| 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 |
| surface-enhanced raman scattering from intracellular and extracellular bacterial locations. | while surface-enhanced raman scattering (sers) can increase the raman cross-section by 4-6 orders of magnitude, for sers to be effective it is necessary for the analyte to be either chemically bonded or within close proximity to the metal surface used. therefore most studies investigating the biochemical constituents of microorganisms have introduced an external supply of gold or silver nanoparticles. as a consequence, the study of bacteria by sers has to date been focused almost exclusively on ... | 2008 | 18661956 |
| cold adaptation of eicosapentaenoic acid-less mutant of shewanella livingstonensis ac10 involving uptake and remodeling of synthetic phospholipids containing various polyunsaturated fatty acids. | an antarctic psychrotrophic bacterium, shewanella livingstonensis ac10, produces cis-5,8,11,14,17-eicosapentaenoic acid (epa), a long-chain polyunsaturated fatty acid (lpufa), as a component of membrane phospholipids at low temperatures. the epa-less mutant generated by disruption of the epa synthesis gene becomes cold-sensitive. we studied whether the cold sensitivity could be suppressed by supplementation of various lpufas. the epa-less mutant was cultured at 6 degrees c in the presence of syn ... | 2008 | 18668196 |
| shewanella basaltis sp. nov., a marine bacterium isolated from black sand. | a gram-negative, motile, rod-shaped bacterium was isolated from black sand collected at soesoggak, jeju island, korea. the strain, designated j83t, was able to grow in the presence of 5 % nacl, at temperatures of 4-45 degrees c and over the ph range 5.5-9.5. the isolate reduced nitrate to nitrite and was positive for oxidase, catalase, alkaline phosphatase and leucine arylamidase. strain j83(t) utilized malate, maltose, mannitol and glucose as sole sources of carbon. phylogenetic analysis based ... | 2008 | 18676478 |
| confounding impacts of iron reduction on arsenic retention. | a transition from oxidizing to reducing conditions has long been implicated to increase aqueous as concentrations, for which reductive dissolution of iron (hydr)oxides is commonly implicated as the primary culprit. confounding our understanding of processes controlling as retention, however, is that reductive transformation of ferrihydrite has recently been shown to promote as retention rather than release. to resolve the role iron phases have in regulating arsenic concentrations, here we examin ... | 2008 | 18678005 |
| 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 |
| spectral dictionaries: integrating de novo peptide sequencing with database search of tandem mass spectra. | database search tools identify peptides by matching tandem mass spectra against a protein database. we study an alternative approach when all plausible de novo interpretations of a spectrum (spectral dictionary) are generated and then quickly matched against the database. we present a new ms-dictionary algorithm for efficiently generating spectral dictionaries and demonstrate that ms-dictionary can identify spectra that are missed in the database search. we argue that ms-dictionary enables prote ... | 2009 | 18703573 |
| 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 |
| enzymatic assay of marine bacterial phosphatases by capillary electrophoresis with laser-induced fluorescence detection. | microbial ectoenzyme activities in aquatic environments are important determinants of polymer hydrolysis and indicators of the state of microbial carbon, nitrogen, and phosphorus nutrition. marine ectoenzymes are found on the cell surface or in the periplasmic space of gram-negative heterotrophic bacteria. phosphatases, which remove phosphate groups from substrates, are one example of an ectoenzyme. enzyme assays based on-capillary electrophoresis (ce) take advantage of ce's high-efficiency sepa ... | 2008 | 18726971 |
| 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 |
| preliminary x-ray diffraction analysis of yqjh from escherichia coli: a putative cytoplasmic ferri-siderophore reductase. | yqjh is a cytoplasmic fad-containing protein from escherichia coli; based on homology to viub of vibrio cholerae, it potentially acts as a ferri-siderophore reductase. this work describes its overexpression, purification, crystallization and structure solution at 3.0 a resolution. yqjh shares high sequence similarity with a number of known siderophore-interacting proteins and its structure was solved by molecular replacement using the siderophore-interacting protein from shewanella putrefaciens ... | 2008 | 18765906 |
| 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 |
