Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study. | lateral gene transfer (lgt) is now accepted as an important factor in the evolution of prokaryotes. establishment of the occurrence of lgt is typically attempted by a variety of methods that includes the comparison of reconstructed phylogenetic trees, the search for unusual gc composition or codon usage within a genome, and identification of similarities between distant species as determined by best blast hits. we explore quantitative assessments of these strategies to study the prokaryotic trai ... | 2006 | 16769896 |
| denitrification ability of rhizobial strains isolated from lotus sp. | ten rhizobial strains isolated from lotus sp. have been characterized by their ability to denitrify. out of the 10 strains, the five slow-growing isolates grew well under oxygen-limiting conditions with nitrate as a sole nitrogen source, and accumulated nitrous oxide in the growth medium when acetylene was used to inhibit nitrous oxide reductase activity. all five strains contained dna homologous to the bradyrhizobium japonicum nirk, norbdq and nosz genes. in contrast, fast-growing lotus rhizobi ... | 2006 | 16779640 |
| comparative genomics and evolution of the hsp90 family of genes across all kingdoms of organisms. | hsp90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. hsp90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. in this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in genbank, and address the diversity, evolution, gene structure, conservation and nomenclature ... | 2006 | 16780600 |
| activation of the global gene regulator prra (rega) from rhodobacter sphaeroides. | prra is a global transcription regulator activated upon phosphorylation by its cognate kinase prrb in response to low oxygen levels in rhodobacter sphaeroides. here we show by gel filtration, analytical ultracentrifugation, and nmr diffusion measurements that treatment of prra with a phosphate analogue, bef(3)(-), results in dimerization of the protein, producing a protein that binds dna. no dimeric species was observed in the absence of bef(3)(-). upon addition of bef(3)(-), the inhibitory acti ... | 2006 | 16784239 |
| fixj: a major regulator of the oxygen limitation response and late symbiotic functions of sinorhizobium meliloti. | sinorhizobium meliloti exists either in a free-living state in the soil or in symbiosis within legume nodules, where the bacteria differentiate into nitrogen-fixing bacteroids. expression of genes involved in nitrogen fixation and associated respiration is governed by two intermediate regulators, nifa and fixk, respectively, which are controlled by a two-component regulatory system fixlj in response to low-oxygen conditions. in order to identify the fixlj regulon, gene expression profiles were d ... | 2006 | 16788198 |
| effects of n-starvation and c-source on bradyrhizobium japonicum exopolysaccharide production and composition, and bacterial infectivity to soybean roots. | the exopolysaccharide (eps) is an extracellular molecule that in bradyrhizobium japonicum affects bacterial efficiency to nodulate soybean. culture conditions such as n availability, type of c-source, or culture age can modify the amount and composition of eps. to better understand the relationship among these conditions for eps production, we analyzed their influence on eps in b. japonicum usda 110 and its derived mutant deltap22. this mutant has a deletion including the 3' region of exop, exot ... | 2006 | 16802172 |
| [model of genes expression regulation in bacteria by means of formation of secondary rna structures]. | in this article a model, first, classical attenuation rna regulation of gene expression by means of transcription termination is offered. the model bases on representation about a macrostate of secondary structure in rna regulatory region between a ribosome and a rna polymerase, on the formulas of a resonant type defining the value of deceleration of a rna polymerase by a set of hairpins in the same region. the special attention is given to selection of parameters of model. to check of model the ... | 2006 | 16813169 |
| a proximal arginine r206 participates in switching of the bradyrhizobium japonicum fixl oxygen sensor. | in oxygen-sensing pas domains, a conserved polar residue on the proximal side of the heme cofactor, usually arginine or histidine, interacts alternately with the protein in the "on-state" or the heme edge in the "off-state" but does not contact the bound ligand directly. we assessed the contributions of this residue in bradyrhizobium japonicum fixl by determining the effects of an r206a substitution on the heme-pas structure, ligand affinity, and regulatory capacity. the crystal structures of th ... | 2006 | 16813836 |
| the brucella abortus cyclic beta-1,2-glucan virulence factor is substituted with o-ester-linked succinyl residues. | brucella periplasmic cyclic beta-1,2-glucan plays an important role during bacterium-host interaction. nuclear magnetic resonance spectrometry analysis, thin-layer chromatography, and deae-sephadex chromatography were used to characterize brucella abortus cyclic glucan. in the present study, we report that a fraction of b. abortus cyclic beta-1,2-glucan is substituted with succinyl residues, which confer anionic character on the cyclic beta-1,2-glucan. the oligosaccharide backbone is substituted ... | 2006 | 16816173 |
| occurrence of two 5-aminolevulinate biosynthetic pathways in streptomyces nodosus subsp. asukaensis is linked with the production of asukamycin. | we report the results of cloning genes for two key biosynthetic enzymes of different 5-aminolevulinic acid (ala) biosynthetic routes from streptomyces. the genes encode the glutamyl-trnaglu reductase (glutr) of the c5 pathway and the ala synthase (alas) of the shemin pathway. while streptomyces coelicolor a3(2) synthesizes ala via the c5 route, both pathways are operational in streptomyces nodosus subsp. asukaensis, a producer of asukamycin. in this strain, the c5 route produces ala for tetrapyr ... | 2006 | 16816183 |
| regulation of liars-dependent gene expression in bacillus subtilis: identification of inhibitor proteins, regulator binding sites, and target genes of a conserved cell envelope stress-sensing two-component system. | the regulatory network of the cell envelope stress response in bacillus subtilis involves both extracytoplasmic function sigma-factors and two-component signal transducing systems. one such system, liars, responds to cell wall antibiotics that interfere with the undecaprenol cycle and to perturbation of the cytoplasmic membrane. it is encoded by the last two genes of the liaihgfsr locus. here, we analyzed the expression of two liar-dependent operons, liaihgfsr and yhcyz-yhda, and characterized a ... | 2006 | 16816187 |
| osmotic upshift transiently inhibits uptake via abc transporters in gram-negative bacteria. | atp-binding cassette transporters from several rhizobia and salmonella enterica serovar typhimurium, but not secondarily coupled systems, were inhibited by high concentrations (100 to 500 mm) of various osmolytes, an effect reversed by the removal of the osmolyte. abc systems were also inactivated in isolated pea bacteroids, probably due to the obligatory use of high-osmolarity isolation media. measurement of nutrient cycling in isolated pea bacteroids is impeded by this effect. | 2006 | 16816205 |
| response of lactobacillus helveticus pr4 to heat stress during propagation in cheese whey with a gradient of decreasing temperatures. | the heat stress response was studied in lactobacillus helveticus pr4 during propagation in cheese whey with a gradient of naturally decreasing temperature (55 to 20 degrees c). growth under a gradient of decreasing temperature was compared to growth at a constant temperature of 42 degrees c. proteinase, peptidase, and acidification activities of l. helveticus pr4 were found to be higher in cells harvested when 40 degrees c was reached by a gradient of decreasing temperature than in cells grown a ... | 2006 | 16820437 |
