Publications

improved prediction of malaria degradomes by supervised learning with svm and profile kernel.	the spread of drug resistance through malaria parasite populations calls for the development of new therapeutic strategies. however, the seemingly promising genomics-driven target identification paradigm is hampered by the weak annotation coverage. to identify potentially important yet uncharacterized proteins, we apply support vector machines using profile kernels, a supervised discriminative machine learning technique for remote homology detection, as a complement to the traditional alignment ...	2009	19057851
delayed maturation of nodules reduces symbiotic effectiveness of the lotus japonicus-rhizobium sp. ngr234 interaction.	lotus japonicus, a model legume, develops an efficient, nitrogen-fixing symbiosis with mesorhizobium loti that promotes plant growth. lotus japonicus also forms functional nodules with rhizobium sp. ngr234 and r. etli. yet, in a plant defence-like reaction, nodules induced by r. etli quickly degenerate, thus limiting plant growth. in contrast, nodules containing ngr234 are long-lasting. it was found that ngr234 initiates nodule formation in a similar way to m. loti maff303099, but that the nodul ...	2009	19060298
delayed maturation of nodules reduces symbiotic effectiveness of the lotus japonicus-rhizobium sp. ngr234 interaction.	lotus japonicus, a model legume, develops an efficient, nitrogen-fixing symbiosis with mesorhizobium loti that promotes plant growth. lotus japonicus also forms functional nodules with rhizobium sp. ngr234 and r. etli. yet, in a plant defence-like reaction, nodules induced by r. etli quickly degenerate, thus limiting plant growth. in contrast, nodules containing ngr234 are long-lasting. it was found that ngr234 initiates nodule formation in a similar way to m. loti maff303099, but that the nodul ...	2009	19060298
functional differences of two distinct catalases in mesorhizobium loti maff303099 under free-living and symbiotic conditions.	protection against reactive oxygen species (ros) is important for legume-nodulating rhizobia during the establishment and maintenance of symbiosis, as well as under free-living conditions, because legume hosts might assail incoming microbes with ros and because nitrogenase is extremely sensitive to ros. we generated mutants of two potential catalase genes in mesorhizobium loti maff303099 to investigate their physiological significance. biochemical results indicated that genes with the locus tags ...	2009	19074374
functional differences of two distinct catalases in mesorhizobium loti maff303099 under free-living and symbiotic conditions.	protection against reactive oxygen species (ros) is important for legume-nodulating rhizobia during the establishment and maintenance of symbiosis, as well as under free-living conditions, because legume hosts might assail incoming microbes with ros and because nitrogenase is extremely sensitive to ros. we generated mutants of two potential catalase genes in mesorhizobium loti maff303099 to investigate their physiological significance. biochemical results indicated that genes with the locus tags ...	2009	19074374
functional mapping of brucella abortus cyclic beta-1,2-glucan synthase: identification of the protein domain required for cyclization.	cyclic beta-1,2-glucans (cbetag) are periplasmic homopolysaccharides that have been shown to play an important role in several symbiotic and pathogenic relationships. cyclic beta-1,2-glucan synthase (cgs), the enzyme responsible for the synthesis of cbetag, is an integral membrane polyfunctional protein that catalyzes the four enzymatic activities (initiation, elongation, phosphorolysis, and cyclization) required for the synthesis of cbetag. recently, we have identified the glycosyltransferase a ...	2009	19074375
functional mapping of brucella abortus cyclic beta-1,2-glucan synthase: identification of the protein domain required for cyclization.	cyclic beta-1,2-glucans (cbetag) are periplasmic homopolysaccharides that have been shown to play an important role in several symbiotic and pathogenic relationships. cyclic beta-1,2-glucan synthase (cgs), the enzyme responsible for the synthesis of cbetag, is an integral membrane polyfunctional protein that catalyzes the four enzymatic activities (initiation, elongation, phosphorolysis, and cyclization) required for the synthesis of cbetag. recently, we have identified the glycosyltransferase a ...	2009	19074375
genetic diversity and host range of rhizobia nodulating lotus tenuis in typical soils of the salado river basin (argentina).	a total of 103 root nodule isolates were used to estimate the diversity of bacteria nodulating lotus tenuis in typical soils of the salado river basin. a high level of genetic diversity was revealed by repetitive extragenic palindromic pcr, and 77 isolates with unique genomic fingerprints were further differentiated into two clusters, clusters a and b, after 16s rrna restriction fragment length polymorphism analysis. cluster a strains appeared to be related to the genus mesorhizobium, whereas cl ...	2009	19074602
genetic diversity and host range of rhizobia nodulating lotus tenuis in typical soils of the salado river basin (argentina).	a total of 103 root nodule isolates were used to estimate the diversity of bacteria nodulating lotus tenuis in typical soils of the salado river basin. a high level of genetic diversity was revealed by repetitive extragenic palindromic pcr, and 77 isolates with unique genomic fingerprints were further differentiated into two clusters, clusters a and b, after 16s rrna restriction fragment length polymorphism analysis. cluster a strains appeared to be related to the genus mesorhizobium, whereas cl ...	2009	19074602
isolation of the bacteriophage dinohi from dichelobacter nodosus and its interactions with other integrated genetic elements.	the gram-negative anaerobic pathogen dichelobacter nodosus carries several genetic elements that integrate into the chromosome. these include the inta, intb, intc and intd elements, which integrate adjacent to csra and pnpa, two putative global regulators of virulence and the virulence-related locus, vrl, which integrates into ssra. treatment of d. nodosus strains with ultraviolet light resulted in the isolation of dinohi, a member of the siphoviridae and the first bacteriophage to be identified ...	2008	19088904
genetic and computational identification of a conserved bacterial metabolic module.	we have experimentally and computationally defined a set of genes that form a conserved metabolic module in the alpha-proteobacterium caulobacter crescentus and used this module to illustrate a schema for the propagation of pathway-level annotation across bacterial genera. applying comprehensive forward and reverse genetic methods and genome-wide transcriptional analysis, we (1) confirmed the presence of genes involved in catabolism of the abundant environmental sugar myo-inositol, (2) defined a ...	2008	19096521
