| ferrichrome utilization in a mesorhizobial population: microevolution of a three-locus system. | the ability to utilize the siderophore ferrichrome as an iron source was found to be a variable trait in a field population of mesorhizobia. to investigate the genetic basis of this variation, genes required for ferrichrome utilization (fhu genes) were characterized in mesorhizobium strain r88b, an fhu(+) member of the population. functional fhu genes were present at three loci. two genes of the ferrichrome abc transporter, fhubd, were identified at an fhu1 locus downstream of the symbiosis isla ... | 2007 | 17991023 |
| multiple phospholipid n-methyltransferases with distinct substrate specificities are encoded in bradyrhizobium japonicum. | phosphatidylcholine (pc) is the major phospholipid in eukaryotic membranes. in contrast, it is found in only a few prokaryotes including members of the family rhizobiaceae. in these bacteria, pc is required for pathogenic and symbiotic plant-microbe interactions, as shown for agrobacterium tumefaciens and bradyrhizobium japonicum. at least two different phospholipid n-methyltransferases (pmta and pmtx) have been postulated to convert phosphatidylethanolamine (pe) to pc in b. japonicum by three c ... | 2008 | 17993534 |
| multiple phospholipid n-methyltransferases with distinct substrate specificities are encoded in bradyrhizobium japonicum. | phosphatidylcholine (pc) is the major phospholipid in eukaryotic membranes. in contrast, it is found in only a few prokaryotes including members of the family rhizobiaceae. in these bacteria, pc is required for pathogenic and symbiotic plant-microbe interactions, as shown for agrobacterium tumefaciens and bradyrhizobium japonicum. at least two different phospholipid n-methyltransferases (pmta and pmtx) have been postulated to convert phosphatidylethanolamine (pe) to pc in b. japonicum by three c ... | 2008 | 17993534 |
| identification of prophages in bacterial genomes by dinucleotide relative abundance difference. | prophages are integrated viral forms in bacterial genomes that have been found to contribute to interstrain genetic variability. many virulence-associated genes are reported to be prophage encoded. present computational methods to detect prophages are either by identifying possible essential proteins such as integrases or by an extension of this technique, which involves identifying a region containing proteins similar to those occurring in prophages. these methods suffer due to the problem of l ... | 2007 | 18030328 |
| crystal structure of mycobacterium tuberculosis lrpa, a leucine-responsive global regulator associated with starvation response. | the bacterial leucine-responsive regulatory protein (lrp) is a global transcriptional regulator that controls the expression of many genes during starvation and the transition to stationary phase. the mycobacterium tuberculosis gene rv3291c encodes a 150-amino acid protein (designated here as mtb lrpa) with homology with escherichia coli lrp. the crystal structure of the native form of mtb lrpa was solved at 2.1 a. the mtb lrpa structure shows an n-terminal dna-binding domain with a helix-turn-h ... | 2008 | 18042675 |
| phylogenomics and signature proteins for the alpha proteobacteria and its main groups. | alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. however, for these bacteria as a whole and for all of its major subgroups (viz. rhizobiales, rhodobacterales, rhodospirillales, rickettsiales, sphingomonadales and caulobacterales), very few or no distinctive molecular or biochemical characteristics are known. | 2007 | 18045498 |
| a mesorhizobium loti mutant with reduced glucan content shows defective invasion of its host plant lotus japonicus. | random transposon mutagenesis led to the isolation of a novel mesorhizobium loti mutant that is defective in nitrogen fixation during symbiosis with lotus japonicus. the mutated locus, designated cep, encodes a putative cell-envelope protein displaying no significant sequence similarity to proteins with known functions. this mutant elicits the formation of nodule-like bumps and root-hair curling, but not the elongation of infection threads, on l. japonicus roots. this is reminiscent of the pheno ... | 2007 | 18048913 |
| defects in rhizobial cyclic glucan and lipopolysaccharide synthesis alter legume gene expression during nodule development. | cdna array technology was used to compare transcriptome profiles of lotus japonicus roots inoculated with a mesorhizobium loti wild-type and two mutant strains affected in cyclic beta(1-2) glucan synthesis (cgs) and in lipopolysaccharide synthesis (lpsbeta2). expression of genes associated with the development of a fully functional nodule was significantly affected in plants inoculated with the cgs mutant. array results also revealed that induction of marker genes for nodule development was dela ... | 2008 | 18052882 |
| binding site determinants for the lysr-type transcriptional regulator pcaq in the legume endosymbiont sinorhizobium meliloti. | lysr-type transcriptional regulators represent one of the largest groups of prokaryotic regulators described to date. in the gram-negative legume endosymbiont sinorhizobium meliloti, enzymes involved in the protocatechuate branch of the beta-ketoadipate pathway are encoded within the pcadchgb operon, which is subject to regulation by the lysr-type protein pcaq. in this work, purified pcaq was shown to bind strongly (equilibrium dissociation constant, 0.54 nm) to a region at positions -78 to -45 ... | 2008 | 18055594 |