| expression of the 1-aminocyclopropane-1-carboxylic acid deaminase gene requires symbiotic nitrogen-fixing regulator gene nifa2 in mesorhizobium loti maff303099. | many soil bacteria contain 1-aminocyclopropane-1-carboxylic acid (acc) deaminase, which degrades acc, a precursor of the phytohormone ethylene. in order to examine the regulation of the acds gene encoding acc deaminase in mesorhizobium loti maff303099 during symbiosis with the host legume lotus japonicus, we introduced the beta-glucuronidase (gus) gene into acds so that gus was expressed under control of the acds promoter, and we also generated disruption mutants with mutations in a nitrogen fix ... | 2006 | 16820494 |
| differential symbiotic response of phage-typed strains of bradyrhizobium japonicum with soybean cultivars. | in this study, native bradyrhizobium strains were isolated from the host plant, glycine max, harvested from fields in madhya pradesh, india, and were typed by lytic rhizobiophages. eight indigenous (soy2, asr011, asr031, asr032, msr091, isr050, isr076 and isr078) and two exotic strains (usda123 and cb1809), all of which evidenced a distinct reaction with six phages, were employed in this study. the symbiotic interaction of these strains was studied initially using soybean cultivar js335 in a san ... | 2006 | 16820768 |
| comparison of aerobic and photosynthetic rhodobacter sphaeroides 2.4.1 proteomes. | the analysis of proteomes from aerobic and photosynthetic rhodobacter sphaeroides 2.4.1 cell cultures by liquid chromatography-mass spectrometry yielded approximately 6,500 high confidence peptides representing 1,675 gene products (39% of the predicted proteins). the identified proteins corresponded primarily to open reading frames (orfs) contained within the two chromosomal elements of this bacterium, but a significant number were also observed from orfs associated with 5 naturally occurring pl ... | 2006 | 16828186 |
| phase variation and genomic architecture changes in azospirillum. | the plant growth-promoting rhizobacterium azospirillum lipoferum 4b generates in vitro at high frequency a stable nonswimming phase variant designated 4v(i), which is distinguishable from the wild type by the differential absorption of dyes. the frequency of variants generated by a reca mutant of a. lipoferum 4b was increased up to 10-fold. the pleiotropic modifications characteristic of the phase variant are well documented, but the molecular processes involved are unknown. here, the objective ... | 2006 | 16855225 |
| quantitative detection of the nosz gene, encoding nitrous oxide reductase, and comparison of the abundances of 16s rrna, narg, nirk, and nosz genes in soils. | nitrous oxide (n2o) is an important greenhouse gas in the troposphere controlling ozone concentration in the stratosphere through nitric oxide production. in order to quantify bacteria capable of n2o reduction, we developed a sybr green quantitative real-time pcr assay targeting the nosz gene encoding the catalytic subunit of the nitrous oxide reductase. two independent sets of nosz primers flanking the nosz fragment previously used in diversity studies were designed and tested (k. kloos, a. mer ... | 2006 | 16885263 |
| characterization of the beta-ketoadipate pathway in sinorhizobium meliloti. | aromatic compounds represent an important source of energy for soil-dwelling organisms. the beta-ketoadipate pathway is a key metabolic pathway involved in the catabolism of the aromatic compounds protocatechuate and catechol, and here we show through enzymatic analysis and mutant analysis that genes required for growth and catabolism of protocatechuate in the soil-dwelling bacterium sinorhizobium meliloti are organized on the psymb megaplasmid in two transcriptional units designated pcadchgb an ... | 2006 | 16885292 |
| peptidoglycan from bacillus cereus mediates commensalism with rhizosphere bacteria from the cytophaga-flavobacterium group. | previous research in our laboratory revealed that the introduction of bacillus cereus uw85 can increase the populations of bacteria from the cytophaga-flavobacterium (cf) group of the bacteroidetes phylum in the soybean rhizosphere, suggesting that these rhizosphere microorganisms have a beneficial relationship (g. s. gilbert, j. l. parke, m. k. clayton, and j. handelsman, ecology 74:840-854, 1993). in the present study, we determined the frequency at which cf bacteria coisolated with b. cereus ... | 2006 | 16885294 |
| metabolic profiles and genetic diversity of denitrifying communities in activated sludge after addition of methanol or ethanol. | external carbon sources can enhance denitrification rates and thus improve nitrogen removal in wastewater treatment plants. the effects of adding methanol and ethanol on the genetic and metabolic diversity of denitrifying communities in activated sludge were compared using a pilot-scale plant with two parallel lines. a full-scale plant receiving the same municipal wastewater, but without external carbon source addition, was the reference. metabolic profiles obtained from potential denitrificatio ... | 2006 | 16885297 |
| activity of rhodobacter sphaeroides rpohii, a second member of the heat shock sigma factor family. | we have identified a second rpoh homolog, rpoh(ii), in the alpha-proteobacterium rhodobacter sphaeroides. primary amino acid sequence comparisons demonstrate that r. sphaeroides rpoh(ii) belongs to a phylogenetically distinct group with rpoh orthologs from alpha-proteobacteria that contain two rpoh genes. like its previously identified paralog, rpoh(i), rpoh(ii) is able to complement the temperature-sensitive phenotype of an escherichia coli sigma(32) (rpoh) mutant. in addition, we show that rec ... | 2006 | 16885439 |
| global gene expression analysis of the heat shock response in the phytopathogen xylella fastidiosa. | xylella fastidiosa is a phytopathogenic bacterium that is responsible for diseases in many economically important crops. although different strains have been studied, little is known about x. fastidiosa stress responses. one of the better characterized stress responses in bacteria is the heat shock response, which induces the expression of specific genes to prevent protein misfolding and aggregation and to promote degradation of the irreversibly denatured polypeptides. to investigate x. fastidio ... | 2006 | 16885450 |
| molecular and functional analysis of nicotinate catabolism in eubacterium barkeri. | the anaerobic soil bacterium eubacterium barkeri catabolizes nicotinate to pyruvate and propionate via a unique fermentation. a full molecular characterization of nicotinate fermentation in this organism was accomplished by the following results: (i) a 23.2-kb dna segment with a gene cluster encoding all nine enzymes was cloned and sequenced, (ii) two chiral intermediates were discovered, and (iii) three enzymes were found, completing the hitherto unknown part of the pathway. nicotinate dehydrog ... | 2006 | 16894175 |
| heme: a versatile signaling molecule controlling the activities of diverse regulators ranging from transcription factors to map kinases. | heme (iron protoporphyrin ix) is an essential molecule for numerous living organisms. not only does it serve as a prosthetic group in enzymes, it also acts as a signaling molecule that controls diverse molecular and cellular processes ranging from signal transduction to protein complex assembly. deficient heme synthesis or function impacts the hematopoietic, hepatic and nervous systems in humans. recent studies have revealed a series of heme-regulated transcription factors and signal transducers ... | 2006 | 16894358 |