| gammaproteobacteria as a possible source of eicosapentaenoic acid in anoxic intertidal sediments. | eicosapentaenoic acid (epa; n-20:5omega3) was found to be a constituent of phospholipids in three mesophilic strains of gammaproteobacteria, which were isolated from anoxic most probable number series prepared with sediments from an intertidal flat of the german north sea coast. their partial 16s rrna gene sequences identified the isolates as close relatives of shewanella colwelliana, vibrio splendidus, and photobacterium lipolyticum. so far, eicosapentaenoic acid has mainly been reported to occ ... | 2009 | 18777187 |
| 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 |
| molecular analysis of microbiota along the digestive tract of juvenile atlantic salmon (salmo salar l.). | dominant bacterial microbiota of the gut of juvenile farmed atlantic salmon was investigated using a combination of molecular approaches. bacterial community composition from the stomach, the pyloric caeca, and the intestine was assessed by extracting dna directly from each gut compartment. temporal temperature gradient gel electrophoresis (ttge) analysis of 16s ribosomal dna (rdna) amplicons showed very similar bacterial compositions throughout the digestive tract. band sequencing revealed a na ... | 2009 | 18797955 |
| 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 |
| study on the synergic effect of natural compounds on the microbial quality decay of packed fish hamburger. | the effectiveness of natural compounds in slowing down the microbial quality decay of refrigerated fish hamburger is addressed in this study. in particular, the control of the microbiological spoilage by combined use of three antimicrobials, and the determination of their optimal composition to extend the fish hamburger microbiological stability limit (mal) are the main objectives of this work. thymol, grapefruit seed extract (gfse) and lemon extract were tested for monitoring the cell growth of ... | 2008 | 18804302 |
| acclimated biomass that degrades sulfonated naphthalene formaldehyde condensate. | a number of aerobic species were isolated from textile industry activated sludge wastewater. the bacterial consortium was acclimated during seven days before testing its capacity of sulfonated naphthalene-formaldehyde condensate (snfc) recalcitrant compound degradation. snfc's degradation was evaluated by using different techniques including: vapour pressure osmometry, spectroscopy uv-visible and chemical oxygen demand (cod). the degradation of snfc by acclimated bacterial consortium was determi ... | 2008 | 18819646 |
| comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. | bacteria can use branched-chain amino acids (ilv, i.e., isoleucine, leucine, valine) and fatty acids (fas) as sole carbon and energy sources converting ilv into acetyl-coenzyme a (coa), propanoyl-coa, and propionyl-coa, respectively. in this work, we used the comparative genomic approach to identify candidate transcriptional factors and dna motifs that control ilv and fa utilization pathways in proteobacteria. the metabolic regulons were characterized based on the identification and comparison o ... | 2009 | 18820024 |
| 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 |
| [toxicity screening and identification of bacteria isolated from snails nassarius semiplicatus and their habitat]. | tetrodotoxin and its analogues (ttxs) were responsible for the poisoning incidents associated with snail nassarius spp. we studied bacteria isolated from toxic snails as well as their habitat to probe into the relationship between bacteria and toxicity of nassariid gastropod. | 2008 | 18837369 |
| microbial production and characterization of superparamagnetic magnetite nanoparticles by shewanella sp. hn-41. | a facultative dissimilatory metal-reducing bacterium, shewanella sp. strain hn-41, was used to produce magnetite nanoparticles from a precursor, poorly crystalline ironoxyhydroxide akaganeite (beta-feooh), by reducing fe(iii). the diameter of the biogenic magnetite nanoparticles ranged from 26 nm to 38 nm, characterized by dynamic light scattering spectrophotometry. the magnetite nanoparticles consisted of mostly uniformly shaped spheres, which were identified by electron microscopy. the magneto ... | 2008 | 18852514 |
| effects of electron transfer mediators on the bioreduction of lepidocrocite (gamma-feooh) by shewanella putrefaciens cn32. | electron transfer mediators (etms) such as low-molecular-mass quinones (e.g., juglone and lawsone) and humic substances are believed to play a role in many redox reactions involved in contaminant transformations and the biogeochemical cycling of many redox-active elements (e.g., fe and mn) in aquatic and terrestrial environments. this study examines the effects of a series of compounds representing major classes of natural and synthetic organic etms, including low-molecular-mass quinones, humic ... | 2008 | 18853803 |
| characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid ftms instruments. | hybrid ftms instruments, such as the ltq-ft and ltq-orbitrap, are capable of generating high duty cycle linear ion trap ms/ms data along with high resolution information without compromising the overall throughput of measurements. combined with online lc separations, these instruments provide powerful capabilities for proteomics research. in the present work, we explore three alternative strategies for high throughput proteomics measurements using hybrid ftms instruments. our accurate mass and t ... | 2008 | 18855412 |
| 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 |
| mutations that affect agrobacterium vitis-induced grape necrosis also alter its ability to cause a hypersensitive response on tobacco. | abstract tn5-induced mutations in agrobacterium vitis f2/5 resulted in both altered grape necrosis and tobacco leaf panel collapse phenotypes, suggesting that the underlying mechanisms of the reactions are related. the reaction on tobacco resembles the classical hypersensitive response (hr) caused by several plant pathogenic bacteria in that it is observable within 14 h, is inhibited by treatment of plants with metabolic inhibitors, and results in the inability to recover the pathogen from the n ... | 2001 | 18944123 |
| 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 |
| studies of iron-uptake mechanisms in two bacterial species of the shewanella genus adapted to middle-range (shewanella putrefaciens) or antarctic (shewanella gelidimarina) temperatures. | iron(iii)-uptake mechanisms in bacteria indigenous to the antarctic, which is the most fe-deficient continent on earth, have not been extensively studied. the cold-adapted, antarctic bacterium, shewanella gelidimarina, does not produce detectable levels of the siderophore, putrebactin, in the supernatant of fe(iii)-deprived cultures. this is distinct from the putrebactin-producing bacterium from the same genus, shewanella putrefaciens, which is adapted to middle-range temperatures. the productio ... | 2008 | 18972501 |
| 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 |
| a structural basis for the regulatory inactivation of dnaa. | regulatory inactivation of dnaa is dependent on hda (homologous to dnaa), a protein homologous to the aaa+ (atpases associated with diverse cellular activities) atpase region of the replication initiator dnaa. when bound to the sliding clamp loaded onto duplex dna, hda can stimulate the transformation of active dnaa-atp into inactive dnaa-adp. the crystal structure of hda from shewanella amazonensis sb2b at 1.75 a resolution reveals that hda resembles typical aaa+ atpases. the arrangement of the ... | 2009 | 19000695 |
| eicosapentaenoic acid plays a beneficial role in membrane organization and cell division of a cold-adapted bacterium, shewanella livingstonensis ac10. | shewanella livingstonensis ac10, a psychrotrophic gram-negative bacterium isolated from antarctic seawater, produces eicosapentaenoic acid (epa) as a component of phospholipids at low temperatures. epa constitutes about 5% of the total fatty acids of cells grown at 4 degrees c. we found that five genes, termed orf2, orf5, orf6, orf7, and orf8, are specifically required for the synthesis of epa by targeted disruption of the respective genes. the mutants lacking epa showed significant growth retar ... | 2009 | 19011019 |
| protein evolution in deep sea bacteria: an analysis of amino acids substitution rates. | abyssal microorganisms have evolved particular features that enable them to grow in their extreme habitat. genes belonging to specific functional categories are known to be particularly susceptible to high-pressure; therefore, they should show some evidence of positive selection. to verify this hypothesis we computed the amino acid substitution rates between two deep-sea microorganisms, photobacterium profundum ss9 and shewanella benthica kt99, and their respective shallow water relatives. | 2008 | 19014525 |
| metabolic flux analysis of shewanella spp. reveals evolutionary robustness in central carbon metabolism. | shewanella spp. are a group of facultative anaerobic bacteria widely distributed in marine and freshwater environments. in this study, we profiled the central metabolic fluxes of eight recently sequenced shewanella species grown under the same condition in minimal medium with [3-13c] lactate. although the tested shewanella species had slightly different growth rates (0.23-0.29 h(-1)) and produced different amounts of acetate and pyruvate during early exponential growth (pseudo-steady state), the ... | 2009 | 19031428 |
| 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 |
| microbial iron redox cycling in a circumneutral-ph groundwater seep. | the potential for microbially mediated redox cycling of iron (fe) in a circumneutral-ph groundwater seep in north central alabama was studied. incubation of freshly collected seep material under anoxic conditions with acetate-lactate or h(2) as an electron donor revealed the potential for rapid fe(iii) oxide reduction (ca. 700 to 2,000 micromol liter(-1) day(-1)). fe(iii) reduction at lower but significant rates took place in unamended controls (ca. 300 micromol liter(-1) day(-1)). culture-based ... | 2009 | 19047399 |
