Publications

poly-beta-hydroxybutyrate production by fast-growing rhizobia cultivated in sludge and in industrial wastewater.	in our study, the potential of producing polyhydroxybutyrate (phb) by cultivating fast-growing rhizobia (sinorhizobium meliloti, rhizobium leguminosarum bv. viciae, r. leguminosarum bv. phaseoli and r. leguminosarum bv. trifolii) in sludge and in industrial wastewater was evaluated. results confirmed the possibility of using sludge as media for rhizobial growth. during growth, substantial quantity of phb was accumulated and yields varied depending on the media and rhizobial species. growing in s ...	2009	18795238
lack of genomic evidence of ai-2 receptors suggests a non-quorum sensing role for luxs in most bacteria.	great excitement accompanied discoveries over the last decade in several gram-negative and gram-positive bacteria of the luxs protein, which catalyzes production of the ai-2 autoinducer molecule for a second quorum sensing system (qs-2). since the luxs gene was found to be widespread among the most diverse bacterial taxa, it was hypothesized that ai-2 may constitute the basis of a universal microbial language, a kind of bacterial esperanto. many of the studies published in this field have drawn ...	2008	18803868
scin is an outer membrane lipoprotein required for type vi secretion in enteroaggregative escherichia coli.	enteroaggregative escherichia coli (eaec) is a pathogen implicated in several infant diarrhea or diarrheal outbreaks in areas of endemicity. although multiple genes involved in eaec pathogenesis have been identified, the overall mechanism of virulence is not well understood. recently, a novel secretion system, called type vi secretion (t6s) system (t6ss), has been identified in eaec and most animal or plant gram-negative pathogens. t6sss are multicomponent cell envelope machines responsible for ...	2008	18805985
psso, a unique extracellular protein important for exopolysaccharide synthesis in rhizobium leguminosarum bv. trifolii.	synthesis and secretion of polysaccharides by gram-negative bacteria are a result of a concerted action of enzymatic and channel-forming proteins localized in different compartments of the cell. the presented work comprises functional characterization of psso protein encoded within the previously identified, chromosomal exopolysaccharide (eps) biosynthesis region (pss-i) of symbiotic bacterium rhizobium leguminosarum bv. trifolii ta1 (rtta1). psso gene localization between pssn and pssp genes en ...	2008	18835420
symbiotic plasmid is required for nolr to fully repress nodulation genes in rhizobium leguminosarum a34.	nolr is a regulator of nodulation genes present in rhizobium and sinorhizobium. however, the mechanism by which nolr participates in the inducible transcription of nodulation genes remains unclear. to investigate whether there are other factors regulating the function of nolr, an insertion mutant of nolr in rhizobium leguminosarum strain 8401, which lacks the symbiotic plasmid, was constructed by homologous recombination. we investigated the effects of nolr inactivation on the expression of nodu ...	2008	18850056
the 52nd annual wind river conference on prokaryotic biology--2008.		2008	18931109
unfolding the relationship between secreted molecular chaperones and macrophage activation states.	over the last 20 years, it has emerged that many molecular chaperones and protein-folding catalysts are secreted from cells and function, somewhat in the manner of cytokines, as pleiotropic signals for a variety of cells, with much attention being focused on the macrophage. during the last decade, it has become clear that macrophages respond to bacterial, protozoal, parasitic and host signals to generate phenotypically distinct states of activation. these activation states have been termed 'clas ...	2008	18958583
unfolding the relationship between secreted molecular chaperones and macrophage activation states.	over the last 20 years, it has emerged that many molecular chaperones and protein-folding catalysts are secreted from cells and function, somewhat in the manner of cytokines, as pleiotropic signals for a variety of cells, with much attention being focused on the macrophage. during the last decade, it has become clear that macrophages respond to bacterial, protozoal, parasitic and host signals to generate phenotypically distinct states of activation. these activation states have been termed 'clas ...	2008	18958583
bacterial heme-transport proteins and their heme-coordination modes.	efficient iron acquisition is critical for an invading microbe's survival and virulence. most of the iron in mammals is incorporated into heme, which can be plundered by certain bacterial pathogens as a nutritional iron source. utilization of exogenous heme by bacteria involves the binding of heme or hemoproteins to the cell surface receptors, followed by the transport of heme into cells. once taken into the cytosol, heme is presented to heme oxygenases where the tetrapyrrole ring is cleaved in ...	2008	18977196
bacterial heme-transport proteins and their heme-coordination modes.	efficient iron acquisition is critical for an invading microbe's survival and virulence. most of the iron in mammals is incorporated into heme, which can be plundered by certain bacterial pathogens as a nutritional iron source. utilization of exogenous heme by bacteria involves the binding of heme or hemoproteins to the cell surface receptors, followed by the transport of heme into cells. once taken into the cytosol, heme is presented to heme oxygenases where the tetrapyrrole ring is cleaved in ...	2008	18977196
expression and physiological relevance of agrobacterium tumefaciens phosphatidylcholine biosynthesis genes.	phosphatidylcholine (pc), or lecithin, is the major phospholipid in eukaryotic membranes, whereas only 10% of all bacteria are predicted to synthesize pc. in rhizobiaceae, including the phytopathogenic bacterium agrobacterium tumefaciens, pc is essential for the establishment of a successful host-microbe interaction. a. tumefaciens produces pc via two alternative pathways, the methylation pathway and the pcs pathway. the responsible genes, pmta (coding for a phospholipid n-methyltransferase) and ...	2009	18978052
