes responsible for anaerobic rdx mineralization pathways ...201020174598
siderophores are not involved in fe(iii) solubilization during anaerobic fe(iii) respiration by shewanella oneidensis mr-1.shewanella oneidensis mr-1 respires a wide range of anaerobic electron acceptors, including sparingly soluble fe(iii) oxides. in the present study, s. oneidensis was found to produce fe(iii)-solubilizing organic ligands during anaerobic fe(iii) oxide respiration, a respiratory strategy postulated to destabilize fe(iii) and produce more readily reducible soluble organic fe(iii). in-frame gene deletion mutagenesis, siderophore detection assays, and voltammetric techniques were combined to determin ...201020190086
enhanced reductive dechlorination of ddt in an anaerobic system of dissimilatory iron-reducing bacteria and iron oxide.the transformation of ddt was studied in an anaerobic system of dissimilatory iron-reducing bacteria (shewanella decolorationis s12) and iron oxide (alpha-feooh). the results showed that s. decolorationis could reduce ddt into ddd, and ddt transformation rate was accelerated by the presence of alpha-feooh. ddd was observed as the primary transformation product, which was demonstrated to be transformed in the abiotic system of fe(2+)+alpha-feooh and the system of dirb+alpha-feooh. the intermediat ...201020031285
the 285 kda bap/rtx hybrid cell surface protein (so4317) of shewanella oneidensis mr-1 is a key mediator of biofilm formation.shewanella oneidensis, a gram-negative bacterium with unusual respiratory versatility, is found in soil and sediment environments, and sporadically as an opportunistic pathogen in humans and aquatic animals. the ability to form biofilms is a critical factor in the environmental spread and survival of this bacterium. we subjected s. oneidensis mr-1 to random transposon insertion mutagenesis to identify genes contributing to the ability of the organism to form biofilms on polystyrene surfaces. fol ...201020034561
possible biosynthetic pathways for all cis-3,6,9,12,15,19,22, 25,28-hentriacontanonaene in bacteria.a very long chain polyunsaturated hydrocarbon, hentriacontanonaene (c31:9), was detected in an eicosapentaenoic acid (epa)-producing marine bacterium, which was isolated from the mid-latitude seashore of hokkaido, japan, and was tentatively identified as mesophilic shewanella sp. strain osh08 from 16s rrna gene sequencing. the geometry and position of the double bonds in this compound were determined physicochemically to be all cis at positions 3, 6, 9, 12, 15, 19, 22, 25, and 28. although c31:9 ...201020037794
development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities.high-density functional gene arrays have become a powerful tool for environmental microbial detection and characterization. however, microarray data normalization and comparison for this type of microarray remain a challenge in environmental microbiology studies because some commonly used normalization methods (e.g., genomic dna) for the study of pure cultures are not applicable. in this study, we developed a common oligonucleotide reference standard (cors) method to address this problem. a uniq ...201020038701
hydrous manganese oxide doped gel probe sampler for measuring in situ reductive dissolution rates. 1. laboratory development.reductive dissolution of redox-sensitive minerals such as manganese (mn) oxides in natural sediments is an important mechanism for trace element mobilization into groundwater. a gel probe sampler has been constructed to study in situ reductive dissolution of mn oxides. the gel consists of a polyacrylamide polymer matrix doped with hydrous mn oxide (hmo). gel slabs are mounted into a probe, which is designed to be inserted into the sediments. the amount of mn released from the gel by reductive di ...201020039731
outer membrane-associated serine protease involved in adhesion of shewanella oneidensis to fe(iii) oxides.the facultative anaerobe shewanella oneidensis mr-1 respires a variety of anaerobic electron acceptors, including insoluble fe(iii) oxides. s. oneidensis employs a number of novel strategies for respiration of insoluble fe(iii) oxides, including localization of respiratory proteins to the cell outer membrane (om). the molecular mechanism by which s. oneidensis adheres to and respires fe(iii) oxides, however, remains poorly understood. in the present study, whole cell fractionation and maldi-tof- ...201020039735