| chitinases produced by paenibacillus illinoisensis and bacillus thuringiensis subsp. pakistani degrade nod factor from bradyrhizobium japonicum. | chitinases are enzymes that hydrolyze internal beta-1,4-n-acetyl-d-glucosamine linkages of chitin. since the backbone of nod factors is a chitin oligomer, we investigated whether chitinases produced by soil bacteria paenibacillus illinoisensis kja-424 and bacillus thuringiensis subsp. pakistani hd 395 are able to degrade nod factor produced by bradyrhizobium japonicum, a phenomenon that could disrupt b. japonicum-soybean signaling and nodule establishment when chitinases are present. purified no ... | 2008 | 16904303 |
| the housekeeping dipeptide permease is the escherichia coli heme transporter and functions with two optional peptide binding proteins. | heme, a major iron source, is transported through the outer membrane of gram-negative bacteria by specific heme/hemoprotein receptors and through the inner membrane by heme-specific, periplasmic, binding protein-dependent, atp-binding cassette permeases. escherichia coli k12 does not use exogenous heme, and no heme uptake genes have been identified. nevertheless, a recombinant e. coli strain expressing just one foreign heme outer membrane receptor can use exogenous heme as an iron source. this r ... | 2006 | 16905647 |
| isolation of a novel nodulin: a molecular marker of osmotic stress in glycine max/bradyrhizobium japonicum nodule. | symbiotic n(2) fixation of legume crops is highly sensitive to drought, which results in a dramatic drop of n accumulation and yield. the symbiosis between soybean (glycine max) and bradyrhizobium japonicum, because of its extreme sensitivity to drought, was chosen as a model to analyse the response to drought stress at a molecular level. the mrna differential display technique was performed to isolate cdna markers differentially expressed in well-watered [100% of n(2) fixation capacity (nfc)] a ... | 2006 | 16913873 |
| a cytosolic arabidopsis d-xylulose kinase catalyzes the phosphorylation of 1-deoxy-d-xylulose into a precursor of the plastidial isoprenoid pathway. | plants are able to integrate exogenous 1-deoxy-d-xylulose (dx) into the 2c-methyl-d-erythritol 4-phosphate pathway, implicated in the biosynthesis of plastidial isoprenoids. thus, the carbohydrate needs to be phosphorylated into 1-deoxy-d-xylulose 5-phosphate and translocated into plastids, or vice versa. an enzyme capable of phosphorylating dx was partially purified from a cell-free arabidopsis (arabidopsis thaliana) protein extract. it was identified by mass spectrometry as a cytosolic protein ... | 2006 | 16920870 |
| evolution of vitamin b2 biosynthesis: 6,7-dimethyl-8-ribityllumazine synthases of brucella. | the penultimate step in the biosynthesis of riboflavin (vitamin b2) involves the condensation of 3,4-dihydroxy-2-butanone 4-phosphate with 5-amino-6-ribitylamino-2,4(1h,3h)-pyrimidinedione, which is catalyzed by 6,7-dimethyl-8-ribityllumazine synthase (lumazine synthase). pathogenic brucella species adapted to an intracellular lifestyle have two genes involved in riboflavin synthesis, ribh1 and ribh2, which are located on different chromosomes. the ribh2 gene was shown previously to specify a lu ... | 2006 | 16923880 |
| regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in rhodopseudomonas palustris. | rhodopseudomonas palustris is a purple, facultatively phototrophic bacterium that uses hydrogen gas as an electron donor for carbon dioxide fixation during photoautotrophic growth or for ammonia synthesis during nitrogen fixation. it also uses hydrogen as an electron supplement to enable the complete assimilation of oxidized carbon compounds, such as malate, into cell material during photoheterotrophic growth. the r. palustris genome predicts a membrane-bound nickel-iron uptake hydrogenase and s ... | 2006 | 16923881 |
| identification and characterization of the bacillus thuringiensis phaz gene, encoding new intracellular poly-3-hydroxybutyrate depolymerase. | a gene that codes for a novel intracellular poly-3-hydroxybutyrate (phb) depolymerase has now been identified in the genome of bacillus thuringiensis subsp. israelensis atcc 35646. this gene, previously annotated as a hypothetical 3-oxoadipate enol-lactonase (pcad) gene and now designated phaz, encodes a protein that shows no significant similarity with any known phb depolymerase. purified his-tagged phaz could efficiently degrade trypsin-activated native phb granules as well as artificial amorp ... | 2006 | 16936025 |
| isocitrate dehydrogenase of bradyrhizobium japonicum is not required for symbiotic nitrogen fixation with soybean. | a mutant strain of bradyrhizobium japonicum usda110 lacking isocitrate dehydrogenase activity was created to determine whether this enzyme was required for symbiotic nitrogen fixation with soybean (glycine max cv. williams 82). the isocitrate dehydrogenase mutant, strain 5051, was constructed by insertion of a streptomycin resistance gene cassette. the mutant was devoid of isocitrate dehydrogenase activity and of immunologically detectable protein, indicating there is only one copy in the genome ... | 2006 | 16936027 |
| the hmuq and hmud genes from bradyrhizobium japonicum encode heme-degrading enzymes. | utilization of heme by bacteria as a nutritional iron source involves the transport of exogenous heme, followed by cleavage of the heme macrocycle to release iron. bradyrhizobium japonicum can use heme as an iron source, but no heme-degrading oxygenase has been described. here, bioinformatics analyses of the b. japonicum genome identified two paralogous genes renamed hmuq (bll7075) and hmud (bll7423) that encode proteins with weak similarity to the heme-degrading monooxygenase isdg from staphylo ... | 2006 | 16952937 |
| thiamine is synthesized by a salvage pathway in rhizobium leguminosarum bv. viciae strain 3841. | in the absence of added thiamine, rhizobium leguminosarum bv. viciae strain 3841 does not grow in liquid medium and forms only "pin" colonies on agar plates, which contrasts with the good growth of sinorhizobium meliloti 1021, mesorhizobium loti 303099, and rhizobium etli cfn42. these last three organisms have thicoge genes, which are essential for de novo thiamine synthesis. while r. leguminosarum bv. viciae 3841 lacks thicoge, it does have thimed. mutation of thim prevented formation of pin co ... | 2006 | 16952958 |
| fourier-transform infrared spectroscopic analysis is a powerful tool for studying the dynamic changes in staphylococcus aureus small-colony variants. | infections due to small-colony variants (scvs) of staphylococcus aureus in patients with chronic and recurrent infections are an emerging problem; however, studies with this subpopulation are hampered by the fact that scvs may exhibit unstable phenotypes, making them difficult to study, particularly in broth media. in this study, two s. aureus sets comprising the (i) normal and the (ii) scv phenotype (clonal with normal phenotype) recovered from clinical specimens, as well as (iii) corresponding ... | 2006 | 16954260 |
| halotolerant cyanobacterium aphanothece halophytica contains a betaine transporter active at alkaline ph and high salinity. | aphanothece halophytica is a halotolerant alkaliphilic cyanobacterium which can grow in media of up to 3.0 m nacl and ph 11. this cyanobacterium can synthesize betaine from glycine by three-step methylation using s-adenosylmethionine as a methyl donor. to unveil the mechanism of betaine uptake and efflux in this alkaliphile, we isolated and characterized a betaine transporter. a gene encoding a protein (bett(a. halophytica)) that belongs to the betaine-choline-carnitine transporter (bcct) family ... | 2006 | 16957224 |