expression and physiological relevance of agrobacterium tumefaciens phosphatidylcholine biosynthesis genes.	phosphatidylcholine (pc), or lecithin, is the major phospholipid in eukaryotic membranes, whereas only 10% of all bacteria are predicted to synthesize pc. in rhizobiaceae, including the phytopathogenic bacterium agrobacterium tumefaciens, pc is essential for the establishment of a successful host-microbe interaction. a. tumefaciens produces pc via two alternative pathways, the methylation pathway and the pcs pathway. the responsible genes, pmta (coding for a phospholipid n-methyltransferase) and ...	2009	18978052
the luxr family quorum-sensing activator mrtr requires its cognate autoinducer for dimerization and activation but not for protein folding.	mrtr, a luxr homolog in mesorhizobium tianshanense, is important for symbiosis. we found that mrtr requires its cognate n-acylhomoserine lactone for forming dimers, binding to a single dna site and activating the downstream promoter. however, mrtr is able to fold independently of its ligand.	2009	18978063
the luxr family quorum-sensing activator mrtr requires its cognate autoinducer for dimerization and activation but not for protein folding.	mrtr, a luxr homolog in mesorhizobium tianshanense, is important for symbiosis. we found that mrtr requires its cognate n-acylhomoserine lactone for forming dimers, binding to a single dna site and activating the downstream promoter. however, mrtr is able to fold independently of its ligand.	2009	18978063
function, regulation, and transcriptional organization of the hemin utilization locus of bartonella quintana.	bartonella quintana is a gram-negative agent of trench fever, chronic bacteremia, endocarditis, and bacillary angiomatosis in humans. b. quintana has the highest known hemin requirement among bacteria, but the mechanisms of hemin acquisition are poorly defined. genomic analyses revealed a potential locus dedicated to hemin utilization (hut) encoding a putative hemin receptor, huta; a tonb-like energy transducer; an abc transport system comprised of three proteins, hutb, hutc, and hmuv; and a hem ...	2009	18981245
function, regulation, and transcriptional organization of the hemin utilization locus of bartonella quintana.	bartonella quintana is a gram-negative agent of trench fever, chronic bacteremia, endocarditis, and bacillary angiomatosis in humans. b. quintana has the highest known hemin requirement among bacteria, but the mechanisms of hemin acquisition are poorly defined. genomic analyses revealed a potential locus dedicated to hemin utilization (hut) encoding a putative hemin receptor, huta; a tonb-like energy transducer; an abc transport system comprised of three proteins, hutb, hutc, and hmuv; and a hem ...	2009	18981245
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
revision of the taxonomic status of the species rhizobium leguminosarum (frank 1879) frank 1889al, rhizobium phaseoli dangeard 1926al and rhizobium trifolii dangeard 1926al. r. trifolii is a later synonym of r. leguminosarum. reclassification of the strain r. leguminosarum dsm 30132 (=ncimb 11478) as rhizobium pisi sp. nov.	the taxonomic status of the species rhizobium leguminosarum, rhizobium trifolii and rhizobium phaseoli was analysed in this study on the basis of their molecular and phenotypic characteristics. according to the results, the type strain r. phaseoli atcc 14482(t) does not belong to any of the already described species of the genus rhizobium and it should therefore be considered as a different species. in contrast, the strains of r. trifolii examined belonged to r. leguminosarum and thus r. trifoli ...	2008	18984681
the pea sym37 receptor kinase gene controls infection-thread initiation and nodule development.	phenotypic characterization of pea symbiotic mutants has provided a detailed description of the symbiosis with rhizobium leguminosarum bv. viciae strains. we show here that two allelic non-nodulating pea mutants, risnod4 and k24, are affected in the pssym37 gene, encoding a lysm receptor kinase similar to lotus japonicus nfr1 and medicago truncatula lyk3. phenotypic analysis of risnod4 and k24 suggests a role for the sym37 in regulation of infection-thread initiation and nodule development from ...	2008	18986256
the transcriptional repressor protein nsrr senses nitric oxide directly via a [2fe-2s] cluster.	the regulatory protein nsrr, a member of the rrf2 family of transcription repressors, is specifically dedicated to sensing nitric oxide (no) in a variety of pathogenic and non-pathogenic bacteria. it has been proposed that no directly modulates nsrr activity by interacting with a predicted [fe-s] cluster in the nsrr protein, but no experimental evidence has been published to support this hypothesis. here we report the purification of nsrr from the obligate aerobe streptomyces coelicolor. we demo ...	2008	18989365
survival of rhizobia in two soils as influenced by storage conditions.	two soils were kept moist at 4 degrees c, -20 degrees c or air-dried at 20-22 degrees c and after one week, one month, two months and six months of storage at these conditions changes in soil populations of rhizobium leguminosarum bv. trifolii (rlt) and rhizobium leguminosarum bv. viciae (rlv) were examined. in one air-dried soil (from grab6w) markedly lower numbers of both rlt and rlv., as compared to the refrigerated or frozen samples, were found already after 1 week of storage. in the case of ...	2008	19004248
characterization of the myo-inositol utilization island of salmonella enterica serovar typhimurium.	knockout mutation of stm4432 resulted in a growth-deficient phenotype of salmonella enterica serovar typhimurium in the presence of myo-inositol (mi) as the sole carbon source. stm4432 is part of a 22.6-kb genomic island which spans stm4417 to stm4436 (genomic island 4417/4436) and is responsible for mi degradation. genome comparison revealed the presence of this island in only six salmonella strains and a high variability of the iol gene organization in gram-negative bacteria. upon nonpolar del ...	2009	19011032
characterization of the myo-inositol utilization island of salmonella enterica serovar typhimurium.	knockout mutation of stm4432 resulted in a growth-deficient phenotype of salmonella enterica serovar typhimurium in the presence of myo-inositol (mi) as the sole carbon source. stm4432 is part of a 22.6-kb genomic island which spans stm4417 to stm4436 (genomic island 4417/4436) and is responsible for mi degradation. genome comparison revealed the presence of this island in only six salmonella strains and a high variability of the iol gene organization in gram-negative bacteria. upon nonpolar del ...	2009	19011032