| binding site determinants for the lysr-type transcriptional regulator pcaq in the legume endosymbiont sinorhizobium meliloti. | lysr-type transcriptional regulators represent one of the largest groups of prokaryotic regulators described to date. in the gram-negative legume endosymbiont sinorhizobium meliloti, enzymes involved in the protocatechuate branch of the beta-ketoadipate pathway are encoded within the pcadchgb operon, which is subject to regulation by the lysr-type protein pcaq. in this work, purified pcaq was shown to bind strongly (equilibrium dissociation constant, 0.54 nm) to a region at positions -78 to -45 ... | 2008 | 18055594 |
| multiple ku orthologues mediate dna non-homologous end-joining in the free-living form and during chronic infection of sinorhizobium meliloti. | the bacterial non-homologous end-joining (nhej) apparatus is a two-component system that uses ku and ligd to repair dna double-strand breaks. although the reaction mechanism has been extensively studied, much less is known about the physiological role of bacterial nhej. recent studies suggest that nhej acts under conditions where dna replication is reduced or absent (such as in a spore or stationary phase). interestingly, genes encoding ku and ligd have been identified in a wide range of bacteri ... | 2008 | 18067541 |
| multiple ku orthologues mediate dna non-homologous end-joining in the free-living form and during chronic infection of sinorhizobium meliloti. | the bacterial non-homologous end-joining (nhej) apparatus is a two-component system that uses ku and ligd to repair dna double-strand breaks. although the reaction mechanism has been extensively studied, much less is known about the physiological role of bacterial nhej. recent studies suggest that nhej acts under conditions where dna replication is reduced or absent (such as in a spore or stationary phase). interestingly, genes encoding ku and ligd have been identified in a wide range of bacteri ... | 2008 | 18067541 |
| identification of chromosomal alpha-proteobacterial small rnas by comparative genome analysis and detection in sinorhizobium meliloti strain 1021. | small untranslated rnas (srnas) seem to be far more abundant than previously believed. the number of srnas confirmed in e. coli through various approaches is above 70, with several hundred more srna candidate genes under biological validation. although the total number of srnas in any one species is still unclear, their importance in cellular processes has been established. however, unlike protein genes, no simple feature enables the prediction of the location of the corresponding sequences in g ... | 2007 | 18093320 |
| salicylic acid and systemic acquired resistance play a role in attenuating crown gall disease caused by agrobacterium tumefaciens. | we investigated the effects of salicylic acid (sa) and systemic acquired resistance (sar) on crown gall disease caused by agrobacterium tumefaciens. nicotiana benthamiana plants treated with sa showed decreased susceptibility to agrobacterium infection. exogenous application of sa to agrobacterium cultures decreased its growth, virulence, and attachment to plant cells. using agrobacterium whole-genome microarrays, we characterized the direct effects of sa on bacterial gene expression and showed ... | 2008 | 18156296 |
| structural studies of the o-polysaccharide chain from the lipopolysaccharide of symbiotically enhanced mutant mlo-13 of mesorhizobium loti nzp2213. | the o-specific polysaccharide (ops) of mesorhizobium loti mutant mlo-13 was obtained by mild-acid degradation of the lipopolysaccharide and studied by sugar and ethylation analyses, smith degradation, as well as (1)h and (13)c nmr spectroscopy. the o-polysaccharide has a trisaccharide repeating unit composed of 6-deoxy-l-talose (l-6dtal), 4-o-acetyl-6-deoxy-l-talose (l-6dtal-4ac) and l-rhamnose residues. an analysis of nmr spectra revealed that the rhamnose residue was substituted nonstoichiomet ... | 2008 | 18160063 |
| pfli, a protein involved in flagellar positioning in caulobacter crescentus. | the bacterial flagellum is important for motility and adaptation to environmental niches. the sequence of events required for the synthesis of the flagellar apparatus has been extensively studied, yet the events that dictate where the flagellum is placed at the onset of flagellar biosynthesis remain largely unknown. we addressed this question for alphaproteobacteria by using the polarly flagellated alphaproteobacterium caulobacter crescentus as an experimental model system. to identify candidate ... | 2008 | 18165296 |
| pfli, a protein involved in flagellar positioning in caulobacter crescentus. | the bacterial flagellum is important for motility and adaptation to environmental niches. the sequence of events required for the synthesis of the flagellar apparatus has been extensively studied, yet the events that dictate where the flagellum is placed at the onset of flagellar biosynthesis remain largely unknown. we addressed this question for alphaproteobacteria by using the polarly flagellated alphaproteobacterium caulobacter crescentus as an experimental model system. to identify candidate ... | 2008 | 18165296 |
| requirement for mesorhizobium loti ornithine transcarbamoylase for successful symbiosis with lotus japonicus as revealed by an unexpected long-range genome deletion. | with the original aim of surveying the role of exopolysaccharide (eps) in lotus-mesorhizobium symbiosis, we carried out tn5 mutagenesis of mesorhizobium loti and obtained 32 mutants with defects in eps biosynthesis. one of the mutants, hia22, formed pseudonodules and failed to fix nitrogen with lotus japonicus. however, complementation analysis unexpectedly revealed that the potential gene with the locus tag, mll2073, interrupted by tn5 was responsible for neither normal eps synthesis nor symbio ... | 2008 | 18184692 |
