| production of amino acids by rhizobium, mesorhizobium and sinorhizobium strains in chemically defined media. | five strains of rhizobium spp, one strain of mesorhizobium loti and two strains of sinorhizobium meliloti were tested for their ability to grow in chemically-defined medium lacking growth factor. qualitative and quantitative production of aspartic acid, serine, glutamic acid, glycine, histidine, threonine, arginine, alanine, proline, cysteine, tyrosine, valine, methionine, lysine, isoleucine, leucine, and phenylalanine was determined by the use of mannitol as sole carbon source. strains of rhizo ... | 2004 | 15378411 |
| release of periplasmic proteins of brucella suis upon acidic shock involves the outer membrane protein omp25. | the survival and replication of brucella in macrophages is initially triggered by a low intraphagosomal ph. in order to identify proteins released by brucella during this early acidification step, we analyzed brucella suis conditioned medium at various ph levels. no significant proteins were released at ph 4.0 in minimal medium or citrate buffer, whereas in acetate buffer, b. suis released a substantial amount of soluble proteins. comparison of 13 n-terminal amino acid sequences determined by ed ... | 2004 | 15385468 |
| the ton system, an abc transporter, and a universally conserved gtpase are involved in iron utilization by brucella melitensis 16m. | brucella spp. are gram-negative intracellular facultative pathogens that are known to produce 2,3-dihydroxybenzoic acid (dhba), a catechol siderophore that is essential for full virulence in the natural host. the mechanism of dhba entry into brucella and other gram-negative bacteria is poorly understood. using mini-tn5kmcat mutagenesis, we created a transposon library of brucella melitensis 16m and isolated 32 mutants with a defect in iron acquisition or assimilation. three of these transposon m ... | 2004 | 15385478 |
| the structure and ligand binding properties of the b. subtilis ykof gene product, a member of a novel family of thiamin/hmp-binding proteins. | the crystal structure of the bacillus subtilis ykof gene product, a protein involved in the hydroxymethyl pyrimidine (hmp) salvage pathway, was solved by the multiwavelength anomalous dispersion (mad) method and refined with data extending to 1.65 a resolution. the atomic model of the protein shows a homodimeric association of two polypeptide chains, each containing an internal repeat of a ferredoxin-like betaalphabetabetaalphabeta fold, as seen in the act and ram-domains. each repeat shows a re ... | 2004 | 15451668 |
| complete genome sequence of the industrial bacterium bacillus licheniformis and comparisons with closely related bacillus species. | bacillus licheniformis is a gram-positive, spore-forming soil bacterium that is used in the biotechnology industry to manufacture enzymes, antibiotics, biochemicals and consumer products. this species is closely related to the well studied model organism bacillus subtilis, and produces an assortment of extracellular enzymes that may contribute to nutrient cycling in nature. | 2004 | 15461803 |
| expression profiling in medicago truncatula identifies more than 750 genes differentially expressed during nodulation, including many potential regulators of the symbiotic program. | in this study, we describe a large-scale expression-profiling approach to identify genes differentially regulated during the symbiotic interaction between the model legume medicago truncatula and the nitrogen-fixing bacterium sinorhizobium meliloti. macro- and microarrays containing about 6,000 probes were generated on the basis of three cdna libraries dedicated to the study of root symbiotic interactions. the experiments performed on wild-type and symbiotic mutant material led us to identify a ... | 2004 | 15466239 |
| expression of an exogenous 1-aminocyclopropane-1-carboxylate deaminase gene in sinorhizobium meliloti increases its ability to nodulate alfalfa. | 1-aminocyclopropane-1-carboxylate (acc) deaminase has been found in various plant growth-promoting rhizobacteria, including rhizobia. this enzyme degrades acc, the immediate precursor of ethylene, and thus decreases the biosynthesis of ethylene in higher plants. the acc deaminase of rhizobium leguminosarum bv. viciae 128c53k was previously reported to be able to enhance nodulation of peas. the acc deaminase structural gene (acds) and its upstream regulatory gene, a leucine-responsive regulatory ... | 2004 | 15466529 |
| functional expression of sinorhizobium meliloti bets, a high-affinity betaine transporter, in bradyrhizobium japonicum usda110. | among the rhizobiaceae, bradyrhizobium japonicum strain usda110 appears to be extremely salt sensitive, and the presence of glycine betaine cannot restore its growth in medium with an increased osmolarity (e. boncompagni, m. osteras, m. c. poggi, and d. le rudulier, appl. environ. microbiol. 65:2072-2077, 1999). in order to improve the salt tolerance of b. japonicum, cells were transformed with the bets gene of sinorhizobium meliloti. this gene encodes a major glycine betaine/proline betaine tra ... | 2004 | 15466533 |
| unexpectedly diverse mesorhizobium strains and rhizobium leguminosarum nodulate native legume genera of new zealand, while introduced legume weeds are nodulated by bradyrhizobium species. | the new zealand native legume flora are represented by four genera, sophora, carmichaelia, clianthus, and montigena. the adventive flora of new zealand contains several legume species introduced in the 19th century and now established as serious invasive weeds. until now, nothing has been reported on the identification of the associated rhizobia of native or introduced legumes in new zealand. the success of the introduced species may be due, at least in part, to the nature of their rhizobial sym ... | 2004 | 15466541 |
| comparative genomics of the ftsk-hera superfamily of pumping atpases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. | recently, it has been shown that a predicted p-loop atpase (the hera or mlaa protein), which is highly conserved in archaea and also present in many bacteria but absent in eukaryotes, has a bidirectional helicase activity and forms hexameric rings similar to those described for the trwb atpase. in this study, the ftsk-hera superfamily of p-loop atpases, in which the hera clade comprises one of the major branches, is analyzed in detail. we show that, in addition to the ftsk and hera clades, this ... | 2004 | 15466593 |
| the complete genomic sequence of nocardia farcinica ifm 10152. | we determined the genomic sequence of nocardia farcinica ifm 10152, a clinical isolate, and revealed the molecular basis of its versatility. the genome consists of a single circular chromosome of 6,021,225 bp with an average g+c content of 70.8% and two plasmids of 184,027 (pnf1) and 87,093 (pnf2) bp with average g+c contents of 67.2% and 68.4%, respectively. the chromosome encoded 5,674 putative protein-coding sequences, including many candidate genes for virulence and multidrug resistance as w ... | 2004 | 15466710 |
| symbiotic phenotypes and translocated effector proteins of the mesorhizobium loti strain r7a virb/d4 type iv secretion system. | the symbiosis island of mesorhizobium loti strain r7a contains genes with strong similarity to the structural vir genes (virb1-11; vird4) of agrobacterium tumefaciens that encode the type iv secretion system (t4ss) required for t-dna transfer to plants. in contrast, m. loti strain maff303099 lacks these genes but contains genes not present in strain r7a that encode a type iii secretion system (t3ss). here we show by hybridization analysis that most m. loti strains contain the virb/d4 t4ss and no ... | 2004 | 15469524 |