the blcc (attm) lactonase of agrobacterium tumefaciens does not quench the quorum-sensing system that regulates ti plasmid conjugative transfer.	the conjugative transfer of agrobacterium plasmids is controlled by a quorum-sensing system consisting of trar and its acyl-homoserine lactone (hsl) ligand. the acyl-hsl is essential for the trar-mediated activation of the ti plasmid tra genes. strains a6 and c58 of agrobacterium tumefaciens produce a lactonase, blcc (attm), that can degrade the quormone, leading some to conclude that the enzyme quenches the quorum-sensing system. we tested this hypothesis by examining the effects of the mutatio ...	2009	19011037
the blcc (attm) lactonase of agrobacterium tumefaciens does not quench the quorum-sensing system that regulates ti plasmid conjugative transfer.	the conjugative transfer of agrobacterium plasmids is controlled by a quorum-sensing system consisting of trar and its acyl-homoserine lactone (hsl) ligand. the acyl-hsl is essential for the trar-mediated activation of the ti plasmid tra genes. strains a6 and c58 of agrobacterium tumefaciens produce a lactonase, blcc (attm), that can degrade the quormone, leading some to conclude that the enzyme quenches the quorum-sensing system. we tested this hypothesis by examining the effects of the mutatio ...	2009	19011037
encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium anoxybacillus flavithermus wk1.	gram-positive bacteria of the genus anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. the ability of a. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be sim ...	2008	19014707
a mutant glnd nitrogen sensor protein leads to a nitrogen-fixing but ineffective sinorhizobium meliloti symbiosis with alfalfa.	the nitrogen-fixing symbiosis between rhizobia and legume plants is a model of coevolved nutritional complementation. the plants reduce atmospheric co(2) by photosynthesis and provide carbon compounds to symbiotically associated bacteria; the rhizobia use these compounds to reduce (fix) atmospheric n(2) to ammonia, a form of nitrogen the plants can use. a key feature of symbiotic n(2) fixation is that n(2) fixation is uncoupled from bacterial nitrogen stress metabolism so that the rhizobia gener ...	2008	19020095
new taxonomic markers for identification of rhizobium leguminosarum and discrimination between closely related species.	rhizobia, producing species-specific exopolysaccharides (epss), comprise a very diverse group of soil bacteria that are able to establish nitrogen-fixing symbioses with legumes. based on the sequences of r. leguminosarum eps synthesis genes, a sensitive and reliable pcr-based method for identification and subsequent discrimination between rhizobium species has been developed and tested. for identification of r. leguminosarum, primer sets i-iii complementary to sequences of rosr, pssa and pssy ge ...	2009	19020864
oryr is a luxr-family protein involved in interkingdom signaling between pathogenic xanthomonas oryzae pv. oryzae and rice.	xanthomonas oryzae pv. oryzae, the causal agent of bacterial leaf blight in rice, contains a regulator that is encoded in the genome, designated oryr, which belongs to the n-acyl homoserine lactone (ahl)-dependent quorum-sensing luxr subfamily of proteins. however, we previously reported that x. oryzae pv. oryzae does not make ahls and does not possess a luxi-family ahl synthase and that the oryr protein is solubilized by a compound present in rice. in this study we obtained further evidence tha ...	2009	19028884
oryr is a luxr-family protein involved in interkingdom signaling between pathogenic xanthomonas oryzae pv. oryzae and rice.	xanthomonas oryzae pv. oryzae, the causal agent of bacterial leaf blight in rice, contains a regulator that is encoded in the genome, designated oryr, which belongs to the n-acyl homoserine lactone (ahl)-dependent quorum-sensing luxr subfamily of proteins. however, we previously reported that x. oryzae pv. oryzae does not make ahls and does not possess a luxi-family ahl synthase and that the oryr protein is solubilized by a compound present in rice. in this study we obtained further evidence tha ...	2009	19028884
identification and characterization of a bacterial transport system for the uptake of pyruvate, propionate, and acetate in corynebacterium glutamicum.	the metabolism of monocarboxylic acids is of central importance for bacteria in their natural habitat as well as during biotechnological production. although biosynthesis and degradation are well understood, the transport of such compounds is still a matter of discussion. here we present the identification and characterization of a new transport system in corynebacterium glutamicum with high affinity for acetate and propionate and with lower affinity for pyruvate. biochemical analysis of this mo ...	2009	19028892
identification and characterization of a bacterial transport system for the uptake of pyruvate, propionate, and acetate in corynebacterium glutamicum.	the metabolism of monocarboxylic acids is of central importance for bacteria in their natural habitat as well as during biotechnological production. although biosynthesis and degradation are well understood, the transport of such compounds is still a matter of discussion. here we present the identification and characterization of a new transport system in corynebacterium glutamicum with high affinity for acetate and propionate and with lower affinity for pyruvate. biochemical analysis of this mo ...	2009	19028892
regulatory and dna repair genes contribute to the desiccation resistance of sinorhizobium meliloti rm1021.	sinorhizobium meliloti can form a nitrogen-fixing symbiotic relationship with alfalfa after bacteria in the soil infect emerging root hairs of the growing plant. to be successful at this, the bacteria must be able to survive in the soil between periods of active plant growth, including when conditions are dry. the ability of s. meliloti to withstand desiccation has been known for years, but genes that contribute to this phenotype have not been identified. transposon mutagenesis was used in combi ...	2009	19028909
regulatory and dna repair genes contribute to the desiccation resistance of sinorhizobium meliloti rm1021.	sinorhizobium meliloti can form a nitrogen-fixing symbiotic relationship with alfalfa after bacteria in the soil infect emerging root hairs of the growing plant. to be successful at this, the bacteria must be able to survive in the soil between periods of active plant growth, including when conditions are dry. the ability of s. meliloti to withstand desiccation has been known for years, but genes that contribute to this phenotype have not been identified. transposon mutagenesis was used in combi ...	2009	19028909
newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the liverpool epidemic strain of pseudomonas aeruginosa.	pseudomonas aeruginosa isolates have a highly conserved core genome representing up to 90% of the total genomic sequence with additional variable accessory genes, many of which are found in genomic islands or islets. the identification of the liverpool epidemic strain (les) in a children's cystic fibrosis (cf) unit in 1996 and its subsequent observation in several centers in the united kingdom challenged the previous widespread assumption that cf patients acquire only unique strains of p. aerugi ...	2009	19047519
cloning, purification, crystallization and preliminary x-ray analysis of a bacterial gaba receptor with a venus flytrap fold.	in response to infection by the pathogen agrobacterium tumefaciens, plants synthesize several stress amino acids, including gamma-aminobutyric acid (gaba), which modulates the expression of bacterial virulence factors. gaba penetrates into the bacterial cytoplasm via an abc transporter that is associated with the periplasmic receptor atu2422. mature receptor atu2422 (without its signal peptide) was overexpressed in escherichia coli, purified and crystallized. a complete data set was collected to ...	2008	19052373
rhizobium fabae sp. nov., a bacterium that nodulates vicia faba.	six strains were isolated from root nodules of vicia faba grown in nanchang, yifeng, taihu, huaibei, bengbu and lujiang, in the middle and lower reaches of the yangtze river. according to phylogenetic analyses of 16s rrna gene, atpd and reca sequences, these strains belong to the genus rhizobium, with rhizobium etli and rhizobium leguminosarum as the closest related species. ccbau 33202(t), a representative of these novel isolates, showed sequence similarity to its closest relatives r. etli cfn ...	2008	19060074
purine utilization by klebsiella oxytoca m5al: genes for ring-oxidizing and -opening enzymes.	the enterobacterium klebsiella oxytoca uses a variety of inorganic and organic nitrogen sources, including purines, nitrogen-rich compounds that are widespread in the biosphere. we have identified a 23-gene cluster that encodes the enzymes for utilizing purines as the sole nitrogen source. growth and complementation tests with insertion mutants, combined with sequence comparisons, reveal functions for the products of these genes. here, we report our characterization of 12 genes, one encoding gua ...	2009	19060149
purine utilization by klebsiella oxytoca m5al: genes for ring-oxidizing and -opening enzymes.	the enterobacterium klebsiella oxytoca uses a variety of inorganic and organic nitrogen sources, including purines, nitrogen-rich compounds that are widespread in the biosphere. we have identified a 23-gene cluster that encodes the enzymes for utilizing purines as the sole nitrogen source. growth and complementation tests with insertion mutants, combined with sequence comparisons, reveal functions for the products of these genes. here, we report our characterization of 12 genes, one encoding gua ...	2009	19060149
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
essential role for the baca protein in the uptake of a truncated eukaryotic peptide in sinorhizobium meliloti.	the inner membrane baca protein is essential for the establishment of chronic intracellular infections by sinorhizobium meliloti and brucella abortus within plant and mammalian hosts, respectively. in their free-living state, s. meliloti and b. abortus mutants lacking baca have reductions in their outer membrane lipid a very-long-chain fatty acid (vlcfa) contents and exhibit low-level resistance to the glycopeptide bleomycin in comparison to their respective parent strains. in this paper we inve ...	2009	19074376
essential role for the baca protein in the uptake of a truncated eukaryotic peptide in sinorhizobium meliloti.	the inner membrane baca protein is essential for the establishment of chronic intracellular infections by sinorhizobium meliloti and brucella abortus within plant and mammalian hosts, respectively. in their free-living state, s. meliloti and b. abortus mutants lacking baca have reductions in their outer membrane lipid a very-long-chain fatty acid (vlcfa) contents and exhibit low-level resistance to the glycopeptide bleomycin in comparison to their respective parent strains. in this paper we inve ...	2009	19074376
engineered biosynthesis of bacterial aromatic polyketides in escherichia coli.	bacterial aromatic polyketides are important therapeutic compounds including front line antibiotics and anticancer drugs. it is one of the last remaining major classes of natural products of which the biosynthesis has not been reconstituted in the genetically superior host escherichia coli. here, we demonstrate the engineered biosynthesis of bacterial aromatic polyketides in e. coli by using a dissected and reassembled fungal polyketide synthase (pks). the minimal pks of the megasynthase pks4 fr ...	2008	19075227
regulation by transcription factors in bacteria: beyond description.	transcription is an essential step in gene expression and its understanding has been one of the major interests in molecular and cellular biology. by precisely tuning gene expression, transcriptional regulation determines the molecular machinery for developmental plasticity, homeostasis and adaptation. in this review, we transmit the main ideas or concepts behind regulation by transcription factors and give just enough examples to sustain these main ideas, thus avoiding a classical ennumeration ...	2008	19076632
regulation by transcription factors in bacteria: beyond description.	transcription is an essential step in gene expression and its understanding has been one of the major interests in molecular and cellular biology. by precisely tuning gene expression, transcriptional regulation determines the molecular machinery for developmental plasticity, homeostasis and adaptation. in this review, we transmit the main ideas or concepts behind regulation by transcription factors and give just enough examples to sustain these main ideas, thus avoiding a classical ennumeration ...	2008	19076632