| the selective value of bacterial shape. | why do bacteria have shape? is morphology valuable or just a trivial secondary characteristic? why should bacteria have one shape instead of another? three broad considerations suggest that bacterial shapes are not accidental but are biologically important: cells adopt uniform morphologies from among a wide variety of possibilities, some cells modify their shape as conditions demand, and morphology can be tracked through evolutionary lineages. all of these imply that shape is a selectable featur ... | 2006 | 16959965 |
| a new assay for nitric oxide reductase reveals two conserved glutamate residues form the entrance to a proton-conducting channel in the bacterial enzyme. | a specific amperometric assay was developed for the membrane-bound nor [no (nitric oxide) reductase] from the model denitrifying bacterium paracoccus denitrificans using its natural electron donor, pseudoazurin, as a co-substrate. the method allows the rapid and specific assay of no reduction catalysed by recombinant nor expressed in the cytoplasmic membranes of escherichia coli. the effect on enzyme activity of substituting alanine, aspartate or glutamine for two highly conserved glutamate resi ... | 2007 | 16961460 |
| a new assay for nitric oxide reductase reveals two conserved glutamate residues form the entrance to a proton-conducting channel in the bacterial enzyme. | a specific amperometric assay was developed for the membrane-bound nor [no (nitric oxide) reductase] from the model denitrifying bacterium paracoccus denitrificans using its natural electron donor, pseudoazurin, as a co-substrate. the method allows the rapid and specific assay of no reduction catalysed by recombinant nor expressed in the cytoplasmic membranes of escherichia coli. the effect on enzyme activity of substituting alanine, aspartate or glutamine for two highly conserved glutamate resi ... | 2007 | 16961460 |
| microbial diversity and bioremediation of a hydrocarbon-contaminated aquifer (vega baja, puerto rico). | hydrocarbon contamination of groundwater resources has become a major environmental and human health concern in many parts of the world. our objectives were to employ both culture and culture-independent techniques to characterize the dynamics of microbial community structure within a fluidized bed reactor used to bioremediate a diesel-contaminated groundwater in a tropical environment. under normal operating conditions, 97 to 99% of total hydrocarbons were removed with only 14 min hydraulic ret ... | 2006 | 16968977 |
| comparative and functional genomic analyses of iron transport and regulation in leptospira spp. | the spirochetes of the leptospira genus contain saprophytic and pathogenic members, the latter being responsible for leptospirosis. despite the recent sequencing of the genome of the pathogen l. interrogans, the slow growth of these bacteria, their virulence in humans, and a lack of genetic tools make it difficult to work with these pathogens. in contrast, the development of numerous genetic tools for the saprophyte l. biflexa enables its use as a model bacterium. leptospira spp. require iron fo ... | 2006 | 16980464 |
| colocation of genes encoding a trna-mrna hybrid and a putative signaling peptide on complementary strands in the genome of the hyperthermophilic bacterium thermotoga maritima. | in the genome of the hyperthermophilic bacterium thermotoga maritima, tm0504 encodes a putative signaling peptide implicated in population density-dependent exopolysaccharide formation. although not noted in the original genome annotation, tm0504 was found to colocate, on the opposite strand, with the gene encoding ssra, a hybrid of trna and mrna (tmrna), which is involved in a trans-translation process related to ribosome rescue and is ubiquitous in bacteria. specific dna probes were designed a ... | 2006 | 16980482 |
| lipoprotein pssn of rhizobium leguminosarum bv. trifolii: subcellular localization and possible involvement in exopolysaccharide export. | surface expression of exopolysaccharides (eps) in gram-negative bacteria depends on the activity of proteins found in the cytoplasmic membrane, the periplasmic space, and the outer membrane. psstnop genes identified in rhizobium leguminosarum bv. trifolii strain ta1 encode proteins that might be components of the eps polymerization and secretion system. in this study, we have characterized pssn protein. employing pssn-phoa and pssn-lacz gene fusions and in vivo acylation with [3h]palmitate, we d ... | 2006 | 16980497 |
| unexpected stereorecognition in nitrilase-catalyzed hydrolysis of beta-hydroxy nitriles. | biocatalytic enantioselective hydrolysis of beta-hydroxy nitriles to corresponding (s)-enriched beta-hydroxy carboxylic acids has been achieved for the first time by an isolated nitrilase bll6402 from bradyrhizobium japonicum usda110. this offers a new "green" approach to optically pure beta-hydroxy nitriles and beta-hydroxy carboxylic acids. the observed remote stereorecognition is surprising because this nitrilase shows no enantioselectivity for the hydrolysis of alpha-hydroxy nitriles such as ... | 2006 | 16986917 |
| crystal structures of the dna-binding domain of escherichia coli proline utilization a flavoprotein and analysis of the role of lys9 in dna recognition. | puta (proline utilization a) from escherichia coli is a 1320-amino-acid residue protein that is both a bifunctional proline catabolic enzyme and an autogenous transcriptional repressor. here, we report the first crystal structure of a puta dna-binding domain along with functional analysis of a mutant puta defective in dna binding. crystals were grown using a polypeptide corresponding to residues 1-52 of e. coli puta (puta52). the 2.1 angstrom resolution structure of puta52 mutant lys9met was det ... | 2006 | 17001030 |
| the crystal structure of the e. coli stress protein ycif. | ycif is a protein that is up-regulated when bacteria experience stress conditions, and is highly conserved in a range of bacterial species. ycif has no known structure or biochemical function. to learn more about its potential molecular function and its role in the bacterial stress response, we solved the crystal structure of ycif at 2.0 angstrom resolution by the multiple wavelength anomalous diffraction (mad) technique. ycif is a dimer in solution, and forms a homodimer in the crystal asymmetr ... | 2006 | 17001035 |
| experimental and computational assessment of conditionally essential genes in escherichia coli. | genome-wide gene essentiality data sets are becoming available for escherichia coli, but these data sets have yet to be analyzed in the context of a genome scale model. here, we present an integrative model-driven analysis of the keio e. coli mutant collection screened in this study on glycerol-supplemented minimal medium. out of 3,888 single-deletion mutants tested, 119 mutants were unable to grow on glycerol minimal medium. these conditionally essential genes were then evaluated using a genome ... | 2006 | 17012394 |
| detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs. | in bacteria, sigma factors and other transcriptional regulatory proteins recognize dna patterns upstream of their target genes and interact with rna polymerase to control transcription. as a consequence of evolution, dna sequences recognized by transcription factors are thought to be enriched in intergenic regions (irs) and depleted from coding regions of prokaryotic genomes. | 2006 | 17014715 |