a portal for rhizobial genomes: rhizogate integrates a sinorhizobium meliloti genome annotation update with postgenome data.	sinorhizobium meliloti is a symbiotic soil bacterium of the alphaproteobacterial subdivision. like other rhizobia, s. meliloti induces nitrogen-fixing root nodules on leguminous plants. this is an ecologically and economically important interaction, because plants engaged in symbiosis with rhizobia can grow without exogenous nitrogen fertilizers. the s. meliloti-medicago truncatula (barrel medic) association is an important symbiosis model. the s. meliloti genome was published in 2001, and the m ...	2009	19103235
a portal for rhizobial genomes: rhizogate integrates a sinorhizobium meliloti genome annotation update with postgenome data.	sinorhizobium meliloti is a symbiotic soil bacterium of the alphaproteobacterial subdivision. like other rhizobia, s. meliloti induces nitrogen-fixing root nodules on leguminous plants. this is an ecologically and economically important interaction, because plants engaged in symbiosis with rhizobia can grow without exogenous nitrogen fertilizers. the s. meliloti-medicago truncatula (barrel medic) association is an important symbiosis model. the s. meliloti genome was published in 2001, and the m ...	2009	19103235
role of melanin pigment in expression of vibrio cholerae virulence factors.	we identified the mutated gene locus in a pigment-overproducing vibrio cholerae mutant of strain a1552. the deduced gene product is suggested to be an oxidoreductase based on partial homology to putative homogentisate 1,2-dioxygenase in pseudomonas aeruginosa and mesorhizobium loti, and we propose that the gene vc1345 in the v. cholerae genome be denoted hmga in accordance with the nomenclature for other species. the hmga::mini-tn5 mutant showed a nonpigmented phenotype after complementation wit ...	2009	19103773
role of melanin pigment in expression of vibrio cholerae virulence factors.	we identified the mutated gene locus in a pigment-overproducing vibrio cholerae mutant of strain a1552. the deduced gene product is suggested to be an oxidoreductase based on partial homology to putative homogentisate 1,2-dioxygenase in pseudomonas aeruginosa and mesorhizobium loti, and we propose that the gene vc1345 in the v. cholerae genome be denoted hmga in accordance with the nomenclature for other species. the hmga::mini-tn5 mutant showed a nonpigmented phenotype after complementation wit ...	2009	19103773
characterization of a {gamma}-aminobutyric acid transport system of rhizobium leguminosarum bv. viciae 3841.	spontaneous mutants of rhizobium leguminosarum bv. viciae 3841 were isolated that grow faster than the wild type on gamma-aminobutyric acid (gaba) as the sole carbon and nitrogen source. these strains (ru1736 and ru1816) have frameshift mutations (gtsr101 and gtsr102, respectively) in a gntr-type regulator (gtsr) that result in a high rate of constitutive gaba transport. tn5 mutagenesis and quantitative reverse transcription-pcr showed that gstr regulates expression of a large operon (prl100242 ...	2009	19103927
characterization of a {gamma}-aminobutyric acid transport system of rhizobium leguminosarum bv. viciae 3841.	spontaneous mutants of rhizobium leguminosarum bv. viciae 3841 were isolated that grow faster than the wild type on gamma-aminobutyric acid (gaba) as the sole carbon and nitrogen source. these strains (ru1736 and ru1816) have frameshift mutations (gtsr101 and gtsr102, respectively) in a gntr-type regulator (gtsr) that result in a high rate of constitutive gaba transport. tn5 mutagenesis and quantitative reverse transcription-pcr showed that gstr regulates expression of a large operon (prl100242 ...	2009	19103927
lotus japonicus castor and pollux are ion channels essential for perinuclear calcium spiking in legume root endosymbiosis.	the mechanism underlying perinuclear calcium spiking induced during legume root endosymbioses is largely unknown. lotus japonicus symbiosis-defective castor and pollux mutants are impaired in perinuclear calcium spiking. homology modeling suggested that the related proteins castor and pollux might be ion channels. here, we show that castor and pollux form two independent homocomplexes in planta. castor reconstituted in planar lipid bilayers exhibited ion channel activity, and the channel charact ...	2008	19106374
the constancy of gene conservation across divergent bacterial orders.	orthologous genes are frequently presumed to perform similar functions. however, outside of model organisms, this is rarely tested. one means of inferring changes in function is if there are changes in the level of gene conservation and selective constraint. here we compare levels of gene conservation across three bacterial groups to test for changes in gene functionality.	2009	19128452
characterization of novel 2-oxoglutarate dependent dioxygenases converting l-proline to cis-4-hydroxy-l-proline.	hydroxyprolines are valuable chiral building blocks for organic synthesis of pharmaceuticals. several microorganisms producing l-proline trans-4- and cis-3-hydroxylase were discovered and these enzymes were applied to the industrial production of trans-4- and cis-3-hydroxy-l-proline, respectively. meanwhile, other hydroxyproline isomers, cis-4- and trans-3-hydroxy-l-proline, were not easily available because the corresponding hydroxylase have not been discovered. herein we report novel l-proline ...	2009	19133227
rearrangement of actin cytoskeleton mediates invasion of lotus japonicus roots by mesorhizobium loti.	infection thread-dependent invasion of legume roots by rhizobia leads to internalization of bacteria into the plant cells, which is one of the salient features of root nodule symbiosis. we found that two genes, nap1 (for nck-associated protein 1) and pir1 (for 121f-specific p53 inducible rna), involved in actin rearrangements were essential for infection thread formation and colonization of lotus japonicus roots by its natural microsymbiont, mesorhizobium loti. nap1 and pir1 mutants developed an ...	2009	19136645
cloning, expression and immunogenicity of the translation initiation factor 3 homologue of brucella abortus.	the infc gene of brucella abortus encoding the translation initiation factor 3 (if3) was cloned, sequenced and expressed in escherichia coli. the amino acid sequence analysis predicted a product with 74-80% identity with the if3 proteins from mesorhizobium loti, sinorhizobium meliloti, aurantimona sp. and mesorhizobium sp. this protein also show 54% amino acid sequence identity with the e. coli if3, sharing most of the residues which were described as responsible for the biological activity of t ...	2009	19167989
the temperature-sensitive brush mutant of the legume lotus japonicus reveals a link between root development and nodule infection by rhizobia.	the brush mutant of lotus japonicus exhibits a temperature-dependent impairment in nodule, root, and shoot development. at 26 degrees c, brush formed fewer nodules, most of which were not colonized by rhizobia bacteria. primary root growth was retarded and the anatomy of the brush root apical meristem revealed distorted cellular organization and reduced cell expansion. reciprocal grafting of brush with wild-type plants indicated that this genotype only affected the root and that the shoot phenot ...	2009	19176723
genomic islands: tools of bacterial horizontal gene transfer and evolution.	bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. the horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. a significant part of the horizontal gene ...	2008	19178566