| 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 |
| functional roles of arca, etra, cyclic amp (camp)-camp receptor protein, and cya in the arsenate respiration pathway in shewanella sp. strain ana-3. | microbial arsenate respiration can enhance arsenic release from arsenic-bearing minerals--a process that can cause arsenic contamination of water. in shewanella sp. strain ana-3, the arsenate respiration genes (arrab) are induced under anaerobic conditions with arsenate and arsenite. here we report how genes that encode anaerobic regulator (arca and etra [fnr homolog]) and carbon catabolite repression (crp and cya) proteins affect arsenate respiration in ana-3. transcription of arca, etra, and c ... | 2009 | 19060154 |
| reductive processes controlling arsenic retention: revealing the relative importance of iron and arsenic reduction. | the fate and transport of arsenic is regulated, in part, by its strong affinity for iron (hydr)oxides. a transition from aerobic to anaerobic conditions resulting in concomitant reduction of both as(v) and iron (hydr)oxides can thus have a pronounced influence on as partitioning. however, it is presently unclear whether as desorption under anaerobic conditions results predominantly from a transformation from as(v) to as(iii) or from mineralogical changes as a consequence of iron and manganese re ... | 2008 | 19068807 |
| 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 |
| self-constructed electrically conductive bacterial networks. | | 2009 | 19072958 |
| tuning of functional heme reduction potentials in shewanella fumarate reductases. | the fumarate reductases from s. frigidimarina ncimb400 and s. oneidensis mr-1 are soluble and monomeric enzymes located in the periplasm of these bacteria. these proteins display two redox active domains, one containing four c-type hemes and another containing fad at the catalytic site. this arrangement of single-electron redox co-factors leading to multiple-electron active sites is widespread in respiratory enzymes. to investigate the properties that allow a chain of single-electron co-factors ... | 2009 | 19081388 |
| 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 |
| identification and characterization of two alternative sigma factors of rna polymerase in the deep-sea piezophilic bacterium shewanella violacea, strain dss12. | two genes for alternative sigma factors, sigma(e2) and sigma(e3), classified in the extracytoplasmic function sigma family for rna polymerases, were identified in the deep-sea piezophilic bacterium shewanella violacea dss12. amino acid alignments revealed that the domains for transcriptional functions were comparatively conserved compared with escherichia coli sigma(e) in both proteins. core-binding analysis suggested that both proteins function as sigma factors. | 2009 | 19129643 |
| identification of psychrophile shewanella sp. kmg427 as an eicosapentaenoic acid producer. | an isolate from holothurians was identified as an eicosapentaenoic acid (epa)-producing bacterium kmg427, which is characterized by epa synthesis efficiency, by thin layer and gas chromatographic analyses. the epa production was maximized to more than 10% of the total fatty acids by incubation at 4o degrees c after cell proliferation at 20 degrees c. the isolated bacterium was categorized as gramnegative, rod-shaped, aerobic, and motile with a single polar flagellum. according to phylogenetic an ... | 2008 | 19131686 |
| analysis by mutagenesis of a chromosomal integron integrase from shewanella amazonensis sb2bt. | integrons are mobile genetic elements that can integrate and disseminate genes as cassettes by a site-specific recombination mechanism. integrons contain an integrase gene (inti) that carries out recombination by interacting with two different target sites; the atti site in cis with the integrase and the palindromic attc site of a cassette. the plasmid-specified inti1 excises a greater variety of cassettes (principally antibiotic resistance genes), and has greater activity, than chromosomal inte ... | 2009 | 19136589 |
| diversity of beta-propeller phytase genes in the intestinal contents of grass carp provides insight into the release of major phosphorus from phytate in nature. | phytate is the most abundant organic phosphorus compound in nature, and microbial mineralization of phytate by phytase is a key process for phosphorus recycling in the biosphere. in the present study, beta-propeller phytase (bpp) gene fragments were readily amplified from the intestinal contents of grass carp (ctenopharyngodon idellus) directly or from phytate-degrading isolates from the same source, confirming the widespread occurrence of bpp in aquatic communities. the amounts of sequences col ... | 2009 | 19151187 |