| endogenous isoflavones are essential for the establishment of symbiosis between soybean and bradyrhizobium japonicum. | legume iso/flavonoids have been implicated in the nodulation process, but questions remain as to their specific role(s), and no unequivocal evidence exists showing that these compounds are essential for nodulation. two hypotheses suggest that the primary role of iso/flavonoids is their ability to induce rhizobial nod gene expression and/or their ability to modulate internal root auxin concentrations. the present work provides direct, genetic evidence that isoflavones are essential for nodulation ... | 2006 | 17018035 |
| culture-independent analysis of indomethacin-induced alterations in the rat gastrointestinal microbiota. | nonsteroidal anti-inflammatory drugs (nsaids) are commonly prescribed for a variety of inflammatory conditions; however, the benefits of this class of drugs are accompanied by deleterious side effects, most commonly gastric irritation and ulceration. nsaid-induced ulceration is thought to be exacerbated by intestinal microbiota, but previous studies have not identified specific microbes that contribute to these adverse effects. in this study, we conducted a culture-independent analysis of approx ... | 2006 | 17021222 |
| whole-genome reciprocal blast analysis reveals that planctomycetes do not share an unusually large number of genes with eukarya and archaea. | the genome sequences of rhodopirellula baltica, formerly pirellula sp. strain 1, blastopirellula marina, gemmata obscuriglobus, and kuenenia stuttgartiensis were used in a series of pairwise reciprocal best-hit analyses to evaluate the contested evolutionary position of planctomycetes. contrary to previous reports which suggested that r. baltica had a high percentage of genes with closest matches to archaea and eukarya, we show here that these planctomycetes do not share an unusually large numbe ... | 2006 | 17021241 |
| overlapping and specialized functions of the molybdenum-dependent regulators mopa and mopb in rhodobacter capsulatus. | the phototrophic purple bacterium rhodobacter capsulatus encodes two similar but functionally not identical molybdenum-dependent regulator proteins (mopa and mopb), which are known to replace each other in repression of the modabc genes (coding for an abc-type high-affinity mo transport system) and anfa (coding for the transcriptional activator of fe-nitrogenase genes). we identified further mo-regulated (mor) genes coding for a putative abc-type transport system of unknown function (morabc) and ... | 2006 | 17028278 |
| the complete genome of rhodococcus sp. rha1 provides insights into a catabolic powerhouse. | rhodococcus sp. rha1 (rha1) is a potent polychlorinated biphenyl-degrading soil actinomycete that catabolizes a wide range of compounds and represents a genus of considerable industrial interest. rha1 has one of the largest bacterial genomes sequenced to date, comprising 9,702,737 bp (67% g+c) arranged in a linear chromosome and three linear plasmids. a targeted insertion methodology was developed to determine the telomeric sequences. rha1's 9,145 predicted protein-encoding genes are exceptional ... | 2006 | 17030794 |
| the bradyrhizobium japonicum fur protein is an iron-responsive regulator in vivo. | the fur protein is a global regulator of iron metabolism in many bacterial species. however, fur homologs from some rhizobia appear not to mediate iron-dependent gene expression in vivo. here, transcriptional profiling analysis showed that more than one-fourth of the genes within the iron stimulon of bradyrhizobium japonicum were aberrantly controlled by iron in a fur mutant. however, fur has only a modest role in regulating iron transport genes. quantitative real time reverse transcriptase pcr ... | 2006 | 17039378 |
| foxb of pseudomonas aeruginosa functions in the utilization of the xenosiderophores ferrichrome, ferrioxamine b, and schizokinen: evidence for transport redundancy at the inner membrane. | expression of the inner membrane protein foxb (pa2465) of pseudomonas aeruginosa in mutants of sinorhizobium meliloti that are defective in the utilization of ferrichrome, ferrioxamine b, and schizokinen resulted in the restoration of siderophore utilization. mutagenesis of foxb in p. aeruginosa did not abolish siderophore utilization, suggesting that the function is redundant. | 2007 | 17056746 |
| foxb of pseudomonas aeruginosa functions in the utilization of the xenosiderophores ferrichrome, ferrioxamine b, and schizokinen: evidence for transport redundancy at the inner membrane. | expression of the inner membrane protein foxb (pa2465) of pseudomonas aeruginosa in mutants of sinorhizobium meliloti that are defective in the utilization of ferrichrome, ferrioxamine b, and schizokinen resulted in the restoration of siderophore utilization. mutagenesis of foxb in p. aeruginosa did not abolish siderophore utilization, suggesting that the function is redundant. | 2007 | 17056746 |
| identification of a histidine-tyrosine cross-link in the active site of the cbb3-type cytochrome c oxidase from rhodobacter sphaeroides. | the heme-copper oxidases constitute a superfamily of terminal dioxygen-reducing enzymes located in the inner mitochondrial or in the bacterial cell membrane. the presence of a mechanistically important covalent bond between a histidine ligand of the copper ion (cu(b)) in the active site and a generally conserved tyrosine residue nearby has been shown to exist in the canonical cytochrome c oxidases. however, according to sequence alignment studies, this critical tyrosine is missing from the subfa ... | 2006 | 17060620 |
| study of the inducer effect of molasses and soybean cake on synthesis and excretion of nodulation factors in different strains of bradyrhizobium japonicum. | it is known that the synthesis of nodulation factors by the bacteria within the genera rhizobium is induced by different compounds, mainly of flavonoid nature exudated by the legume plants. the capacity of different compounds to act as inducers of nod genes on three bradyrhizobium japonicum strains was studied in this paper and this effect was compared using two concentrations of the inducer. induced nod factors were observed among the strains exposed to the inducers. the profiles and amount of ... | 2001 | 17061566 |
| an inventory of yeast proteins associated with nucleolar and ribosomal components. | although baker's yeast is a primary model organism for research on eukaryotic ribosome assembly and nucleoli, the list of its proteins that are functionally associated with nucleoli or ribosomes is still incomplete. we trained a naïve bayesian classifier to predict novel proteins that are associated with yeast nucleoli or ribosomes based on parts lists of nucleoli in model organisms and large-scale protein interaction data sets. phylogenetic profiling and gene expression analysis were carried ou ... | 2006 | 17067374 |
| malic enzyme cofactor and domain requirements for symbiotic n2 fixation by sinorhizobium meliloti. | the nad(+)-dependent malic enzyme (dme) and the nadp(+)-dependent malic enzyme (tme) of sinorhizobium meliloti are representatives of a distinct class of malic enzymes that contain a 440-amino-acid n-terminal region homologous to other malic enzymes and a 330-amino-acid c-terminal region with similarity to phosphotransacetylase enzymes (pta). we have shown previously that dme mutants of s. meliloti fail to fix n(2) (fix(-)) in alfalfa root nodules, whereas tme mutants are unimpaired in their n(2 ... | 2007 | 17071765 |