genomic islands: tools of bacterial horizontal gene transfer and evolution.	bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. the horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. a significant part of the horizontal gene ...	2008	19178566
pathway of gamma-aminobutyrate metabolism in rhizobium leguminosarum 3841 and its role in symbiosis.	pea plants incubated in 15n2 rapidly accumulated labeled gamma-aminobutyrate (gaba) in the plant cytosol and in bacteroids of rhizobium leguminosarum bv. viciae 3841. two pathways of gaba metabolism were identified in r. leguminosarum 3841. in the first, glutamate is formed by gaba aminotransferase (gabt), transferring the amino group from gaba to 2-oxoglutarate. in the second, alanine is formed by two omega-aminotransferases (opaa and opab), transferring the amino group from gaba to pyruvate. w ...	2009	19181799
role of potassium uptake systems in sinorhizobium meliloti osmoadaptation and symbiotic performance.	stimulation of potassium uptake is the most rapid response to an osmotic upshock in bacteria. this cation accumulates by a number of different transport systems whose importance has not been previously addressed for rhizobia. in silico analyses reveal the presence of genes encoding four possible potassium uptake systems in the genome of sinorhizobium meliloti 1021: kup1, kup2, trk, and kdp. the study of the relevance of these systems under a number of different growth conditions and in symbiosis ...	2009	19181803
construction of disarmed ti plasmids transferable between escherichia coli and agrobacterium species.	agrobacterium-mediated plant transformation has been used widely, but there are plants that are recalcitrant to this type of transformation. this transformation method uses bacterial strains harboring a modified tumor-inducing (ti) plasmid that lacks the transfer dna (t-dna) region (disarmed ti plasmid). it is desirable to develop strains that can broaden the host range. a large number of agrobacterium strains have not been tested yet to determine whether they can be used in transformation. in o ...	2009	19181833
genome sequence of desulfobacterium autotrophicum hrm2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide.	sulfate-reducing bacteria (srb) belonging to the metabolically versatile desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. desulfobacterium autotrophicum hrm2 is the first member of this ecophysiologically important group with a now available genome sequence. with 5.6 megabasepairs (mbp) the genome of db. autotrophicum hrm2 is about 2 mbp larger than the sequenced genomes of other sulfate reducers (srb). a h ...	2009	19187283
rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life.	completed genome sequences are rapidly increasing for rickettsia, obligate intracellular alpha-proteobacteria responsible for various human diseases, including epidemic typhus and rocky mountain spotted fever. in light of phylogeny, the establishment of orthologous groups (ogs) of open reading frames (orfs) will distinguish the core rickettsial genes and other group specific genes (class 1 ogs or c1ogs) from those distributed indiscriminately throughout the rickettsial tree (class 2 og or c2ogs) ...	2008	19194535
evolution of the antibiotic resistance protein, fosa, is linked to a catalytically promiscuous progenitor.	the fosfomycin (1) resistance proteins fosa and fosx in pathogenic microorganisms are related to a catalytically promiscuous progenitor encoded in a phn operon in mesorhizobium loti. the mlr3345 gene product (fosx(ml)) from m. loti has a very low epoxide hydrolase activity and even lower glutathione transferase activity toward 1 and does not confer resistance to the antibiotic. in vitro homologous recombination of the mlr3345 and pa1129 genes (a fosa gene from pseudomonas aeruginosa that does co ...	2009	19196010
minimum contradiction matrices in whole genome phylogenies.	minimum contradiction matrices are a useful complement to distance-based phylogenies. a minimum contradiction matrix represents phylogenetic information under the form of an ordered distance matrix y(i) (,) (j) (n). a matrix element corresponds to the distance from a reference vertex n to the path (i, j). for an x-tree or a split network, the minimum contradiction matrix is a robinson matrix. it therefore fulfills all the inequalities defining perfect order: y(i) (,) (j) (n) >or= y(i) (,) (k) (n ...	2008	19204821
gene identification and characterization of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an nad+-dependent dismutase.	a chromosomal gene, mlr6793, in mesorhizobium loti was identified as the gene encoding 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid (fhmpc) dehydrogenase (dismutase) involved in the degradation pathway for pyridoxine (vitamin b(6)). the homogenously purified recombinant enzyme has a molecular mass of 59.1 kda and is a homodimeric protein. fhmpc dehydrogenase catalyses practically irreversible oxidation (k(cat) = 204 s(-1)) of fhmpc (k(m) = 48.2 microm) by nad(+) (k(m) = 34.3 microm) to ...	2009	19218190
characterization of a mesorhizobium loti alpha-type carbonic anhydrase and its role in symbiotic nitrogen fixation.	carbonic anhydrase (ca) (ec 4.2.1.1) is a widespread enzyme catalyzing the reversible hydration of co(2) to bicarbonate, a reaction that participates in many biochemical and physiological processes. mesorhizobium loti, the microsymbiont of the model legume lotus japonicus, possesses on the symbiosis island a gene (msi040) encoding an alpha-type ca homologue, annotated as caa1. in the present work, the caa1 open reading frame from m. loti strain r7a was cloned, expressed, and biochemically charac ...	2009	19218391
target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.	to study the substrate specificity of enzymes, we use the amidohydrolase and enolase superfamilies as model systems; members of these superfamilies share a common tim barrel fold and catalyze a wide range of chemical reactions. here, we describe a collaboration between the enzyme specificity consortium (enspec) and the new york sgx research center for structural genomics (nysgxrc) that aims to maximize the structural coverage of the amidohydrolase and enolase superfamilies. using sequence- and s ...	2009	19219566
genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria.	the family rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. within this family, many rhizobium and sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as agrobacterium are plant pathogens. these contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. members of the rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, ...	2009	19251847
identification of a novel udp-n-acetylglucosamine enolpyruvyl transferase (mura) from vibrio fischeri that confers high fosfomycin resistance in escherichia coli.	mura [udp-n-acetylglucosamine (udp-nag) enolpyruvyl transferase] is a key enzyme involved in bacterial cell wall peptidoglycan synthesis and a target for the antimicrobial agent fosfomycin, a structural analog of the mura substrate phosphoenol pyruvate. in this study, we identified, cloned and sequenced a novel mura gene from an environmental isolate of vibrio fischeri that is naturally resistant to fosfomycin. the fosfomycin resistance gene was isolated from a genomic dna library of v. fischeri ...	2009	19277606