| a large scale analysis of protein-protein interactions in the nitrogen-fixing bacterium mesorhizobium loti. | global viewing of protein-protein interactions (ppis) is a useful way to assign biological roles to large numbers of proteins predicted by complete genome sequence. here, we systematically analyzed ppis in the nitrogen-fixing soil bacterium mesorhizobium loti using a modified high-throughput yeast two-hybrid system. the aims of this study are primarily on the providing functional clues to m. loti proteins that are relevant to symbiotic nitrogen fixation and conserved in other rhizobium species, ... | 2008 | 18192278 |
| split-root study of autoregulation of nodulation in the model legume lotus japonicus. | we used a split-root system to determine the timing for induction of the autoregulation of nodulation (aut) in lotus japonicus (regel) larsen after inoculation with mesorhizobium loti. the signal took at least five days for full induction of aut and inhibition of infection thread formation. strain ml108 (able to nodulate but unable to fix nitrogen) induced full aut, but ml101 (unable to nodulate or to fix nitrogen) did not induce autoregulation. these results indicate that nod factor-producing s ... | 2008 | 18202823 |
| codon choice in genes depends on flanking sequence information--implications for theoretical reverse translation. | algorithms for theoretical reverse translation have direct applications in degenerate pcr. the conventional practice is to create several degenerate primers each of which variably encode the peptide region of interest. in the current work, for each codon we have analyzed the flanking residues in proteins and determined their influence on codon choice. from this, we created a method for theoretical reverse translation that includes information from flanking residues of the protein in question. ou ... | 2008 | 18203741 |
| gene identification and characterization of the pyridoxine degradative enzyme 4-pyridoxic acid dehydrogenase from the nitrogen-fixing symbiotic bacterium mesorhizobium loti maff303099. | the gene encoding 4-pyridoxic acid dehydrogenase was identified as mlr6792 in a chromosome of a nitrogen-fixing symbiotic bacterium mesorhizobium loti maff303099. the enzyme is the fourth enzyme in the vitamin b(6) (pyridoxine)-degradation pathway i. the recombinant enzyme with a his-tag over-expressed in escherichia coli cells was a membrane-bound protein, and purified to homogeneity. the enzyme was a monomeric protein with a molecular weight of 59,000, and a flavoprotein containing one mole of ... | 2008 | 18216065 |
| alteration of o-specific polysaccharide structure of symbiotically defective mesorhizobium loti mutant 2213.1 derived from strain nzp2213. | mesorhizobium loti mutant 2213.1 derived from the wild-type strain nzp2213 by tn5 mutagenesis showed impaired effectiveness of symbiosis with the host plant lotus corniculatus (turska-szewczuk et al., 2007 microbiol res, in press). the inability of lipopolysaccharide (lps) isolated from the mutant 2213.1 strain or de-o-acetylated lps of the parental cells to inactivate phage a1 particles implicated alterations in the lps structure. the o-specific polysaccharide of the mutant was studied by chemi ... | 2008 | 18217107 |
| evolution of a family of metazoan active-site-serine enzymes from penicillin-binding proteins: a novel facet of the bacterial legacy. | bacterial penicillin-binding proteins and beta-lactamases (pbp-betals) constitute a large family of serine proteases that perform essential functions in the synthesis and maintenance of peptidoglycan. intriguingly, genes encoding pbp-betal homologs occur in many metazoan genomes including humans. the emerging role of lactb, a mammalian mitochondrial pbp-betal homolog, in metabolic signaling prompted us to investigate the evolutionary history of metazoan pbp-betal proteins. | 2008 | 18226203 |
| comparative secretome analysis suggests low plant cell wall degrading capacity in frankia symbionts. | frankia sp. strains, the nitrogen-fixing facultative endosymbionts of actinorhizal plants, have long been proposed to secrete hydrolytic enzymes such as cellulases, pectinases, and proteases that may contribute to plant root penetration and formation of symbiotic root nodules. these or other secreted proteins might logically be involved in the as yet unknown molecular interactions between frankia and their host plants. we compared the genome-based secretomes of three frankia strains representing ... | 2008 | 18226217 |
| identification of protein secretion systems and novel secreted proteins in rhizobium leguminosarum bv. viciae. | proteins secreted by bacteria play an important role in infection of eukaryotic hosts. rhizobia infect the roots of leguminous plants and establish a mutually beneficial symbiosis. proteins secreted during the infection process by some rhizobial strains can influence infection and modify the plant defence signalling pathways. the aim of this study was to systematically analyse protein secretion in the recently sequenced strain rhizobium leguminosarum bv. viciae 3841. | 2008 | 18230162 |
