| the sinorhizobium meliloti abc transporter cho is highly specific for choline and expressed in bacteroids from medicago sativa nodules. | in sinorhizobium meliloti, choline is the direct precursor of phosphatidylcholine, a major lipid membrane component in the rhizobiaceae family, and glycine betaine, an important osmoprotectant. moreover, choline is an efficient energy source which supports growth. using a pcr strategy, we identified three chromosomal genes (choxwv) which encode components of an abc transporter: chox (binding protein), chow (permease), and chov (atpase). whereas the best homology scores were obtained with compone ... | 2004 | 15342567 |
| sinorhizobium meliloti exor and exos proteins regulate both succinoglycan and flagellum production. | the production of the sinorhizobium meliloti exopolysaccharide, succinoglycan, is required for the formation of infection threads inside root hairs, a critical step during the nodulation of alfalfa (medicago sativa) by s. meliloti. two bacterial mutations, exor95::tn5 and exos96::tn5, resulted in the overproduction of succinoglycan and a reduction in symbiosis. systematic analyses of the symbiotic phenotypes of the two mutants demonstrated their reduced efficiency of root hair colonization. in a ... | 2004 | 15342573 |
| microbial products trigger amino acid exudation from plant roots. | plants naturally cycle amino acids across root cell plasma membranes, and any net efflux is termed exudation. the dominant ecological view is that microorganisms and roots passively compete for amino acids in the soil solution, yet the innate capacity of roots to recover amino acids present in ecologically relevant concentrations is unknown. we find that, in the absence of culturable microorganisms, the influx rates of 16 amino acids (each supplied at 2.5 microm) exceed efflux rates by 5% to 545 ... | 2004 | 15347793 |
| co-sensing mechanisms. | carbon monoxide (co) has long been known to have dramatic physiological effects on organisms ranging from bacteria to humans, but recently there have a number of suggestions that organisms might have specific sensors for co. this article reviews the current evidence for a variety of proteins with demonstrated or potential co-sensing ability. particular emphasis is placed on the molecular description of cooa, a heme-containing co sensor from rhodospirillum rubrum, since its biological role as a c ... | 2004 | 15353565 |
| sinorhizobium meliloti strain 1021 produces a low-molecular-mass capsular polysaccharide that is a homopolymer of 3-deoxy-d-manno-oct-2-ulosonic acid harboring a phospholipid anchor. | sinorhizobium meliloti strain 1021 possesses the particularity to synthesize biologically inefficient capsular polysaccharides (kps). it has been assumed that this class of compounds is not produced in high-molecular-mass (hmm) forms, even if many genetic analyses show the existence of expression of genes involved in the biosynthesis of capsular polysaccharides. the expression of these genes that are involved in the export of a kps throughout the membrane and in the attachment of a lipid moiety ... | 2005 | 15355932 |
| occurrence and potential diagnostic applications of serological cross-reactivities between brucella and other alpha-proteobacteria. | agrobacterium, sinorhizobium, and ochrobactrum are genera closely related to brucella but, in contrast to the latter, are not pathogenic for humans and animals. we studied by an indirect enzyme-linked immunosorbent assay (elisa) the reactivities of brucellosis sera against cytosolic (cyt) and membrane (ma) antigens from these nonpathogenic bacteria, and we evaluated the potential usefulness of these cross-reactions for the diagnosis of brucellosis in humans, sheep, cows, and dogs. canine infecti ... | 2004 | 15358645 |
| nod factor-treated medicago truncatula roots and seeds show an increased number of nodules when inoculated with a limiting population of sinorhizobium meliloti. | medicago truncatula is a model legume plant that interacts symbiotically with sinorhizobium meliloti, the alfalfa symbiont. this process involves a molecular dialogue between the bacterium and the plant. legume roots exude flavonoids that induce the expression of a set of rhizobial genes, the nod genes, which are essential for nodulation and determination of the host range. in turn, nod genes control the synthesis of lipo-chito-oligosaccharides (lcos), nod factors, which are bacteria-to-plant si ... | 2004 | 15361530 |
| wide-range transcriptional modulating effect of ntrr under microaerobiosis in sinorhizobium meliloti. | a mutation in the second gene in the ntrpr operon results in increased expression of nodulation (nod) and nitrogen fixation (nif) genes in sinorhizobium meliloti. since this pleiotropic effect is particularly pronounced in the presence of external combined nitrogen, a nitrogen regulatory function has been suggested for ntrr. to identify the complete set of protein-coding genes influenced by loss of ntrr function, microarray hybridizations were carried out to compare transcript levels in the wild ... | 2004 | 15365818 |
| comprehensive metabolite profiling of sinorhizobium meliloti using gas chromatography-mass spectrometry. | a metabolite analysis of the soil bacterium sinorhizobium meliloti was established as a first step towards a better understanding of the symbiosis with its host plant medicago truncatula. a crucial step was the development of fast harvesting and extraction methods for the bacterial metabolites because of rapid changes in their composition. s. meliloti 1021 cell cultures grown in minimal medium were harvested by centrifugation, filtration or immediate freezing in liquid nitrogen followed by a lyo ... | 2004 | 15372312 |
| genome-wide molecular clock and horizontal gene transfer in bacterial evolution. | we describe a simple theoretical framework for identifying orthologous sets of genes that deviate from a clock-like model of evolution. the approach used is based on comparing the evolutionary distances within a set of orthologs to a standard intergenomic distance, which was defined as the median of the distribution of the distances between all one-to-one orthologs. under the clock-like model, the points on a plot of intergenic distances versus intergenomic distances are expected to fit a straig ... | 2004 | 15375139 |