protein secretion systems in bacterial-host associations, and their description in the gene ontology.	protein secretion plays a central role in modulating the interactions of bacteria with their environments. this is particularly the case when symbiotic bacteria (whether pathogenic, commensal or mutualistic) are interacting with larger host organisms. in the case of gram-negative bacteria, secretion requires translocation across the outer as well as the inner membrane, and a diversity of molecular machines have been elaborated for this purpose. a number of secreted proteins are destined to enter ...	2009	19278550
localization of the attachment site of oligoglucans to mesorhizobium loti hambi 1148 murein.	the location and nature of the linkage between peptidoglycan and oligoglucans in the cell wall of mesorhizobium loti hambi 1148 have been defined by the analysis of nitrous acid deamination of peptidoglycan glucosaminyl residues. the murnh(2)-glc(n) fraction was obtained after converting deaminoacylated and n-deacetylated muramyl residues in the cell wall preparation to lactam forms which were stable during subsequent deamination, followed by reduction and opening of the lactams. gc/ms analysis ...	2009	19294234
functional analysis of three ahl autoinducer synthase genes in mesorhizobium loti reveals the important role of quorum sensing in symbiotic nodulation.	one of the most important signal transduction pathways in bacteria, quorum sensing, is involved in many regulatory circuits in rhizobia, especially in the control of communication between rhizobia and their plant hosts. in this study, we identified 3 autoinducer synthase genes - mrli1, mrli2, and mrli3 - in mesorhizobium loti nzp 2213. we found that mrli1 and mrli2 could synthesize distinct n-acyl homoserine lactone (ahl) autoinducers in rich medium cultures, and the expression of mrli1 was show ...	2009	19295655
the mnth gene encodes the major mn(2+) transporter in bradyrhizobium japonicum and is regulated by manganese via the fur protein.	the bacterial nramp family protein mnth is a divalent metal transporter, but mnth mutants have little or no phenotype in organisms where it has been studied. here, we identify the mnth homologue of bradyrhizobium japonicum, and demonstrate that it is essential for mn(2+) transport and for maintenance of cellular manganese homeostasis. transport activity was induced under manganese deficiency, and fe(2+) did not compete with (54)mn(2+) for uptake by cells. the steady-state level of mnth mrna was ...	2009	19298371
structure of the plp degradative enzyme 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from mesorhizobium loti maff303099 and its mechanistic implications.	a vitamin b(6) degradative pathway has recently been identified and characterized in mesorhizobium loti maff303099. one of the enzymes on this pathway, 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (mhpco), is a flavin-dependent enzyme and catalyzes the oxidative ring-opening of 2-methyl-3-hydroxypyridine-5-carboxylic acid to form e-2-(acetamino-methylene)succinate. the gene for this enzyme has been cloned, and the corresponding protein has been overexpressed in escherichia coli and pur ...	2009	19317437
developmental gene expression profiles of the human pathogen schistosoma japonicum.	the schistosome blood flukes are complex trematodes and cause a chronic parasitic disease of significant public health importance worldwide, schistosomiasis. their life cycle is characterised by distinct parasitic and free-living phases involving mammalian and snail hosts and freshwater. microarray analysis was used to profile developmental gene expression in the asian species, schistosoma japonicum. total rnas were isolated from the three distinct environmental phases of the lifecycle -- aquati ...	2009	19320991
analysis of ten brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle.	the facultative intracellular bacterial pathogen brucella infects a wide range of warm-blooded land and marine vertebrates and causes brucellosis. currently, there are nine recognized brucella species based on host preferences and phenotypic differences. the availability of 10 different genomes consisting of two chromosomes and representing six of the species allowed for a detailed comparison among themselves and relatives in the order rhizobiales. phylogenomic analysis of ortholog families show ...	2009	19346311
characterization of the mesorhizobium loti maff303099 type-three protein secretion system.	type iii secretion systems (t3ss) have been found in several species of rhizobia. proteins (termed effectors) secreted by this system are involved in host-range determination and influence nodulation efficiency. mesorhizobium loti maff303099 possesses a functional t3ss in its symbiotic island whose expression is induced by flavonoids. as in other rhizobia, conserved cis-elements (tts box) were found in the promoter regions of genes or operons encoding t3ss components. using a bioinformatics appr ...	2009	19348570
the structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains.	the recent characterization of the prokaryotic cys(2)his(2) zinc-finger domain, identified in ros protein from agrobacterium tumefaciens, has demonstrated that, although possessing a similar zinc coordination sphere, this domain is structurally very different from its eukaryotic counterpart. a search in the databases has identified approximately 300 homologues with a high sequence identity to the ros protein, including the amino acids that form the extensive hydrophobic core in ros. surprisingly ...	2009	19369210
transcriptomic analysis of rhizobium leguminosarum biovar viciae in symbiosis with host plants pisum sativum and vicia cracca.	rhizobium leguminosarum bv. viciae forms nitrogen-fixing nodules on several legumes, including pea (pisum sativum) and vetch (vicia cracca), and has been widely used as a model to study nodule biochemistry. to understand the complex biochemical and developmental changes undergone by r. leguminosarum bv. viciae during bacteroid development, microarray experiments were first performed with cultured bacteria grown on a variety of carbon substrates (glucose, pyruvate, succinate, inositol, acetate, a ...	2009	19376875
rhizobium sp. strain ngr234 possesses a remarkable number of secretion systems.	rhizobium sp. strain ngr234 is a unique alphaproteobacterium (order rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other microsymbiont. we report here that the 3.93-mbp chromosome (cngr234) encodes most functions required for cellular growth. few essential functions are encoded on the 2.43-mbp megaplasmid (pngr234b), and none are present on the second 0.54-mbp symbiotic plasmid (pngr234a). among many striking features, the 6.9-mbp genome encodes more different secreti ...	2009	19376903
extensive genomic diversity of closely related wolbachia strains.	using microarray-based comparative genome hybridization (mcgh), the genomic content of wolbachia pipientis wmel from drosophila melanogaster was compared to the closely related wolbachia from d. innubila (winn), d. santomea (wsan), and three strains from d. simulans (wau, wri, wsim). a large number of auxiliary genes are identified in these five strains, with most absent/divergent genes being unique to a given strain. each strain caused an average of approximately 60 genes to be removed from the ...	2009	19389774