| variation suggestive of horizontal gene transfer at a lipopolysaccharide (lps) biosynthetic locus in xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen of rice. | in animal pathogenic bacteria, horizontal gene transfer events (hgt) have been frequently observed in genomic regions that encode functions involved in biosynthesis of the outer membrane located lipopolysaccharide (lps). as a result, different strains of the same pathogen can have substantially different lps biosynthetic gene clusters. since lps is highly antigenic, the variation at lps loci is attributed to be of advantage in evading the host immune system. although lps has been suggested as a ... | 2004 | 15473911 |
| generation of the brucella melitensis orfeome version 1.1. | the bacteria of the brucella genus are responsible for a worldwide zoonosis called brucellosis. they belong to the alpha-proteobacteria group, as many other bacteria that live in close association with a eukaryotic host. importantly, the brucellae are mainly intracellular pathogens, and the molecular mechanisms of their virulence are still poorly understood. using the complete genome sequence of brucella melitensis, we generated a database of protein-coding open reading frames (orfs) and constru ... | 2004 | 15489343 |
| the prc-barrel domain of the ribosome maturation protein rimm mediates binding to ribosomal protein s19 in the 30s ribosomal subunits. | the rimm protein in escherichia coli is associated with free 30s ribosomal subunits but not with 70s ribosomes. a deltarimm mutant is defective in 30s maturation and accumulates 17s rrna. to study the interaction of rimm with the 30s and its involvement in 30s maturation, rimm amino acid substitution mutants were constructed. a mutant rimm (rimm-yy-->aa), containing alanine substitutions for two adjacent tyrosines within the prc beta-barrel domain, showed a reduced binding to 30s and an accumula ... | 2004 | 15496525 |
| large-scale analysis of gene expression profiles during early stages of root nodule formation in a model legume, lotus japonicus. | gene expression profiles during early stages of formation of symbiotic nitrogen-fixing nodules in a model legume lotus japonicus were analyzed by means of a cdna array of 18,144 non-redundant expressed sequence tags (ests) isolated from l. japonicus. expression of a total of 1,076 genes was significantly accelerated during the successive stages that represent infection of mesorhizobium loti, nodule primordium initiation, nodule organogenesis, and the onset of nitrogen fixation. these include 32 ... | 2004 | 15500251 |
| oxa-60, a chromosomal, inducible, and imipenem-hydrolyzing class d beta-lactamase from ralstonia pickettii. | a chromosomally encoded oxacillinase, oxa-22, had been characterized from ralstonia pickettii pic-1 that did not explain by itself the resistance profile of this strain to beta-lactams. thus, further analysis of the genetic background of this species led to the identification of another oxacillinase, oxa-60, that was expressed only after beta-lactam induction. this chromosomally encoded oxacillinase shared 19% amino acid identity with oxa-22. it has a narrow-spectrum hydrolysis profile that incl ... | 2004 | 15504844 |
| transfer of the symbiotic plasmid of rhizobium etli cfn42 requires cointegration with p42a, which may be mediated by site-specific recombination. | plasmid p42a from rhizobium etli cfn42 is self-transmissible and indispensable for conjugative transfer of the symbiotic plasmid (psym). most psym transconjugants also inherit p42a. psym transconjugants that lack p42a always contain recombinant psyms, which we designated rpsyms*. rpsyms* do not contain some psym segments and instead have p42a sequences, including the replication and transfer regions. these novel recombinant plasmids are compatible with wild-type psym, incompatible with p42a, and ... | 2004 | 15516565 |
| a novel archaeal alanine dehydrogenase homologous to ornithine cyclodeaminase and mu-crystallin. | a novel alanine dehydrogenase (aladh) showing no significant amino acid sequence homology with previously known bacterial aladhs was purified to homogeneity from the soluble fraction of the hyperthermophilic archaeon archaeoglobus fulgidus. aladh catalyzed the reversible, nad+-dependent deamination of l-alanine to pyruvate and nh4+. nadp(h) did not serve as a coenzyme. the enzyme is a homodimer of 35 kda per subunit. the km values for l-alanine, nad+, pyruvate, nadh, and nh4+ were estimated at 0 ... | 2004 | 15516582 |
| characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16s ribosomal dna terminal restriction fragment length polymorphism profiling. | progressive loss of lung function resulting from the inflammatory response to bacterial colonization is the leading cause of mortality in cystic fibrosis (cf) patients. a greater understanding of these bacterial infections is needed to improve lung disease management. as culture-based diagnoses are associated with fundamental drawbacks, we used terminal restriction fragment (t-rf) length polymorphism profiling and 16s rrna clone data to characterize, without prior cultivation, the bacterial comm ... | 2004 | 15528712 |
| bartonella adhesin a mediates a proangiogenic host cell response. | bartonella henselae causes vasculoproliferative disorders in humans. we identified a nonfimbrial adhesin of b. henselae designated as bartonella adhesin a (bada). bada is a 340-kd outer membrane protein encoded by the 9.3-kb bada gene. it has a modular structure and contains domains homologous to the yersinia enterocolitica nonfimbrial adhesin (yersinia adhesin a). expression of bada was restored in a bada-deficient transposon mutant by complementation in trans. bada mediates the binding of b. h ... | 2004 | 15534369 |
| a genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. | the timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. however, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. we assembled a data set of sequences from 32 proteins (approximately 7600 amino acids) common to 72 species ... | 2004 | 15535883 |
| structural basis of ligand activation in a cyclic nucleotide regulated potassium channel. | here we describe the initial functional characterization of a cyclic nucleotide regulated ion channel from the bacterium mesorhizobium loti and present two structures of its cyclic nucleotide binding domain, with and without camp. the domains are organized as dimers with the interface formed by the linker regions that connect the nucleotide binding pocket to the pore domain. together, structural and functional data suggest the domains form two dimers on the cytoplasmic face of the channel. we pr ... | 2004 | 15550244 |
| widespread presence of "bacterial-like" ppp phosphatases in eukaryotes. | in eukaryotes, ppp (protein phosphatase p) family is one of the two known protein phosphatase families specific for ser and thr. the role of ppp phosphatases in multiple signaling pathways in eukaryotic cell has been extensively studied. unlike eukaryotic ppp phosphatases, bacterial members of the family have broad substrate specificity or may even be tyr-specific. moreover, one group of bacterial ppps are diadenosine tetraphosphatases, indicating that bacterial ppp phosphatases may not necessar ... | 2004 | 15555063 |
| complete nucleotide sequence of the conjugative tetracycline resistance plasmid pfbaot6, a member of a group of incu plasmids with global ubiquity. | this study presents the first complete sequence of an incu plasmid, pfbaot6. this plasmid was originally isolated from a strain of aeromonas caviae from hospital effluent (westmorland general hospital, kendal, united kingdom) in september 1997 (g. rhodes, g. huys, j. swings, p. mcgann, m. hiney, p. smith, and r. w. pickup, appl. environ. microbiol. 66:3883-3890, 2000) and belongs to a group of related plasmids with global ubiquity. pfbaot6 is 84,748 bp long and has 94 predicted coding sequences, ... | 2004 | 15574953 |
