| refuting phylogenetic relationships. | phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. this constitutes an important methodologic dimension not often taken into account. here we address this dimension in the context of concatenation approaches to phylogeny. | 2006 | 16956399 |
| exopolysaccharide production by some rhizobium strain in culture. | eight rhizobium strains were screened for exopolysaccharide production during growth in yeast extract mannitol medium. a strain of rhizobium loti produced more than 250 mg of exopolysaccharide/100 ml of culture during the stationary phase of growth. exopolysaccharide production was favoured by maltose and mannitol but n2 supplementation could not affect the production siginificantly. preliminary studies indicate that the polymer contains 16% protein and 73.5% carbohydrate being composed of gluco ... | 1998 | 16961205 |
| complete nucleotide sequence of an exogenously isolated plasmid, plb1, involved in gamma-hexachlorocyclohexane degradation. | the alpha-proteobacterial strain sphingobium japonicum ut26 utilizes a highly chlorinated pesticide, gamma-hexachlorocyclohexane (gamma-hch), as a sole source of carbon and energy, and haloalkane dehalogenase linb catalyzes the second step of gamma-hch degradation in ut26. functional complementation of a linb mutant of ut26, ut26db, was performed by the exogenous plasmid isolation technique using hch-contaminated soil, leading to our successful identification of a plasmid, plb1, carrying the lin ... | 2006 | 16963556 |
| lipoprotein pssn of rhizobium leguminosarum bv. trifolii: subcellular localization and possible involvement in exopolysaccharide export. | surface expression of exopolysaccharides (eps) in gram-negative bacteria depends on the activity of proteins found in the cytoplasmic membrane, the periplasmic space, and the outer membrane. psstnop genes identified in rhizobium leguminosarum bv. trifolii strain ta1 encode proteins that might be components of the eps polymerization and secretion system. in this study, we have characterized pssn protein. employing pssn-phoa and pssn-lacz gene fusions and in vivo acylation with [3h]palmitate, we d ... | 2006 | 16980497 |
| the crystal structure of the e. coli stress protein ycif. | ycif is a protein that is up-regulated when bacteria experience stress conditions, and is highly conserved in a range of bacterial species. ycif has no known structure or biochemical function. to learn more about its potential molecular function and its role in the bacterial stress response, we solved the crystal structure of ycif at 2.0 angstrom resolution by the multiple wavelength anomalous diffraction (mad) technique. ycif is a dimer in solution, and forms a homodimer in the crystal asymmetr ... | 2006 | 17001035 |
| two metallocarboxypeptidases from the protozoan trypanosoma cruzi belong to the m32 family, found so far only in prokaryotes. | mcps (metallocarboxypeptidases) of the m32 family of peptidases have been identified in a number of prokaryotic organisms, and only a few of them have been characterized biochemically. members of this family are absent from eukaryotic genomes, with the remarkable exception of those of trypanosomatids. the genome of the cl brener clone of trypanosoma cruzi, the causative agent of chagas' disease, encodes two such mcps, with 64% identity between them: tcmcp-1 and tcmcp-2. both genes, which are pre ... | 2007 | 17007610 |
| two metallocarboxypeptidases from the protozoan trypanosoma cruzi belong to the m32 family, found so far only in prokaryotes. | mcps (metallocarboxypeptidases) of the m32 family of peptidases have been identified in a number of prokaryotic organisms, and only a few of them have been characterized biochemically. members of this family are absent from eukaryotic genomes, with the remarkable exception of those of trypanosomatids. the genome of the cl brener clone of trypanosoma cruzi, the causative agent of chagas' disease, encodes two such mcps, with 64% identity between them: tcmcp-1 and tcmcp-2. both genes, which are pre ... | 2007 | 17007610 |
| intrinsic and selected resistance to antibiotics binding the ribosome: analyses of brucella 23s rrn, l4, l22, ef-tu1, ef-tu2, efflux and phylogenetic implications. | brucella spp. are highly similar, having identical 16s rna. however, they have important phenotypic differences such as differential susceptibility to antibiotics binding the ribosome. neither the differential susceptibility nor its basis has been rigorously studied. differences found among other conserved ribosomal loci could further define the relationships among the classical brucella spp. | 2006 | 17014718 |
| interrelations between glycine betaine catabolism and methionine biosynthesis in sinorhizobium meliloti strain 102f34. | methionine is produced by methylation of homocysteine. sinorhizobium meliloti 102f34 possesses only one methionine synthase, which catalyzes the transfer of a methyl group from methyl tetrahydrofolate to homocysteine. this vitamin b(12)-dependent enzyme is encoded by the meth gene. glycine betaine can also serve as an alternative methyl donor for homocysteine. this reaction is catalyzed by betaine-homocysteine methyl transferase (bhmt), an enzyme that has been characterized in humans and rats. a ... | 2006 | 17015658 |
| a plasmid-borne truncated luxi homolog controls quorum-sensing systems and extracellular carbohydrate production in methylobacterium extorquens am1. | a cryptic plasmid of methylobacterium extorquens am1 was found to encode tsli, a truncated luxi homolog. tsli was shown to be expressed and to control transcription of the acyl-homoserine lactone (hsl) synthase gene msai and thus, indirectly, acyl-hsl production. in addition, tsli was found to positively regulate extracellular polysaccharide production. | 2006 | 17015673 |
| whole-genome reciprocal blast analysis reveals that planctomycetes do not share an unusually large number of genes with eukarya and archaea. | the genome sequences of rhodopirellula baltica, formerly pirellula sp. strain 1, blastopirellula marina, gemmata obscuriglobus, and kuenenia stuttgartiensis were used in a series of pairwise reciprocal best-hit analyses to evaluate the contested evolutionary position of planctomycetes. contrary to previous reports which suggested that r. baltica had a high percentage of genes with closest matches to archaea and eukarya, we show here that these planctomycetes do not share an unusually large numbe ... | 2006 | 17021241 |
| genetic suppressors of the lotus japonicus har1-1 hypernodulation phenotype. | lotus japonicus har1 mutants respond to inoculation with mesorhizobium loti by forming an excessive number of nodules due to genetic lesions in the har1 autoregulatory receptor kinase gene. in order to expand the repertoire of mutants available for the genetic dissection of the root nodule symbiosis (rns), a screen for suppressors of the l. japonicus har1-1 hypernodulation phenotype was performed. of 150,000 m2 plants analyzed, 61 stable l. japonicus double-mutant lines were isolated. in the con ... | 2006 | 17022172 |
| mesorhizobium loti produces nodpq-dependent sulfated cell surface polysaccharides. | leguminous plants and bacteria from the family rhizobiaceae form a symbiotic relationship, which culminates in novel plant structures called root nodules. the indeterminate symbiosis that forms between sinorhizobium meliloti and alfalfa requires biosynthesis of nod factor, a beta-1,4-linked lipochitooligosaccharide that contains an essential 6-o-sulfate modification. s. meliloti also produces sulfated cell surface polysaccharides, such as lipopolysaccharide (lps). the physiological function of s ... | 2006 | 17028279 |