| origin and evolution of gala-lrr, a new member of the cc-lrr subfamily: from plants to bacteria? | the phytopathogenic bacterium ralstonia solanacearum encodes type iii effectors, called gala proteins, which contain f-box and lrr domains. the gala lrrs do not perfectly fit any of the previously described lrr subfamilies. by applying protein sequence analysis and structural prediction, we clarify this ambiguous case of lrr classification and assign gala-lrrs to cc-lrr subfamily. we demonstrate that side-by-side packing of lrrs in the 3d structures may control the limits of repeat variability w ... | 2008 | 18301771 |
| arrhythmogenic right ventricular cardiomyopathy type 5 is a fully penetrant, lethal arrhythmic disorder caused by a missense mutation in the tmem43 gene. | autosomal-dominant arrhythmogenic right ventricular cardiomyopathy/dysplasia (arvc/d) causes sudden cardiac death and is characterized by clinical and genetic heterogeneity. fifteen unrelated arvc families with a disease-associated haplotype on chromosome 3p (arvd5) were ascertained from a genetically isolated population. identification of key recombination events reduced the disease region to a 2.36 mb interval containing 20 annotated genes. bidirectional resequencing showed one rare variant in ... | 2008 | 18313022 |
| symrk defines a common genetic basis for plant root endosymbioses with arbuscular mycorrhiza fungi, rhizobia, and frankiabacteria. | root endosymbioses vitally contribute to plant nutrition and fitness worldwide. nitrogen-fixing root nodulation, confined to four plant orders, encompasses two distinct types of associations, the interaction of legumes (fabales) with rhizobia bacteria and actinorhizal symbioses, where the bacterial symbionts are actinomycetes of the genus frankia. although several genetic components of the host-symbiont interaction have been identified in legumes, the genetic basis of actinorhiza formation is un ... | 2008 | 18316735 |
| functional adaptation of a plant receptor-kinase paved the way for the evolution of intracellular root symbioses with bacteria. | nitrogen-fixing root nodule symbioses (rns) occur in two major forms-actinorhiza and legume-rhizobium symbiosis-which differ in bacterial partner, intracellular infection pattern, and morphogenesis. the phylogenetic restriction of nodulation to eurosid angiosperms indicates a common and recent evolutionary invention, but the molecular steps involved are still obscure. in legumes, at least seven genes-including the symbiosis receptor-kinase gene symrk-are essential for the interaction with rhizob ... | 2008 | 18318603 |
| focal point theory models for dissecting dynamic duality problems of microbial infections. | extending along the dynamic continuum from conflict to cooperation, microbial infections always involve symbiosis (sym) and pathogenesis (pat). there exists a dynamic sym-pat duality (dspd) in microbial infection that is the most fundamental problem in infectomics. dspd is encoded by the genomes of both the microbes and their hosts. three focal point (fp) theory-based game models (pure cooperative, dilemma, and pure conflict) are proposed for resolving those problems. our health is associated wi ... | 2008 | 18350122 |
| ttsi regulates symbiotic genes in rhizobium species ngr234 by binding to tts boxes. | infection of legumes by rhizobium sp. ngr234 and subsequent development of nitrogen-fixing nodules are dependent on the coordinated actions of nod factors, proteins secreted by a type iii secretion system (t3ss) and modifications to surface polysaccharides. the production of these signal molecules is dependent on plant flavonoids which trigger a regulatory cascade controlled by the transcriptional activators nodd1, nodd2, syrm2 and ttsi. ttsi is known to control the genes responsible for t3ss fu ... | 2008 | 18363648 |
| phosphorylation-independent regulation of the diguanylate cyclase wspr. | environmental signals that trigger bacterial pathogenesis and biofilm formation are mediated by changes in the level of cyclic dimeric guanosine monophosphate (c-di-gmp), a unique eubacterial second messenger. tight regulation of cellular c-di-gmp concentration is governed by diguanylate cyclases and phosphodiesterases, which are responsible for its production and degradation, respectively. here, we present the crystal structure of the diguanylate cyclase wspr, a conserved ggdef domain-containin ... | 2008 | 18366254 |
| structural characterization of the primary o-antigenic polysaccharide of the rhizobium leguminosarum 3841 lipopolysaccharide and identification of a new 3-acetimidoylamino-3-deoxyhexuronic acid glycosyl component: a unique o-methylated glycan of uniform size, containing 6-deoxy-3-o-methyl-d-talose, n-acetylquinovosamine, and rhizoaminuronic acid (3-acetimidoylamino-3-deoxy-d-gluco-hexuronic acid). | rhizobium are gram-negative bacteria that survive intracellularly, within host membrane-derived plant cell compartments called symbiosomes. within the symbiosomes the bacteria differentiate to bacteroids, the active form that carries out nitrogen fixation. the progression from free-living bacteria to bacteroid is characterized by physiological and morphological changes at the bacterial surface, a phase shift with an altered array of cell surface glycoconjugates. lipopolysaccharides undergo struc ... | 2008 | 18387959 |
| transcriptional interference and repression modulate the conjugative ability of the symbiotic plasmid of rhizobium etli. | bacteria of the order rhizobiales are able to establish nitrogen-fixing symbioses with legumes. commonly, genes for symbiosis are harbored on large symbiotic plasmids. although the transfer of symbiotic plasmids is commonly detected in nature, there are few experimentally characterized examples. in rhizobium etli, the product of rcta inhibits the conjugation of the symbiotic plasmid by reducing the transcription of the virb operon. rcta is transcribed divergently from this operon, and its produc ... | 2008 | 18424522 |