| symbiotic autoregulation of nifa expression in rhizobium leguminosarum bv. viciae. | nifa is the general transcriptional activator of nitrogen fixation genes in diazotrophic bacteria. in rhizobium leguminosarum bv. viciae upm791, the nifa gene is part of a gene cluster (orf71 orf79 fixw orf5 fixabcx nifab) separated by 896 bp from an upstream and divergent truncated duplication of nifh (deltanifh). symbiotic expression analysis of genomic nifa::lacz fusions revealed that in strain upm791 nifa is expressed mainly from a sigma54-dependent promoter (p(nifa1)) located upstream of or ... | 2004 | 15375140 |
| an energy taxis transducer promotes root colonization by azospirillum brasilense. | motility responses triggered by changes in the electron transport system are collectively known as energy taxis. in azospirillum brasilense, energy taxis was shown to be the principal form of locomotor control. in the present study, we have identified a novel chemoreceptor-like protein, named tlp1, which serves as an energy taxis transducer. the tlp1 protein is predicted to have an n-terminal periplasmic region and a cytoplasmic c-terminal signaling module homologous to those of other chemorecep ... | 2004 | 15375141 |
| involvement of exo5 in production of surface polysaccharides in rhizobium leguminosarum and its role in nodulation of vicia sativa subsp. nigra. | analysis of two exopolysaccharide-deficient mutants of rhizobium leguminosarum, rbl5808 and rbl5812, revealed independent tn5 transposon integrations in a single gene, designated exo5. as judged from structural and functional homology, this gene encodes a udp-glucose dehydrogenase responsible for the oxidation of udp-glucose to udp-glucuronic acid. a mutation in exo5 affects all glucuronic acid-containing polysaccharides and, consequently, all galacturonic acid-containing polysaccharides. exo5-d ... | 2004 | 15375143 |
| 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 |
| functional difference between sinorhizobium meliloti nifa and enterobacter cloacae nifa. | the nifa gene is an important regulatory gene and its product, nifa protein, regulates the expression of many nif genes involved in the nitrogen fixation process. we introduced multiple copies of the constitutively expressed sinorhizobium meliloti (sm) or enterobacter cloacae (ec) nifa gene into both the nifa mutant strain smy and the wild-type strain sm1021. root nodules produced by smy containing a constitutively expressed sm nifa gene were capable of fixing nitrogen, while nodules produced by ... | 2004 | 15384181 |
| complete nucleotide sequence of a 92-kilobase plasmid harboring the ctx-m-15 extended-spectrum beta-lactamase involved in an outbreak in long-term-care facilities in toronto, canada. | a major outbreak involving an escherichia coli strain that was resistant to expanded-spectrum cephalosporins occurred in toronto and surrounding regions in 2000 to 2002. we report the complete sequence of a plasmid, pc15-1a, that was found associated with the outbreak strain. plasmid pc15-1a is a circular molecule of 92,353 bp consisting of two distinct regions. the first is a 64-kb region that is essentially homologous to the non-r-determinant region of plasmid r100 except for several point mut ... | 2004 | 15388431 |
| purification and physical-chemical characterization of the three hydroperoxidases from the symbiotic bacterium sinorhizobium meliloti. | three genes encoding heme hydroperoxidases (kata, katb, and katc) have been identified in the soil bacterium sinorhizobium meliloti. the recombinant proteins were overexpressed in escherichia coli and purified in order to achieve a spectral and kinetic characterization. the three proteins contain heme b with high-spin fe(iii). katb is an acidic bifunctional homodimeric catalase-peroxidase exhibiting both catalase (k(cat) = 2400 s(-1)) and peroxidase activity and having a high affinity for hydrog ... | 2004 | 15449959 |
| abortive transposition by a group ii intron in yeast mitochondria. | group ii intron homing in yeast mitochondria is initiated at active target sites by activities of intron-encoded ribonucleoprotein (rnp) particles, but is completed by competing recombination and repair mechanisms. intron ai1 transposes in haploid cells at low frequency to target sites in mtdna that resemble the exon 1-exon 2 (e1/e2) homing site. this study investigates a system in which ai1 can transpose in crosses (i.e., in trans). surprisingly, replacing an inefficient transposition site with ... | 2004 | 15454528 |
| is autoinducer-2 a universal signal for interspecies communication: a comparative genomic and phylogenetic analysis of the synthesis and signal transduction pathways. | quorum sensing is a process of bacterial cell-to-cell communication involving the production and detection of extracellular signaling molecules called autoinducers. recently, it has been proposed that autoinducer-2 (ai-2), a furanosyl borate diester derived from the recycling of s-adenosyl-homocysteine (sah) to homocysteine, serves as a universal signal for interspecies communication. | 2004 | 15456522 |
| novel substitutions in the sigma54-dependent activator dctd that increase dependence on upstream activation sequences or uncouple atp hydrolysis from transcriptional activation. | sinorhizobium meliloti dctd is an activator of sigma(54)-rna polymerase holoenzyme and member of the aaa+ superfamily of atpases. dctd uses energy released from atp hydrolysis to stimulate the isomerization of a closed promoter complex to an open complex. dctd binds to upstream activation sequences (uas) and contacts the closed complex through dna looping to activate transcription, but the uas is not essential for activation if dctd is expressed at higher than normal levels. introduction of spec ... | 2004 | 15458403 |
| replicon-specific regulation of small heat shock genes in agrobacterium tumefaciens. | four genes coding for small heat shock proteins (shsps) were identified in the genome sequence of agrobacterium tumefaciens, one on the circular chromosome (hspc), one on the linear chromosome (hspl), and two on the pat plasmid (hspat1 and hspat2). induction of shsps at elevated temperatures was revealed by immunoblot analyses. primer extension experiments and translational lacz fusions demonstrated that expression of the pat-derived genes and hspl is controlled by temperature in a regulon-speci ... | 2004 | 15466035 |