| nucleotide sequences, genetic organization, and distribution of peu30 and pel60 from erwinia amylovora. | the nucleotide sequences, genetic organization, and distribution of plasmids peu30 (30,314 bp) and pel60 (60,145 bp) from the plant pathogen erwinia amylovora are described. the newly characterized peu30 and pel60 plasmids inhabited strains isolated in the western united states and lebanon, respectively. the gene content of peu30 resembled plasmids found in plant-associated bacteria, while that of pel60 was most similar to incl/m plasmids inhabiting enteric bacteria. | 2004 | 15574957 |
| a genetic locus necessary for rhamnose uptake and catabolism in rhizobium leguminosarum bv. trifolii. | rhizobium leguminosarum bv. trifolii mutants unable to catabolize the methyl-pentose rhamnose are unable to compete effectively for nodule occupancy. in this work we show that the locus responsible for the transport and catabolism of rhamnose spans 10,959 bp. mutations in this region were generated by transposon mutagenesis, and representative mutants were characterized. the locus contains genes coding for an abc-type transporter, a putative dehydrogenase, a probable isomerase, and a sugar kinas ... | 2004 | 15576793 |
| new insights into type ii nad(p)h:quinone oxidoreductases. | type ii nad(p)h:quinone oxidoreductases (ndh-2) catalyze the two-electron transfer from nad(p)h to quinones, without any energy-transducing site. ndh-2 accomplish the turnover of nad(p)h, regenerating the nad(p)(+) pool, and may contribute to the generation of a membrane potential through complexes iii and iv. these enzymes are usually constituted by a nontransmembrane polypeptide chain of approximately 50 kda, containing a flavin moiety. there are a few compounds that can prevent their activity ... | 2004 | 15590775 |
| glutathione plays a fundamental role in growth and symbiotic capacity of sinorhizobium meliloti. | rhizobia form a symbiotic relationship with plants of the legume family to produce nitrogen-fixing root nodules under nitrogen-limiting conditions. we have examined the importance of glutathione (gsh) during free-living growth and symbiosis of sinorhizobium meliloti. an s. meliloti mutant strain (smgsha) which is unable to synthesize gsh due to a gene disruption in gsha, encoding the enzyme for the first step in the biosynthesis of gsh, was unable to grow under nonstress conditions, precluding a ... | 2005 | 15601700 |
| luxr homolog avhr in agrobacterium vitis affects the development of a grape-specific necrosis and a tobacco hypersensitive response. | the luxr homolog avir in agrobacterium vitis strain f2/5 was recently shown to be associated with induction of a hypersensitive response (hr) on tobacco and necrosis on grape plants, indicating that the responses are regulated by quorum sensing. we now report a second luxr homolog, avhr, whose disruption (mutant m1320) results in hr-negative and reduced grape necrosis phenotypes. the deduced avhr protein has characteristic autoinducer binding and dna binding domains and is unique among reported ... | 2005 | 15601702 |
| the kata catalase gene is regulated by oxyr in both free-living and symbiotic sinorhizobium meliloti. | the characterization of an oxyr insertion mutant provides evidences that kata, which encodes the unique h2o2-inducible hpii catalase, is regulated by oxyr not only in free-living sinorhizobium meliloti but also in symbiotic s. meliloti. moreover, oxyr is expressed independently of exogenous h2o2 and downregulates its own expression in s. meliloti. | 2005 | 15601722 |
| positive charge is an important feature of the c-terminal transport signal of the virb/d4-translocated proteins of agrobacterium. | several human pathogens and the plant pathogen agrobacterium tumefaciens use a type iv secretion system for translocation of effector proteins into host cells. how effector proteins are selected for transport is unknown, but a c-terminal transport signal is present in the proteins translocated by the a. tumefaciens virb/d4 type iv secretion system. we characterized this signal in the virulence protein virf by alanine scanning and further site-directed mutagenesis. the cre recombinase was used as ... | 2005 | 15644442 |
| nopb, a type iii secreted protein of rhizobium sp. strain ngr234, is associated with pilus-like surface appendages. | rhizobium sp. strain ngr234 possesses a functional type three secretion system (ttss), through which a number of proteins, called nodulation outer proteins (nops), are delivered to the outside of the cell. a major constraint to the identification of nops is their low abundance in the supernatants of ngr234 strains grown in culture. to overcome this limitation, a more sensitive proteomics-based strategy was developed. secreted proteins from wild-type ngr234 were separated by two-dimensional gel e ... | 2005 | 15659692 |
| symbiotic rhizobium and nitric oxide induce gene expression of non-symbiotic hemoglobin in lotus japonicus. | we characterized the expression profiles of ljhb1 and ljhb2, non-symbiotic hemoglobin (non-sym-hb) genes of lotus japonicus. although ljhb1 and ljhb2 showed 77% homology in their cdna sequences, ljhb2 is located in a unique position in the phylogenetic tree of plant hbs. the 5'-upstream regions of both genes contain the motif aaaggg at a position similar to that in promoters of other non-sym-hb genes. expression profiles obtained by using quantitative rt-pcr showed that ljhb1 and ljhb2 were expr ... | 2005 | 15668209 |
| ectoine-induced proteins in sinorhizobium meliloti include an ectoine abc-type transporter involved in osmoprotection and ectoine catabolism. | to understand the mechanisms of ectoine-induced osmoprotection in sinorhizobium meliloti, a proteomic examination of s. meliloti cells grown in minimal medium supplemented with ectoine was undertaken. this revealed the induction of 10 proteins. the protein products of eight genes were identified by using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. five of these genes, with four other genes whose products were not detected on two-dimensional gels, belong to the s ... | 2005 | 15687193 |
| protein domains and architectural innovation in plant-associated proteobacteria. | evolution of new complex biological behaviour tends to arise by novel combinations of existing building blocks. the functional and evolutionary building blocks of the proteome are protein domains, the function of a protein being dependent on its constituent domains. we clustered completely-sequenced proteomes of prokaryotes on the basis of their protein domain content, as defined by pfam (release 16.0). this revealed that, although there was a correlation between phylogeny and domain content, ot ... | 2005 | 15715905 |
| variation in the strength of selected codon usage bias among bacteria. | among bacteria, many species have synonymous codon usage patterns that have been influenced by natural selection for those codons that are translated more accurately and/or efficiently. however, in other species selection appears to have been ineffective. here, we introduce a population genetics-based model for quantifying the extent to which selection has been effective. the approach is applied to 80 phylogenetically diverse bacterial species for which whole genome sequences are available. the ... | 2005 | 15728743 |