| identification and characterization of kpss, a novel polysaccharide sulphotransferase in mesorhizobium loti. | plants enter into symbiotic relationships with bacteria that allow survival in nutrient-limiting environments. the bacterium mesorhizobium loti enters into a symbiosis with the legume host, lotus japonicus, which results in the formation of novel plant structures called root nodules. the bacteria colonize the nodules, and are internalized into the cytoplasm of the plant cells, where they reduce molecular dinitrogen for the plant. symbiosis between m. loti and l. japonicus requires bacterial synt ... | 2008 | 18430142 |
| glucomannan-mediated attachment of rhizobium leguminosarum to pea root hairs is required for competitive nodule infection. | the rhizobium leguminosarum biovar viciae genome contains several genes predicted to determine surface polysaccharides. mutants predicted to affect the initial steps of polysaccharide synthesis were identified and characterized. in addition to the known cellulose (cel) and acidic exopolysaccharide (eps) (pss) genes, we mutated three other loci; one of these loci (gmsa) determines glucomannan synthesis and one (gela) determines a gel-forming polysaccharide, but the role of the other locus (an exo ... | 2008 | 18441060 |
| rhizobium cellulase celc2 is essential for primary symbiotic infection of legume host roots. | the rhizobia-legume, root-nodule symbiosis provides the most efficient source of biologically fixed ammonia fertilizer for agricultural crops. its development involves pathways of specificity, infectivity, and effectivity resulting from expressed traits of the bacterium and host plant. a key event of the infection process required for development of this root-nodule symbiosis is a highly localized, complete erosion of the plant cell wall through which the bacterial symbiont penetrates to establi ... | 2008 | 18458328 |
| triad pattern algorithm for predicting strong promoter candidates in bacterial genomes. | bacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. this difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes. | 2008 | 18471287 |
| plp catabolism: identification of the 2-(acetamidomethylene)succinate hydrolase gene in mesorhizobium loti maff303099. | the function of the mlr6787 gene from mesorhizobium loti maff303099 has been identified. this gene encodes 2-(acetamidomethylene)succinate hydrolase, an enzyme involved in the catabolism of pyridoxal 5'-phosphate (vitamin b 6). this enzyme was overexpressed in escherichia coli, purified to homogeneity, and characterized. 2-(acetamidomethylene)succinate hydrolase catalyzes the hydrolysis of 2-(acetamidomethylene)succinate to yield succinic semialdehyde, acetic acid, carbon dioxide, and ammonia. t ... | 2008 | 18476725 |
| unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context. | the phosphoenolpyruvate phosphotransferase system (pts) plays a major role in sugar transport and in the regulation of essential physiological processes in many bacteria. the pts couples solute transport to its phosphorylation at the expense of phosphoenolpyruvate (pep) and it consists of general cytoplasmic phosphoryl transfer proteins and specific enzyme ii complexes which catalyze the uptake and phosphorylation of solutes. previous studies have suggested that the evolution of the constituents ... | 2008 | 18485189 |
| symbiosis-promoting and deleterious effects of nopt, a novel type 3 effector of rhizobium sp. strain ngr234. | establishment of symbiosis between certain host plants and nitrogen-fixing bacteria ("rhizobia") depends on type 3 effector proteins secreted via the bacterial type 3 secretion system (t3ss). here, we report that the open reading frame y4zc of strain ngr234 encodes a novel rhizobial type 3 effector, termed nopt (for nodulation outer protein t). analysis of secreted proteins from ngr234 and t3ss mutants revealed that nopt is secreted via the t3ss. nopt possessed autoproteolytic activity when expr ... | 2008 | 18487326 |
| genome sequence of the beta-rhizobium cupriavidus taiwanensis and comparative genomics of rhizobia. | we report the first complete genome sequence of a beta-proteobacterial nitrogen-fixing symbiont of legumes, cupriavidus taiwanensis lmg19424. the genome consists of two chromosomes of size 3.42 mb and 2.50 mb, and a large symbiotic plasmid of 0.56 mb. the c. taiwanensis genome displays an unexpected high similarity with the genome of the saprophytic bacterium c. eutrophus h16, despite being 0.94 mb smaller. both organisms harbor two chromosomes with large regions of synteny interspersed by speci ... | 2008 | 18490699 |
| a genomic search approach to identify esterases in propionibacterium freudenreichii involved in the formation of flavour in emmental cheese. | abstract: | 2008 | 18498642 |
| genetic and functional characterization of the type iv secretion system in wolbachia. | a type iv secretion system (t4ss) is used by many symbiotic and pathogenic intracellular bacteria for the successful infection of and survival, proliferation, and persistence within hosts. in this study, the presence and function of the t4ss in wolbachia strains were investigated by a combination of genetic screening and immunofluorescence microscopy. two operons of virb-vird4 loci were found in the genome of wolbachia pipientis strain watab3, from the hymenoptera asobara tabida, and strain wri, ... | 2008 | 18502862 |