| infection-related activation of the cg12 promoter is conserved between actinorhizal and legume-rhizobia root nodule symbiosis. | two nitrogen-fixing root nodule symbioses between soil bacteria and higher plants have been described: the symbiosis between legume and rhizobia and actinorhizal symbioses between plants belonging to eight angiosperm families and the actinomycete frankia. we have recently shown that the subtilisin-like ser protease gene cg12 (isolated from the actinorhizal plant casuarina glauca) is specifically expressed during plant cell infection by frankia. here we report on the study of c. glauca cg12 promo ... | 2004 | 15466224 |
| 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 |
| chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, spartobacteria classis nov., of the phylum verrucomicrobia. | the phylum verrucomicrobia is increasingly recognized as an environmentally significant group of bacteria, particularly in soil habitats. at least six subdivisions of the verrucomicrobia are resolved by comparative analysis of 16s rrna genes, mostly obtained directly from environmental samples. to date, only two of these subdivisions (1 and 4) have characterized pure-culture representatives. we have isolated and characterized the first known pure-culture representative of subdivision 2. strain e ... | 2004 | 15466527 |
| 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 |
| transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium thermotoga maritima. | thermotoga maritima, a fermentative, anaerobic, hyperthermophilic bacterium, was found to attach to bioreactor glass walls, nylon mesh, and polycarbonate filters during chemostat cultivation on maltose-based media at 80 degrees c. a whole-genome cdna microarray was used to examine differential expression patterns between biofilm and planktonic populations. mixed-model statistical analysis revealed differential expression (twofold or more) of 114 open reading frames in sessile cells (6% of the ge ... | 2004 | 15466556 |
| comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. | itsf and itsreub, constituting a new primer set designed for the amplification of the 16s-23s rrna intergenic transcribed spacers, have been compared with primer sets consisting of 1406f and 23sr (m. m. fisher and e. w. triplett, appl. environ. microbiol. 65:4630-4636, 1999) and s-d-bact-1522-b-s-20 and l-d-bact-132-a-a-18 (l. ranjard et al., appl. environ. microbiol. 67:4479-4487, 2001), previously proposed for automated ribosomal intergenic spacer analysis (arisa) of complex bacterial communit ... | 2004 | 15466561 |
| 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 |
| [positional analysis of a gene related to salt tolerance in sinorhizobium meliloti by transposon rescue]. | salt sensitive mutant 042bml-2 was obtained by mutating sinorhizobium meliloti 042bm with transposon tn5 carried on the plasmid prl1063a. by transposon rescue, a 1.179 kb of dna sequence of s. meliloti flanking the tn5 insertion site was obtained. the sequence similarity analysis through blast analysis in genbank revealed the transposon was inserted into a functionally unknown gene, which is 6 270 bp in length, of s. meliloti, and the gene was named rtsc. this study indicated that rtsc was assoc ... | 2004 | 15468925 |
| analysis of the n-terminal dna binding domain of the is30 transposase. | is30 is the founding member of a large family of widely spread bacterial insertion sequences with closely related transposases. the n-terminal end of the is30 transposase had been shown to retain sequence-specific dna binding activity and to protect the is30 terminal inverted repeats. structural predictions revealed the presence of a helix-helix-turn-helix motif (h-hth2) which, in the case of is30, is preceded by an additional helix-turn-helix motif (hth1). analysis of deletion and point mutants ... | 2004 | 15469518 |
| regulated communication between the upstream face of rna polymerase and the beta' subunit jaw domain. | we used bacteriophage t7-encoded transcription inhibitor gene protein 2 (gp2) as a probe to study the contribution of the escherichia coli rna polymerase (rnap) beta' subunit jaw domain--the site of gp2 binding--to activator and atp hydrolysis-dependent open complex formation by the sigma(54)-rnap. we show that, unlike sigma(70)-dependent transcription, activated transcription by sigma(54)-rnap is resistant to gp2. in contrast, activator and atp hydrolysis-independent transcription by sigma(54)- ... | 2004 | 15470503 |
| reorganisation of an rna polymerase-promoter dna complex for dna melting. | sigma factors, the key regulatory components of the bacterial rna polymerase (rnap), direct promoter dna binding and dna melting. the sigma(54)-rnap forms promoter complexes in which dna melting is only triggered by an activator and atp hydrolysis-driven reorganisation of an initial sigma(54)-rnap-promoter complex. we report that an initial bacterial rnap-dna complex can be reorganised by an activator to form an intermediate transcription initiation complex where full dna melting has not yet occ ... | 2004 | 15470504 |
| gas chromatography-mass spectrometry analysis of indoleacetic acid and tryptophan following aqueous chloroformate derivatisation of rhizobium exudates. | a new method for preparing alkyl esters of indole-3-acetic acid (iaa) in aqueous solution is adapted from the chloroformate method originally described by husek for the analysis of amino acids. this method has the significant advantage of avoiding the generation and use of diazomethane, and is done in aqueous solution without the need to dry the sample with concomitant non-specific losses of iaa. the effectiveness of this method is demonstrated by its use in an isotope dilution gas chromatograph ... | 2004 | 15474378 |
| heterologous complementation of the exopolysaccharide synthesis and carbon utilization phenotypes of sinorhizobium meliloti rm1021 polyhydroxyalkanoate synthesis mutants. | a reduced exopolysaccharide phenotype is associated with inability to synthesize polyhydroxyalkanaote (pha) stores in sinorhizobium meliloti strain rm1021. loss of function mutations in phbb and phbc result in non-mucoid colony morphology on yeast mannitol agar, compared to the mucoid phenotype exhibited by the parental strain. this phenotype is attributed to reduction in succinoglycan synthesis. we have used complementation of this phenotype and the previously described d-3-hydroxybutyrate/acet ... | 2004 | 15476977 |