| molecular and biochemical characterization of 2-hydroxyisoflavanone dehydratase. involvement of carboxylesterase-like proteins in leguminous isoflavone biosynthesis. | isoflavonoids are ecophysiologically active secondary metabolites of the leguminosae and known for health-promoting phytoestrogenic functions. isoflavones are synthesized by 1,2-elimination of water from 2-hydroxyisoflavanones, the first intermediate with the isoflavonoid skeleton, but details of this dehydration have been unclear. we screened the extracts of repeatedly fractionated escherichia coli expressing a glycyrrhiza echinata cdna library for the activity to convert a radiolabeled precurs ... | 2005 | 15734910 |
| crystal structure of a novel polyisoprenoid-binding protein from thermus thermophilus hb8. | the isoprenoid quinones exist widely among prokaryotes and eukaryotes. they play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. in the isoprenoid quinone biosynthetic pathway, polyprenyl pyrophosphates are used as isoprenoid side-chain precursors. here we report the crystal structure of a novel polyprenyl pyrophosphate binding protein, tt1927b, from thermus thermophilus hb8, complexed with its ligand. this protein belongs to the ycei-li ... | 2005 | 15741337 |
| rhizobial 16s rrna and dnak genes: mosaicism and the uncertain phylogenetic placement of rhizobium galegae. | the phylogenetic relatedness among 12 agriculturally important species in the order rhizobiales was estimated by comparative 16s rrna and dnak sequence analyses. two groups of related species were identified by neighbor-joining and maximum-parsimony analysis. one group consisted of mesorhizobium loti and mesorhizobium ciceri, and the other group consisted of agrobacterium rhizogenes, rhizobium tropici, rhizobium etli, and rhizobium leguminosarum. although bootstrap support for the placement of t ... | 2005 | 15746335 |
| quantitative molecular assay for fingerprinting microbial communities of wastewater and estrogen-degrading consortia. | a quantitative fingerprinting method, called the real-time terminal restriction fragment length polymorphism (real-time-t-rflp) assay, was developed for simultaneous determination of microbial diversity and abundance within a complex community. the real-time-t-rflp assay was developed by incorporating the quantitative feature of real-time pcr and the fingerprinting feature of t-rflp analysis. the assay was validated by using a model microbial community containing three pure strains, an escherich ... | 2005 | 15746346 |
| genomic analysis of bacteriophage phijl001: insights into its interaction with a sponge-associated alpha-proteobacterium. | bacteriophage phijl001 infects a novel marine bacterium in the alpha subclass of the proteobacteria isolated from the marine sponge ircinia strobilina. phijl001 is a siphovirus and forms turbid plaques on its host. the genome sequence of phijl001 was determined in order to better understand the interaction between the marine phage and its sponge-associated host bacterium. the complete genome sequence of phijl001 comprised 63,469 bp with an overall g+c content of 62%. the genome has 91 predicted ... | 2005 | 15746365 |
| lotus japonicus metabolic profiling. development of gas chromatography-mass spectrometry resources for the study of plant-microbe interactions. | symbiotic nitrogen fixation (snf) in legume root nodules requires differentiation and integration of both plant and bacterial metabolism. classical approaches of biochemistry, molecular biology, and genetics have revealed many aspects of primary metabolism in legume nodules that underpin snf. functional genomics approaches, especially transcriptomics and proteomics, are beginning to provide a more holistic picture of the metabolic potential of nodules in model legumes like medicago truncatula an ... | 2005 | 15749991 |
| potential limitations of the 16s-23s rrna intergenic region for molecular detection of bartonella species. | pcr targeting the 16s-23s rrna gene intergenic transcribed spacer (its) region has been proposed as a rapid and reliable method for the detection of bartonella species dna in clinical samples. because of variation in its sequences among bartonella species, a single pcr amplification can be used to detect different species within this genus. therefore, by targeting the its region, multiple pcrs or additional sample-processing steps beyond the primary amplification can be avoided when attempting t ... | 2005 | 15750079 |
| detection of and response to signals involved in host-microbe interactions by plant-associated bacteria. | diverse interactions between hosts and microbes are initiated by the detection of host-released chemical signals. detection of these signals leads to altered patterns of gene expression that culminate in specific and adaptive changes in bacterial physiology that are required for these associations. this concept was first demonstrated for the members of the family rhizobiaceae and was later found to apply to many other plant-associated bacteria as well as to microbes that colonize human and anima ... | 2005 | 15755957 |
| gene fusions and gene duplications: relevance to genomic annotation and functional analysis. | escherichia coli a model organism provides information for annotation of other genomes. our analysis of its genome has shown that proteins encoded by fused genes need special attention. such composite (multimodular) proteins consist of two or more components (modules) encoding distinct functions. multimodular proteins have been found to complicate both annotation and generation of sequence similar groups. previous work overstated the number of multimodular proteins in e. coli. this work corrects ... | 2005 | 15757509 |
| bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-iii secretion. | like many other pathogens, enterohaemorrhagic and enteropathogenic strains of escherichia coli employ a type-iii secretion system to translocate bacterial effector proteins into host cells, where they then disrupt a range of cellular functions. this system is encoded by the locus for enterocyte effacement. many of the genes within this locus have been assigned names and functions through homology with the better characterised ysc-yop system from yersinia spp. however, the functions and homologie ... | 2005 | 15757514 |
| a novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement. | in micrococcus luteus growth and resuscitation from starvation-induced dormancy is controlled by the production of a secreted growth factor. this autocrine resuscitation-promoting factor (rpf) is the founder member of a family of proteins found throughout and confined to the actinobacteria (high g + c gram-positive bacteria). the aim of this work was to search for and characterise a cognate gene family in the firmicutes (low g + c gram-positive bacteria) and obtain information about how they may ... | 2005 | 15774001 |
| the presumptive magnetosome protein mms16 is a poly(3-hydroxybutyrate) granule-bound protein (phasin) in magnetospirillum gryphiswaldense. | the mms16 protein has been previously found to be associated with isolated magnetosomes from two magnetospirillum strains. a function of this protein as a magnetosome-specific gtpase involved in the formation of intracellular magnetosome membrane vesicles was suggested. here we present a study of the mms16 protein from magnetospirillum gryphiswaldense to clarify its function. insertion-duplication mutagenesis of the mms16 gene did not affect the formation of magnetosome particles but resulted in ... | 2005 | 15774885 |
| invasion of lotus japonicus root hairless 1 by mesorhizobium loti involves the nodulation factor-dependent induction of root hairs. | in many legumes, including lotus japonicus and medicago truncatula, susceptible root hairs are the primary sites for the initial signal perception and physical contact between the host plant and the compatible nitrogen-fixing bacteria that leads to the initiation of root invasion and nodule organogenesis. however, diverse mechanisms of nodulation have been described in a variety of legume species that do not rely on root hairs. to clarify the significance of root hairs during the l. japonicus-me ... | 2005 | 15778455 |