| kinase activity of overexpressed hipa is required for growth arrest and multidrug tolerance in escherichia coli. | overexpression of the hipa protein of the hipba toxin/antitoxin module leads to multidrug tolerance in escherichia coli. hipa is a "toxin" that causes reversible dormancy, whereas hipb is an antitoxin that binds hipa and acts as a transcriptional repressor of the hipba operon. comparative sequence analysis shows that hipa is a member of the phosphatidylinositol 3/4-kinase superfamily. the kinase activity of hipa was examined. hipa was autophosphorylated in the presence of atp in vitro, and the p ... | 2006 | 17041039 |
| ljnsring, a novel ring finger protein, is required for symbiotic interactions between mesorhizobium loti and lotus japonicus. | nodule-specific (nodulin) genes are thought to play crucial roles during establishment of the nitrogen-fixing symbiosis between legume plants and rhizobium bacteria. on the basis of a gene expression database for early stages of the nodulation process of lotus japonicus, previously constructed by a cdna macroarray analysis, we identified a novel nodulin gene, ljnsring, which encodes a protein with a typical ring-h2 finger domain that is well conserved in a number of plant e3 ubiquitin ligases. l ... | 2006 | 17056617 |
| ftcr is a new master regulator of the flagellar system of brucella melitensis 16m with homologs in rhizobiaceae. | the flagellar regulon of brucella melitensis 16m contains 31 genes clustered in three loci on the small chromosome. these genes encode a polar sheathed flagellum that is transiently expressed during vegetative growth and required for persistent infection in a mouse model. by following the expression of three flagellar genes (flif, flge, and flic, corresponding to the ms ring, hook, and filament monomer, respectively), we identified a new regulator gene, ftcr (flagellar two-component regulator). ... | 2007 | 17056750 |
| ftcr is a new master regulator of the flagellar system of brucella melitensis 16m with homologs in rhizobiaceae. | the flagellar regulon of brucella melitensis 16m contains 31 genes clustered in three loci on the small chromosome. these genes encode a polar sheathed flagellum that is transiently expressed during vegetative growth and required for persistent infection in a mouse model. by following the expression of three flagellar genes (flif, flge, and flic, corresponding to the ms ring, hook, and filament monomer, respectively), we identified a new regulator gene, ftcr (flagellar two-component regulator). ... | 2007 | 17056750 |
| an inventory of yeast proteins associated with nucleolar and ribosomal components. | although baker's yeast is a primary model organism for research on eukaryotic ribosome assembly and nucleoli, the list of its proteins that are functionally associated with nucleoli or ribosomes is still incomplete. we trained a naïve bayesian classifier to predict novel proteins that are associated with yeast nucleoli or ribosomes based on parts lists of nucleoli in model organisms and large-scale protein interaction data sets. phylogenetic profiling and gene expression analysis were carried ou ... | 2006 | 17067374 |
| lotus japonicus nodulation requires two gras domain regulators, one of which is functionally conserved in a non-legume. | a new nodulation-defective mutant of lotus japonicus does not initiate nodule cortical cell division in response to mesorhizobium loti, but induces root hair deformation, nod factor-induced calcium spiking, and mycorrhization. this phenotype, together with mapping data, suggested that the mutation could be in the ortholog of the medicago truncatula nsp1 gene (mtnsp1). the sequence of the orthologous gene (ljnsp1) in the l. japonicus mutant (ljnsp1-1) revealed a mutation causing a premature stop ... | 2006 | 17071642 |
| alpha-proteobacterial symbionts of marine bryozoans in the genus watersipora. | bacterial symbionts that resembled mollicutes were discovered in the marine bryozoan watersipora arcuata in the 1980s. in this study, we used pcr and sequencing of 16s rrna genes, specific fluorescence in situ hybridization, and phylogenetic analysis to determine that the bacterial symbionts of "w. subtorquata" and "w. arcuata" from several locations along the california coast are actually closely related alpha-proteobacteria, not mollicutes. we propose the names "candidatus endowatersipora palo ... | 2007 | 17071786 |
| alpha-proteobacterial symbionts of marine bryozoans in the genus watersipora. | bacterial symbionts that resembled mollicutes were discovered in the marine bryozoan watersipora arcuata in the 1980s. in this study, we used pcr and sequencing of 16s rrna genes, specific fluorescence in situ hybridization, and phylogenetic analysis to determine that the bacterial symbionts of "w. subtorquata" and "w. arcuata" from several locations along the california coast are actually closely related alpha-proteobacteria, not mollicutes. we propose the names "candidatus endowatersipora palo ... | 2007 | 17071786 |
| excision and transfer of the mesorhizobium loti r7a symbiosis island requires an integrase ints, a novel recombination directionality factor rdfs, and a putative relaxase rlxs. | the mesorhizobium loti strain r7a symbiosis island is an integrative conjugative element (ice), herein termed icemlsymr7a, which integrates into a phetrna gene. integration reconstructs the phetrna gene at one junction with the core chromosome, and a direct repeat of the 3-prime 17 bp of the gene is formed at the other junction. we show that the icemlsymr7aints gene, which encodes an integrase of the phage p4 family, is required for integration and excision of the island. excision also depended ... | 2006 | 17076666 |
| aph(3')-iic, an aminoglycoside resistance determinant from stenotrophomonas maltophilia. | we report the characterization of an intrinsic, chromosomally carried aph(3')-iic gene from stenotrophomonas maltophilia clinical isolate k279a, encoding an aminoglycoside phosphotransferase enzyme that significantly increases mics of kanamycin, neomycin, butirosin, and paromomycin when expressed in escherichia coli. disruption of aph(3')-iic in k279a results in decreased mics of these drugs. | 2007 | 17088477 |
| aph(3')-iic, an aminoglycoside resistance determinant from stenotrophomonas maltophilia. | we report the characterization of an intrinsic, chromosomally carried aph(3')-iic gene from stenotrophomonas maltophilia clinical isolate k279a, encoding an aminoglycoside phosphotransferase enzyme that significantly increases mics of kanamycin, neomycin, butirosin, and paromomycin when expressed in escherichia coli. disruption of aph(3')-iic in k279a results in decreased mics of these drugs. | 2007 | 17088477 |
| crystal structures of leucyl/phenylalanyl-trna-protein transferase and its complex with an aminoacyl-trna analog. | eubacterial leucyl/phenylalanyl-trna protein transferase (l/f-transferase), encoded by the aat gene, conjugates leucine or phenylalanine to the n-terminal arg or lys residue of proteins, using leu-trna(leu) or phe-trna(phe) as a substrate. the resulting n-terminal leu or phe acts as a degradation signal for the clps-clpap-mediated n-end rule protein degradation pathway. here, we present the crystal structures of escherichia coli l/f-transferase and its complex with an aminoacyl-trna analog, puro ... | 2006 | 17110926 |