| the binary protein interactome of treponema pallidum--the syphilis spirochete. | protein interaction networks shed light on the global organization of proteomes but can also place individual proteins into a functional context. if we know the function of bacterial proteins we will be able to understand how these species have adapted to diverse environments including many extreme habitats. here we present the protein interaction network for the syphilis spirochete treponema pallidum which encodes 1,039 proteins, 726 (or 70%) of which interact via 3,649 interactions as revealed ... | 2008 | 18509523 |
| soybean seed extracts preferentially express genomic loci of bradyrhizobium japonicum in the initial interaction with soybean, glycine max (l.) merr. | initial interaction between rhizobia and legumes actually starts via encounters of both partners in the rhizosphere. in this study, the global expression profiles of bradyrhizobium japonicum usda 110 in response to soybean (glycine max) seed extracts (sse) and genistein, a major soybean-released isoflavone for nod genes induction of b. japonicum, were compared. sse induced many genomic loci as compared with genistein (5.0 microm), nevertheless sse-supplemented medium contained 4.7 microm geniste ... | 2008 | 18511436 |
| the genome of the versatile nitrogen fixer azorhizobium caulinodans ors571. | biological nitrogen fixation is a prokaryotic process that plays an essential role in the global nitrogen cycle. azorhizobium caulinodans ors571 has the dual capacity to fix nitrogen both as free-living organism and in a symbiotic interaction with sesbania rostrata. the host is a fast-growing, submergence-tolerant tropical legume on which a. caulinodans can efficiently induce nodule formation on the root system and on adventitious rootlets located on the stem. | 2008 | 18522759 |
| structure, function, and evolution of bacterial atp-binding cassette systems. | summary: atp-binding cassette (abc) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. abc transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. in a classical transport reaction, two highly conserved atp-binding domains or subunits couple the binding/hydrolysis of atp to the translocat ... | 2008 | 18535149 |
| a positive regulatory role for ljerf1 in the nodulation process is revealed by systematic analysis of nodule-associated transcription factors of lotus japonicus. | we have used reverse genetics to identify genes involved in legume-rhizobium symbiosis in lotus japonicus. we obtained the sequences of 20 putative transcription factors from previously reported large-scale transcriptome data. the transcription factors were classified according to their dna binding domains and patterns of expression during the nodulation process. we identified two homologues of medicago truncatula mthap2-1, which encodes a ccaat-binding protein and has been shown to play a role ... | 2008 | 18567832 |
| a common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria. | this work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, rhizobium leguminosarum biovar viciae 3841 and rhizobium etli cfn42. these strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. the chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. the pairs of plasmids p42f-prl12, p42e-prl11 and p42b-prl9 ... | 2008 | 18596979 |
| the rpg gene of medicago truncatula controls rhizobium-directed polar growth during infection. | rhizobia can infect roots of host legume plants and induce new organs called nodules, in which they fix atmospheric nitrogen. infection generally starts with root hair curling, then proceeds inside newly formed, intracellular tubular structures called infection threads. a successful symbiotic interaction relies on infection threads advancing rapidly at their tips by polar growth through successive cell layers of the root toward developing nodule primordia. to identify a plant component that cont ... | 2008 | 18621693 |
| a novel arid dna-binding protein interacts with symrk and is expressed during early nodule development in lotus japonicus. | during the establishment of symbiosis in legume roots, the rhizobial nod factor signal is perceived by the host cells via receptor-like kinases, including symrk. the nodule inception (nin) gene in lotus japonicus is required for rhizobial entry into root cells and for nodule organogenesis. we describe here a novel dna-binding protein from l. japonicus, referred to as sip1, because it was identified as a symrk-interacting protein. sip1 contains a conserved at-rich interaction domain (arid) and re ... | 2008 | 18633121 |
| gene identification and characterization of the pyridoxine degradative enzyme alpha-(n-acetylaminomethylene)succinic acid amidohydrolase from mesorhizobium loti maff303099. | we have found for the first time that a chromosomal gene, mlr6787, in mesorhizobium loti encodes the pyridoxine degradative enzyme alpha-(n-acetylaminomethylene)succinic acid (aams) amidohydrolase. the recombinant enzyme expressed in escherichia coli cells was homogeneously purified and characterized. the enzyme consisted of two subunits each with a molecular mass of 34,000+/-1,000 da, and exhibited km and kcat values of 53.7+/-6 microm and 307.3+/-12 min(-1), respectively. the enzyme required n ... | 2008 | 18635903 |
| enzymatic, immunological and phylogenetic characterization of brucella suis urease. | the sequenced genomes of the brucella spp. have two urease operons, ure-1 and ure-2, but there is evidence that only one is responsible for encoding an active urease. the present work describes the purification and the enzymatic and phylogenomic characterization of urease from brucella suis strain 1330. additionally, the urease reactivity of sera from patients diagnosed with brucellosis was examined. | 2008 | 18638408 |