cloning and characterization of dihydrofolate reductases from deep-sea bacteria.enzymes from organisms living in deep-sea are thought to have characteristic pressure-adaptation mechanisms in structure and function. to better understand these mechanisms in dihydrofolate reductase (dhfr), an essential enzyme in living cells, we cloned, overexpressed and purified four new dhfrs from the deep-sea bacteria shewanella violacea (svdhfr), photobacterium profundum (ppdhfr), moritella yayanosii (mydhfr) and moritella japonica (mjdhfr), and compared their structure and function with t ...201020040594
towards structural studies of the old yellow enzyme homologue sye4 from shewanella oneidensis and its complexes at atomic resolution.shewanella oneidensis is an environmentally versatile gram-negative gamma-proteobacterium that is endowed with an unusually large proteome of redox proteins. of the four old yellow enzyme (oye) homologues found in s. oneidensis, sye4 is the homologue most implicated in resistance to oxidative stress. sye4 was recombinantly expressed in escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. the crystals belonged to the orthorhombic space group p2(1)2(1)2(1) an ...201020057079
crystal structure of cold-active alkaline phosphatase from the psychrophile shewanella sp.the crystal structure of a cold-active alkaline phosphatase from a psychrophile, shewanella sp. (scap), was solved at 2.2 a. a refined model showed a homodimer with six metal-ligand sites. the arrangement of the catalytic residues resembled those of alkaline phosphatases (aps), suggesting that the reaction mechanism of scap was fundamentally identical to those of other aps. scap had two distinct structural features: (i) a loop with arg122 that bound to the phosphate moiety of the substrate suffe ...201020057143
[biosynthesis and function of long-chain polyunsaturated fatty acids in cold-adapted bacteria]. 201020058713
partial degradation mechanisms of malachite green and methyl violet b by shewanella decolorationis ntou1 under anaerobic conditions.this work demonstrated that shewanella decolorationis ntou1 decolorized 200 mg l(-1) of crystal violet, malachite green, or methyl violet b within 2-11h under anaerobic conditions at 35 degrees c. the initial color removal rate of malachite green was highest, while that of methyl violet was lowest. gc/ms analyses of the intermediate compounds produced during and after decolorization of malachite green and methyl violet b suggested that biodegradation of these dyes involved reduction to leuco for ...201020060225
comparative study of the gating motif and c-type inactivation in prokaryotic voltage-gated sodium channels.prokaryotic voltage-gated sodium channels (na(v)s) are homotetramers and are thought to inactivate through a single mechanism, named c-type inactivation. here we report the voltage dependence and inactivation rate of the nachbac channel from bacillus halodurans, the first identified prokaryotic na(v), as well as of three new homologues cloned from bacillus licheniformis (na(v)bacl), shewanella putrefaciens (na(v)shep), and roseobacter denitrificans (na(v)rosd). we found that, although activated ...201019959480
the periplasmic nitrate reductase in shewanella: the resolution, distribution and functional implications of two nap isoforms, napedabc and napdaghb.in the bacterial periplasm, the reduction of nitrate to nitrite is catalysed by a periplasmic nitrate reductase (nap) system, which is a species-dependent assembly of protein subunits encoded by the nap operon. the reduction of nitrate catalysed by nap takes place in the 90 kda napa subunit, which contains a mo-bis-molybdopterin guanine dinucleotide cofactor and one [4fe-4s] iron-sulfur cluster. a review of the nap operons in the genomes of 19 strains of shewanella shows that most genomes contai ...201019959582
rust-dissolving bugs may chow down with variety of utensils.s. oneidensis mutant impaired in adhering to an iron oxide can still reduce it.201019994884
aerated shewanella oneidensis in continuously fed bioelectrochemical systems for power and hydrogen production.we studied the effects of aeration of shewanella oneidensis on potentiostatic current production, hydrogen production in a microbial electrolysis cell, and electric power generation in a microbial fuel cell (mfc). the potentiostatic performance of aerated s. oneidensis was considerably enhanced to a maximum current density of 0.45 a/m(2) or 80.3 a/m(3) (mean: 0.34 a/m(2), 57.2 a/m(3)) compared to anaerobically grown cultures. biocatalyzed hydrogen production rates with aerated s. oneidensis were ...201019998276