exploiting structural classifications for function prediction: towards a domain grammar for protein function.	the ability to assign function to proteins has become a major bottleneck for comprehensively understanding cellular mechanisms at the molecular level. here we discuss the extent to which structural domain classifications can help in deciphering the complex relationship between the functions of proteins and their sequences and structures. structural classifications are particularly helpful in understanding the mosaic manner in which new proteins and functions emerge through evolution. this is par ...	2009	19398323
molecular and biochemical characterization of the parvulin-type ppiases in lotus japonicus.	the cis/trans isomerization of the peptide bond preceding proline is an intrinsically slow process, although important in many biological processes in both prokaryotes and eukaryotes. in vivo, this isomerization is catalyzed by peptidyl-prolyl cis/trans-isomerases (ppiases). here, we present the molecular and biochemical characterization of parvulin-type ppiase family members of the model legume lotus japonicus, annotated as ljpar1, ljpar2, and ljpar3. although ljpar1 and ljpar2 were found to be ...	2009	19403733
an acetyltransferase conferring tolerance to toxic aromatic amine chemicals: molecular and functional studies.	aromatic amines (aa) are a major class of environmental pollutants that have been shown to have genotoxic and cytotoxic potentials toward most living organisms. fungi are able to tolerate a diverse range of chemical compounds including certain aa and have long been used as models to understand general biological processes. deciphering the mechanisms underlying this tolerance may improve our understanding of the adaptation of organisms to stressful environments and pave the way for novel pharmace ...	2009	19416981
evolution in the amidohydrolase superfamily: substrate-assisted gain of function in the e183k mutant of a phosphotriesterase-like metal-carboxylesterase.	the recent specialization for utilization of pesticides reported for pseudomonas diminuta phosphotriesterase (ppte) strongly suggests that this activity evolved from an enzyme endowed with promiscuous phosphotriesterase activity. such a putative "generalist" enzyme was recently proposed to be a member of the new phoshotriesterase-like lactonase family (pll). the promiscuous carboxylesterase and phosphodiesterase activities detected in ppte and plls in turn paved the way for the prediction of the ...	2009	19438255
methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of c1 compounds from natural and industrial sources.	methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. the genomes of two pink-pigmented facultative methylotrophic bacteria of the alpha-proteobacterial genus methylobacterium, the reference species methylobacterium extorquens strain am1 and the dichloromethane-degrading strain dm4, were compared.	2009	19440302
nicotianamine synthase specifically expressed in root nodules of lotus japonicus.	in dicotyledonous plants, nicotianamine synthase (nas) is thought to play a role in the intercellular transport of iron (fe). fe is an essential metal for nitrogen-fixing root nodules of legumes, prompting us to characterize the role of the nas gene in detail. we previously compared gene-expression profiles in ineffective nodules formed on a lotus japonicus fix(-) mutant, sen1, with those in wild-type-effective nodules, and showed that expression of an expressed sequence tag (est) clone encoding ...	2009	19455352
solution structure of the mesorhizobium loti k1 channel cyclic nucleotide-binding domain in complex with camp.	cyclic nucleotide-sensitive ion channels, known as hcn and cng channels, are crucial in neuronal excitability and signal transduction of sensory cells. hcn and cng channels are activated by binding of cyclic nucleotides to their intracellular cyclic nucleotide-binding domain (cnbd). however, the mechanism by which the binding of cyclic nucleotides opens these channels is not well understood. here, we report the solution structure of the isolated cnbd of a cyclic nucleotide-sensitive k(+) channel ...	2009	19465888
a cytosolic invertase is required for normal growth and cell development in the model legume, lotus japonicus.	neutral/alkaline invertases are a subgroup, confined to plants and cyanobacteria, of a diverse family of enzymes. a family of seven closely-related genes, ljinv1-ljinv7, is described here and their expression in the model legume, lotus japonicus, is examined. ljinv1 previously identified as encoding a nodule-enhanced isoform is the predominant isoform present in all parts of the plant. mutants for two isoforms, ljinv1 and ljinv2, were isolated using tilling. a premature stop codon allele of ljin ...	2009	19474088
ensifer meliloti bv. lancerottense establishes nitrogen-fixing symbiosis with lotus endemic to the canary islands and shows distinctive symbiotic genotypes and host range.	eleven strains were isolated from root nodules of lotus endemic to the canary islands and they belonged to the genus ensifer, a genus never previously described as a symbiont of lotus. according to their 16s rrna and atpd gene sequences, two isolates represented minority genotypes that could belong to previously undescribed ensifer species, but most of the isolates were classified within the species ensifer meliloti. these isolates nodulated lotus lancerottensis, lotus corniculatus and lotus jap ...	2009	19477097
plant lectins: the ties that bind in root symbiosis and plant defense.	lectins are a diverse group of carbohydrate-binding proteins that are found within and associated with organisms from all kingdoms of life. several different classes of plant lectins serve a diverse array of functions. the most prominent of these include participation in plant defense against predators and pathogens and involvement in symbiotic interactions between host plants and symbiotic microbes, including mycorrhizal fungi and nitrogen-fixing rhizobia. extensive biological, biochemical, and ...	2009	19488786
comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes.	the prokaryotic toxin-antitoxin systems (tas, also referred to as ta loci) are widespread, mobile two-gene modules that can be viewed as selfish genetic elements because they evolved mechanisms to become addictive for replicons and cells in which they reside, but also possess "normal" cellular functions in various forms of stress response and management of prokaryotic population. several distinct tas of type 1, where the toxin is a protein and the antitoxin is an antisense rna, and numerous, unr ...	2009	19493340
symbiotic competence in lotus japonicus is affected by plant nitrogen status: transcriptomic identification of genes affected by a new signalling pathway.	in leguminous plants, symbiotic nitrogen (n) fixation performances and n environmental conditions are linked because nodule initiation, development and functioning are greatly influenced by the amount of available n sources. we demonstrate here that n supply also controls, beforehand, the competence of leguminous plants to perform the nodulation program. lotus japonicus plants preincubated for 10 d in high-n conditions, and then transferred to low n before the mesorhizobium loti inoculation, had ...	2009	19500268