| complete genome sequence of the n2-fixing broad host range endophyte klebsiella pneumoniae 342 and virulence predictions verified in mice. | we report here the sequencing and analysis of the genome of the nitrogen-fixing endophyte, klebsiella pneumoniae 342. although k. pneumoniae 342 is a member of the enteric bacteria, it serves as a model for studies of endophytic, plant-bacterial associations due to its efficient colonization of plant tissues (including maize and wheat, two of the most important crops in the world), while maintaining a mutualistic relationship that encompasses supplying organic nitrogen to the host plant. genomic ... | 2008 | 18654632 |
| phenotypic plasticity with respect to salt stress response by lotus glaber: the role of its am fungal and rhizobial symbionts. | our hypothesis is that lotus glaber (a glycophytic species, highly tolerant to saline-alkaline soils) displays a plastic root phenotypic response to soil salinity that may be influenced by mycorrhizal and rhizobial microorganisms. uninoculated plants and plants colonised by glomus intraradices or mesorhizobium loti were exposed to either 150 or 0 mm nacl. general plant growth and root architectural parameters (morphology and topology) were measured and phenotypic plasticity determined at the end ... | 2008 | 18654803 |
| construction of signature-tagged mutant library in mesorhizobium loti as a powerful tool for functional genomics. | rhizobia are nitrogen-fixing soil bacteria that establish endosymbiosis with some leguminous plants. the completion of several rhizobial genome sequences provides opportunities for genome-wide functional studies of the physiological roles of many rhizobial genes. in order to carry out genome-wide phenotypic screenings, we have constructed a large mutant library of the nitrogen-fixing symbiotic bacterium, mesorhizobium loti, by transposon mutagenesis. transposon insertion mutants were generated u ... | 2008 | 18658183 |
| structural characterization of neutral and anionic glucans from mesorhizobium loti. | the periplasmic glucans of mesorhizobium loti were isolated and separated into fractions according to their acidity. nmr spectroscopy confirmed their backbone structure to be a cyclic beta-(1-->2)-d-glucan as in the case of other rhizobia, and revealed no non-glycosidic substituents in the neutral fraction, and glycerophosphoryl and succinyl residues as major and minor substituents, respectively, in the anionic fractions. maldi-tof mass spectrometry showed that the anionic glucans contain one, t ... | 2008 | 18667198 |
| structure/function evaluations of single nucleotide polymorphisms in human n-acetyltransferase 2. | arylamine n-acetyltransferase 2 (nat2) modifies drug efficacy/toxicity and cancer risk due to its role in bioactivation and detoxification of arylamine and hydrazine drugs and carcinogens. human nat2 alleles possess a combination of single nucleotide polymorphisms (snps) associated with slow acetylation phenotypes. clinical and molecular epidemiology studies investigating associations of nat2 genotype with drug efficacy/toxicity and/or cancer risk are compromised by incomplete and sometimes conf ... | 2008 | 18680467 |
| identification and functional characterization of gene components of type vi secretion system in bacterial genomes. | a new secretion system, called the type vi secretion system (t6ss), was recently reported in vibrio cholerae, pseudomonas aeruginosa and burkholderia mallei. a total of 18 genes have been identified to be belonging to this secretion system in v. cholerae. here we attempt to identify presence of t6ss in other bacterial genomes. this includes identification of orthologous sequences, conserved motifs, domains, families, 3d folds, genomic islands containing t6ss components, phylogenetic profiles and ... | 2008 | 18698408 |
| expression of a class 1 hemoglobin gene and production of nitric oxide in response to symbiotic and pathogenic bacteria in lotus japonicus. | symbiotic nitrogen fixation by the collaboration between leguminous plants and rhizobia is an important system in the global nitrogen cycle, and some molecular aspects during the early stage of host-symbiont recognition have been revealed. to understand the responses of a host plant against various bacteria, we examined expression of hemoglobin (hb) genes and production of nitric oxide (no) in lotus japonicus after inoculation with rhizobia or plant pathogens. when the symbiotic rhizobium mesorh ... | 2008 | 18700822 |
| prediction of sinorhizobium meliloti srna genes and experimental detection in strain 2011. | small non-coding rnas (srnas) have emerged as ubiquitous regulatory elements in bacteria and other life domains. however, few srnas have been identified outside several well-studied species of gamma-proteobacteria and thus relatively little is known about the role of rna-mediated regulation in most other bacterial genera. here we have conducted a computational prediction of putative srna genes in intergenic regions (igrs) of the symbiotic alpha-proteobacterium s. meliloti 1021 and experimentally ... | 2008 | 18793445 |