rhizobium leguminosarum bv. trifolii rosr gene expression is regulated by catabolic repression.	rhizobium leguminosarum bv. trifolii rosr gene encodes a transcriptional regulator involved in the positive regulation of exopolysaccharide synthesis. transcription of rosr is directed by two promoters, distal p1 and proximal p2, of different strengths. we demonstrated that rosr p1 functions as the main promoter and, besides the -35 and -10 sequences, it contains two other important regulatory elements, an extended -10 motif and an upstream promoter element, that play a significant role in the i ...	2009	19077060
pleiotropic effects of a rel mutation on stress survival of rhizobium etli cnpaf512.	the rel gene of rhizobium etli (relret), the nodulating endosymbiont of the common bean plant, determines the cellular level of the alarmone (p)ppgpp and was previously shown to affect free-living growth and symbiosis. here, we demonstrate its role in cellular adaptation and survival in response to various stresses.	2008	19077212
an orphan luxr homolog of sinorhizobium meliloti affects stress adaptation and competition for nodulation.	the sin/expr quorum-sensing system of sinorhizobium meliloti plays an important role in the symbiotic association with its host plant, medicago sativa. the luxr-type response regulators of the sin system include the synthase (sini)-associated sinr and the orphan regulator expr. interestingly, the s. meliloti rm1021 genome codes for four additional putative orphan luxr homologs whose regulatory roles remain to be identified. these response regulators contain the characteristic domains of the luxr ...	2009	19088317
an orphan luxr homolog of sinorhizobium meliloti affects stress adaptation and competition for nodulation.	the sin/expr quorum-sensing system of sinorhizobium meliloti plays an important role in the symbiotic association with its host plant, medicago sativa. the luxr-type response regulators of the sin system include the synthase (sini)-associated sinr and the orphan regulator expr. interestingly, the s. meliloti rm1021 genome codes for four additional putative orphan luxr homologs whose regulatory roles remain to be identified. these response regulators contain the characteristic domains of the luxr ...	2009	19088317
identification of a novel regulator for the escherichia coli fit iron transport system.	the escherichia coli fit iron transport system consists of 6 genes, fita, b, c, d, e and fitr. based on in silico analysis, fita-e composes a typical bacterial iron transporter, while fitr was deduced to be a regulator. in this paper the regulation of fit expression by fitr was studied using a quantitative rt-pcr technique and a lacz reporter assay. it was found that fit expression was repressed when fitr was over-expressed and de-repressed when fitr was knocked out by mutation. when the mutatio ...	2008	19088918
heme-dependent metalloregulation by the iron response regulator (irr) protein in rhizobium and other alpha-proteobacteria.	perception and response to nutritional iron by bacteria is essential for viability, and for the ability to adapt to the environment. the iron response regulator (irr) is part of a novel regulatory scheme employed by rhizobium and other alpha-proteobacteria to control iron-dependent gene expression. bradyrhizobium japonicum senses iron through the status of heme biosynthesis to regulate gene expression, thus it responds to an iron-dependent process rather than to iron directly. irr mediates this ...	2009	19093075
heme-dependent metalloregulation by the iron response regulator (irr) protein in rhizobium and other alpha-proteobacteria.	perception and response to nutritional iron by bacteria is essential for viability, and for the ability to adapt to the environment. the iron response regulator (irr) is part of a novel regulatory scheme employed by rhizobium and other alpha-proteobacteria to control iron-dependent gene expression. bradyrhizobium japonicum senses iron through the status of heme biosynthesis to regulate gene expression, thus it responds to an iron-dependent process rather than to iron directly. irr mediates this ...	2009	19093075
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
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
oxygene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes.	oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ros, rns) and cellular antioxidant defence. to defend themselves against ros/rns, bacteria possess a subsystem of detoxification enzymes, which are classified with regard to their substrates. to identify such enzymes in prokaryotic genomes, different approaches based on similarity, enzyme profiles or patterns exist. unfortunately, several prob ...	2008	19117520
rhizobia with different symbiotic efficiencies nodulate acaciella angustissima in mexico, including sinorhizobium chiapanecum sp. nov. which has common symbiotic genes with sinorhizobium mexicanum.	bacteria from nodules of the legume acaciella angustissima native to the south of mexico were characterized genetically and their nodulation and competitiveness were evaluated. phylogenetic studies derived from rpob gene sequences indicated that a. angustissima is nodulated by sinorhizobium mexicanum, rhizobium tropici, mesorhizobium plurifarium and agrobacterium tumefaciens and by bacteria related to sinorhizobium americanum, sinorhizobium terangae, rhizobium etli and rhizobium gallicum. a new ...	2009	19120461
rhizobia with different symbiotic efficiencies nodulate acaciella angustissima in mexico, including sinorhizobium chiapanecum sp. nov. which has common symbiotic genes with sinorhizobium mexicanum.	bacteria from nodules of the legume acaciella angustissima native to the south of mexico were characterized genetically and their nodulation and competitiveness were evaluated. phylogenetic studies derived from rpob gene sequences indicated that a. angustissima is nodulated by sinorhizobium mexicanum, rhizobium tropici, mesorhizobium plurifarium and agrobacterium tumefaciens and by bacteria related to sinorhizobium americanum, sinorhizobium terangae, rhizobium etli and rhizobium gallicum. a new ...	2009	19120461
architectural phenotypes in the transparent testa mutants of arabidopsis thaliana.	flavonoids are low molecular weight secondary plant metabolites with a myriad of functions. as flavonoids affect auxin transport (an important growth-controlling hormone) and are biologically active in eukaryotes, flavonoid mutants were expected to have undescribed architectural phenotypes. the arabidopsis thaliana transparent testa (tt) mutants are compromised in the enzymatic steps or transcriptional regulators affecting flavonoid synthesis. tt mutant seedlings were grown on hard-slanted agar ...	2009	19129166