ethylene insensitivity conferred by a mutated arabidopsis ethylene receptor gene alters nodulation in transgenic lotus japonicus.	transgenics are used to demonstrate a causal relationship between ethylene insensitivity of a seedling legume plant, the level of ethylene receptor gene expression, lateral root growth and mesorhizobium loti-induced nodule initiation.	2009	19505874
cerberus, a novel u-box protein containing wd-40 repeats, is required for formation of the infection thread and nodule development in the legume-rhizobium symbiosis.	endosymbiotic infection of legume plants by rhizobium bacteria is initiated through infection threads (its) which are initiated within and penetrate from root hairs and deliver the endosymbionts into nodule cells. despite recent progress in understanding the mutual recognition and early symbiotic signaling cascades in host legumes, the molecular mechanisms underlying bacterial infection processes and successive nodule organogenesis are still poorly understood. we isolated a novel symbiotic mutan ...	2009	19508425
cytokinin induces expansin gene expression in melilotus alba desr. wild-type and the non-nodulating, non-mycorrhizal (nodmyc) mutant masym3.	we previously showed that applying 10(-6) m of the cytokinin 6-benzylaminopurine (bap) to uninoculated roots of masym3, a nod(-)myc(-)melilotus alba (desr.) mutant, resulted in the accumulation of maenod40 transcripts to levels similar to bap-treated wild-type roots. in contrast, inoculation with a nod(-)s. meliloti mutant expressing the trans-zeatin synthase gene of agrobacterium tumefaciens (nod(-)/ptzs(+)) did not induce maenod40 transcript accumulation in either wild-type or masym3 roots. ho ...	2008	19513217
the symbiosis interactome: a computational approach reveals novel components, functional interactions and modules in sinorhizobium meliloti.	rhizobium-legume symbiosis is an attractive biological process that has been studied for decades because of its importance in agriculture. however, this system has undergone extensive study and although many of the major factors underpinning the process have been discovered using traditional methods, much remains to be discovered.	2009	19531251
fine-structured multi-scaling long-range correlations in completely sequenced genomes--features, origin, and classification.	the sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 x 10(6) to 3.0 x 10(7) bp from archaea, bacteria, arabidopsis thaliana, saccharomyces cerevisiae, schizosaccharomyces po ...	2009	19533117
characterization and isolation of a t-dna tagged banana promoter active during in vitro culture and low temperature stress.	next-generation transgenic plants will require a more precise regulation of transgene expression, preferably under the control of native promoters. a genome-wide t-dna tagging strategy was therefore performed for the identification and characterization of novel banana promoters. embryogenic cell suspensions of a plantain-type banana were transformed with a promoterless, codon-optimized luciferase (luc+) gene and low temperature-responsive luciferase activation was monitored in real time.	2009	19552803
the complete genome of teredinibacter turnerae t7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms).	here we report the complete genome sequence of teredinibacter turnerae t7901. t. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family teredinidae (shipworms). this species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host's nitrogen-deficient diet. t. t ...	2009	19568419
conserved amino acid sequence features in the alpha subunits of mofe, vfe, and fefe nitrogenases.	this study examines the structural features and phylogeny of the alpha subunits of 69 full-length nifd (mofe subunit), vnfd (vfe subunit), and anfd (fefe subunit) sequences.	2009	19578539
detection of genomic islands via segmental genome heterogeneity.	while the recognition of genomic islands can be a powerful mechanism for identifying genes that distinguish related bacteria, few methods have been developed to identify them specifically. rather, identification of islands often begins with cataloging individual genes likely to have been recently introduced into the genome; regions with many putative alien genes are then examined for other features suggestive of recent acquisition of a large genomic region. when few phylogenetic relatives are av ...	2009	19589805
origin of an alternative genetic code in the extremely small and gc-rich genome of a bacterial symbiont.	the genetic code relates nucleotide sequence to amino acid sequence and is shared across all organisms, with the rare exceptions of lineages in which one or a few codons have acquired novel assignments. recoding of uga from stop to tryptophan has evolved independently in certain reduced bacterial genomes, including those of the mycoplasmas and some mitochondria. small genomes typically exhibit low guanine plus cytosine (gc) content, and this bias in base composition has been proposed to drive ug ...	2009	19609354
persistent wolbachia and cultivable bacteria infection in the reproductive and somatic tissues of the mosquito vector aedes albopictus.	commensal and symbiotic microbes have a considerable impact on the behavior of many arthropod hosts, including hematophagous species that transmit pathogens causing infectious diseases to human and animals. little is known about the bacteria associated with mosquitoes other than the vectorized pathogens. this study investigated wolbachia and cultivable bacteria that persist through generations in ae. albopictus organs known to host transmitted arboviruses, such as dengue and chikungunya.	2009	19633721
resonance assignment of the cyclic nucleotide binding domain from a cyclic nucleotide-gated k(+) channel in complex with camp.	in order to determine the structure of the 15 kda cyclic nucleotide binding domain of a cyclic nucleotide-activated k(+) channel from mesorhizobium loti and its interaction with camp, nearly complete (1)h, (13)c, and (15)n chemical shifts were assigned.	2007	19636859
tilling in lotus japonicus identified large allelic series for symbiosis genes and revealed a bias in functionally defective ethyl methanesulfonate alleles toward glycine replacements.	we have established tools for forward and reverse genetic analysis of the legume lotus (lotus japonicus). a structured population of m2 progeny of 4,904 ethyl methanesulfonate-mutagenized m1 embryos is available for single nucleotide polymorphism mutation detection, using a tilling (for targeting induced local lesions in genomes) protocol. scanning subsets of this population, we identified a mutation load of one per 502 kb of amplified fragment. moreover, we observed a 1:10 ratio between homozyg ...	2009	19641028
mesorhizobium shangrilense sp. nov., isolated from root nodules of caragana species.	five strains of bacteria isolated from nodules of caragana bicolor and caragana erinacea in yunnan province of china were classified within the genus mesorhizobium in the class alphaproteobacteria. the highest degree of 16s rrna gene sequence similarity was determined to be to mesorhizobium loti lmg 6125(t) (99.7 %) and mesorhizobium ciceri upm-ca7(t) (99.7 %). polyphasic taxonomic methods including sds-page of whole-cell soluble proteins, comparative housekeeping sequence analysis of atpd, glni ...	2009	19643905