| characterization of the lotus japonicus symbiotic mutant lot1 that shows a reduced nodule number and distorted trichomes. | we isolated a recessive symbiotic mutant of lotus japonicus that defines a genetic locus, lot1 (for low nodulation and trichome distortion). the nodule number per plant of the mutant was about one-fifth of that of the wild type. the lot1 mutant showed a moderate dwarf phenotype and distorted trichomes, but its root hairs showed no apparent differences to those of the wild type. infection thread formation after inoculation of mesorhizobium loti was repressed in lot1 compared to that in the wild t ... | 2005 | 15793069 |
| transgenic expression of the soybean apyrase in lotus japonicus enhances nodulation. | the soybean apyrase, gs52, was previously characterized as an early nodulin that is expressed in roots and localized to the plasma membrane. transgenic lotus japonicus plants were constructed constitutively expressing the gs52 apyrase. segregation and southern-blot analysis identified four single-copy sense lines, several double-copy sense lines, and one double-copy antisense line for further analysis. the single- and double-copy sense gs52 l. japonicus lines had enhanced nodulation that correla ... | 2005 | 15793071 |
| acetylation of a fucosyl residue at the reducing end of mesorhizobium loti nod factors is not essential for nodulation of lotus japonicus. | nodml-v(c(18:1), me, cb, acfuc) is a major component of lipo-chitin oligosaccharides (lcos), or nod factors, produced by mesorhizobium loti. the presence of a 4-o-acetylated fucosyl residue (acfuc) at the reducing end has been thought to be essential for symbiotic interactions with the compatible host plant, lotus japonicus. we generated an m. loti mutant in which the noll gene is disrupted; noll has been shown to encode acetyltransferase that is responsible for acetylation of the fucosyl residu ... | 2005 | 15805124 |
| the sulfate transporter sst1 is crucial for symbiotic nitrogen fixation in lotus japonicus root nodules. | symbiotic nitrogen fixation (snf) by intracellular rhizobia within legume root nodules requires the exchange of nutrients between host plant cells and their resident bacteria. little is known at the molecular level about plant transporters that mediate such exchanges. several mutants of the model legume lotus japonicus have been identified that develop nodules with metabolic defects that cannot fix nitrogen efficiently and exhibit retarded growth under symbiotic conditions. map-based cloning of ... | 2005 | 15805486 |
| completion of the genome sequence of brucella abortus and comparison to the highly similar genomes of brucella melitensis and brucella suis. | brucellosis is a worldwide disease of humans and livestock that is caused by a number of very closely related classical brucella species in the alpha-2 subdivision of the proteobacteria. we report the complete genome sequence of brucella abortus field isolate 9-941 and compare it to those of brucella suis 1330 and brucella melitensis 16 m. the genomes of these brucella species are strikingly similar, with nearly identical genetic content and gene organization. however, a number of insertion-dele ... | 2005 | 15805518 |
| biochemical and molecular characterization of a periplasmic hydrolase for oxidized polyvinyl alcohol from sphingomonas sp. strain 113p3. | oxidized polyvinyl alcohol hydrolase (oph) and polyvinyl alcohol dehydrogenase were found to be constitutively present in the periplasm of sphingomonas sp. strain 113p3 (formerly pseudomonas sp. 113p3). the oph was purified to homogeneity with a yield of 40 % and a 5.9-fold increase in specific activity. the enzyme was a homodimer consisting of 35 kda subunits. its activity was inhibited by pmsf, hg(2+) and zn(2+). the enzyme hydrolysed oxidized polyvinyl alcohol (oxidized pva) and p-nitrophenyl ... | 2005 | 15817792 |
| grafting between model legumes demonstrates roles for roots and shoots in determining nodule type and host/rhizobia specificity. | previous grafting experiments have demonstrated that legume shoots play a critical role in symbiotic development of nitrogen-fixing root nodules by regulating nodule number. here, reciprocal grafting experiments between the model legumes lotus japonicus and medicago truncatula were carried out to investigate the role of the shoot in the host-specificity of legume-rhizobia symbiosis and nodule type. lotus japonicus is nodulated by mesorhizobium loti and makes determinate nodules, whereas m. trunc ... | 2005 | 15824071 |
| processive lipid galactosyl/glucosyltransferases from agrobacterium tumefaciens and mesorhizobium loti display multiple specificities. | the glycosyltransferase family 21 (gt21) includes both enzymes of eukaryotic and prokaryotic organisms. many of the eukaryotic enzymes from animal, plant, and fungal origin have been characterized as uridine diphosphoglucose (udp-glc):ceramide glucosyltransferases (glucosylceramide synthases [gcs], ec 2.4.1.80). as the acceptor molecule ceramide is not present in most bacteria, the enzymatic specificities and functions of the corresponding bacterial glycosyltransferases remain elusive. in this s ... | 2005 | 15843594 |
| requirement of mgtc for brucella suis intramacrophage growth: a potential mechanism shared by salmonella enterica and mycobacterium tuberculosis for adaptation to a low-mg2+ environment. | a brucella suis mgtc mutant is defective for growth within macrophages and in low-mg(2+) medium. these phenotypes are strikingly similar to those observed with mgtc mutants from salmonella enterica and mycobacterium tuberculosis, two other pathogens that proliferate within phagosomes. mgtc appears as a remarkable virulence factor that would have been acquired by distantly related intracellular pathogens to contribute to the adaptation to a low-mg(2+) environment in the phagosome. | 2005 | 15845525 |
| microtubule dynamics in living root hairs: transient slowing by lipochitin oligosaccharide nodulation signals. | the incorporation of a fusion of green fluorescent protein and tubulin-alpha 6 from arabidopsis thaliana in root hairs of lotus japonicus has allowed us to visualize and quantify the dynamic parameters of the cortical microtubules in living root hairs. analysis of individual microtubule turnover in real time showed that only plus polymer ends contributed to overall microtubule dynamicity, exhibiting dynamic instability as the main type of microtubule behavior in lotus root hairs. comparison of t ... | 2005 | 15863517 |
| horizontal transfer of the high-pathogenicity island of yersinia pseudotuberculosis. | the horizontal transfer of genetic elements plays a major role in bacterial evolution. the high-pathogenicity island (hpi), which codes for an iron uptake system, is present and highly conserved in various enterobacteriaceae, suggesting its recent acquisition by lateral gene transfer. the aim of this work was to determine whether the hpi has kept its ability to be transmitted horizontally. we demonstrate here that the hpi is indeed transferable from a donor to a recipient yersinia pseudotubercul ... | 2005 | 15866919 |
| investigation of the catalytic triad of arylamine n-acetyltransferases: essential residues required for acetyl transfer to arylamines. | the nats (arylamine n-acetyltransferases) are a well documented family of enzymes found in both prokaryotes and eukaryotes. nats are responsible for the acetylation of a range of arylamine, arylhydrazine and hydrazine compounds. we present here an investigation into the catalytic triad of residues (cys-his-asp) and other structural features of nats using a variety of methods, including site-directed mutagenesis, x-ray crystallography and bioinformatics analysis, in order to investigate whether e ... | 2005 | 15869465 |
| genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes. | bacterial, archaeal, yeast, and fly genomes are compared with respect to predicted highly expressed (phx) genes and several genomic properties. there is a striking difference in the status of phx ribosomal protein (rp) genes where the archaeal genome generally encodes more rp genes and fewer phx rps compared with bacterial genomes. the increase in rps in archaea and eukaryotes compared with that in bacteria may reflect a more complex set of interactions in archaea and eukaryotes in regulating tr ... | 2005 | 15883367 |
| an sos-regulated operon involved in damage-inducible mutagenesis in caulobacter crescentus. | dna polymerases of the y-family, such as escherichia coli umuc and dinb, are specialized enzymes induced by the sos response, which bypass lesions allowing the continuation of dna replication. umudc orthologs are absent in caulobacter crescentus and other bacteria, raising the question about the existence of sos mutagenesis in these organisms. here, we report that the c.crescentus dinb ortholog is not involved in damage-induced mutagenesis. however, an operon composed of two hypothetical genes a ... | 2005 | 15886391 |
| promoter trapping in lotus japonicus reveals novel root and nodule gus expression domains. | agrobacterium-based transformation was used to introduce a promoter-less glucuronidase uida gene (beta-glucuronidase; gus) into lotus japonicus. transgenic plants were screened for gus activation at different stages after inoculation with its symbiont, mesorhizobium loti. functional gus fusion frequencies ranged from about 2 to 5% of the total number of transgenic lines. these lines provide excellent histological markers for tissue ontogeny analysis. some of the activations generated gus express ... | 2005 | 15899881 |
| prediction of functional modules based on comparative genome analysis and gene ontology application. | we present a computational method for the prediction of functional modules encoded in microbial genomes. in this work, we have also developed a formal measure to quantify the degree of consistency between the predicted and the known modules, and have carried out statistical significance analysis of consistency measures. we first evaluate the functional relationship between two genes from three different perspectives--phylogenetic profile analysis, gene neighborhood analysis and gene ontology ass ... | 2005 | 15901854 |
| nodule development induced by mesorhizobium loti mutant strains affected in polysaccharide synthesis. | the role of mesorhizobium loti surface polysaccharides on the nodulation process is not yet fully understood. in this article, we describe the nodulation phenotype of mutants affected in the synthesis of lipopolysaccharide (lps) and beta(1,2) cyclic glucan. m. loti lpsbeta2 mutant produces lps with reduced amount of o-antigen, whereas m. loti lpsbeta1 mutant produces lps totally devoid of o-antigen. both genes are clustered in the chromosome. based on amino acid sequence homology, lps sugar comp ... | 2005 | 15915643 |
| the tetr family of transcriptional repressors. | we have developed a general profile for the proteins of the tetr family of repressors. the stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix dna binding motif and adjacent regions in the three-dimensional structures of tetr, qacr, cprb, and ethr, four family members for which the function and three-dimensional structure are known. we have detected a set of 2,353 nonredundant proteins belonging to this family by scree ... | 2005 | 15944459 |
| a census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial iq, extroverts and introverts. | analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction. | 2005 | 15955239 |
| signature proteins that are distinctive of alpha proteobacteria. | the alpha (alpha) proteobacteria, a very large and diverse group, are presently characterized solely on the basis of 16s rrna trees, with no known molecular characteristic that is unique to this group. the genomes of three alpha-proteobacteria, rickettsia prowazekii (rp), caulobacter crescentus (cc) and bartonella quintana (bq), were analyzed in order to search for proteins that are unique to this group. | 2005 | 15960851 |
| pyd genes of rhizobium sp. strain tal1145 are required for degradation of 3-hydroxy-4-pyridone, an aromatic intermediate in mimosine metabolism. | rhizobium sp. strain tal1145 degrades the leucaena toxin mimosine and its degradation product 3-hydroxy-4-pyridone (hp). the aim of this investigation is to characterize the rhizobium genes for hp degradation and transport. these genes were localized by subcloning and mutagenesis on a previously isolated cosmid, puhr263, containing mid genes of tal1145 required for mimosine degradation. two structural genes, pyda and pydb, encoding a metacleavage dioxygenase and a hydrolase, respectively, are re ... | 2005 | 15968058 |
| codon usage comparison of novel genes in clinical isolates of haemophilus influenzae. | a similarity statistic for codon usage was developed and used to compare novel gene sequences found in clinical isolates of haemophilus influenzae with a reference set of 80 prokaryotic, eukaryotic and viral genomes. these analyses were performed to obtain an indication as to whether individual genes were haemophilus-like in nature, or if they probably had more recently entered the h.influenzae gene pool via horizontal gene transfer from other species. the average and sd values were calculated f ... | 2005 | 15983137 |
| purification and characterization of a novel alcohol dehydrogenase from leifsonia sp. strain s749: a promising biocatalyst for an asymmetric hydrogen transfer bioreduction. | to find microorganisms that could reduce phenyl trifluoromethyl ketone (ptk) to (s)-1-phenyltrifluoroethanol [(s)-pte], styrene-assimilating bacteria (ca. 900 strains) isolated from soil samples were screened. we found that leifsonia sp. strain s749 was the most suitable strain for the conversion of ptk to (s)-pte in the presence of 2-propanol as a hydrogen donor. the enzyme corresponding to the reaction was purified homogeneity, characterized and designated leifsonia alcohol dehydrogenase (lsad ... | 2005 | 16000771 |
| l: -stereoselective amino acid amidase with broad substrate specificity from brevundimonas diminuta: characterization of a new member of the leucine aminopeptidase family. | brevundimonas diminuta tpu 5720 produces an amidase acting l-stereoselectively on phenylalaninamide. the enzyme (laaa(bd)) was purified to electrophoretic homogeneity by ammonium sulfate fractionation and four steps of column chromatography. the final preparation gave a single band on sds-page with a molecular weight of approximately 53,000. the native molecular weight of the enzyme was about 288,000 based on gel filtration chromatography, suggesting that the enzyme is active as a homohexamer. i ... | 2006 | 16001251 |
| variant tricarboxylic acid cycle in mycobacterium tuberculosis: identification of alpha-ketoglutarate decarboxylase. | mycobacterium tuberculosis (mtb) has adapted its metabolism for persistence in the human macrophage. the adaptations are likely to involve mtb's core intermediary metabolism, whose enzymes have been little studied. the tricarboxylic acid cycle is expected to yield precursors for energy, lipids, amino acids, and heme. the genome sequence of mtb h37rv predicts the presence of a complete tricarboxylic acid cycle, but we recently found that alpha-ketoglutarate dehydrogenase (kdh) activity is lacking ... | 2005 | 16027371 |