| malic enzyme cofactor and domain requirements for symbiotic n2 fixation by sinorhizobium meliloti. | the nad(+)-dependent malic enzyme (dme) and the nadp(+)-dependent malic enzyme (tme) of sinorhizobium meliloti are representatives of a distinct class of malic enzymes that contain a 440-amino-acid n-terminal region homologous to other malic enzymes and a 330-amino-acid c-terminal region with similarity to phosphotransacetylase enzymes (pta). we have shown previously that dme mutants of s. meliloti fail to fix n(2) (fix(-)) in alfalfa root nodules, whereas tme mutants are unimpaired in their n(2 ... | 2007 | 17071765 |
| reconstructing the mosaic glycolytic pathway of the anaerobic eukaryote monocercomonoides. | all eukaryotes carry out glycolysis, interestingly, not all using the same enzymes. anaerobic eukaryotes face the challenge of fewer molecules of atp extracted per molecule of glucose due to their lack of a complete tricarboxylic acid cycle. this may have pressured anaerobic eukaryotes to acquire the more atp-efficient alternative glycolytic enzymes, such as pyrophosphate-fructose 6-phosphate phosphotransferase and pyruvate orthophosphate dikinase, through lateral gene transfers from bacteria an ... | 2006 | 17071828 |
| arg-158 is critical in both binding the substrate and stabilizing the transition-state oxyanion for the enzymatic reaction of malonamidase e2. | malonamidase e2 (mae2) from bradyrhizobium japonicum is an enzyme that hydrolyzes malonamate to malonate and has a ser-cis-ser-lys catalytic triad at the active site. the crystal structures of wild type and mutant mae2 exhibited that the guanido group of arg-158 could be involved in the binding of malonamate in which the negative charge of the carboxyl group could destabilize a negatively charged transition-state oxyanion in the enzymatic reaction. in an attempt to elucidate the specific roles o ... | 2006 | 17077089 |
| the evolution of two-component systems in bacteria reveals different strategies for niche adaptation. | two-component systems including histidine protein kinases represent the primary signal transduction paradigm in prokaryotic organisms. to understand how these systems adapt to allow organisms to detect niche-specific signals, we analyzed the phylogenetic distribution of nearly 5,000 histidine protein kinases from 207 sequenced prokaryotic genomes. we found that many genomes carry a large repertoire of recently evolved signaling genes, which may reflect selective pressure to adapt to new environm ... | 2006 | 17083272 |
| proteolytic adaptor for transfer-messenger rna-tagged proteins from alpha-proteobacteria. | we have identified an analog of sspb, the proteolytic adaptor for transfer-messenger rna (tmrna)-tagged proteins, in caulobacter crescentus. c. crescentus sspb shares limited sequence similarity with escherichia coli sspb but binds the tmrna tag in vitro and is required for optimal proteolysis of tagged proteins in vivo. | 2007 | 17085560 |
| proteolytic adaptor for transfer-messenger rna-tagged proteins from alpha-proteobacteria. | we have identified an analog of sspb, the proteolytic adaptor for transfer-messenger rna (tmrna)-tagged proteins, in caulobacter crescentus. c. crescentus sspb shares limited sequence similarity with escherichia coli sspb but binds the tmrna tag in vitro and is required for optimal proteolysis of tagged proteins in vivo. | 2007 | 17085560 |
| the tolc homologue of brucella suis is involved in resistance to antimicrobial compounds and virulence. | brucella spp., like other pathogens, must cope with the environment of diverse host niches during the infection process. in doing this, pathogens evolved different type of transport systems to help them survive and disseminate within the host. members of the tolc family have been shown to be involved in the export of chemically diverse molecules ranging from large protein toxins to small toxic compounds. the role of proteins from the tolc family in brucella and other alpha-2-proteobacteria has b ... | 2007 | 17088356 |
| the tolc homologue of brucella suis is involved in resistance to antimicrobial compounds and virulence. | brucella spp., like other pathogens, must cope with the environment of diverse host niches during the infection process. in doing this, pathogens evolved different type of transport systems to help them survive and disseminate within the host. members of the tolc family have been shown to be involved in the export of chemically diverse molecules ranging from large protein toxins to small toxic compounds. the role of proteins from the tolc family in brucella and other alpha-2-proteobacteria has b ... | 2007 | 17088356 |
| nod factor enhances calcium uptake by soybean. | inoculation with rhizobia or application of nod factors (lipo-chitooligosaccharides, lcos) causes transient increases in cytosolic calcium concentration in root hairs of legume plants. we conducted experiments to evaluate whether application of lco and inoculation with rhizobia improved (45)cacl(2) uptake into soybean (glycine max [l.] merr.) leaves. roots of soybean seedlings with one developing trifoliolate were immersed in murashige and skoog (ms) basal liquid medium containing treatment solu ... | 2006 | 17092733 |
| dynamic state of dna topology is essential for genome condensation in bacteria. | in bacteria, dps is one of the critical proteins to build up a condensed nucleoid in response to the environmental stresses. in this study, we found that the expression of dps and the nucleoid condensation was not simply correlated in escherichia coli, and that fis, which is an e. coli (gamma-proteobacteria)-specific nucleoid protein, interfered with the dps-dependent nucleoid condensation. atomic force microscopy and northern blot analyses indicated that the inhibitory effect of fis was due to ... | 2006 | 17093499 |
| denitrifying degradation of dimethyl phthalate. | results of batch experiments on the denitrifying degradation of dimethyl phthalate (dmp) was most favorable at ph 7-9 and 30-35 degrees c. dmp was first degraded to monomethyl phthalate (mmp), which was in turn degraded to phthalate before complete mineralization. there was no fatty acid residue in the mixed liquor throughout the experiments. the maximum specific degradation rates were 0.32 mm/(gvss x h) for dmp, 0.19 mm/(gvss x h) for mmp, and 0.14 mm/(gvss x h) for phthalate. about 86% of avai ... | 2007 | 17096122 |
| the complete genome sequence of roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. | purple aerobic anoxygenic phototrophs (aaps) are the only organisms known to capture light energy to enhance growth only in the presence of oxygen but do not produce oxygen. the highly adaptive aaps compose more than 10% of the microbial community in some euphotic upper ocean waters and are potentially major contributors to the fixation of the greenhouse gas co2. we present the complete genomic sequence and feature analysis of the aap roseobacter denitrificans, which reveal clues to its physiolo ... | 2007 | 17098896 |
| the complete genome sequence of roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. | purple aerobic anoxygenic phototrophs (aaps) are the only organisms known to capture light energy to enhance growth only in the presence of oxygen but do not produce oxygen. the highly adaptive aaps compose more than 10% of the microbial community in some euphotic upper ocean waters and are potentially major contributors to the fixation of the greenhouse gas co2. we present the complete genomic sequence and feature analysis of the aap roseobacter denitrificans, which reveal clues to its physiolo ... | 2007 | 17098896 |
| characterization of two sets of subpolar flagella in bradyrhizobium japonicum. | bradyrhizobium japonicum is one of the soil bacteria that form nodules on soybean roots. the cell has two sets of flagellar systems, one thick flagellum and a few thin flagella, uniquely growing at subpolar positions. the thick flagellum appears to be semicoiled in morphology, and the thin flagella were in a tight-curly form as observed by dark-field microscopy. flagellin genes were identified from the amino acid sequence of each flagellin. flagellar genes for the thick flagellum are scattered i ... | 2007 | 17098908 |