crystallization and preliminary x-ray analysis of aams amidohydrolase, the final enzyme in degradation pathway i of pyridoxine.	alpha-(n-acetylaminomethylene)succinic acid (aams) amidohydrolase from mesorhizobium loti maff303099, which is involved in a degradation pathway of vitamin b(6) and catalyzes the degradation of aams to acetic acid, ammonia, carbon dioxide and succinic semialdehyde, has been overexpressed in escherichia coli. to elucidate the reaction mechanism based on the tertiary structure, the recombinant enzyme was purified and crystallized by the sitting-drop vapour-diffusion method using peg 8000 as precip ...	2009	19652351
deciphering evolutionary mechanisms between mutualistic and pathogenic symbioses.	the continuum between mutualistic and pathogenic symbioses has been an underlying theme for understanding the evolution of infection and disease in a number of eukaryotic-microbe associations. the ability to monitor and then predict the spread of infectious diseases may depend upon our knowledge and capabilities of anticipating the behavior of virulent pathogens by studying related, benign symbioses. for instance, the ability of a symbiotic species to infect, colonize, and proliferate efficientl ...	2008	19655044
dissection of symbiosis and organ development by integrated transcriptome analysis of lotus japonicus mutant and wild-type plants.	genetic analyses of plant symbiotic mutants has led to the identification of key genes involved in rhizobium-legume communication as well as in development and function of nitrogen fixing root nodules. however, the impact of these genes in coordinating the transcriptional programs of nodule development has only been studied in limited and isolated studies. here, we present an integrated genome-wide analysis of transcriptome landscapes in lotus japonicus wild-type and symbiotic mutant plants. enc ...	2009	19662091
chelativorans multitrophicus gen. nov., sp. nov. and chelativorans oligotrophicus sp. nov., aerobic edta-degrading bacteria.	two previously isolated strains (dsm 9103(t) and lpm-4(t)) able to grow with edta (facultatively and obligately, respectively) as the source of carbon, nitrogen and energy were investigated in order to clarify their taxonomic positions. the strains were strictly aerobic, gram-negative, asporogenous and non-motile rods that required biotin for growth. reproduction occurred by binary fission. the strains were mesophilic and neutrophilic. their major fatty acids were summed feature 7 (consisting of ...	2010	19666787
a genome-wide compilation of the two-component systems in lotus japonicus.	the two-component systems (tcs), or histidine-to-aspartate phosphorelays, are evolutionarily conserved common signal transduction mechanisms that are implicated in a wide variety of cellular responses to environmental stimuli in both prokaryotes and eukaryotes including plants. among higher plants, legumes including lotus japonicus have a unique ability to engage in beneficial symbiosis with nitrogen-fixing bacteria. we previously presented a genome-wide compiled list of tcs-associated component ...	2009	19675111
a luxri-family regulatory system controls excision and transfer of the mesorhizobium loti strain r7a symbiosis island by activating expression of two conserved hypothetical genes.	the symbiosis island icemlsym(r7a) of mesorhizobium loti r7a is an integrative and conjugative element (ice) that carries genes required for a nitrogen-fixing symbiosis with lotus species. icemlsym(r7a) encodes homologues (trar, trai1 and trai2) of proteins that regulate plasmid transfer by quorum sensing in rhizobia and agrobacteria. introduction of trar cloned on a plasmid induced excision of icemlsym(r7a) in all cells, a 1000-fold increase in the production of 3-oxo-c6-homoserine lactone (3-o ...	2009	19682258
responses of the model legume medicago truncatula to the rhizobial exopolysaccharide succinoglycan.	many species of rhizobial bacteria can invade their plant hosts and induce development of symbiotic nitrogen-fixing nodules only if they are able to produce an acidic exopolysaccharide (eps) with certain structural and molecular weight characteristics.1-3sinorhizobium meliloti that produces the functional form of the exopolysaccharide succinoglycan induces formation of invasion structures called infection threads in the root hair cells of its plant hosts alfalfa and medicago truncatula. however, ...	2008	19704531
prokaryotic homologs of argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements.	in eukaryotes, rna interference (rnai) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mrnas. the rnai systems recognize the target rna molecules via small guide rnas that are completely or partially complementary to a region of the target. key components of the rnai systems are proteins of the argonaute-piwi family some of which function as slicers, the nucleases that cleave the target rna that is base-paired to a guide r ...	2009	19706170
convergent evolution of metabolic roles in bacterial co-symbionts of insects.	a strictly host-dependent lifestyle has profound evolutionary consequences for bacterial genomes. most prominent is a sometimes-dramatic amount of gene loss and genome reduction. recently, highly reduced genomes from the co-resident intracellular symbionts of sharpshooters were shown to exhibit a striking level of metabolic interdependence. one symbiont, called sulcia muelleri (bacteroidetes), can produce eight of the 10 essential amino acids, despite having a genome of only 245 kb. the other, b ...	2009	19706397
epigenetic modification of rhizobial genome is essential for efficient nodulation.	ccrm is one of the solitary bacterial dna methyltransferases which does not have corresponding restriction enzymes. we established a stable ccrm-overexpressing mutant of mesorhizobium loti, mlccrm-ox, and performed molecular and phenotypic characterization of this strain. in the m. loti mlccrm-ox infected plants, nodulation was apparently delayed at 7 days after inoculation (dai), however, the nodules that eventually formed on the mlccrm-ox roots showed nitrogen fixing ability by at least 21 dai ...	2009	19720053
a possible role of class 1 plant hemoglobin at the early stage of legume-rhizobium symbiosis.		2009	19721749
crystallization and preliminary x-ray analysis of 4-pyridoxolactonase from mesorhizobium loti.	4-pyridoxolactonase from mesorhizobium loti maff303099 has been overexpressed in escherichia coli. the recombinant enzyme was purified and was crystallized by the sitting-drop vapour-diffusion method using peg 4000 and ammonium sulfate as precipitants. crystals of the free enzyme (form i) and of the 5-pyridoxolactone-bound enzyme (form ii) grew under these conditions. crystals of form i diffracted to 2.0 a resolution and belonged to the monoclinic space group c2, with unit-cell parameters a = 77 ...	2009	19724124