| pharmacological evidence that multiple phospholipid signaling pathways link rhizobium nodulation factor perception in medicago truncatula root hairs to intracellular responses, including ca2+ spiking and specific enod gene expression. | rhizobium nodulation (nod) factors are specific lipochito-oligosaccharide signals essential for initiating in root hairs of the host legume developmental responses that are required for controlled entry of the microsymbiont. in this article, we focus on the nod factor signal transduction pathway leading to specific and cell autonomous gene activation in medicago truncatula cv jemalong in a study making use of the nod factor-inducible mtenod11 gene. first, we show that pharmacological antagonists ... | 2004 | 15489277 |
| 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 |
| use of in vivo expression technology to identify genes important in growth and survival of pseudomonas fluorescens pf0-1 in soil: discovery of expressed sequences with novel genetic organization. | studies were undertaken to determine the genetic needs for the survival of pseudomonas fluorescens pf0-1, a gram-negative soil bacterium potentially important for biocontrol and bioremediation, in soil. in vivo expression technology (ivet) identified 22 genes with elevated expression in soil relative to laboratory media. soil-induced sequences included genes with probable functions of nutrient acquisition and use, and of gene regulation. ten sequences, lacking similarity to known genes, overlapp ... | 2004 | 15489453 |
| beta-1,3 glucan sulfate, but not beta-1,3 glucan, induces the salicylic acid signaling pathway in tobacco and arabidopsis. | sulfate substituents naturally occurring in biomolecules, such as oligosaccharides and polysaccharides, can play a critical role in major physiological functions in plants and animals. we show that laminarin, a beta-1,3 glucan with elicitor activity in tobacco (nicotiana tabacum), becomes, after chemical sulfation, an inducer of the salicylic acid (sa) signaling pathway in tobacco and arabidopsis thaliana. in tobacco cell suspensions, the oxidative burst induced by the laminarin sulfate ps3 was ... | 2004 | 15494557 |
| nip, a symbiotic medicago truncatula mutant that forms root nodules with aberrant infection threads and plant defense-like response. | to investigate the legume-rhizobium symbiosis, we isolated and studied a novel symbiotic mutant of the model legume medicago truncatula, designated nip (numerous infections and polyphenolics). when grown on nitrogen-free media in the presence of the compatible bacterium sinorhizobium meliloti, the nip mutant showed nitrogen deficiency symptoms. the mutant failed to form pink nitrogen-fixing nodules that occur in the wild-type symbiosis, but instead developed small bump-like nodules on its roots ... | 2004 | 15516506 |
| lin, a medicago truncatula gene required for nodule differentiation and persistence of rhizobial infections. | ethyl methanesulfonate mutagenesis of the model legume medicago truncatula has previously identified several genes required for early steps in nodulation. here, we describe a new mutant that is defective in intermediate steps of nodule differentiation. the lin (lumpy infections) mutant is characterized by a 4-fold reduction in the number of infections, all of which arrest in the root epidermis, and by nodule primordia that initiate normally but fail to mature. genetic analyses indicate that the ... | 2004 | 15516512 |
| 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 |
| selenophosphate synthetase genes from lung adenocarcinoma cells: sps1 for recycling l-selenocysteine and sps2 for selenite assimilation. | a labile selenium donor compound monoselenophosphate is synthesized from selenide and atp by selenophosphate synthetase (sps). in the present study, sps1 and sps2 were cloned from a cdna library prepared from human lung adenocarcinoma cells (ncih441). the human lung sps1 has been cloned as an orf of 1,179 bp, identical in sequence to that of the recently revised human liver sps1. the in-frame tga codon of the lung sps2 was genetically altered to tgt (cys) to obtain the sps2cys gene. expression o ... | 2004 | 15534230 |
| 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 |
| a dual-genome symbiosis chip for coordinate study of signal exchange and development in a prokaryote-host interaction. | the soil-dwelling alpha-proteobacterium sinorhizobium meliloti engages in a symbiosis with legumes: s. meliloti elicits the formation of plant root nodules where it converts dinitrogen to ammonia for use by the plant in exchange for plant photosynthate. to study the coordinate differentiation of s. meliloti and its legume partner during nodule development, we designed a custom affymetrix genechip with the complete s. meliloti genome and approximately 10,000 probe sets for the plant host, medicag ... | 2004 | 15542588 |
| katg is the primary detoxifier of hydrogen peroxide produced by aerobic metabolism in bradyrhizobium japonicum. | bacteria are exposed to reactive oxygen species from the environment and from those generated by aerobic metabolism. catalases are heme proteins that detoxify h(2)o(2), and many bacteria contain more than one catalase enzyme. also, the nonheme peroxidase alkyl hydroperoxide reductase (ahp) is the major scavenger of endogenous h(2)o(2) in escherichia coli. here, we show that aerobically grown bradyrhizobium japonicum cells express a single catalase activity. four genes encoding putative catalases ... | 2004 | 15547258 |
| the recombination genes addab are not restricted to gram-positive bacteria: genetic analysis of the recombination initiation enzymes recf and addab in rhizobium etli. | single-strand gaps (ssgs) and double-strand breaks (dsbs) are the major initiation sites for recombination. in bacteria, the ssgs are repaired by recfor, while the dsbs are processed by recbcd in gram-negative bacteria and addab in gram-positive bacteria. unexpectedly, instead of recbcd genes, the addab genes were found in members of the alpha-proteobacteria group (gram negative). taking rhizobium etli as a model, the role of recf and addab genes in homologous recombination and repair of damaged ... | 2004 | 15547262 |