| characterization of two sets of subpolar flagella in bradyrhizobium japonicum. | bradyrhizobium japonicum is one of the soil bacteria that form nodules on soybean roots. the cell has two sets of flagellar systems, one thick flagellum and a few thin flagella, uniquely growing at subpolar positions. the thick flagellum appears to be semicoiled in morphology, and the thin flagella were in a tight-curly form as observed by dark-field microscopy. flagellin genes were identified from the amino acid sequence of each flagellin. flagellar genes for the thick flagellum are scattered i ... | 2007 | 17098908 |
| [glutamate dehydrogenase activity of bradyrhizobium japonicum in the presence of phytoregulators]. | influence of plant growth regulators ivin and emistim c, and flavonoids daidzein and quercetin on the glutamate dehydrogenase activity of soybean nodule bacteria, with contrasting symbiotic properties, were studied. it was shown that all used phytoregulators stimulated glutamate dehydrogenase activity of bradyrhizobium japonicum 71t (the strain with highly efficient symbiotic properties) 1.2-4.9 times. bradyrhizobium japonicum 21110 (the strain with inefficient symbiotic properties) diminished t ... | 2006 | 17100324 |
| the genome of deep-sea vent chemolithoautotroph thiomicrospira crunogena xcl-2. | presented here is the complete genome sequence of thiomicrospira crunogena xcl-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. this gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. it has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. a ... | 2006 | 17105352 |
| jasmonates induce nod factor production by bradyrhizobium japonicum. | jasmonates are signaling molecules involved in induced systemic resistance, wounding and stress responses of plants. we have previously demonstrated that jasmonates can induce nod genes of bradyrhizobium japonicum when measured by beta-galactosidase activity. in order to test whether jasmonates can effectively induce the production and secretion of nod factors (lipo-chitooligosaccharides, lcos) from b. japonicum, we induced two b. japonicum strains, 532c and usda3, with jasmonic acid (ja), methy ... | 2006 | 17107814 |
| involvement of the cynabds operon and the co2-concentrating mechanism in the light-dependent transport and metabolism of cyanate by cyanobacteria. | the cyanobacteria synechococcus elongatus strain pcc7942 and synechococcus sp. strain utex625 decomposed exogenously supplied cyanate (nco-) to co2 and nh3 through the action of a cytosolic cyanase which required hco3- as a second substrate. the ability to metabolize nco- relied on three essential elements: proteins encoded by the cynabds operon, the biophysical activity of the co2-concentrating mechanism (ccm), and light. inactivation of cyns, encoding cyanase, and cyna yielded mutants unable t ... | 2007 | 17122352 |
| involvement of the cynabds operon and the co2-concentrating mechanism in the light-dependent transport and metabolism of cyanate by cyanobacteria. | the cyanobacteria synechococcus elongatus strain pcc7942 and synechococcus sp. strain utex625 decomposed exogenously supplied cyanate (nco-) to co2 and nh3 through the action of a cytosolic cyanase which required hco3- as a second substrate. the ability to metabolize nco- relied on three essential elements: proteins encoded by the cynabds operon, the biophysical activity of the co2-concentrating mechanism (ccm), and light. inactivation of cyns, encoding cyanase, and cyna yielded mutants unable t ... | 2007 | 17122352 |
| phytohormone production by three strains of bradyrhizobium japonicum and possible physiological and technological implications. | the aim of this work was to evaluate phytohormone biosynthesis, siderophores production, and phosphate solubilization in three strains (e109, usda110, and semia5080) of bradyrhizobium japonicum, most commonly used for inoculation of soybean and nonlegumes in usa, canada, and south america. siderophore production and phosphate solubilization were evaluated in selective culture conditions, which had negative results. indole-3-acetic acid (iaa), gibberellic acid (ga(3)), and abscisic acid (aba) pro ... | 2007 | 17136369 |
| a diffusible signal from arbuscular mycorrhizal fungi elicits a transient cytosolic calcium elevation in host plant cells. | the implication of calcium as intracellular messenger in the arbuscular mycorrhizal (am) symbiosis has not yet been directly demonstrated, although often envisaged. we used soybean (glycine max) cell cultures stably expressing the bioluminescent ca(2+) indicator aequorin to detect intracellular ca(2+) changes in response to the culture medium of spores of gigaspora margarita germinating in the absence of the plant partner. rapid and transient elevations in cytosolic free ca(2+) were recorded, in ... | 2007 | 17142489 |
| evolution of enzymatic activities in the enolase superfamily: d-tartrate dehydratase from bradyrhizobium japonicum. | we focus on the assignment of function to and elucidation of structure-function relationships for a member of the mechanistically diverse enolase superfamily encoded by the bradyrhizobium japonicum genome (bll6730; gi:27381841). as suggested by sequence alignments, the active site contains the same functional groups found in the active site of mandelate racemase (mr) that catalyzes a 1,1-proton transfer reaction: two acid/base catalysts, lys 184 at the end of the second beta-strand, and a his 32 ... | 2006 | 17144653 |
| coverage of whole proteome by structural genomics observed through protein homology modeling database. | we have been developing famsbase, a protein homology-modeling database of whole orfs predicted from genome sequences. the latest update of famsbase ( http://daisy.nagahama-i-bio.ac.jp/famsbase/ ), which is based on the protein three-dimensional (3d) structures released by november 2003, contains modeled 3d structures for 368,724 open reading frames (orfs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. those 276 genomes are pr ... | 2006 | 17146617 |
| only one of five groel genes is required for viability and successful symbiosis in sinorhizobium meliloti. | many bacterial species contain multiple copies of the genes that encode the chaperone groel and its cochaperone, groes, including all of the fully sequenced root-nodulating bacteria that interact symbiotically with legumes to generate fixed nitrogen. in particular, in sinorhizobium meliloti there are four groesl operons and one groel gene. to uncover functional redundancies of these genes during growth and symbiosis, we attempted to construct strains containing all combinations of groel mutation ... | 2007 | 17158666 |
| only one of five groel genes is required for viability and successful symbiosis in sinorhizobium meliloti. | many bacterial species contain multiple copies of the genes that encode the chaperone groel and its cochaperone, groes, including all of the fully sequenced root-nodulating bacteria that interact symbiotically with legumes to generate fixed nitrogen. in particular, in sinorhizobium meliloti there are four groesl operons and one groel gene. to uncover functional redundancies of these genes during growth and symbiosis, we attempted to construct strains containing all combinations of groel mutation ... | 2007 | 17158666 |