| electronic absorption spectra and redox properties of c type cytochromes in living microbes. | shewanella is an electrogenic microbe that has significant content of c type cytochromes (ca. 0.5 mm). this feature allows the optical absorption spectra of the cell-membrane-associated proteins to be monitored in vivo in the course of extracellular respiratory electron-transfer reactions. the results show significant differences to those obtained in vitro with purified proteins. | 2009 | 19156795 |
| exploration of csp genes from temperate and glacier soils of the indian himalayas and in silico analysis of encoding proteins. | the metagenomic csp library was constructed from the temperate and glacier soils of central himalaya, india followed by polymerase chain reaction (pcr) amplification. the library was further screened for low-temperature adaptation, and the positive recombinants were sorted out by determining changes in the melting temperature (tm). a homology search of cloned sequence showed their identity with the csp genes of pseudomonas fluorescens, psychrobacter cryohalolentis k5, and shewanella spp mr-4. am ... | 2009 | 19159976 |
| 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 |
| [acute dermohypodermitis of the right leg (s. putrefaciens) after sea bathing]. | | 2009 | 19171235 |
| 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 |
| energy generation coupled to azoreduction by membranous vesicles from shewanella decolorationis s12. | previous studies have demonstrated that shewanella decolorationis s12 can grow on the azo compound amaranth as the sole electron acceptor. thus, to explore the mechanism of energy generation in this metabolism, membranous vesicles (mvs) were prepared and the mechanism of energy generation investigated. the membrane, which was fragmentized during preparation, automatically formed vesicles ranging from 37.5-112.5 nm in diameter under electron micrograph observation. energy was conserved when coupl ... | 2009 | 19190406 |
| shewanella vesiculosa sp. nov., a psychrotolerant bacterium isolated from an antarctic coastal area. | two strains of psychrotolerant bacteria, designated m7(t) and m5, isolated from antarctic coastal marine environments were studied to determine their taxonomic position. the organisms comprised gram-negative, rod-shaped, facultatively anaerobic cells that were motile by means of single polar flagella. neither of the bacterial isolates had a requirement for na(+). these two psychrotolerant strains grew at temperatures ranging from -4 to 30 degrees c. both strains were capable of producing h(2)s f ... | 2009 | 19196774 |
| 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 |
| [taxonomic characteristics and physiological properties of microorganisms from the gut of pike (esox lucius)]. | the taxonomic composition and distribution of microorganisms differing in the degree of association with the intestinal mucosa of the pike (lucius lucius) has been studied. microorgansism of the families enterobacteriaceae, aeromonadaceae, and vibrionaceae dominate in the gut microflora. numerically prevailing bacterial species are characterized by high proteolytic and amylolytic enzyme activities as well as by high persistence accounted for by antilysozyme and antihistone activities. the result ... | 2008 | 19198074 |
| microbial production of ultrafine-grained magnetite by fermentation processes at room temperature. | a method of producing magnetite nanoparticles was developed through culturing a microorganism designated haejae-1, shewanella sp., in the presence of glucose and akaganeite (beta-feooh). haejae-1 isolated from inter-tidal flat sediments was able to produce copious amount of ultrafine magnetite via glucose fermentation extracellularly under anaerobic conditions at room temperature, allowing for easy production, separation, and recovery of the magnetite. tem observation revealed aggregates of smal ... | 2008 | 19198424 |
| degeneration of biogenic superparamagnetic magnetite. | magnetite crystals precipitated as a consequence of fe(iii) reduction by shewanella algae bry after 265 h incubation and 5-year anaerobic storage were investigated with transmission electron microscopy, mössbauer spectroscopy and x-ray diffraction. the magnetite crystals were typically superparamagnetic with an approximate size of 13 nm. the lattice constants of the 265 h and 5-year crystals are 8.4164a and 8.3774a, respectively. the mössbauer spectra indicated that the 265 h magnetite had exces ... | 2009 | 19200144 |
| preliminary characterization and biological reduction of putative biogenic iron oxides (bios) from the tonga-kermadec arc, southwest pacific ocean. | sediment samples were obtained from areas of diffuse hydrothermal venting along the seabed in the tonga sector of the tonga-kermadec arc, southwest pacific ocean. sediments from volcano 1 and volcano 19 were analyzed by x-ray diffraction (xrd) and found to be composed primarily of the iron oxyhydroxide mineral, two-line ferrihydrite. xrd also suggested the possible presence of minor amounts of more ordered iron (hydr)oxides (including six-line ferrihydrite, goethite/lepidocrocite and magnetite) ... | 2009 | 19200145 |