| degradation and mineralization of nanomolar concentrations of the herbicide dichlobenil and its persistent metabolite 2,6-dichlorobenzamide by aminobacter spp. isolated from dichlobenil-treated soils. | 2,6-dichlorobenzamide (bam), a persistent metabolite from the herbicide 2,6-dichlorobenzonitrile (dichlobenil), is the pesticide residue most frequently detected in danish groundwater. a bam-mineralizing bacterial community was enriched from dichlobenil-treated soil sampled from the courtyard of a former plant nursery. a bam-mineralizing bacterium (designated strain msh1) was cultivated and identified by 16s rrna gene sequencing and fatty acid analysis as being closely related to members of the ... | 2007 | 17114317 |
| degradation and mineralization of nanomolar concentrations of the herbicide dichlobenil and its persistent metabolite 2,6-dichlorobenzamide by aminobacter spp. isolated from dichlobenil-treated soils. | 2,6-dichlorobenzamide (bam), a persistent metabolite from the herbicide 2,6-dichlorobenzonitrile (dichlobenil), is the pesticide residue most frequently detected in danish groundwater. a bam-mineralizing bacterial community was enriched from dichlobenil-treated soil sampled from the courtyard of a former plant nursery. a bam-mineralizing bacterium (designated strain msh1) was cultivated and identified by 16s rrna gene sequencing and fatty acid analysis as being closely related to members of the ... | 2007 | 17114317 |
| identification of symbiotically defective mutants of lotus japonicus affected in infection thread growth. | during the symbiotic interaction between legumes and rhizobia, the host cell plasma membrane and associated plant cell wall invaginate to form a tunnel-like infection thread, a structure in which bacteria divide to reach the plant root cortex. we isolated four lotus japonicus mutants that make infection pockets in root hairs but form very few infection threads after inoculation with mesorhizobium loti. the few infection threads that did initiate in the mutants usually did not progress further th ... | 2006 | 17153928 |
| only one of five groel genes is required for viability and successful symbiosis in sinorhizobium meliloti. | many bacterial species contain multiple copies of the genes that encode the chaperone groel and its cochaperone, groes, including all of the fully sequenced root-nodulating bacteria that interact symbiotically with legumes to generate fixed nitrogen. in particular, in sinorhizobium meliloti there are four groesl operons and one groel gene. to uncover functional redundancies of these genes during growth and symbiosis, we attempted to construct strains containing all combinations of groel mutation ... | 2007 | 17158666 |
| only one of five groel genes is required for viability and successful symbiosis in sinorhizobium meliloti. | many bacterial species contain multiple copies of the genes that encode the chaperone groel and its cochaperone, groes, including all of the fully sequenced root-nodulating bacteria that interact symbiotically with legumes to generate fixed nitrogen. in particular, in sinorhizobium meliloti there are four groesl operons and one groel gene. to uncover functional redundancies of these genes during growth and symbiosis, we attempted to construct strains containing all combinations of groel mutation ... | 2007 | 17158666 |
| the type iv secretion system of sinorhizobium meliloti strain 1021 is required for conjugation but not for intracellular symbiosis. | the type iv secretion system (t4ss) of the plant intracellular symbiont sinorhizobium meliloti 1021 is required for conjugal transfer of dna. however, it is not required for host invasion and persistence, unlike the t4sss of closely related mammalian intracellular pathogens. a comparison of the requirement for a bacterial t4ss in plant versus animal host invasion suggests an important difference in the intracellular niches occupied by these bacteria. | 2007 | 17158676 |
| the type iv secretion system of sinorhizobium meliloti strain 1021 is required for conjugation but not for intracellular symbiosis. | the type iv secretion system (t4ss) of the plant intracellular symbiont sinorhizobium meliloti 1021 is required for conjugal transfer of dna. however, it is not required for host invasion and persistence, unlike the t4sss of closely related mammalian intracellular pathogens. a comparison of the requirement for a bacterial t4ss in plant versus animal host invasion suggests an important difference in the intracellular niches occupied by these bacteria. | 2007 | 17158676 |
| characterization of the thermotoga maritima chemotaxis methylation system that lacks pentapeptide-dependent methyltransferase cher:mcp tethering. | sensory adaptation in bacterial chemotaxis is mediated by covalent modifications of specific glutamate and glutamine residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins (mcps). in escherichia coli and salmonella enterica, efficient methylation of mcps depends on the localization of methyltransferase cher to mcp clusters through an interaction between the cher beta-subdomain and a pentapeptide sequence (nwetf or nwesf) at the c-terminus of the mcp. in vitro methylation ... | 2007 | 17163981 |
| characterization of the thermotoga maritima chemotaxis methylation system that lacks pentapeptide-dependent methyltransferase cher:mcp tethering. | sensory adaptation in bacterial chemotaxis is mediated by covalent modifications of specific glutamate and glutamine residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins (mcps). in escherichia coli and salmonella enterica, efficient methylation of mcps depends on the localization of methyltransferase cher to mcp clusters through an interaction between the cher beta-subdomain and a pentapeptide sequence (nwetf or nwesf) at the c-terminus of the mcp. in vitro methylation ... | 2007 | 17163981 |
| high precision multi-genome scale reannotation of enzyme function by eficaz. | the functional annotation of most genes in newly sequenced genomes is inferred from similarity to previously characterized sequences, an annotation strategy that often leads to erroneous assignments. we have performed a reannotation of 245 genomes using an updated version of eficaz, a highly precise method for enzyme function prediction. | 2006 | 17166279 |
| the sphingomonas plasmid pcar3 is involved in complete mineralization of carbazole. | we determined the complete 254,797-bp nucleotide sequence of the plasmid pcar3, a carbazole-degradative plasmid from sphingomonas sp. strain ka1. a region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pnl1 isolated from the aromatic-degrading novosphingobium aromaticivorans strain f199. the presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. alth ... | 2007 | 17172338 |
| the sphingomonas plasmid pcar3 is involved in complete mineralization of carbazole. | we determined the complete 254,797-bp nucleotide sequence of the plasmid pcar3, a carbazole-degradative plasmid from sphingomonas sp. strain ka1. a region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pnl1 isolated from the aromatic-degrading novosphingobium aromaticivorans strain f199. the presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. alth ... | 2007 | 17172338 |
| phytochelatin synthases of the model legume lotus japonicus. a small multigene family with differential response to cadmium and alternatively spliced variants. | the biosynthesis of phytochelatins and homophytochelatins has been studied in nodulated plants of the model legume lotus (lotus japonicus). in the first 6 to 24 h of treatment with cadmium (cd), roots started to synthesize elevated amounts of both polypeptides, with a concomitant increase of glutathione and a decrease of homoglutathione, indicating the presence of active phytochelatin synthase (pcs) genes. screening of transformation-competent artificial chromosome libraries allowed identificati ... | 2007 | 17208961 |