| messing with bacterial quorum sensing. | quorum sensing is widely recognized as an efficient mechanism to regulate expression of specific genes responsible for communal behavior in bacteria. several bacterial phenotypes essential for the successful establishment of symbiotic, pathogenic, or commensal relationships with eukaryotic hosts, including motility, exopolysaccharide production, biofilm formation, and toxin production, are often regulated by quorum sensing. interestingly, eukaryotes produce quorum-sensing-interfering (qsi) compo ... | 2006 | 17158701 |
| stimulus perception in bacterial signal-transducing histidine kinases. | two-component signal-transducing systems are ubiquitously distributed communication interfaces in bacteria. they consist of a histidine kinase that senses a specific environmental stimulus and a cognate response regulator that mediates the cellular response, mostly through differential expression of target genes. histidine kinases are typically transmembrane proteins harboring at least two domains: an input (or sensor) domain and a cytoplasmic transmitter (or kinase) domain. they can be identifi ... | 2006 | 17158704 |
| how phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. | the phosphoenolpyruvate(pep):carbohydrate phosphotransferase system (pts) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. to carry out its catalytic function in sugar transport and phosphorylation, the pts uses pep as an energy source and phosphoryl donor. the phosphoryl group of pep is usually transferred via four distinct proteins (domains) to the transported sugar bo ... | 2006 | 17158705 |
| membrane physical state as key parameter for the resistance of the gram-negative bradyrhizobium japonicum to hyperosmotic treatments. | the survival of bradyrhizobium japonicum under hyperosmotic treatments achieved at various temperatures was investigated. the bacterial viability was measured at a combination of different levels of osmotic pressure (1.4-49.2 mpa) in glycerol solutions and temperature (4-28 degrees c). viability was dependent on these two variables, with low temperatures (10 and 4 degrees c) exhibiting a protective effect against exposure to high levels of osmotic pressure. to understand these results, the relat ... | 2007 | 17160674 |
| characterization of the thermotoga maritima chemotaxis methylation system that lacks pentapeptide-dependent methyltransferase cher:mcp tethering. | sensory adaptation in bacterial chemotaxis is mediated by covalent modifications of specific glutamate and glutamine residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins (mcps). in escherichia coli and salmonella enterica, efficient methylation of mcps depends on the localization of methyltransferase cher to mcp clusters through an interaction between the cher beta-subdomain and a pentapeptide sequence (nwetf or nwesf) at the c-terminus of the mcp. in vitro methylation ... | 2007 | 17163981 |
| characterization of the thermotoga maritima chemotaxis methylation system that lacks pentapeptide-dependent methyltransferase cher:mcp tethering. | sensory adaptation in bacterial chemotaxis is mediated by covalent modifications of specific glutamate and glutamine residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins (mcps). in escherichia coli and salmonella enterica, efficient methylation of mcps depends on the localization of methyltransferase cher to mcp clusters through an interaction between the cher beta-subdomain and a pentapeptide sequence (nwetf or nwesf) at the c-terminus of the mcp. in vitro methylation ... | 2007 | 17163981 |
| high precision multi-genome scale reannotation of enzyme function by eficaz. | the functional annotation of most genes in newly sequenced genomes is inferred from similarity to previously characterized sequences, an annotation strategy that often leads to erroneous assignments. we have performed a reannotation of 245 genomes using an updated version of eficaz, a highly precise method for enzyme function prediction. | 2006 | 17166279 |
| [cloning and identification of cellulase genes from uncultured microorganisms in pulp sediments from paper mill effluent]. | the metagenomic dna of pulp sediments from paper mill effluent was extracted and purified. the 16s rdna was amplified using the purified metagenomic dna as template and a 16s rdna library was prepared. sequence analysis of 16s rdna clones showed that diverse of uncultured bacteria inhabit in this environment, which can be classified into 4 clusters as spirochaetes, proteobacteria, bacteroidetes and firmicutes. a metagenomic library containing 10000 clones was constructed into cosmid vector, and ... | 2006 | 17172029 |
| oxygen reactivity of both respiratory oxidases in campylobacter jejuni: the cydab genes encode a cyanide-resistant, low-affinity oxidase that is not of the cytochrome bd type. | the microaerophilic bacterium campylobacter jejuni is a significant food-borne pathogen and is predicted to possess two terminal respiratory oxidases with unknown properties. inspection of the genome reveals an operon (cydab) apparently encoding a cytochrome bd-like oxidase homologous to oxidases in escherichia coli and azotobacter vinelandii. however, c. jejuni cells lacked all spectral signals characteristic of the high-spin hemes b and d of these oxidases. mutation of the cydab operon of c. j ... | 2007 | 17172349 |
| oxygen reactivity of both respiratory oxidases in campylobacter jejuni: the cydab genes encode a cyanide-resistant, low-affinity oxidase that is not of the cytochrome bd type. | the microaerophilic bacterium campylobacter jejuni is a significant food-borne pathogen and is predicted to possess two terminal respiratory oxidases with unknown properties. inspection of the genome reveals an operon (cydab) apparently encoding a cytochrome bd-like oxidase homologous to oxidases in escherichia coli and azotobacter vinelandii. however, c. jejuni cells lacked all spectral signals characteristic of the high-spin hemes b and d of these oxidases. mutation of the cydab operon of c. j ... | 2007 | 17172349 |
| computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria. | we used comparative genomics to investigate the distribution of conserved dna-binding motifs in the regulatory regions of genes involved in iron and manganese homeostasis in alpha-proteobacteria. combined with other computational approaches, this allowed us to reconstruct the metal regulatory network in more than three dozen species with available genome sequences. we identified several classes of cis-acting regulatory dna motifs (irr-boxes or ices, rira-boxes, iron-rhodo-boxes, fur-alpha-boxes, ... | 2006 | 17173478 |
| identification of important regions for ethylene binding and signaling in the transmembrane domain of the etr1 ethylene receptor of arabidopsis. | the ethylene binding domain (ebd) of the arabidopsis thaliana etr1 receptor is modeled as three membrane-spanning helices. we surveyed ethylene binding activity in different kingdoms and performed a bioinformatic analysis of the ebd. ethylene binding is confined to land plants, chara, and a group of cyanobacteria but is largely absent in other organisms, consistent with our finding that ebd-like sequences are overrepresented among plant and cyanobacterial species. we made amino acid substitution ... | 2006 | 17189345 |
| direct response of bradyrhizobium japonicum nifa-mediated nif gene regulation to cellular oxygen status. | the nifa genes of klebsiella pneumoniae and bradyrhizobium japonicum were constitutively expressed from the pbr329-derived chloramphenicol resistance promoter. the inserts of these nifa plasmid constructs were devoid of any other intact flanking genes. the nifa genes thus expressed led to a marked activation of a b. japonicum nifd-lacz fusion under microaerobic conditions. under aerobic growth conditions, however, activation was mediated only by the k. pneumoniae nifa gene but not by the b. japo ... | 1987 | 17193716 |