| the n terminus of bacterial elongation factor tu elicits innate immunity in arabidopsis plants. | innate immunity is based on the recognition of pathogen-associated molecular patterns (pamps). here, we show that elongation factor tu (ef-tu), the most abundant bacterial protein, acts as a pamp in arabidopsis thaliana and other brassicaceae. ef-tu is highly conserved in all bacteria and is known to be n-acetylated in escherichia coli. arabidopsis plants specifically recognize the n terminus of the protein, and an n-acetylated peptide comprising the first 18 amino acids, termed elf18, is fully ... | 2004 | 15548740 |
| 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 |
| nitrogen regulation in sinorhizobium meliloti probed with whole genome arrays. | using whole genome arrays, we systematically investigated nitrogen regulation in the plant symbiotic bacterium sinorhizobium meliloti. the use of glutamate instead of ammonium as a nitrogen source induced nitrogen catabolic genes independently of the carbon source, including two glutamine synthetase genes, various aminoacid transporters and the glnkamtb operon. these responses depended on both the ntrc and glnb nitrogen regulators. glutamate repressible genes included glutamate synthase and a h+ ... | 2004 | 15556707 |
| modulation of swarming and virulence by fatty acids through the rsba protein in proteus mirabilis. | after sensing external signals, proteus mirabilis undergoes a multicellular behavior called swarming which is coordinately regulated with the expression of virulence factors. here we report that exogenously added fatty acids could act as signals to regulate swarming in p. mirabilis. specifically, while oleic acid enhanced swarming, some saturated fatty acids, such as lauric acid, myristic acid, palmitic acid, and stearic acid, inhibited swarming. we also found that expression of hemolysin, which ... | 2004 | 15557604 |
| characterisation of new symbiotic medicago truncatula (gaertn.) mutants, and phenotypic or genotypic complementary information on previously described mutants. | from a pool of medicago truncatula mutants--obtained by gamma-irradiation or ethyl methanesulfonate mutagenesis--impaired in symbiosis with the n-fixing bacterium sinorhizobium meliloti, new mutants are described and genetically analysed, and for already reported mutants, complementary data are given on their phenotypic and genetic analysis. phenotypic data relate to nodulation and mycorrhizal phenotypes. among the five new mutants, three were classified as [nod+ fix- myc+] and the mutations wer ... | 2005 | 15558330 |
| the symbiotic defect in a sinorhizobium meliloti lipopolysaccharide mutant can be overcome by expression of other surface polysaccharides. | in this work we have examined the extent of functional complementation in symbiosis among different sinorhizobium meliloti surface polysaccharides including lipopolysaccharide (lps). we show that a symbiotic deficiency associated with an lps defect can be reversed by appropriate expression of other surface polysaccharides such as galactoglucan (epsii) and a particular form of capsular polysaccharide (kdops). it is noteworthy that, while succinoglycan epsi and lps cannot functionally substitute f ... | 2004 | 15567281 |
| domain structure and three-dimensional model of a group ii intron-encoded reverse transcriptase. | group ii intron-encoded proteins (ieps) have both reverse transcriptase (rt) activity, which functions in intron mobility, and maturase activity, which promotes rna splicing by stabilizing the catalytically active rna structure. the ltra protein encoded by the lactococcus lactis ll.ltrb group ii intron contains an n-terminal rt domain, with conserved sequence motifs rt1 to 7 found in the fingers and palm of retroviral rts; domain x, associated with maturase activity; and c-terminal dna-binding a ... | 2004 | 15574519 |
| bacterial life and dinitrogen fixation at a gypsum rock. | the organisms of a bluish-green layer beneath the shards of a gypsum rock were characterized by molecular techniques. the cyanobacterial consortium consisted almost exclusively of chroococcidiopsis spp. the organisms of the shards expressed nitrogenase activity (c2h2 reduction) aerobically and in light. after a prolonged period of drought at the rock, the cells were inactive, but they resumed nitrogenase activity 2 to 3 days after the addition of water. in a suspension culture of chroococcidiops ... | 2004 | 15574902 |
| 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 |
| role of a nosx homolog in streptococcus gordonii in aerobic growth and biofilm formation. | oral streptococci such as streptococcus gordonii are facultative anaerobes that initiate biofilm formation on tooth surfaces. an isolated s. gordonii::tn917-lac biofilm-defective mutant contained a transposon insertion in an open reading frame (orf) encoding a homolog of nosx of ralstonia eutropha, a putative maturation factor of nitrous oxide reductase. located downstream are two genes, qor1 and qor2, predicted to encode two putative nadph quinone oxidoreductases. these three genes are cotransc ... | 2004 | 15576767 |
| 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 |
| effect of salinity on root-nodule conductance to the oxygen diffusion in the medicago truncatula-sinorhizobium meliloti symbiosis. | in order to determine the effect of salinity on the nodule conductance, oxygen uptake by the nodulated roots was measured by registering the concentration of o(2) as a function of time in a tight incubator of known volume containing the nodulated roots of medicago truncatula. four lines, namely tn8.20 and tn6.18, originated from local populations, f83005.5 originated from var (france) and jemalong 6, a cultivar from australia, were hydroponically grown in 250 ml glass bottles under semi-controll ... | 2004 | 15596103 |