| sinorhizobium meliloti syra mediates the transcriptional regulation of genes involved in lipopolysaccharide sulfation and exopolysaccharide biosynthesis. | sinorhizobium meliloti is a gram-negative soil bacterium found either in free-living form or as a nitrogen-fixing endosymbiont of leguminous plants such as medicago sativa (alfalfa). s. meliloti synthesizes an unusual sulfate-modified form of lipopolysaccharide (lps). a recent study reported the identification of a gene, lpss, which encodes an lps sulfotransferase activity in s. meliloti. mutants bearing a disrupted version of lpss exhibit an altered symbiosis, in that they elicit more nodules t ... | 2007 | 17209018 |
| sequencing and analysis of the biosynthetic gene cluster of the lipopeptide antibiotic friulimicin in actinoplanes friuliensis. | actinoplanes friuliensis produces the lipopeptide antibiotic friulimicin, which is a cyclic peptide with one exocyclic amino acid linked to a branched-chain fatty acid acyl residue. the structural relationship to daptomycin and the excellent antibacterial performance of friulimicin make the antibiotic an attractive drug candidate. the complete friulimicin biosynthetic gene cluster of 24 open reading frames from a. friuliensis was sequenced and analyzed. in addition to genes for regulation, self- ... | 2007 | 17220414 |
| dna adenine methylation changes dramatically during establishment of symbiosis. | the dna adenine methylation status on specific 5'-gantc-3' sites and its change during the establishment of plant-microbe interactions was demonstrated in several species of alpha-proteobacteria. restriction landmark genome scanning (rlgs), which is a high-resolution two dimensional dna electrophoresis method, was used to monitor the genomewide change in methylation. in the case of mesorhizobium loti maff303099, real rlgs images obtained with the restriction enzyme mboi, which digests at gatc si ... | 2007 | 17250744 |
| exploitation of eukaryotic ubiquitin signaling pathways by effectors translocated by bacterial type iii and type iv secretion systems. | the specific and covalent addition of ubiquitin to proteins, known as ubiquitination, is a eukaryotic-specific modification central to many cellular processes, such as cell cycle progression, transcriptional regulation, and hormone signaling. polyubiquitination is a signal for the 26s proteasome to destroy earmarked proteins, but depending on the polyubiquitin chain topology, it can also result in new protein properties. both ubiquitin-orchestrated protein degradation and modification have also ... | 2007 | 17257058 |
| molecular cloning, identification and characterization of 2-methyl-3-hydroxypyridine-5-carboxylic-acid-dioxygenase-coding gene from the nitrogen-fixing symbiotic bacterium mesorhizobium loti. | the gene (mlr6788) of a nitrogen-fixing symbiotic bacterium mesorhizobium loti maff303099 has been identified as a gene coding for 2-methyl-3-hydroxypyridine-5-carboxylic acid dioxygenase (mhpco), the seventh enzyme in degradation pathway i for pyridoxine, a free form of vitamin b(6). the gene was cloned and overexpressed in escherichia coli cells co-transformed with chaperonin genes. the homogeneous recombinant enzyme showed similar enzymatic properties to the enzyme from pseudomonas sp. ma-1. ... | 2006 | 17270714 |
| a novel ankyrin-repeat membrane protein, ign1, is required for persistence of nitrogen-fixing symbiosis in root nodules of lotus japonicus. | nitrogen-fixing symbiosis of legume plants with rhizobium bacteria is established through complex interactions between two symbiotic partners. similar to the mutual recognition and interactions at the initial stages of symbiosis, nitrogen fixation activity of rhizobia inside root nodules of the host legume is also controlled by specific interactions during later stages of nodule development. we isolated a novel fix(-) mutant, ineffective greenish nodules 1 (ign1), of lotus japonicus, which forms ... | 2007 | 17277093 |
| purification, crystallization and preliminary x-ray diffraction studies of d-tagatose 3-epimerase from pseudomonas cichorii. | d-tagatose 3-epimerase (d-te) from pseudomonas cichorii catalyzes the epimerization of various ketohexoses at the c3 position. the epimerization of d-psicose has not been reported with epimerases other than p. cichorii d-te and d-psicose 3-epimerase from agrobacterium tumefaciens. recombinant p. cichorii d-te has been purified and crystallized. crystals of p. cichorii d-te were obtained by the sitting-drop method at room temperature. the crystal belongs to the monoclinic space group p2(1), with ... | 2007 | 17277456 |
| the role of laterally transferred genes in adaptive evolution. | bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. acquisition of new genes by lateral gene transfer may be one of the dominant ways of adaptation in bacterial genome evolution. lateral gene transfer provides the bacterial genome with a new set of genes that help it to explore and adapt to new ecological niches. | 2007 | 17288581 |
| a complete set of flagellar genes acquired by horizontal transfer coexists with the endogenous flagellar system in rhodobacter sphaeroides. | bacteria swim in liquid environments by means of a complex rotating structure known as the flagellum. approximately 40 proteins are required for the assembly and functionality of this structure. rhodobacter sphaeroides has two flagellar systems. one of these systems has been shown to be functional and is required for the synthesis of the well-characterized single subpolar flagellum, while the other was found only after the genome sequence of this bacterium was completed. in this work we found th ... | 2007 | 17293429 |
| [recombinant expression of an autoinducer synthase of mesorhizobium loti in escherichia coli and analysis of the autoinducer produced in recombinant strain]. | although the autoinducers of mesorhizobium loti could not be detected under the conditions of experimentally pure culture, and even adding some root exact of lotus japonicus into the medium in which m. loti grew to detect the acyl-homoserine lactone (ahl) production, no positive result has been available. however, analysis of homologous comparison showed that there were at least four annotated acylated homoserine lactone (ahl) synthase genes from m. loti genome sequences. the amino acids of all ... | 2006 | 17302171 |
| nucleoporin85 is required for calcium spiking, fungal and bacterial symbioses, and seed production in lotus japonicus. | in lotus japonicus, seven genetic loci have been identified thus far as components of a common symbiosis (sym) pathway shared by rhizobia and arbuscular mycorrhizal fungi. we characterized the nup85 mutants (nup85-1, -2, and -3) required for both symbioses and cloned the corresponding gene. when inoculated with glomus intraradices, the hyphae managed to enter between epidermal cells, but they were unable to penetrate the cortical cell layer. the nup85-2 mutation conferred a weak and temperature- ... | 2007 | 17307929 |