role of outer-membrane cytochromes mtrc and omca in the biomineralization of ferrihydrite by shewanella oneidensis mr-1.in an effort to improve the understanding of electron transfer mechanisms at the microbe-mineral interface, shewanella oneidensis mr-1 mutants with in-frame deletions of outer-membrane cytochromes (omcs), mtrc and omca, were characterized for the ability to reduce ferrihydrite (fh) using a suite of microscopic, spectroscopic, and biochemical techniques. analysis of purified recombinant proteins demonstrated that both cytochromes undergo rapid electron exchange with fh in vitro with mtrc displayi ...201020002197
impact of silver(i) on the metabolism of shewanella oneidensis.anaerobic cultures of shewanella oneidensis mr-1 reduced toxic ag(i), forming nanoparticles of elemental ag(0), as confirmed by x-ray diffraction analyses. the addition of 1 to 50 microm ag(i) had a limited impact on growth, while 100 microm ag(i) reduced both the doubling time and cell yields. at this higher ag(i) concentration transmission electron microscopy showed the accumulation of elemental silver particles within the cell, while at lower concentrations the metal was exclusively reduced a ...201020008067
a large-scale epidemiological study to identify bacteria pathogenic to pacific oyster crassostrea gigas and correlation between virulence and metalloprotease-like activity.a 4-year bacteriological survey (2003-2007) of four molluscs cultivated in france and faced with mortality episodes was performed by the french shellfish pathology network. the more abundant bacteria isolated during 92 mortality episodes, occurring mainly in pacific oyster crassostrea gigas, were identified by genotyping methods. it allowed us both to confirm the representativeness of vibrio splendidus and vibrio aestuarianus bacterial strains and to identify both a large number of vibrio harvey ...201020012275
two different electron transfer pathways may involve in azoreduction in shewanella decolorationis s12.electron transfer pathways for azoreduction by s. decolorationis s12 were studied using a mutant s12-22 which had a transposon insertion in ccma. the results imply that there are two different pathways for electron transport to azo bonds. the colony of s12-22 was whitish and incapable of producing mature c-type cytochromes whose alpha-peak was at 553 nm in the wild type s12. the mutant s12-22 could not use formate as the sole electron donor for azoreduction either in vivo or in vitro, but intact ...201020012540
electrokinesis is a microbial behavior that requires extracellular electron transport.we report a previously undescribed bacterial behavior termed electrokinesis. this behavior was initially observed as a dramatic increase in cell swimming speed during reduction of solid mno(2) particles by the dissimilatory metal-reducing bacterium shewanella oneidensis mr-1. the same behavioral response was observed when cells were exposed to small positive applied potentials at the working electrode of a microelectrochemical cell and could be tuned by adjusting the potential on the working ele ...201020018675
late ventriculoperitoneal shunt infection caused by shewanella algae.we present a case of ventriculitis and peritonitis in a child with ventriculoperitoneal shunt, which occurred 5 years after the surgery. the infection developed after contact with seawater and began as otitis. for the first time, shewanella algae, a marine microorganism, was identified as the cause of ventriculoperitoneal shunt infection.201019952978
bioreduction of nitrobenzene, natural organic matter, and hematite by shewanella putrefaciens cn32.we examined the reduction of nitrobenzene by shewanella putrefaciens cn32 in the presence of natural organic matter (nom) and hematite. bioreduction experiments were conducted with combinations and varied concentrations of nitrobenzene, soil humic acid, georgetown nom, hematite, and cn32. abiotic experiments were conducted to quantify nitrobenzene reduction by biogenic fe(ii) and by bioreduced noms. we show that s. putrefaciens cn32 can directly reduce nitrobenzene. both noms enhanced nitrobenze ...201019957913