| the stringent response is required for amino acid and nitrate utilization, nod factor regulation, nodulation, and nitrogen fixation in rhizobium etli. | a rhizobium etli tn5 insertion mutant, lm01, was selected for its inability to use glutamine as the sole carbon and nitrogen source. the tn5 insertion in lm01 was localized to the rsh gene, which encodes a member of the rela/spot family of proteins. the lm01 mutant was affected in the ability to use amino acids and nitrate as nitrogen sources and was unable to accumulate (p)ppgpp when grown under carbon and nitrogen starvation, as opposed to the wild-type strain, which accumulated (p)ppgpp under ... | 2005 | 16030199 |
| de novo alanine synthesis by bacteroids of mesorhizobium loti is not required for nitrogen transfer in the determinate nodules of lotus corniculatus. | deletion of both alanine dehydrogenase genes (alda) in mesorhizobium loti resulted in the loss of alda enzyme activity from cultured bacteria and bacteroids but had no effect on the symbiotic performance of lotus corniculatus plants. thus, neither indeterminate pea nodules nor determinate l. corniculatus nodules export alanine as the sole nitrogen secretion product. | 2005 | 16030244 |
| role of trehalose transport and utilization in sinorhizobium meliloti--alfalfa interactions. | genes thua and thub in sinorhizobium meliloti rm1021 code for a major pathway for trehalose catabolism and are induced by trehalose but not by related structurally similar disaccharides like sucrose or maltose. s. meliloti strains mutated in either of these two genes were severely impaired in their ability to grow on trehalose as the sole source of carbon. thua and thub show no homology to any known enzymes in trehalose utilization. thua has similarity to proteins of unknown function in mesorhiz ... | 2005 | 16042015 |
| nodulation phenotypes of gibberellin and brassinosteroid mutants of pea. | the initiation and development of legume nodules induced by compatible rhizobium species requires a complex signal exchange involving both plant and bacterial compounds. phytohormones have been implicated in this process, although in many cases direct evidence is lacking. here, we characterize the root and nodulation phenotypes of various mutant lines of pea (pisum sativum) that display alterations in their phytohormone levels and/or perception. mutants possessing root systems deficient in gibbe ... | 2005 | 16055684 |
| comparative analyses of codon and amino acid usage in symbiotic island and core genome in nitrogen-fixing symbiotic bacterium bradyrhizobium japonicum. | genes involved in the symbiotic interactions between the nitrogen-fixing endosymbiont bradyrhizobium japonicum, and its leguminous host are mostly clustered in a symbiotic island (si), acquired by the bacterium through a process of horizontal transfer. a comparative analysis of the codon and amino acid usage in core and si genes/proteins of b. japonicum has been carried out in the present study. the mutational bias, translational selection, and gene length are found to be the major sources of va ... | 2005 | 16060695 |
| carboxyl-terminal protease regulates brucella suis morphology in culture and persistence in macrophages and mice. | the putative carboxyl-terminal processing protease (ctpa) of brucella suis 1330 is a member of a novel family of endoproteases involved in the maturation of proteins destined for the cell envelope. the b. suis ctpa protein shared up to 77% homology with ctpa proteins of other bacteria. a ctpa-deficient brucella strain (1330deltactpa), generated by allelic exchange, produced smaller colonies on enriched agar plates and exhibited a 50% decrease in growth rate in enriched liquid medium and no growt ... | 2005 | 16077124 |
| genome wide identification of dna binding motifs of nodd-factor in sinorhizobium meliloti and mesorhizobium loti. | nodd transcription factor is a regulatory protein of nitrogen fixing bacteria, which activates expression of nod genes participating in nodulation during interaction with its symbiont legumes. it's dna binding motifs have been characterized and reported in sinorhizobium meliloti and this pattern information has been used in our theoretical analyses to detect its novel regulated genes in genomes of s. meliloti and mesorhizobium loti. m. loti, a symbiont to model legume plant lotus japonicus, show ... | 2005 | 16078361 |
| two rhizobial strains, mesorhizobium loti maff303099 and bradyrhizobium japonicum usda110, encode haloalkane dehalogenases with novel structures and substrate specificities. | haloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. two rhizobial strains, mesorhizobium loti maff303099 and bradyrhizobium japonicum usda110, have open reading frames (orfs), mlr5434 and blr1087, respectively, that encode putative haloalkane dehalogenase homologues. the crude extracts of escherichia coli strains expressing mlr5434 and blr1087 showed the ability to dehalogenate 18 halogenated compounds, indicating that these orfs indeed encode haloal ... | 2005 | 16085827 |
| allophanate hydrolase, not urease, functions in bacterial cyanuric acid metabolism. | growth substrates containing an s-triazine ring are typically metabolized by bacteria to liberate 3 mol of ammonia via the intermediate cyanuric acid. over a 25-year period, a number of original research papers and reviews have stated that cyanuric acid is metabolized in two steps to the 2-nitrogen intermediate urea. in the present study, allophanate, not urea, was shown to be the 2-nitrogen intermediate in cyanuric acid metabolism in all the bacteria examined. six different experimental results ... | 2005 | 16085834 |
| proteins encoded by sphingomonas elodea atcc 31461 rmla and ugpg genes, involved in gellan gum biosynthesis, exhibit both dtdp- and udp-glucose pyrophosphorylase activities. | the commercial gelling agent gellan is a heteropolysaccharide produced by sphingomonas elodea atcc 31461. in this work, we carried out the biochemical characterization of the enzyme encoded by the first gene (rmla) of the rml 4-gene cluster present in the 18-gene cluster required for gellan biosynthesis (gel cluster). based on sequence homology, the putative rml operon is presumably involved in the biosynthesis of dtdp-rhamnose, the sugar necessary for the incorporation of rhamnose in the gellan ... | 2005 | 16085866 |
| transcriptome-based identification of the sinorhizobium meliloti nodd1 regulon. | the nodd1 regulon of sinorhizobium meliloti was determined through the analysis of the s. meliloti transcriptome in response to the plant flavone luteolin and the overexpression of nodd1. nine new genes regulated by both nodd1 and luteolin were identified, demonstrating that nodd1 controls few functions behind nodulation in s. meliloti. | 2005 | 16085895 |
| evidence for a second class of s-adenosylmethionine riboswitches and other regulatory rna motifs in alpha-proteobacteria. | riboswitches are rna elements in the 5' untranslated leaders of bacterial mrnas that directly sense the levels of specific metabolites with a structurally conserved aptamer domain to regulate expression of downstream genes. riboswitches are most common in the genomes of low gc gram-positive bacteria (for example, bacillus subtilis contains examples of all known riboswitches), and some riboswitch classes seem to be restricted to this group. | 2005 | 16086852 |
| structural and dynamic properties of bacterial type iv secretion systems (review). | the type iv secretion systems (t4ss) are widely distributed among the gram-negative and -positive bacteria. these systems mediate the transfer of dna and protein substrates across the cell envelope to bacterial or eukaryotic cells generally through a process requiring direct cell-to-cell contact. bacteria have evolved t4ss for survival during establishment of pathogenic or symbiotic relationships with eukaryotic hosts. the agrobacterium tumefaciens virb/d4 t4ss and related conjugation machines s ... | 2005 | 16092524 |