| evidence of horizontal transfer of symbiotic genes from a bradyrhizobium japonicum inoculant strain to indigenous diazotrophs sinorhizobium (ensifer) fredii and bradyrhizobium elkanii in a brazilian savannah soil. | the importance of horizontal gene transfer (hgt) in the evolution and speciation of bacteria has been emphasized; however, most studies have focused on genes clustered in pathogenesis and very few on symbiosis islands. both soybean (glycine max [l.] merrill) and compatible bradyrhizobium japonicum and bradyrhizobium elkanii strains are exotic to brazil and have been massively introduced in the country since the early 1960s, occupying today about 45% of the cropped land. for the past 10 years, ou ... | 2007 | 17308185 |
| the incomplete substitution of lipopolysaccharide with o-chain prevents the establishment of effective symbiosis between mesorhizobium loti nzp2213.1 and lotus corniculatus. | mesorhizobium loti nzp2213.1 mutant obtained after random tn5 mutagenesis of m. loti nzp2213 was inefficient in nitrogen fixation on lotus corniculatus. the transposon insertion was located within an orf with a sequence similarity to a putative glycosyl transferase from caulobacter crescentus. the results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated that the mutant produced lps of the same o-chain length but only half of the entire smooth lps, compared to that of the pa ... | 2009 | 17321732 |
| hpdr is a transcriptional activator of sinorhizobium meliloti hpda, which encodes a herbicide-targeted 4-hydroxyphenylpyruvate dioxygenase. | sinorhizobium meliloti hpda, which encodes the herbicide target 4-hydroxyphenylpyruvate dioxygenase, is positively regulated by hpdr. gel mobility shift and dnase i footprinting analyses revealed that hpdr binds to a region that spans two conserved direct-repeat sequences within the hpdr-hpda intergenic space. hpdr-dependent hpda transcription occurs in the presence of 4-hydroxyphenylpyruvate, tyrosine, and phenylalanine, as well as during starvation. | 2007 | 17337579 |
| characterization of sinorhizobium meliloti triose phosphate isomerase genes. | a tn5 mutant strain of sinorhizobium meliloti with an insertion in tpia (systematic identifier smc01023), a putative triose phosphate isomerase (tpi)-encoding gene, was isolated. the tpia mutant grew more slowly than the wild type on rhamnose and did not grow with glycerol as a sole carbon source. the genome of s. meliloti wild-type rm1021 contains a second predicted tpi-encoding gene, tpib (smc01614). we have constructed mutations and confirmed that both genes encode functional tpi enzymes. tpi ... | 2007 | 17337584 |
| genome analysis of dna repair genes in the alpha proteobacterium caulobacter crescentus. | the integrity of dna molecules is fundamental for maintaining life. the dna repair proteins protect organisms against genetic damage, by removal of dna lesions or helping to tolerate them. dna repair genes are best known from the gamma-proteobacterium escherichia coli, which is the most understood bacterial model. however, genome sequencing raises questions regarding uniformity and ubiquity of these dna repair genes and pathways, reinforcing the need for identifying genes and proteins, which may ... | 2007 | 17352799 |
| signal transduction-related responses to phytohormones and environmental challenges in sugarcane. | sugarcane is an increasingly economically and environmentally important c4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. sugarcane originated from crosses of saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. environmental stresses limit enormously sugarcane productivity worldwide. to investigate transcriptome changes in response to environmental inputs that alter yield we used cdna microarrays to profi ... | 2007 | 17355627 |
| quorum-sensing regulation in rhizobia and its role in symbiotic interactions with legumes. | legume-nodulating bacteria (rhizobia) usually produce n-acyl homoserine lactones, which regulate the induction of gene expression in a quorum-sensing (or population-density)-dependent manner. there is significant diversity in the types of quorum-sensing regulatory systems that are present in different rhizobia and no two independent isolates worked on in detail have the same complement of quorum-sensing genes. the genes regulated by quorum sensing appear to be rather diverse and many are associa ... | 2007 | 17360278 |
| nodulation deficiency caused by fast neutron mutagenesis of the model legume lotus japonicus. | fast neutron mutagenesis of lotus japonicus wild-type genotype gifu resulted in the isolation of a stable mutant (fnn5-2) unable to form nitrogen-fixing nodules in symbiosis with mesorhizobium loti, though being infected by mycorrhizal fungi. the mutation behaves as a loss-of-function recessive, and has no other apparent phenotypic effects. molecular characterization indicates a partial loss of the lysin motif domain (lysm) type receptor kinase gene (ljnfr1). additionally part of the ljnin gene ... | 2007 | 17363108 |
| medicago truncatula nin is essential for rhizobial-independent nodule organogenesis induced by autoactive calcium/calmodulin-dependent protein kinase. | the symbiotic association between legumes and nitrogen-fixing bacteria collectively known as rhizobia results in the formation of a unique plant root organ called the nodule. this process is initiated following the perception of rhizobial nodulation factors by the host plant. nod factor (nf)-stimulated plant responses, including nodulation-specific gene expression, is mediated by the nf signaling pathway. plant mutants in this pathway are unable to nodulate. we describe here the cloning and char ... | 2007 | 17369436 |
| computational and experimental analyses of mammalian arylamine n-acetyltransferase structure and function. | arylamine n-acetyltransferases (nats) play an important role in the metabolism of arylamine and hydrazine drugs and many arylamine procarcinogens. the two human n-acetyltransferases, nat1 and nat2, are widely distributed in human tissues and are highly polymorphic. although many xenobiotic procarcinogens and drugs are known mammalian nat substrates, it is unclear what physiological roles these enzymes might play, what endogenous substrates they primarily act upon, or the mechanisms underlying th ... | 2007 | 17371801 |
| kinetic characterisation of arylamine n-acetyltransferase from pseudomonas aeruginosa. | arylamine n-acetyltransferases (nats) are important drug- and carcinogen-metabolising enzymes that catalyse the transfer of an acetyl group from a donor, such as acetyl coenzyme a, to an aromatic or heterocyclic amine, hydrazine, hydrazide or n-hydroxylamine acceptor substrate. nats are found in eukaryotes and prokaryotes, and they may also have an endogenous function in addition to drug metabolism. for example, nat from mycobacterium tuberculosis has been proposed to have a role in cell wall li ... | 2007 | 17374145 |
| symbiosis-induced cascade regulation of the mesorhizobium loti r7a virb/d4 type iv secretion system. | the mesorhizobium loti r7a symbiosis island contains genes encoding a virb/d4 type iv secretion system (t4ss) similar to that of agrobacterium tumefaciens. this system has host-dependent effects on symbiosis that probably are due to translocation of two effector proteins, msi059 and msi061, into host cells. here we report that, as in a. tumefaciens, the m. loti vir genes are transcriptionally regulated by a vira/virg two-component regulatory system. a virgn54d mutant gene of m. loti caused const ... | 2007 | 17378428 |
| an extracytoplasmic function sigma factor acts as a general stress response regulator in sinorhizobium meliloti. | sinorhizobium meliloti genes transcriptionally up-regulated after heat stress, as well as upon entry into stationary phase, were identified by microarray analyses. sixty stress response genes were thus found to be up-regulated under both conditions. one of them, rpoe2 (smc01506), encodes a putative extracytoplasmic function (ecf) sigma factor. we showed that this sigma factor controls its own transcription and is activated by various stress conditions, including heat and salt, as well as entry i ... | 2007 | 17400745 |