bacterial responses to cu-doped tio(2) nanoparticles.the toxicity of cu-doped tio(2) nanoparticles (nps, 20nm), synthesized by a flame aerosol reactor, to mycobacterium smegmatis and shewanella oneidensis mr-1, is the primary focus of this study. both doped and non-doped tio(2) nps (20nm) tended to agglomerate in the medium solution, and therefore did not penetrate into the cell and damage cellular structures. tio(2) particles (<100mg/l) did not apparently interfere with the growth of the two species in aqueous cultures. cu-doped tio(2) nps (20mg/ ...201019931887
microbesonline: an integrated portal for comparative and functional genomics.since 2003, microbesonline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. the portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as escherichia coli and saccharomyces cerevisiae to environmental microbes such as desulfovibrio vulgaris and shewanella oneidensis. to assist in annotating genes and in reconstr ...201019906701
combined effects of salting, oregano oil and vacuum-packaging on the shelf-life of refrigerated trout fillets.the present study evaluated the effect of salt, oregano essential oil (eo) and packaging on fresh rainbow trout fillets during storage at 4 degrees c. treatments included the following: a1 (control samples, unsalted: air packaged), a2 (salted: air packaged), vp1 (salted, vacuum packaged), vp2 (salted, vacuum packaged with added oregano eo 0.2% v/wt), and vp3 salted, vacuum packaged with added oregano eo 0.4% v/wt). lactic acid bacteria (lab) (to a greater extent), followed by h(2)s-producing bac ...201019913701
shewanella corallii sp. nov., a marine bacterium isolated from a red sea coral.a marine bacterial strain, designated fav-2-10-05(t), was isolated from the mucus layer of a coral of the genus favia, collected from the coral reef in the gulf of eilat, israel (29.5 ° n 34.9 ° e). on the basis of 16s rrna gene sequence comparisons, strain fav-2-10-05(t) was affiliated with the family shewanellaceae. the closest relatives of strain fav-2-10-05(t) were shewanella marisflavi sw-117(t) (96.0 % 16s rrna gene sequence similarity) and shewanella haliotis dw-1(t) (95.9 %). strain fav- ...201019915103
molecular analysis of intestinal microbiota of rainbow trout (oncorhynchus mykiss).the aim of this study was to evaluate different molecular tools based on the 16s rrna gene, internal transcribed spacer, and the rpob gene to examine the bacterial populations present in juvenile rainbow trout intestines. dna was extracted from both pooled intestinal samples and bacterial strains. genes were pcr-amplified and analysed using both temporal temperature gradient gel electrophoresis (ttge) and restriction fragment length polymorphism methods. because of the high cultivability of the ...201019780831
power production in mfcs inoculated with shewanella oneidensis mr-1 or mixed cultures.power densities and oxidation-reduction potentials (orps) of mfcs containing a pure culture of shewanella oneidensis mr-1 were compared to mixed cultures (wastewater inoculum) in cube shaped, 1-, 2-, and 3-bottle batch-fed mfc reactor configurations. the reactor architecture influenced the relative power produced by the different inocula, with the mixed culture generating 68-480% more power than mr-1 in each mfc configuration. the mixed culture produced the maximum power density of 858 +/- 9 mw ...201019787640
electricity generation at high ionic strength in microbial fuel cell by a newly isolated shewanella marisflavi ep1.increasing the ionic strength of the electrolyte in a microbial fuel cell (mfc) can remarkably increase power output due to the reduction of internal resistance. however, only a few bacterial strains are capable of producing electricity at a very high ionic strength. in this report, we demonstrate a newly isolated strain ep1, belonging to shewanella marisflavi based on polyphasic analysis, which could reduce fe(iii) and generate power at a high ionic strength of up to 1,488 mm (8% nacl) using la ...201019789866
regprecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.the regprecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. a significant number of high-quality inferences of transcriptional regulatory interactions have been already accumulated for diverse taxonomic groups of bacteria. the reconstructed regulons include transcription factors, their cognate dna mot ...201019884135
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