| systematic targeted mutagenesis of brucella melitensis 16m reveals a major role for gntr regulators in the control of virulence. | in order to identify transcriptional regulators involved in virulence gene control in brucella melitensis, we generated a collection of 88 mutants in the arac, arsr, crp, deor, gntr, iclr, lysr, merr, rpir, and tetr families of regulators. this collection was named limur (library of mutants for regulators). we developed a method to test several mutants simultaneously in one animal in order to identify those unable to survive. this method, called the plasmid-tagged mutagenesis method, was used to ... | 2005 | 16113274 |
| organization and metabolism of plastids and mitochondria in arbuscular mycorrhizal roots of medicago truncatula. | colonization of root cortical cells by arbuscular mycorrhizal fungi leads to marked cytological changes of plastids and mitochondria. plastids in particular are forming tubular extensions partially connecting individual organelles in a network-like way. these cytological changes correspond to an increased need for plastid and mitochondrial products during establishment and functioning of the symbiosis. the analysis of metabolite and transcript levels in mycorrhizal and nonmycorrhizal roots from ... | 2005 | 16126866 |
| establishment of tn5096-based transposon mutagenesis in gordonia polyisoprenivorans. | the transposons tn5, tn10, tn611, and tn5096 were characterized regarding transposition in gordonia polyisoprenivorans strain vh2. no insertional mutants were obtained employing tn5 or tn10. the thermosensitive plasmid pcg79 harboring tn611 integrated into the chromosome of g. polyisoprenivorans; however, the insertional mutants were fairly unstable und reverted frequently to the wild-type phenotype. in contrast, various stable mutants were obtained employing tn5096-mediated transposon mutagenes ... | 2005 | 16151089 |
| biogenesis, architecture, and function of bacterial type iv secretion systems. | type iv secretion (t4s) systems are ancestrally related to bacterial conjugation machines. these systems assemble as a translocation channel, and often also as a surface filament or protein adhesin, at the envelopes of gram-negative and gram-positive bacteria. these organelles mediate the transfer of dna and protein substrates to phylogenetically diverse prokaryotic and eukaryotic target cells. many basic features of t4s are known, including structures of machine subunits, steps of machine assem ... | 2005 | 16153176 |
| cog3926 and cog5526: a tale of two new lysozyme-like protein families. | we have identified two new lysozyme-like protein families by using a combination of sequence similarity searches, domain architecture analysis, and structural predictions. first, the p5 protein from bacteriophage phi8, which belongs to cog3926 and pfam family duf847, is predicted to have a new lysozyme-like domain. this assignment is consistent with the lytic function of p5 proteins observed in several related double-stranded rna bacteriophages. domain architecture analysis reveals two lysozyme- ... | 2005 | 16155206 |
| structural characterization of a flavonoid-inducible pseudomonas aeruginosa a-band-like o antigen of rhizobium sp. strain ngr234, required for the formation of nitrogen-fixing nodules. | rhizobium (sinorhizobium) sp. strain ngr234 contains three replicons, the smallest of which (pngr234a) carries most symbiotic genes, including those required for nodulation and lipo-chito-oligosaccharide (nod factor) biosynthesis. activation of nod gene expression depends on plant-derived flavonoids, nodd transcriptional activators, and nod box promoter elements. nod boxes nb6 and nb7 delimit six different types of genes, one of which (fixf) is essential for the formation of effective nodules on ... | 2005 | 16159781 |
| diversity in domain architectures of ser/thr kinases and their homologues in prokaryotes. | ser/thr/tyr kinases (styks) commonly found in eukaryotes have been recently reported in many bacterial species. recent studies elucidating their cellular functions have established their roles in bacterial growth and development. however functions of a large number of bacterial styks still remain elusive. the organisation of domains in a large dataset of bacterial styks has been investigated here in order to recognise variety in domain combinations which determine functions of bacterial styks. | 2005 | 16171520 |
| two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. | two-component signal transduction systems, comprised of histidine kinases and their response regulator substrates, are the predominant means by which bacteria sense and respond to extracellular signals. these systems allow cells to adapt to prevailing conditions by modifying cellular physiology, including initiating programs of gene expression, catalyzing reactions, or modifying protein-protein interactions. these signaling pathways have also been demonstrated to play a role in coordinating bact ... | 2005 | 16176121 |
| novel pathway for arsenic detoxification in the legume symbiont sinorhizobium meliloti. | we report a novel pathway for arsenic detoxification in the legume symbiont sinorhizobium meliloti. although a majority of ars operons consist of three genes, arsr (transcriptional regulator), arsb [as(oh)3/h+ antiporter], and arsc (arsenate reductase), the s. meliloti ars operon includes an aquaglyceroporin (aqps) in place of arsb. the presence of aqps in an arsenic resistance operon is interesting, since aquaglyceroporin channels have previously been shown to adventitiously facilitate uptake o ... | 2005 | 16199569 |
| cloning and expression of ispdf from mesorhizobium loti. characterization of a bifunctional protein that catalyzes non-consecutive steps in the methylerythritol phosphate pathway. | gram-negative bacteria, plant chloroplasts, green algae and some gram-positive bacteria utilize the 2-c-methyl-d-erythritol phosphate (mep) pathway for the biosynthesis of isoprenoids. ispd, ispe, and ispf encode the enzymes required to convert mep to 2-c-methyl-d-erythritol 2,4-cyclodiphosphate (cmedp) during the biosynthesis of isopentenyl diphosphate and dimethylallyl diphosphate in the mep pathway. upon analysis of the mesorhizobium loti genome, orf mll0395 showed homology to both ispd and i ... | 2006 | 16203191 |
| role of the regulatory gene rira in the transcriptional response of sinorhizobium meliloti to iron limitation. | a regulatory network of sinorhizobium meliloti genes involved in adaptation to iron-limiting conditions and the involvement of the rhizobial iron regulator gene (rira) were analyzed by mutation and microarray analyses. a constructed s. meliloti rira mutant exhibited growth defects and enhanced h2o2 sensitivity in the presence of iron, but symbiotic nitrogen fixation was not affected. to identify iron-responsive and rira-regulated s. meliloti genes, a transcriptome approach using whole-genome mic ... | 2005 | 16204511 |
| 4-pyridoxolactonase from a symbiotic nitrogen-fixing bacterium mesorhizobium loti: cloning, expression, and characterization. | 4-pyridoxolactonase is involved in the degradation pathway for pyridoxine, a free form of vitamin b6. the gene (mlr6805) encoding the putative 4-pyridoxolactonase of nitrogen fixing symbiotic microorganism mesorhizobium loti maff303099 has been identified based on the genome database. the gene was cloned and overexpressed in a cotransformant escherichia coli cell. the recombinant enzyme was dimeric protein and contained one mole of zn2+ per mole of subunit. the enzyme showed about 30% identity w ... | 2005 | 16226926 |