| ammonia-oxidizing beta-proteobacteria from the oxygen minimum zone off northern chile. | the composition of ammonia-oxidizing bacteria from the beta-proteobacteria subclass (betaaob) was studied in the surface and upper-oxycline oxic waters (2- to 50-m depth, approximately 200 to 44 microm o(2)) and within the oxygen minimum zone (omz) suboxic waters (50- to 400-m depth, < or =10 microm o(2)) of the eastern south pacific off northern chile. this study was carried out through cloning and sequencing of genes coding for 16s rrna and the ammonia monooxygenase enzyme active subunit (amoa ... | 2007 | 17416686 |
| functional characterization of single-nucleotide polymorphisms and haplotypes of human n-acetyltransferase 2. | human n-acetyltransferase 2 (nat2) is polymorphic in humans and may associate with cancer risk by modifying individual susceptibility to cancers from carcinogen exposure. since molecular epidemiological studies investigating these associations usually include determining nat2 single-nucleotide polymorphisms (snps), haplotypes or genotypes, their conclusions can be compromised by the uncertainty of genotype-phenotype relationships. we characterized nat2 snps and haplotypes by cloning and expressi ... | 2007 | 17434923 |
| comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. | magnetotactic bacteria (mtb) are a heterogeneous group of aquatic prokaryotes with a unique intracellular organelle, the magnetosome, which orients the cell along magnetic field lines. magnetotaxis is a complex phenotype, which depends on the coordinate synthesis of magnetosomes and the ability to swim and orient along the direction caused by the interaction with the earth's magnetic field. although a number of putative magnetotaxis genes were recently identified within a conserved genomic magne ... | 2007 | 17449609 |
| trehalose biosynthesis in rhizobium leguminosarum bv. trifolii and its role in desiccation tolerance. | rhizobium leguminosarum bv. trifolii forms nitrogen-fixing root nodules on the pasture legume trifolium repens, and t. repens seed is often coated with a compatible r. leguminosarum bv. trifolii strain prior to sowing. however, significant losses in bacterial viability occur during the seed-coating process and during storage of the coated seeds, most likely due to desiccation stress. the disaccharide trehalose is known to function as an osmoprotectant, and trehalose accumulation due to de novo b ... | 2007 | 17449695 |
| mesorhizobium ciceri biovar biserrulae, a novel biovar nodulating the pasture legume biserrula pelecinus l. | biserrula pelecinus l. is a pasture legume species that forms a highly specific nitrogen-fixing symbiotic interaction with a group of bacteria that belong to mesorhizobium. these mesorhizobia have >98.8 % sequence similarity to mesorhizobium ciceri and mesorhizobium loti for the 16s rrna gene (1440 bp) and >99.3 % sequence similarity to m. ciceri for the dnak gene (300 bp), and strain wsm1271 has 100 % sequence similarity to m. ciceri for gsii (600 bp). strain wsm1271 had 85 % relatedness to m. ... | 2007 | 17473255 |
| characterization of agrobacterium tumefaciens dna ligases c and d. | agrobacterium tumefaciens encodes a single nad+-dependent dna ligase and six putative atp-dependent ligases. two of the ligases are homologs of ligd, a bacterial enzyme that catalyzes end-healing and end-sealing steps during nonhomologous end joining (nhej). agrobacterium ligd1 and atuligd2 are composed of a central ligase domain fused to a c-terminal polymerase-like (pol) domain and an n-terminal 3'-phosphoesterase (pe) module. both ligd proteins seal dna nicks, albeit inefficiently. the ligd2 ... | 2007 | 17488851 |
| ecological genomics of marine roseobacters. | bacterioplankton of the marine roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. an unexpectedly large number of genes are ... | 2007 | 17526795 |
| a versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with brucella as a use case. | we present a bacterial genome computational analysis pipeline, called genvar. the pipeline, based on the program genewise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence variants such as genes with disrupted reading frames (split genes) and those with insertions and deletions (indels). for a given genome to be analyzed, genvar relies on a database containing closely related genomes (such as other species or strains) as well as a few additiona ... | 2007 | 17553834 |
| putative porin of bradyrhizobium sp. (lupinus) bacteroids induced by glyphosate. | application of glyphosate (n-[phosphonomethyl] glycine) to bradyrhizobium sp. (lupinus)-nodulated lupin plants caused modifications in the protein pattern of bacteroids. the most significant change was the presence of a 44-kda polypeptide in bacteroids from plants treated with the higher doses of glyphosate employed (5 and 10 mm). the polypeptide has been characterized by the amino acid sequencing of its n terminus and the isolation and nucleic acid sequencing of its encoding gene. it is putativ ... | 2007 | 17557843 |
| [biosynthesis of chitooligosaccharides by recombinant escherichia coli]. | acetyl-n-glucosaminyltransferase gene (nodc) was successfully cloned to escherichia coli from mesorhizobium loti. the recombinant e. coli harboring nodc gene was able to synthesize chitooligosaccharides (cos) in mmyng medium. in optimized condition, a yield of 526 mg/l was obtained after 26 h cultivation in 10 l bioreactor. cos concentration reached up to 4.5% of the cell dry weight. the cos products were purified by charcoal adsorption and bio-gel p4 chromatography, penta-n-acetylchitopentaose ... | 2007 | 17578006 |
| brucella suis urease encoded by ure1 but not ure2 is necessary for intestinal infection of balb/c mice. | in prokaryotes, the ureases are multi-subunit, nickel-containing enzymes that catalyze the hydrolysis of urea to carbon dioxide and ammonia. the brucella genomes contain two urease operons designated as ure1 and ure2. we investigated the role of the two brucella suis urease operons on the infection, intracellular persistence, growth, and resistance to low-ph killing. | 2007 | 17578575 |
| bigr, a transcriptional repressor from plant-associated bacteria, regulates an operon implicated in biofilm growth. | xylella fastidiosa is a plant pathogen that colonizes the xylem vessels, causing vascular occlusion due to bacterial biofilm growth. however, little is known about the molecular mechanisms driving biofilm formation in xylella-plant interactions. here we show that bigr (for "biofilm growth-associated repressor") is a novel helix-turn-helix repressor that controls the transcription of an operon implicated in biofilm growth. this operon, which encodes bigr, membrane proteins, and an unusual beta-la ... | 2007 | 17586627 |
| patch clamp and phenotypic analyses of a prokaryotic cyclic nucleotide-gated k+ channel using escherichia coli as a host. | prokaryotic ion channels have been valuable in providing structural models for understanding ion filtration and channel-gating mechanisms. however, their functional examinations have remained rare and usually been carried out by incorporating purified channel protein into artificial lipid membranes. here we demonstrate the utilization of escherichia coli to host the functional analyses by examining a putative cyclic nucleotide-gated k+ channel cloned from magnetospirillum magnetotacticum, mmak. ... | 2007 | 17588940 |