the dif/xer recombination systems in proteobacteria.	in e. coli, 10 to 15% of growing bacteria produce dimeric chromosomes during dna replication. these dimers are resolved by xerc and xerd, two tyrosine recombinases that target the 28-nucleotide motif (dif) associated with the chromosome's replication terminus. in streptococci and lactococci, an alternative system is composed of a unique, xer-like recombinase (xers) genetically linked to a dif-like motif (dif(sl)) located at the replication terminus. preliminary observations have suggested that t ...	2009	19727445
disruption of the bmei0066 gene attenuates the virulence of brucella melitensis and decreases its stress tolerance.	brucella melitensis is a facultative intracellular pathogen. an operon composed of bmei0066, which encodes a two-component response regulator cenr, and bmei0067, which encodes a camp-dependent protein kinase regulatory subunit, has been predicted to exist in many bacterial species. however, little is known about the function of this operon. in order to characterize this operon and assess its role in virulence, we constructed a marked deletion mutant of bmei0066. the mutant was less able to withs ...	2009	19742243
identification of functional lsrb-like autoinducer-2 receptors.	although a variety of bacterial species have been reported to use the interspecies communication signal autoinducer-2 (ai-2) to regulate multiple behaviors, the molecular mechanisms of ai-2 recognition and signal transduction remain poorly understood. to date, two types of ai-2 receptors have been identified: luxp, present in vibrio spp., and lsrb, first identified in salmonella enterica serovar typhimurium. in s. typhimurium, lsrb is the ligand binding protein of a transport system that enables ...	2009	19749048
complete genome sequence of the sugarcane nitrogen-fixing endophyte gluconacetobacter diazotrophicus pal5.	gluconacetobacter diazotrophicus pal5 is an endophytic diazotrophic bacterium that lives in association with sugarcane plants. it has important biotechnological features such as nitrogen fixation, plant growth promotion, sugar metabolism pathways, secretion of organic acids, synthesis of auxin and the occurrence of bacteriocins.	2009	19775431
evidence for calcium-mediated perception of plant symbiotic signals in aequorin-expressing mesorhizobium loti.	during the interaction between rhizobia and leguminous plants the two partners engage in a molecular conversation that leads to reciprocal recognition and ensures the beginning of a successful symbiotic integration. in host plants, intracellular ca(2+) changes are an integral part of the signalling mechanism. in rhizobia it is not yet known whether ca(2+) can act as a transducer of symbiotic signals.	2009	19775463
enhanced nodulation and nitrogen fixation in the abscisic acid low-sensitive mutant enhanced nitrogen fixation1 of lotus japonicus.	the phytohormone abscisic acid (aba) is known to be a negative regulator of legume root nodule formation. by screening lotus japonicus seedlings for survival on an agar medium containing 70 microm aba, we obtained mutants that not only showed increased root nodule number but also enhanced nitrogen fixation. the mutant was designated enhanced nitrogen fixation1 (enf1) and was confirmed to be monogenic and incompletely dominant. the low sensitivity to aba phenotype was thought to result from eithe ...	2009	19776164
pgpr-arabidopsis interactions is a useful system to study signaling pathways involved in plant developmental control.		2009	19794852
horizontal gene transfer and recombination shape mesorhizobial populations in the gene center of the host plants astragalus luteolus and astragalus ernestii in sichuan, china.	thirty-three rhizobial strains isolated from the root nodules of astragalus luteolus and astragalus ernestii growing on the west plateau at two different altitudes in sichuan province, china, were characterized by amplified rdna restriction analysis (ardra), amplified fragment length polymorphism (aflp), and by sequencing of rrs, glna, glnii and nifh. the ardra analysis revealed considerable genomic diversity. in aflp analysis, 20 of 33 astragalus rhizobia formed three distinct clades, with othe ...	2009	19796139
chemoenzymatic synthesis of gdp-l-fucose and the lewis x glycan derivatives.	lewis x (le(x))-containing glycans play important roles in numerous cellular processes. however, the absence of robust, facile, and cost-effective methods for the synthesis of le(x) and its structurally related analogs has severely hampered the elucidation of the specific functions of these glycan epitopes. here we demonstrate that chemically defined guanidine 5'-diphosphate-beta-l-fucose (gdp-fucose), the universal fucosyl donor, the le(x) trisaccharide, and their c-5 substituted derivatives ca ...	2009	19805264
genetic analysis of ethylene regulation of legume nodulation.	the gaseous hormone ethylene has multiple roles in plant development and responses to external cues. among these is the regulation of "rhizobium"-induced nodulation in legumes. extensive descriptive literature exists, but has been expanded to allow more mechanistic analysis through the application of genetics. both mutants and transgenics displaying ethylene insensitivity have now been described, suggesting an intimate interplay of ethylene response, plant development and nodulation.	2009	19847106
structure of the o-polysaccharides of the lipopolysaccharides of mesorhizobium loti hambi 1148 and mesorhizobium amorphae atcc 19655 containing two o-methylated monosaccharides.	the o-polysaccharide of mesorhizobium loti hambi 1148 was obtained by mild acid degradation of the lipopolysaccharide and studied by sugar and methylation analyses, smith degradation, and (1)h and (13)c nmr spectroscopies, including 2d (1)h/(1)h cosy, tocsy, roesy, and h-detected (1)h/(13)c hsqc experiments. the o-polysaccharide was found to have a branched hexasaccharide-repeating unit of the following structure: [formula: see text] where 2-acetamido-2-deoxy-4-o-methyl-d-glucose (d-glcnac4me) a ...	2009	19850286
metabolic control of virulence genes in brucella abortus: hutc coordinates virb expression and the histidine utilization pathway by direct binding to both promoters.	type iv secretion systems (t4ss) are multicomponent machineries involved in the translocation of effector molecules across the bacterial cell envelope. the virb operon of brucella abortus codes for a t4ss that is essential for virulence and intracellular multiplication of the bacterium in the host. previous studies showed that the virb operon of b. abortus is tightly regulated within the host cells. in order to identify factors implicated in the control of virb expression, we searched for protei ...	2010	19854911
metabolic control of virulence genes in brucella abortus: hutc coordinates virb expression and the histidine utilization pathway by direct binding to both promoters.	type iv secretion systems (t4ss) are multicomponent machineries involved in the translocation of effector molecules across the bacterial cell envelope. the virb operon of brucella abortus codes for a t4ss that is essential for virulence and intracellular multiplication of the bacterium in the host. previous studies showed that the virb operon of b. abortus is tightly regulated within the host cells. in order to identify factors implicated in the control of virb expression, we searched for protei ...	2010	19854911