remodelling of vipa/vipb tubules by clpv-mediated threading is crucial for type vi protein secretion.	the recently identified type vi secretion systems (t6ss) have a crucial function in the virulence of various proteobacteria, including the human pathogen vibrio cholerae. t6ss are encoded by a conserved gene cluster comprising approximately 15 open reading frames, mediating the appearance of hcp and vgrg proteins in cell culture supernatants. here, we analysed the function of the v. cholerae t6ss member clpv, a specialized aaa+ protein. clpv is crucial for a functional t6ss and interacts through ...	2009	19131969
complete genome sequence of the aerobic co-oxidizing thermophile thermomicrobium roseum.	in order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an "assembling the tree of life" project, we determined the genome sequence of thermomicrobium roseum dsm 5159. t. roseum dsm 5159 is a red-pigmented, rod-shaped, gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. its genome is composed o ...	2009	19148287
identification of undecaprenyl phosphate-beta-d-galactosamine in francisella novicida and its function in lipid a modification.	francisella tularensis is a highly infectious pathogen that causes tularemia. francisella lipid a contains an unusual galactosamine (galn) unit, attached to its 1-phosphate moiety. two genes, flmf2 and flmk, are required for the addition of galn to francisella lipid a, but the relevant enzymes and the galn donor substrate have not been characterized. we now report the purification and identification of a novel minor lipid from francisella novicida that functions as the galn donor. on the basis o ...	2009	19166327
roles of agrobacterium tumefaciens rira in iron regulation, oxidative stress response, and virulence.	the analysis of genetics and physiological functions of agrobacterium tumefaciens rira (rhizobial iron regulator) has shown that it is a transcription regulator and a repressor of iron uptake systems. the rira mutant strain (ntlrira) overproduced siderophores and exhibited a highly constitutive expression of genes involved in iron uptake (fhua, irp6a, and fbpa) compared to that of the wild-type strain (ntl4). the deregulation in the iron control of iron uptake in ntlrira led to iron overload in ...	2009	19168612
changes in barotolerance, thermotolerance, and cellular morphology throughout the life cycle of listeria monocytogenes.	changes in barotolerance, thermotolerance, and cellular morphology throughout the life cycle of listeria monocytogenes were investigated. for part 1 of this analysis, l. monocytogenes atcc 19115 was grown to log, stationary, death, and long-term-survival phases at 35 degrees c in tryptic soy broth with yeast extract (tsbye). cells were diluted in whole milk that had been subjected to ultrahigh temperatures (uht whole milk) and then high-pressure processed (hpp) at 400 mpa for 180 s or thermally ...	2009	19168646
the metal-dependent regulators fura and furb from mycobacterium tuberculosis.	the ferric uptake regulators (fur) form a large family of bacterial metal-activated dna-binding proteins that control a diverse set of genes at the transcriptional level. mycobacterium tuberculosis, the causative agent of tuberculosis, expresses two members of the fur family, designated fura and furb. although both belong to the same family, they share only approximately 25% sequence identity and as a consequence, they differ significantly in some of their key biological functions. fura appears ...	2008	19169435
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
high abundance of virulence gene homologues in marine bacteria.	marine bacteria can cause harm to single-celled and multicellular eukaryotes. however, relatively little is known about the underlying genetic basis for marine bacterial interactions with higher organisms. we examined whole-genome sequences from a large number of marine bacteria for the prevalence of homologues to virulence genes and pathogenicity islands known from bacteria that are pathogenic to terrestrial animals and plants. as many as 60 out of 119 genomes of marine bacteria, with no known ...	2009	19207573
comparative genomic analyses of nickel, cobalt and vitamin b12 utilization.	nickel (ni) and cobalt (co) are trace elements required for a variety of biological processes. ni is directly coordinated by proteins, whereas co is mainly used as a component of vitamin b12. although a number of ni and co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited.	2009	19208259
the time course of the transcriptomic response of sinorhizobium meliloti 1021 following a shift to acidic ph.	the symbiotic soil bacterium sinorhizobium meliloti often has to face low ph in its natural habitats. to identify genes responding to ph stress a global transcriptional analysis of s. meliloti strain 1021 following a ph shift from ph 7.0 to ph 5.75 was carried out. in detail, oligo-based whole genome microarrays were used in a time course experiment. the monitoring period covered a time span of about one hour after the ph shift. the obtained microarray data was filtered and grouped by k-means cl ...	2009	19216801
two small c-type cytochromes affect virulence gene expression in bacillus anthracis.	regulated expression of the genes for anthrax toxin proteins is essential for the virulence of the pathogenic bacterium bacillus anthracis. induction of toxin gene expression depends on several factors, including temperature, bicarbonate levels, and metabolic state of the cell. to identify factors that regulate toxin expression, transposon mutagenesis was performed under non-inducing conditions and mutants were isolated that untimely expressed high levels of toxin. a number of these mutations cl ...	2009	19222757
distinct and essential morphogenic functions for wall- and lipo-teichoic acids in bacillus subtilis.	teichoic acids (tas) are anionic polymers that constitute a major component of the cell wall in most gram-positive bacteria. despite decades of study, their function has remained unclear. tas are covalently linked either to the cell wall peptidoglycan (wall ta (wta)) or to the membrane (lipo-ta (lta)). we have characterized the key enzyme of lta synthesis in bacillus subtilis, lta synthase (ltas). we show that lta is needed for divalent cation homoeostasis and that its absence has severe effects ...	2009	19229300