| virb1* promotes t-pilus formation in the vir-type iv secretion system of agrobacterium tumefaciens. | the vir-type iv secretion system of agrobacterium is assembled from 12 proteins encoded by the virb operon and vird4. virb1 is one of the least-studied proteins encoded by the virb operon. its n terminus is a lytic transglycosylase. the c-terminal third of the protein, virb1*, is cleaved from virb1 and secreted to the outside of the bacterial cell, suggesting an additional function. we show that both nopaline and octopine strains produce abundant amounts of virb1* and perform detailed studies on ... | 2007 | 17631630 |
| how rhizobial symbionts invade plants: the sinorhizobium-medicago model. | nitrogen-fixing rhizobial bacteria and leguminous plants have evolved complex signal exchange mechanisms that allow a specific bacterial species to induce its host plant to form invasion structures through which the bacteria can enter the plant root. once the bacteria have been endocytosed within a host-membrane-bound compartment by root cells, the bacteria differentiate into a new form that can convert atmospheric nitrogen into ammonia. bacterial differentiation and nitrogen fixation are depend ... | 2007 | 17632573 |
| transcriptome profiling of lotus japonicus roots during arbuscular mycorrhiza development and comparison with that of nodulation. | to better understand the molecular responses of plants to arbuscular mycorrhizal (am) fungi, we analyzed the differential gene expression patterns of lotus japonicus, a model legume, with the aid of a large-scale cdna macroarray. experiments were carried out considering the effects of contaminating microorganisms in the soil inoculants. when the colonization by am fungi, i.e. glomus mosseae and gigaspora margarita, was well established, four cysteine protease genes were induced. in situ hybridiz ... | 2007 | 17634281 |
| the conserved glycine/alanine residue of the active-site loop containing the putative acetylcoa-binding motif is essential for the overall structural integrity of mesorhizobium loti arylamine n-acetyltransferase 1. | the arylamine n-acetyltransferases are important xenobiotic-metabolizing enzymes that catalyze an acetyl group transfer from acetylcoa to arylamine substrates. nat enzymes possess an active-site loop (the active-site p-loop) involved in substrate binding and selectivity. the gly/ala residue present at the start of the active-site p-loop, although conserved in all nat enzymes, is not involved in the catalytic mechanism or substrate binding. here we show that a small amino acid (such as gly or ala ... | 2007 | 17658468 |
| subunits act independently in a cyclic nucleotide-activated k(+) channel. | ion channels gated by cyclic nucleotides have crucial roles in neuronal excitability and signal transduction of sensory neurons. here, we studied ligand binding of a cyclic nucleotide-activated k(+) channel from mesorhizobium loti and its isolated cyclic nucleotide-binding domain. the channel and the binding domain alone bind cyclic amp with similar affinity in a non-cooperative manner. the camp sensitivities of binding and activation coincide. thus, each subunit in the tetrameric channel acts i ... | 2007 | 17668006 |
| homologous cpn60 genes in rhizobium leguminosarum are not functionally equivalent. | many bacteria possess 2 or more genes for the chaperonin groel and the cochaperonin groes. in particular, rhizobial species often have multiple groel and groes genes, with a high degree of amino-acid similarity, in their genomes. the rhizobium leguminosarum strain a34 has 3 complete groe operons, which we have named cpn.1, cpn.2 and cpn.3. previously we have shown the cpn. 1 operon to be essential for growth, but the two other cpn operons to be dispensable. here, we have investigated the extent ... | 2007 | 17688191 |
| lysm domains mediate lipochitin-oligosaccharide recognition and nfr genes extend the symbiotic host range. | legume-rhizobium symbiosis is an example of selective cell recognition controlled by host/non-host determinants. individual bacterial strains have a distinct host range enabling nodulation of a limited set of legume species and vice versa. we show here that expression of lotus japonicus nfr1 and nfr5 nod-factor receptor genes in medicago truncatula and l. filicaulis, extends their host range to include bacterial strains, mesorhizobium loti or dzl, normally infecting l. japonicus. as a result, th ... | 2007 | 17690687 |
| biosynthesis and immunogenicity of glucosylceramide in cryptococcus neoformans and other human pathogens. | | 2007 | 17693597 |
| a two-step fermentation process for efficient production of penta-n-acetyl-chitopentaose in recombinant escherichia coli. | the nodc gene from mesorhizobium loti was cloned into e. coli, leading to production of chitin oligosaccharides (cos)-mainly penta-n-acetyl-chitopentaose. a two-step fermentation procedure was then developed which gave 930 mg co/l with a productivity of 37 mg/l.h. | 2007 | 17710376 |
| partial protection against brucella infection in mice by immunization with nonpathogenic alphaproteobacteria. | previous findings indicate that brucella antigens and those from nonpathogenic alphaproteobacteria (npap) are cross-recognized by the immune system. we hypothesized that immunization with npap would protect mice from brucella infection. mice were immunized subcutaneously with heat-killed ochrobactrum anthropi, sinorhizobium meliloti, mesorhizobium loti, agrobacterium tumefaciens, or brucella melitensis h38 (standard positive control) before intravenous challenge with brucella abortus 2308. cross ... | 2007 | 17715332 |
| genetic analysis of the histidine utilization (hut) genes in pseudomonas fluorescens sbw25. | the histidine utilization (hut) locus of pseudomonas fluorescens sbw25 confers the ability to utilize histidine as a sole carbon and nitrogen source. genetic analysis using a combination of site-directed mutagenesis and chromosomally integrated lacz fusions showed the hut locus to be composed of 13 genes organized in 3 transcriptional units: hutf, hutcd, and 10 genes from hutu to hutg (which includes 2 copies of huth, 1 of which is nonfunctional). inactivation of hutf eliminated the ability to g ... | 2007 | 17717196 |
| differential effects of combined n sources on early steps of the nod factor-dependent transduction pathway in lotus japonicus. | the development of nitrogen-fixing nodules in legumes is induced by perception of lipochitin-oligosaccharide signals secreted by a bacterial symbiont. nitrogen (n) starvation is a prerequisite for the formation, development, and function of root nodules, and high levels of combined n in the form of nitrate or ammonium can completely abolish nodule formation. we distinguished between nitrate and ammonium inhibitory effects by identifying when and where these combined n sources interfere with the ... | 2007 | 17722702 |
| the mesorhizobium loti purb gene is involved in infection thread formation and nodule development in lotus japonicus. | the purb and purh mutants of mesorhizobium loti exhibited purine auxotrophy and nodulation deficiency on lotus japonicus. in the presence of adenine, only the purh mutant induced nodule formation and the purb mutant produced few infection threads, suggesting that 5-aminoimidazole-4-carboxamide ribonucleotide biosynthesis catalyzed by purb is required for the establishment of symbiosis. | 2007 | 17827288 |