| insertion of transposon tn5tac1 in the sinorhizobium meliloti malate dehydrogenase (mdh) gene results in conditional polar effects on downstream tca cycle genes. | to isolate sinorhizobium meliloti mutants deficient in malate dehydrogenase (mdh) activity, random transposon tn5tac1 insertion mutants were screened for conditional lethal phenotypes on complex medium. tn5tac1 has an outward-oriented isopropyl-beta-d-thiogalactopyranoside (iptg)-inducible promoter (ptac). the insertion in strain rm30049 was mapped to the mdh gene, which was found to lie directly upstream of the genes encoding succinyl-coa synthetase (succd) and 2-oxoglutarate dehydrogenase (suc ... | 2004 | 15597737 |
| fungal elicitation of signal transduction-related plant genes precedes mycorrhiza establishment and requires the dmi3 gene in medicago truncatula. | suppressive subtractive hybridization and expressed sequence tag sequencing identified 29 plant genes which are upregulated during the appressorium stage of mycorrhiza establishment between medicago truncatula j5 (myc+) and glomus mosseae. eleven genes coding plant proteins with predicted functions in signal transduction, transcription, and translation were investigated in more detail for their relation to early events of symbiotic interactions. expression profiling showed that the genes are act ... | 2004 | 15597744 |
| identification of two new genes involved in diazotrophic growth via the alternative fe-only nitrogenase in the phototrophic purple bacterium rhodobacter capsulatus. | growth of rhodobacter capsulatus with molecular dinitrogen as the sole n source via the alternative fe-only nitrogenase requires all seven gene products of the anfhdgk-1-2-3 operon. in contrast to mutant strains carrying lesions in the structural genes of nitrogenase (anfh, anfd, anfg, and anfk), strains defective for either anf1, anf2, or anf3 are still able to reduce the artificial substrate acetylene, although with diminished activity. to obtain further information on the role of anf1, we scr ... | 2005 | 15601692 |
| 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 |
| molecular cloning, sequence analysis, and heterologous expression of the phosphinothricin tripeptide biosynthetic gene cluster from streptomyces viridochromogenes dsm 40736. | a fosmid library from genomic dna of streptomyces viridochromogenes dsm 40736 was constructed and screened for the presence of genes known to be involved in the biosynthesis of phosphinothricin tripeptide (ptt). eight positives were identified, one of which was able to confer ptt biosynthetic capability upon streptomyces lividans after integration of the fosmid into the chromosome of this heterologous host. sequence analysis of the 40,241-bp fosmid insert revealed 29 complete open reading frames ... | 2005 | 15616300 |
| characterization of bdha, encoding the enzyme d-3-hydroxybutyrate dehydrogenase, from sinorhizobium sp. strain ngr234. | a genomic library of sinorhizobium sp. strain ngr234 was introduced into escherichia coli ls5218, a strain with a constitutively active pathway for acetoacetate degradation, and clones that confer the ability to utilize d-3-hydroxybutyrate as a sole carbon source were isolated. subcloning experiments identified a 2.3 kb ecori fragment that retained complementing ability, and an orf that appeared orthologous with known bdha genes was located within this fragment. the deduced ngr234 bdha amino aci ... | 2005 | 15621424 |
| azide resistance in rhizobium ciceri linked with superior symbiotic nitrogen fixation. | isolated azide resistant (azr) native r. ciceri strain 18-7 was resistant to sodium azide at 10 microg/ml. to find if nif-reiteration is responsible for azide resistance and linked to superior symbiotic nitrogen fixation, transposon (tn5) induced azide sensitive mutants were generated. using 4 kb nif-reiterated sinorhizobium meliloti dna, a clone c4 that complemented azide sensitivity was isolated by dna hybridization from genomic library of chickpea rhizobium strain rcd301. ecori restriction ma ... | 2004 | 15623228 |
| genome organization of the sars-cov. | annotation of the genome sequence of the sars-cov (severe acute respiratory syndrome-associated coronavirus) is indispensable to understand its evolution and pathogenesis. we have performed a full annotation of the sars-cov genome sequences by using annotation programs publicly available or developed by ourselves. totally, 21 open reading frames (orfs) of genes or putative uncharacterized proteins (pups) were predicted. seven pups had not been reported previously, and two of them were predicted ... | 2003 | 15629035 |
| the bldc developmental locus of streptomyces coelicolor encodes a member of a family of small dna-binding proteins related to the dna-binding domains of the merr family. | the bldc locus, required for formation of aerial hyphae in streptomyces coelicolor, was localized by map-based cloning to the overlap between cosmids d17 and d25 of a minimal ordered library. subcloning and sequencing showed that bldc encodes a member of a previously unrecognized family of small (58- to 78-residue) dna-binding proteins, related to the dna-binding domains of the merr family of transcriptional activators. bldc family members are found in a wide range of gram-positive and gram-nega ... | 2005 | 15629942 |
| detailed studies of the binding mechanism of the sinorhizobium meliloti transcriptional activator expg to dna. | the exopolysaccharide galactoglucan promotes the establishment of symbiosis between the nitrogen-fixing gram-negative soil bacterium sinorhizobium meliloti 2011 and its host plant alfalfa. the transcriptional regulator expg activates expression of galactoglucan biosynthesis genes by direct binding to the expa1, expg/expd1 and expe1 promoter regions. expg is a member of the marr family of regulatory proteins. analysis of target sequences of an expg(his)(6) fusion protein in the exp promoter regio ... | 2005 | 15632443 |
| diversity of green-like and red-like ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbl) in differently managed agricultural soils. | a pcr-based approach was developed to detect ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) form i large-subunit genes (cbbl) as a functional marker of autotrophic bacteria that fix carbon dioxide via the calvin-benson-bassham cycle. we constructed two different primer sets, targeting the green-like and red-like phylogenetic groups of cbbl genes. the diversity of these cbbl genes was analyzed by the use of three differently managed agricultural soils from a long-term field experiment. ... | 2005 | 15640185 |