[effects of natural and hybrid lectins on the legume-rhizobium interactions].	the effects of hybrid lectins--full-sized pea pisum sativum lectin (psl) with the carbohydrate-binding region of white melilot melilotus albus lectin or wild licorice astragalus glycyphyllos lectin substituted for the corresponding psl region (psl/mal and psl/agl, correspondingly)--on the legume-rhizobium symbiosis were studied. the treatment of the rhizobium leguminosarum bv. viciae in the alfalfa (medicago sativa) rhizosphere with psl induced formation of uninfected pseudonodules on its roots, ...	2009	19235514
uridine-based inhibitors as new leads for antibiotics targeting escherichia coli lpxc.	the udp-3-o-(r-3-hydroxyacyl)-n-acetylglucosamine deacetylase lpxc catalyzes the committed reaction of lipid a (endotoxin) biosynthesis in gram-negative bacteria and is a validated antibiotic target. although several previously described compounds bind to the unique acyl chain binding passage of lpxc with high affinity, strategies to target the enzyme's udp-binding site have not been reported. here the identification of a series of uridine-based lpxc inhibitors is presented. the most potent exam ...	2009	19256534
nematode indicators of organic enrichment.	the organisms of the soil food web, dependent on resources from plants or on amendment from other sources, respond characteristically to enrichment of their environment by organic matter. primary consumers of the incoming substrate, including bacteria, fungi, plant-feeding nematodes, annelids, and some microarthropods, are entry-level indicators of enrichment. however, the quantification of abundance and biomass of this diverse group, as an indicator of resource status, requires a plethora of ex ...	2006	19259424
the cin and rai quorum-sensing regulatory systems in rhizobium leguminosarum are coordinated by expr and cins, a small regulatory protein coexpressed with cini.	to understand how the rhizobium leguminosarum raii-rair quorum-sensing system is regulated, we identified mutants with decreased levels of raii-made n-acyl homoserine lactones (ahls). a luxr-type regulator, expr, is required for rair expression, and rair is required to induce raii. since rair (and raii) expression is also reduced in cini and cinr quorum-sensing mutants, we thought cini-made ahls may activate expr to induce rair. however, added cini-made ahls did not induce rair expression in a c ...	2009	19270098
structural similarity of tailed phages and pathogenic bacterial secretion systems.		2009	19276114
protein secretion systems in bacterial-host associations, and their description in the gene ontology.	protein secretion plays a central role in modulating the interactions of bacteria with their environments. this is particularly the case when symbiotic bacteria (whether pathogenic, commensal or mutualistic) are interacting with larger host organisms. in the case of gram-negative bacteria, secretion requires translocation across the outer as well as the inner membrane, and a diversity of molecular machines have been elaborated for this purpose. a number of secreted proteins are destined to enter ...	2009	19278550
growmatch: an automated method for reconciling in silico/in vivo growth predictions.	genome-scale metabolic reconstructions are typically validated by comparing in silico growth predictions across different mutants utilizing different carbon sources with in vivo growth data. this comparison results in two types of model-prediction inconsistencies; either the model predicts growth when no growth is observed in the experiment (gng inconsistencies) or the model predicts no growth when the experiment reveals growth (ngg inconsistencies). here we propose an optimization-based framewo ...	2009	19282964
diversity and transcription of proteases involved in the maturation of hydrogenases in nostoc punctiforme atcc 29133 and nostoc sp. strain pcc 7120.	the last step in the maturation process of the large subunit of [nife]-hydrogenases is a proteolytic cleavage of the c-terminal by a hydrogenase specific protease. contrary to other accessory proteins these hydrogenase proteases are believed to be specific whereby one type of hydrogenases specific protease only cleaves one type of hydrogenase. in cyanobacteria this is achieved by the gene product of either hupw or hoxw, specific for the uptake or the bidirectional hydrogenase respectively. the f ...	2009	19284580
characterization of the hupsl promoter activity in nostoc punctiforme atcc 29133.	in cyanobacteria three enzymes are directly involved in the hydrogen metabolism; a nitrogenase that produces molecular hydrogen, h2, as a by-product of nitrogen fixation, an uptake hydrogenase that recaptures h2 and oxidize it, and a bidirectional hydrogenase that can both oxidize and produce h2.nostoc punctiforme atcc 29133 is a filamentous dinitrogen fixing cyanobacterium containing a nitrogenase and an uptake hydrogenase but no bidirectional hydrogenase. generally, little is known about the t ...	2009	19284581
dissecting the bacterial type vi secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?	the availability of hundreds of bacterial genomes allowed a comparative genomic study of the type vi secretion system (t6ss), recently discovered as being involved in pathogenesis. by combining comparative and phylogenetic approaches using more than 500 prokaryotic genomes, we characterized the global t6ss genetic structure in terms of conservation, evolution and genomic organization.	2009	19284603
the mnth gene encodes the major mn(2+) transporter in bradyrhizobium japonicum and is regulated by manganese via the fur protein.	the bacterial nramp family protein mnth is a divalent metal transporter, but mnth mutants have little or no phenotype in organisms where it has been studied. here, we identify the mnth homologue of bradyrhizobium japonicum, and demonstrate that it is essential for mn(2+) transport and for maintenance of cellular manganese homeostasis. transport activity was induced under manganese deficiency, and fe(2+) did not compete with (54)mn(2+) for uptake by cells. the steady-state level of mnth mrna was ...	2009	19298371
indole acts as an extracellular cue regulating gene expression in vibrio cholerae.	indole has been proposed to act as an extracellular signal molecule influencing biofilm formation in a range of bacteria. for this study, the role of indole in vibrio cholerae biofilm formation was examined. it was shown that indole activates genes involved in vibrio polysaccharide (vps) production, which is essential for v. cholerae biofilm formation. in addition to activating these genes, it was determined using microarrays that indole influences the expression of many other genes, including t ...	2009	19329638