| the structure of the prokaryotic cyclic nucleotide-modulated potassium channel mlok1 at 16 a resolution. | the gating ring of cyclic nucleotide-modulated channels is proposed to be either a two-fold symmetric dimer of dimers or a four-fold symmetric tetramer based on high-resolution structure data of soluble cyclic nucleotide-binding domains and functional data on intact channels. we addressed this controversy by obtaining structural data on an intact, full-length, cyclic nucleotide-modulated potassium channel, mlok1, from mesorhizobium loti, which also features a putative voltage-sensor. we present ... | 2007 | 17850745 |
| plp catabolism: identification of the 4-pyridoxic acid dehydrogenase gene in mesorhizobium loti maff303099. | the function of the mlr6793 gene from mesorhizobium loti maff303099 has been identified. this gene encodes 4-pyridoxic acid dehydrogenase, an enzyme involved in the catabolism of plp (vitamin b6). this enzyme was overexpressed in escherichia coli and characterized. 4-pyridoxic acid dehydrogenase is a 33kda protein that catalyzes the four electron oxidation of 4-pyridoxic acid to 3-hydroxy-2-methylpyridine-4,5-dicarboxylate, using nicotinamide adenine dinucleotide as a cofactor. the k cat for nad ... | 2007 | 17868768 |
| l-rhamnose transport is sugar kinase (rhak) dependent in rhizobium leguminosarum bv. trifolii. | strains of rhizobium leguminosarum which are unable to catabolize l-rhamnose, a methyl-pentose sugar, are compromised in the ability to compete for nodule occupancy versus wild-type strains. previous characterization of the 11-kb region necessary for the utilization of rhamnose identified a locus carrying catabolic genes and genes encoding the components of an abc transporter. genetic evidence suggested that the putative kinase rhak carried out the first step in the catabolism of rhamnose. chara ... | 2007 | 17890304 |
| evolution and functional characterization of the rh50 gene from the ammonia-oxidizing bacterium nitrosomonas europaea. | the family of ammonia and ammonium channel proteins comprises the amt proteins, which are present in all three domains of life with the notable exception of vertebrates, and the homologous rh proteins (rh50 and rh30) that have been described thus far only in eukaryotes. the existence of an rh50 gene in bacteria was first revealed by the genome sequencing of the ammonia-oxidizing bacterium nitrosomonas europaea. here we have used a phylogenetic approach to study the evolution of the n. europaea r ... | 2007 | 17921289 |
| the mlotik1 channel transports ions along the canonical conduction pore. | although the cyclic nucleotide-modulated potassium channel from mesorhizobium loti, mlotik1, is easily studied using a 86rb+ flux assay, its comparatively low activity raises serious concerns about the integrity of the purified protein. we investigated the pathway of uptake using a multi-pronged approach. first, we probed the conduction pathway using quaternary ammonium compounds known to block conduction in eukaryotic k+ channels. second, we examined the effect of chemical modification of putat ... | 2007 | 17935718 |
| identification of two gene clusters and a transcriptional regulator required for pseudomonas aeruginosa glycine betaine catabolism. | glycine betaine (gb), which occurs freely in the environment and is an intermediate in the catabolism of choline and carnitine, can serve as a sole source of carbon or nitrogen in pseudomonas aeruginosa. twelve mutants defective in growth on gb as the sole carbon source were identified through a genetic screen of a nonredundant pa14 transposon mutant library. further growth experiments showed that strains with mutations in two genes, gbca (pa5410) and gbcb (pa5411), were capable of growth on dim ... | 2008 | 17951379 |
| identification of two gene clusters and a transcriptional regulator required for pseudomonas aeruginosa glycine betaine catabolism. | glycine betaine (gb), which occurs freely in the environment and is an intermediate in the catabolism of choline and carnitine, can serve as a sole source of carbon or nitrogen in pseudomonas aeruginosa. twelve mutants defective in growth on gb as the sole carbon source were identified through a genetic screen of a nonredundant pa14 transposon mutant library. further growth experiments showed that strains with mutations in two genes, gbca (pa5410) and gbcb (pa5411), were capable of growth on dim ... | 2008 | 17951379 |
| novel hexamerization motif is discovered in a conserved cytoplasmic protein from salmonella typhimurium. | the cytoplasmic protein stm3548 of unknown function obtained from a strain of salmonella typhimurium was determined by x-ray crystallography at a resolution of 2.25 a. the asymmetric unit contains a hexamer of structurally identical monomers. the monomer is a globular domain with a long beta-hairpin protrusion that distinguishes this structure. this beta-hairpin occupies a central position in the hexamer, and its residues participate in the majority of interactions between subunits of the hexame ... | 2007 | 17968677 |
| identification of differentially expressed small non-coding rnas in the legume endosymbiont sinorhizobium meliloti by comparative genomics. | bacterial small non-coding rnas (srnas) are being recognized as novel widespread regulators of gene expression in response to environmental signals. here, we present the first search for srna-encoding genes in the nitrogen-fixing endosymbiont sinorhizobium meliloti, performed by a genome-wide computational analysis of its intergenic regions. comparative sequence data from eight related alpha-proteobacteria were obtained, and the interspecies pairwise alignments were scored with the programs eqrn ... | 2007 | 17971083 |
| gene identification and structural characterization of the pyridoxal 5'-phosphate degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase from mesorhizobium loti maff303099. | the function of the mlr6791 gene from mesorhizobium loti maff303099 has been identified. this gene encodes 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase (hmpddc), an enzyme involved in the catabolism of pyridoxal 5'-phosphate (vitamin b6). this enzyme was overexpressed in escherichia coli and characterized. hmpddc is a 26 kda protein that catalyzes the decarboxylation of 3-hydroxy-2-methylpyridine-4,5-dicarboxylate to 3-hydroxy-2-methylpyridine-5-carboxylate. the km and kcat were fo ... | 2007 | 17973403 |
| from endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism. | mitochondria are eukaryotic organelles that originated from the endosymbiosis of an alpha-proteobacterium. to gain insight into the evolution of the mitochondrial proteome as it proceeded through the transition from a free-living cell to a specialized organelle, we compared a reconstructed ancestral proteome of the mitochondrion with the proteomes of alpha-proteobacteria as well as with the mitochondrial proteomes in yeast and man. overall, there has been a large turnover of the mitochondrial pr ... | 2007 | 17983265 |
| crystal structure of pyridoxamine-pyruvate aminotransferase from mesorhizobium loti maff303099. | pyridoxamine-pyruvate aminotransferase (ppat; ec 2.6.1.30) is a pyridoxal 5'-phosphate-independent aminotransferase and catalyzes reversible transamination between pyridoxamine and pyruvate to form pyridoxal and l-alanine. the crystal structure of ppat from mesorhizobium loti has been solved in space group p4(3)2(1)2 and was refined to an r factor of 15.6% (r(free) = 20.6%) at 2.0 a resolution. in addition, the structures of ppat in complexes with pyridoxamine, pyridoxal, and pyridoxyl-l-alanine ... | 2008 | 17989071 |