| role and regulation of fatty acid biosynthesis in the response of shewanella piezotolerans wp3 to different temperatures and pressures. | members of the genus shewanella inhabit various environments; they are capable of synthesizing various types of low-melting-point fatty acids, including monounsaturated fatty acids (mufa) and branched-chain fatty acids (bcfa) with and without eicosapentanoic acid (epa). the genes involved in fatty acid synthesis in 15 whole-genome-sequenced shewanella strains were identified and compared. a typical type ii fatty acid synthesis pathway in shewanella was constructed. a complete epa synthesis gene ... | 2009 | 19201790 |
| microbial colonization of an in situ sediment cap and correlation to stratified redox zones. | in situ capping is a management technique for contaminated sediments involving the placement of clean material at the sediment-water interface. this work combined porewater geochemical profiling with quantitative microbial data to investigate the intrinsic microbial colonization of a sand cap. geochemical characterization using voltammetric microelectrodes indicated vertical stratification of biogeochemical processes within a capped sediment column. following dissection of the column, quantitati ... | 2009 | 19209586 |
| 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 |
| detection of bacterioplankton in immersed cadavers using selective agar plates. | we measured bacterioplankton in blood from cadavers retrieved from the sea (n=12), near estuaries (n=4), rivers (fresh water, n=8) and from bathtubs (n=4) as well as from non-drowned victims (n=10) discovered near aquatic environments. blood from 11 victims drowned in seawater developed bioluminescent and/or blue colonies (oxidase test positive) on selective media containing 2-4% nacl. homology analyses of the 16s rrna gene showed that all of them were marine bacteria (genera: photobacterium, vi ... | 2009 | 19261520 |
| [non necrotizing bacterial cellulitis and bacteriemia due to shewanella putrefaciens]. | shewanella putrefaciens is a gram negative opportunistic pathogen which causes skin and soft tissue infections and bacteriemia in immunocompromized patients. we report a 86-year-old man, who presented with an infectious cellulitis of the leg associated with shewanella putrefaciens bacteriemia. this patient was treated by mycophenolate mofetil for a bullous pemphigoid resistant to corticotherapy. | 2009 | 19282070 |
| isolation and characterization of shewanella oneidensis wl-7 capable of decolorizing azo dye reactive black 5. | | 2009 | 19282633 |
| respiratory arsenate reductase as a bidirectional enzyme. | the haloalkaliphilic bacterium alkalilimnicola ehrlichii is capable of anaerobic chemolithoautotrophic growth by coupling the oxidation of arsenite (as(iii)) to the reduction of nitrate and carbon dioxide. analysis of its complete genome indicates that it lacks a conventional arsenite oxidase (aox), but instead possesses two operons that each encode a putative respiratory arsenate reductase (arr). here we show that one homolog is expressed under chemolithoautotrophic conditions and exhibits both ... | 2009 | 19285953 |
| 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 |
| diversity of both the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the south china sea. | protease-producing bacteria are known to play an important role in degrading sedimentary particular organic nitrogen, and yet, their diversity and extracellular proteases remain largely unknown. in this paper, the diversity of the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the south china sea was investigated. the richness of the cultivable protease-producing bacteria reached 10(6) cells/g in all sediment samples. analysis of the 16s rrna gene se ... | 2009 | 19301066 |
| bacterial loads and microbial composition in high pressure treated oysters during storage. | analysis of bacterial communities present in high-pressure (hp)-treated, quick-frozen (qf), and raw oysters was carried out during three different seasons. bacterial numbers and species diversity in each sample were determined at 0, 7, 14, and 21 days of storage. results showed that numbers of total aerobic bacterial counts (tabc) in treated oysters were significantly lower than in untreated oysters at day 0 by 10 to 10(5) colony forming units per gram of oyster meat (cfu/g) in all samplings. ho ... | 2009 | 19303653 |
| 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 |
| skin and soft tissue infections (patera foot) in immigrants, spain. | an unusual skin and soft tissue infection of the lower limbs has been observed in immigrants from sub-saharan africa who cross the atlantic ocean crowded on small fishing boats (pateras). response to conventional treatment is usually poor. extreme extrinsic factors (including new pathogens) may contribute to the etiology of the infection and its pathogenesis. | 2009 | 19331742 |