structural basis for the specialization of nur, a nickel-specific fur homolog, in metal sensing and dna recognition.	nur, a member of the fur family, is a nickel-responsive transcription factor that controls nickel homeostasis and anti-oxidative response in streptomyces coelicolor. here we report the 2.4-a resolution crystal structure of nur. it contains a unique nickel-specific metal site in addition to a nonspecific common metal site. the identification of the 6-5-6 motif of the nur recognition box and a nur/dna complex model reveals that nur mainly interacts with terminal bases of the palindrome on complex ...	2009	19336416
sequence-specific binding to a subset of iscr-regulated promoters does not require iscr fe-s cluster ligation.	iscr is an fe-s protein that functions as a transcriptional regulator of fe-s biogenesis and other fe-s protein-encoding genes in escherichia coli. in this study, we investigated the requirement for the ligation of the [2fe-2s] cluster of iscr to regulate a subset of iscr target promoters (p(hyaa), p(ydiu), p(napf), and p(hybo)) and defined the requirements for sequence-specific binding to the iscr target site in the hyaa promoter region. in contrast to previous results with the iscr promoter, w ...	2009	19361432
identification and characterization of hemolysin-like proteins similar to rtx toxin in pasteurella pneumotropica.	pasteurella pneumotropica is an opportunistic pathogen that causes lethal pneumonia in immunodeficient rodents. the virulence factors of this bacterium remain unknown. in this study, we identified the genes encoding two rtx toxins, designated as pnxi and pnxii, from the genomic dna of p. pneumotropica atcc 35149 and characterized with respect to hemolysis. the pnxi operon was organized according to the manner in which the genes encoded the structural rtx toxin (pnxia), the type i secretion syste ...	2009	19363112
biosynthesis of polyketide synthase extender units.	this review covers the biosynthesis of extender units that are utilized for the assembly of polyketides by polyketide synthases. the metabolic origins of each of the currently known polyketide synthase extender units are covered.	2009	19374124
transcriptomic analysis of rhizobium leguminosarum biovar viciae in symbiosis with host plants pisum sativum and vicia cracca.	rhizobium leguminosarum bv. viciae forms nitrogen-fixing nodules on several legumes, including pea (pisum sativum) and vetch (vicia cracca), and has been widely used as a model to study nodule biochemistry. to understand the complex biochemical and developmental changes undergone by r. leguminosarum bv. viciae during bacteroid development, microarray experiments were first performed with cultured bacteria grown on a variety of carbon substrates (glucose, pyruvate, succinate, inositol, acetate, a ...	2009	19376875
strategies for acquiring the phospholipid metabolite inositol in pathogenic bacteria, fungi and protozoa: making it and taking it.	myo-inositol (inositol) is an essential nutrient that is used for building phosphatidylinositol and its derivatives in eukaryotes and even in some eubacteria such as the mycobacteria. as a consequence, fungal, protozoan and mycobacterial pathogens must be able to acquire inositol in order to proliferate and cause infection in their hosts. there are two primary mechanisms for acquiring inositol. one is to synthesize inositol from glucose 6-phosphate using two sequentially acting enzymes: inositol ...	2009	19383710
an icmf family protein, implm, is an integral inner membrane protein interacting with impkl, and its walker a motif is required for type vi secretion system-mediated hcp secretion in agrobacterium tumefaciens.	an intracellular multiplication f (icmf) family protein is a conserved component of a newly identified type vi secretion system (t6ss) encoded in many animal and plant-associated proteobacteria. we have previously identified impl(m), an icmf family protein that is required for the secretion of the t6ss substrate hemolysin-coregulated protein (hcp) from the plant-pathogenic bacterium agrobacterium tumefaciens. in this study, we characterized the topology of impl(m) and the importance of its nucle ...	2009	19395482
proteomic analysis of the response of the plant growth-promoting bacterium pseudomonas putida uw4 to nickel stress.	plant growth-promoting bacteria can alleviate the inhibitory effects of various heavy metals on plant growth, via decreasing levels of stress-induced ethylene. however, little has been done to detect any mechanisms specific for heavy metal resistance of this kind of bacteria. here, we investigate the response of the wild-type plant growth-promoting bacterium pseudomonas putida uw4 to nickel stress using proteomic approaches. the mutant strain p. putida uw4/acds-, lacking a functional 1-aminocycl ...	2009	19422705
the sinorhizobium meliloti lpxxl and acpxl proteins play important roles in bacteroid development within alfalfa.	free-living sinorhizobium meliloti lpxxl and acpxl mutants lack lipid a very-long-chain fatty acids (vlcfas) and have reduced competitiveness in alfalfa. we demonstrate that lpxxl and acpxl play important but distinct roles in bacteroid development and that lpxxl is essential for the modification of s. meliloti bacteroid lipid a with vlcfas.	2009	19429615
genome degradation in brucella ovis corresponds with narrowing of its host range and tissue tropism.	brucella ovis is a veterinary pathogen associated with epididymitis in sheep. despite its genetic similarity to the zoonotic pathogens b. abortus, b. melitensis and b. suis, b. ovis does not cause zoonotic disease. genomic analysis of the type strain atcc25840 revealed a high percentage of pseudogenes and increased numbers of transposable elements compared to the zoonotic brucella species, suggesting that genome degradation has occurred concomitant with narrowing of the host range of b. ovis. th ...	2009	19436743
rnai phenotypes and the localization of a protein::gus fusion imply a role for medicago truncatula pin genes in nodulation.	the symbiosis between legumes and rhizobia results in the development of a new plant organ, the nodule. a role for polar auxin transport in nodule development in medicago truncatula has been demonstrated using molecular genetic tools. the expression of a dr5::gus auxin-responsive promoter in uninoculated m. truncatula roots mirrored that reported in arabidopsis, and expression of the construct in nodulating roots confirmed results reported in white clover. the localization of a root-specific pin ...	2006	19444321