| a bipartite signal mediates the transfer of type iv secretion substrates of bartonella henselae into human cells. | bacterial type iv secretion (t4s) systems mediate the transfer of macromolecular substrates into various target cells, e.g., the conjugative transfer of dna into bacteria or the transfer of virulence proteins into eukaryotic host cells. the t4s apparatus virb of the vascular tumor-inducing pathogen bartonella henselae causes subversion of human endothelial cell (hec) function. here we report the identification of multiple protein substrates of virb, which, upon translocation into hec, mediate al ... | 2005 | 15642951 |
| experimental evidence for plasmid-borne nor-nir genes in sinorhizobium meliloti jj1c10. | in denitrification, nir and nor genes are respectively required for the sequential dissimilatory reduction of nitrite and nitric oxide to form nitrous oxide. their location on the psyma megaplasmid of sinorhizobium meliloti was confirmed by southern hybridization of its clones with specific structural gene probes for nirk and norcb. a 20-kb region of psyma containing the nor-nir genes was delineated by nucleotide sequence analysis. these genes were linked to the nap genes encoding periplasmic pr ... | 2004 | 15644918 |
| rep code: defining bacterial identity in extragenic space. | through the analysis of 57 bacterial genomes we have detected repetitive extragenic palindromic dna sequences (reps) in 11 species. for a sequence to be considered as rep, the following criteria should be met: (i) it should be extragenic, (ii) palindromic, (iii) of a length between 21 and 65 bases and (iv) should constitute more than 0.5% of the total extragenic space. species-specific reps have been found in human pathogens such as escherichia coli, salmonella enterica, neisseria meningitidis, ... | 2005 | 15658989 |
| the expression of a novel antisense gene mediates incompatibility within the large repabc family of alpha-proteobacterial plasmids. | large extrachromosomal replicons in many members of the alpha-proteobacteria encode genes that are required for plant or animal pathogenesis or symbiosis. most of these replicons encode repabc genes that control their replication and faithful segregation during cell division. in addition to its chromosome, the plant endosymbiont sinorhizobium meliloti also maintains the 1.4 mb psyma and 1.7 mb psymb symbiotic megaplasmids both of which are repabc-type replicons. in all repabc loci that have been ... | 2005 | 15659174 |
| the generalized transducing salmonella bacteriophage es18: complete genome sequence and dna packaging strategy. | the generalized transducing double-stranded dna bacteriophage es18 has an icosahedral head and a long noncontractile tail, and it infects both rough and smooth salmonella enterica strains. we report here the complete 46,900-bp genome nucleotide sequence and provide an analysis of the sequence. its 79 genes and their organization clearly show that es18 is a member of the lambda-like (lambdoid) phage group; however, it contains a novel set of genes that program assembly of the virion head. most of ... | 2005 | 15659686 |
| sinorhizobium meliloti dcta mutants with partial ability to transport dicarboxylic acids. | sinorhizobium meliloti dcta encodes a transport protein needed for a successful nitrogen-fixing symbiosis between the bacteria and alfalfa. using the toxicity of the dcta substrate fluoroorotic acid as a selective agent in an iterated selection procedure, four independent s. meliloti dcta mutants were isolated that retained some ability to transport dicarboxylates. two mutations were located in a region called motif b located in a predicted transmembrane helix of the protein that has been shown ... | 2005 | 15659691 |
| 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 |
| origin of asymmetry in adenylyl cyclases: structures of mycobacterium tuberculosis rv1900c. | rv1900c, a mycobacterium tuberculosis adenylyl cyclase, is composed of an n-terminal alpha/beta-hydrolase domain and a c-terminal cyclase homology domain. it has an unusual 7% guanylyl cyclase side-activity. a canonical substrate-defining lysine and a catalytic asparagine indispensable for mammalian adenylyl cyclase activity correspond to n342 and h402 in rv1900c. mutagenic analysis indicates that these residues are dispensable for activity of rv1900c. structures of the cyclase homology domain, ... | 2005 | 15678099 |
| the high-affinity maltose/trehalose abc transporter in the extremely thermophilic bacterium thermus thermophilus hb27 also recognizes sucrose and palatinose. | we have studied the transport of trehalose and maltose in the thernophilic bacterium thermus thermophilus hb27, which grows optimally in the range of 70 to 75 degrees c. the k(m) values at 70 degrees c were 109 nm for trehalose and 114 nm for maltose; also, a high k(m) (424 nm) was found for the uptake of sucrose. competition studies showed that a single transporter recognizes trehalose, maltose, and sucrose, while d-galactose, d-fucose, l-rhamnose, l-arabinose, and d-mannose were not competitiv ... | 2005 | 15687184 |
| glnd is essential for nifa activation, ntrb/ntrc-regulated gene expression, and posttranslational regulation of nitrogenase activity in the photosynthetic, nitrogen-fixing bacterium rhodospirillum rubrum. | glnd is a bifunctional uridylyltransferase/uridylyl-removing enzyme and is thought to be the primary sensor of nitrogen status in the cell. it plays an important role in nitrogen assimilation and metabolism by reversibly regulating the modification of p(ii) proteins, which in turn regulate a variety of other proteins. we report here the characterization of glnd mutants from the photosynthetic, nitrogen-fixing bacterium rhodospirillum rubrum and the analysis of the roles of glnd in the regulation ... | 2005 | 15687189 |
| 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 |