| 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 |
| characterization of a cryptic plasmid psfkw33 from shewanella sp. 33b. | a cryptic plasmid psfkw33 from psychrotrophic bacterium shewanella sp. 33b, an isolate from the gulf of gdansk (the baltic sea), was sequenced and characterized. it is an 8021bp circular molecule with 38% gc content, which shows a distinctive nucleotide sequence without homology to other known plasmids. the nucleotide sequence analysis predicts eight open reading frames. the deduced amino acid sequence of orf-1 shared significant similarity with the phage integrase protein from pseudomonas putid ... | 2009 | 19336243 |
| discovering cis-regulatory rnas in shewanella genomes by support vector machines. | an increasing number of cis-regulatory rna elements have been found to regulate gene expression post-transcriptionally in various biological processes in bacterial systems. effective computational tools for large-scale identification of novel regulatory rnas are strongly desired to facilitate our exploration of gene regulation mechanisms and regulatory networks. we present a new computational program named rssvm (rna sampler+support vector machine), which employs support vector machines (svms) f ... | 2009 | 19343219 |
| 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 |
| tandem acyl carrier protein domains in polyunsaturated fatty acid synthases. | polyunsaturated fatty acids (pufas) can be biosynthesized via aerobic pathways that rely on combinations of desaturases and elongases to convert saturated fatty acids to pufas or anaerobic pathways that exploit polyketide synthase (pks)-like enzymes known as pufa synthases for de novo synthesis from acyl coa precursors. in contrast to most fatty acid synthases (fass) and pkss that contain a single acyl carrier protein (acp) domain for each cycle of fatty acid or polyketide chain elongation, all ... | 2009 | 19362636 |
| 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 |
| involvement of a membrane-bound class iii adenylate cyclase in regulation of anaerobic respiration in shewanella oneidensis mr-1. | unlike other bacteria that use fnr to regulate anaerobic respiration, shewanella oneidensis mr-1 uses the cyclic amp receptor protein (crp) for this purpose. three putative genes, cyaa, cyab, and cyac, predicted to encode class i, class iv, and class iii adenylate cyclases, respectively, have been identified in the genome sequence of this bacterium. functional validation through complementation of an escherichia coli cya mutant confirmed that these genes encode proteins with adenylate cyclase ac ... | 2009 | 19395492 |
| [influence of amino acid and dipeptide composition on protein stability of piezophilic microbes]. | to compare the amino acid and dipeptide composition of proteins from piezophilic and non-piezophilic microbes is of great significance for understanding the stability of piezophilic protein and directed mutation of them. | 2009 | 19445175 |
| using genomic data to determine the diversity and distribution of target site motifs recognized by class c-attc group ii introns. | the attc sites are well-known integrase-targeted elements involved in the insertion and excision of gene cassettes from integrons. recently, functional analysis of sma.i2, a class c-attc group ii intron, showed that this mobile element invades the attc sites through a specific process. the analysis of genomic data indicates that class c-attc group ii introns are independently acquired by their bacterial hosts and evolve in the recognition of a variety of target sites, including the attcs. in add ... | 2009 | 19449055 |
| pfab products determine the molecular species produced in bacterial polyunsaturated fatty acid biosynthesis. | when pdha4, a vector carrying all five pfaa-pfae genes responsible for docosahexaenoic acid (dha; 22:6) biosynthesis in moritella marina mp-1, was coexpressed in escherichia coli with the individual pfaa-pfad genes for eicosapentaenoic acid (epa; 20:5) biosynthesis from shewanella pneumatophori scrc-2738, both polyunsaturated fatty acids were synthesized only in the recombinant carrying pfab for epa synthesis. escherichia coli coexpressing a deleted construct comprising pfaa, pfac, pfad and pfae ... | 2009 | 19453514 |
| anti-microfouling activity of lipidic metabolites from the invasive brown alga sargassum muticum (yendo) fensholt. | the purification of the chloroform extract from the brown invasive macroalga sargassum muticum, through a series of chromatographic separations, yielded 12 fractions that were tested against strains of bacteria, microalgae, and fungi involved in marine biofilm formation. the chemical composition of four (a, c, g, and k) out of the six fractions that exhibited anti-microfouling activity was investigated. fraction a contained saturated and unsaturated linear hydrocarbons (c12-c27). arachidonic aci ... | 2010 | 19468792 |