| overexpression of class 1 plant hemoglobin genes enhances symbiotic nitrogen fixation activity between mesorhizobium loti and lotus japonicus. | plant hemoglobins (hbs) have been divided into three groups: class 1, class 2, and truncated hbs. the various physiological functions of class 1 hb include its role as a modulator of nitric oxide (no) levels in plants. to gain more insight into the functions of class 1 hbs, we investigated the physical properties of ljhb1 and afhb1, class 1 hbs of a model legume lotus japonicus and an actinorhizal plant alnus firma, respectively. spectrophotometric analysis showed that the recombinant form of th ... | 2009 | 18801013 |
| the bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands. | the major birch pollen allergen, bet v 1, is a member of the ubiquitous pr-10 family of plant pathogenesis-related proteins. in recent years, a number of diverse plant proteins with low sequence similarity to bet v 1 was identified. in addition, determination of the bet v 1 structure revealed the existence of a large superfamily of structurally related proteins. in this study, we aimed to identify and classify all bet v 1-related structures from the protein data bank and all bet v 1-related sequ ... | 2008 | 18922149 |
| ion channels in microbes. | studies of ion channels have for long been dominated by the animalcentric, if not anthropocentric, view of physiology. the structures and activities of ion channels had, however, evolved long before the appearance of complex multicellular organisms on earth. the diversity of ion channels existing in cellular membranes of prokaryotes is a good example. although at first it may appear as a paradox that most of what we know about the structure of eukaryotic ion channels is based on the structure of ... | 2008 | 18923187 |
| efd is an erf transcription factor involved in the control of nodule number and differentiation in medicago truncatula. | mechanisms regulating legume root nodule development are still poorly understood, and very few regulatory genes have been cloned and characterized. here, we describe efd (for ethylene response factor required for nodule differentiation), a gene that is upregulated during nodulation in medicago truncatula. the efd transcription factor belongs to the ethylene response factor (erf) group v, which contains ern1, 2, and 3, three erfs involved in nod factor signaling. the role of efd in the regulation ... | 2008 | 18978033 |
| molecular determinants of a symbiotic chronic infection. | rhizobial bacteria colonize legume roots for the purpose of biological nitrogen fixation. a complex series of events, coordinated by host and bacterial signal molecules, underlie the development of this symbiotic interaction. rhizobia elicit de novo formation of a novel root organ within which they establish a chronic intracellular infection. legumes permit rhizobia to invade these root tissues while exerting control over the infection process. once rhizobia gain intracellular access to their ho ... | 2008 | 18983260 |
| purification and characterization of the lipid a 1-phosphatase lpxe of rhizobium leguminosarum. | lpxe, a membrane-bound phosphatase found in rhizobium leguminosarum and some other gram-negative bacteria, selectively dephosphorylates the 1-position of lipid a on the outer surface of the inner membrane. lpxe belongs to the family of lipid phosphate phosphatases that contain a tripartite active site motif and six predicted transmembrane helices. here we report the purification and characterization of r. leguminosarum lpxe. a modified lpxe gene, encoding a protein with an n-terminal his6 tag, w ... | 2009 | 18984595 |
| mesorhizobium gobiense sp. nov. and mesorhizobium tarimense sp. nov., isolated from wild legumes growing in desert soils of xinjiang, china. | twenty-four mesorhizobium strains were isolated from desert soils in the xinjiang region of china and were characterized by a polyphasic approach. these strains grouped into three clusters in igs-rflp, sds-page analysis of whole-cell proteins and box-pcr analysis, corresponding to genomic species v, vi and vii as found in a previous study. the results were supported by sequencing analyses of rrs, igs, atpd and reca genes. genospecies vii was most related to mesorhizobium septentrionale, while ge ... | 2008 | 18984702 |
| identification of vcea and vcec, two members of the vjbr regulon that are translocated into macrophages by the brucella type iv secretion system. | survival and replication inside host cells by brucella spp. requires a type iv secretion system (t4ss), encoded by the virb locus. however, the identity of the molecules secreted by the t4ss has remained elusive. we hypothesized that proteins translocated by the t4ss would be co-regulated with the virb operon. the luxr family regulator vjbr, known to regulate virb, bound a fragment of the virb promoter containing an 18 bp palindromic motif (virb promoter box), showing that vjbr regulated the vir ... | 2008 | 19019140 |
| gs52 ecto-apyrase plays a critical role during soybean nodulation. | apyrases are non-energy-coupled nucleotide phosphohydrolases that hydrolyze nucleoside triphosphates and nucleoside diphosphates to nucleoside monophosphates and orthophosphates. gs52, a soybean (glycine soja) ecto-apyrase, was previously shown to be induced very early in response to inoculation with the symbiotic bacterium bradyrhizobium japonicum. overexpression of the gs52 ecto-apyrase in lotus japonicus increased the level of rhizobial infection and enhanced nodulation. these data suggest a ... | 2009 | 19036836 |
| 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 |
| 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 |
| 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 |
| 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 |