| novel mobilizable prokaryotic two-hybrid system vectors for high-throughput protein interaction mapping in escherichia coli by bacterial conjugation. | since its initial description, the yeast two-hybrid (y2h) system has been widely used for the detection and analysis of protein-protein interactions. mating-based strategies have been developed permitting its application for automated proteomic interaction mapping projects using both exhaustive and high-throughput strategies. more recently, a number of prokaryotic two-hybrid (p2h) systems have been developed but, despite the many advantages such escherichia coli-based systems have over the y2h s ... | 2005 | 15687376 |
| lipopolysaccharides as a communication signal for progression of legume endosymbiosis. | establishment of a successful symbiosis between rhizobia and legumes results from an elaborate molecular dialogue between both partners. bacterial nodulation (nod) factors are indispensable for initiating plant responses, whereas bacterial surface polysaccharides are important for infection progression and nodule development. the mutant ors571-oac2 of azorhizobium caulinodans, affected in its surface polysaccharides, provokes a defective interaction with its host sesbania rostrata. ors571-oac2 i ... | 2005 | 15699329 |
| 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 |
| experimental identification and quantification of glucose metabolism in seven bacterial species. | the structurally conserved and ubiquitous pathways of central carbon metabolism provide building blocks and cofactors for the biosynthesis of cellular macromolecules. the relative uses of pathways and reactions, however, vary widely among species and depend upon conditions, and some are not used at all. here we identify the network topology of glucose metabolism and its in vivo operation by quantification of intracellular carbon fluxes from 13c tracer experiments. specifically, we investigated a ... | 2005 | 15716428 |
| cupin-type phosphoglucose isomerases (cupin-pgis) constitute a novel metal-dependent pgi family representing a convergent line of pgi evolution. | cupin-type phosphoglucose isomerases (cpgis) were identified in some archaeal and bacterial genomes and the respective coding function of cpgi's from the euryarchaeota archaeoglobus fulgidus and methanosarcina mazei, as well as the bacteria salmonella enterica serovar typhimurium and ensifer meliloti, was proven by functional overexpression. these cpgis and the cpgis from pyrococcus and thermococcus spp. represent the cpgi family and were compared with respect to kinetic, inhibitory, thermophili ... | 2005 | 15716432 |
| probing the sinorhizobium meliloti-alfalfa symbiosis using temperature-sensitive and impaired-function citrate synthase mutants. | to study the role of the decarboxylating leg of the bacterial tca cycle in symbiotic nitrogen fixation, we used dna shuffling and localized random polymerase chain reaction mutagenesis to construct a series of temperature-sensitive and impaired-function mutants in the sinorhizobium meliloti rm104a14 citrate synthase (glta) gene. reducing citrate synthase (cs) activity by mutation led to a corresponding decrease in the free-living growth rate; however, alfalfa plants formed fully effective nodule ... | 2005 | 15720082 |
| the lipid a substructure of the sinorhizobium meliloti lipopolysaccharides is sufficient to suppress the oxidative burst in host plants. | medicago sativa (alfalfa), medicago truncatula and nicotiana tabacum cell suspension cultures, responding to elicitation with the production of reactive oxygen species (ros), were used to analyse the suppressor (and elicitor) activity of lipopolysaccharides (lps) of the symbiotic soil bacterium sinorhizobium meliloti. in order to identify the epitopes of the lps molecule recognized by the plant, s. meliloti mutants defective in lps biosynthesis and hydrolytically obtained lipid a were analysed f ... | 2005 | 15720666 |
| 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 |
| functional domains of nosr, a novel transmembrane iron-sulfur flavoprotein necessary for nitrous oxide respiration. | bacterial nitrous oxide (n2o) respiration depends on the polytopic membrane protein nosr for the expression of n2o reductase from the nosz gene. we constructed his-tagged nosr and purified it from detergent-solubilized membranes of pseudomonas stutzeri atcc 14405. nosr is an iron-sulfur flavoprotein with redox centers positioned at opposite sides of the cytoplasmic membrane. the flavin cofactor is presumably bound covalently to an invariant threonine residue of the periplasmic domain. nosr also ... | 2005 | 15743947 |
| magnesium promotes flagellation of vibrio fischeri. | the bacterium vibrio fischeri requires bacterial motility to initiate colonization of the hawaiian squid euprymna scolopes. once colonized, however, the bacterial population becomes largely unflagellated. to understand environmental influences on v. fischeri motility, we investigated migration of this organism in tryptone-based soft agar media supplemented with different salts. we found that optimal migration required divalent cations and, in particular, mg2+. at concentrations naturally present ... | 2005 | 15743954 |
| nodulation of lupinus albus by strains of ochrobactrum lupini sp. nov. | the nodulation of legumes has for more than a century been considered an exclusive capacity of a group of microorganisms commonly known as rhizobia and belonging to the alpha-proteobacteria. however, in the last 3 years four nonrhizobial species, belonging to alpha and beta subclasses of the proteobacteria, have been described as legume-nodulating bacteria. in the present study, two fast-growing strains, lup21 and lup23, were isolated from nodules of lupinus honoratus. the phylogenetic analysis ... | 2005 | 15746334 |
| 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 |
| a copper(i) protein possibly involved in the assembly of cua center of bacterial cytochrome c oxidase. | sco1 and cox17 are accessory proteins required for the correct assembly of eukaryotic cytochrome c oxidase. at variance with sco1, cox17 orthologs are found only in eukaryotes. we browsed bacterial genomes to search proteins functionally equivalent to cox17, and we identified a class of proteins of unknown function displaying a conserved gene neighborhood to bacterial sco1 genes, all sharing a potential metal binding motif h(m)x10mx21hxm. two members of this group, dr1885 from deinococcus radiod ... | 2005 | 15753304 |
| 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 |