Publications

the diversity of rhizobia nodulating beans in northwest argentina as a source of more efficient inoculant strains.	the common bean (phaseolus vulgaris l.) is cultivated widely in central and south america and particularly in the northwest of argentina. in order to describe the diversity of the common bean nodulating rhizobial population from the bean producing area in northwest argentina (nwa), a collection of about 400 isolates of common beans recovered from nodules and soil samples from nwa were characterized by using nifh-pcr, analysis of genes coding for 16s rrna and nodc, and rep-fingerprinting, respect ...	2001	11566389
improved soybean root association of n-starved bradyrhizobium japonicum.	in this study, we addressed the effects of n limitation in bradyrhizobium japonicum for its association with soybean roots. the wild-type strain lp 3001 grew for six generations with a growth rate of 1.2 day(-1) in a minimal medium with 28 mm mannitol as the carbon source and with the n source [(nh(4))(2)so(4)] limited to only 20 microm. under these conditions, the glutamine synthetase (gs) activity was five to six times higher than in similar cultures grown with 1 or 0.1 mm (nh(4))(2)so(4). the ...	2001	11717284
site-specific integrative elements of rhizobiophage 16-3 can integrate into proline trna (cgg) genes in different bacterial genera.	the integrase protein of the rhizobium meliloti 41 phage 16-3 has been classified as a member of the int family of tyrosine recombinases. the site-specific recombination system of the phage belongs to the group in which the target site of integration (attb) is within a trna gene. since trna genes are conserved, we expected that the target sequence of the site-specific recombination system of the 16-3 phage could occur in other species and integration could take place if the required putative hos ...	2002	11741858
characterization of a family of arabidopsis genes related to xyloglucan fucosyltransferase1.	to understand primary cell wall assembly in arabidopsis, we have focused on identifying and characterizing enzymes involved in xyloglucan biosynthesis. nine genes (atfut2-10) were identified that share between 47% and 62% amino acid similarity with the xyloglucan-specific fucosyltransferase atfut1. reverse transcriptase-pcr analysis indicates that all these genes are expressed. bioinformatic analysis predicts that these family members are fucosyltransferases, and we first hypothesized that some ...	2001	11743104
[diversity of sinorhizobium fredii strains].	rhizobial strains were isolated from soils growing with soybean cultivar heilong 33 and willimas. fifty sinorhizobium fredii strains were chosen, and their biological characteristics including growth velocity, acid-alkali endurance, resistance of intrinsic antibiotics, utilization of carbon and nitrogen sources, absorption of congo red, ability of melanin production, and plasmid profiles were comparatively researched. the dendrogram was described using the method of cluster analysis, and the bio ...	2001	11758392
[effect of ph on nodulation of soybean rhizobia from weifang and huayuankou soils].	the effect of ph on the nodulation of sinorhizobium fredii and bradyrhizobium japonicum was examined by analyzing the indigent soybean rhizobia, predominant indigent rhizobia, and specific rhizobia, respectively. the results showed that very acid and very alkaline environment could retard the nodulation and inhibit the growth of the rhizobia. sinorhizohium fredii could endure environment more strongly than bradyrhizobium japonicum, and had a high competitive nodulation capacity. bradyhizobium ja ...	2001	11758403
characterization of a sinorhizobium isolate and its extracellular polymer implicated in pollutant transport in soil.	a bacterium isolated from soil (designated 9702-m4) synthesizes an extracellular polymer that facilitates the transport of such hydrophobic pollutants as polynuclear aromatic hydrocarbons, as well as the toxic metals lead and cadmium in soil. biolog analysis, growth rate determinations, and percent g+c content identify 9702-m4 as a strain of sinorhizobium meliloti. sequence analysis of a 16s rdna fragment gives 9702-m4 a phylogenetic designation most closely related to sinorhizobium fredii. the ...	2002	11772656
nolx of sinorhizobium fredii usda257, a type iii-secreted protein involved in host range determination, iis localized in the infection threads of cowpea (vigna unguiculata [l.] walp) and soybean (glycine max [l.] merr.) nodules.	sinorhizobium fredii usda257 forms nitrogen-fixing nodules on soybean (glycine max [l.] merr.) in a cultivar-specific manner. this strain forms nodules on primitive soybean cultivars but fails to nodulate agronomically improved north american cultivars. soybean cultivar specificity is regulated by the nolxwbtuv locus, which encodes part of a type iii secretion system (ttss). nolx, a soybean cultivar specificity protein, is secreted by ttss and shows homology to hrpf of the plant pathogen xanthom ...	2002	11790754
identification of two myo-inositol transporter genes of bacillus subtilis.	among hundreds of mutants constructed systematically by the japanese groups participating in the functional analysis of the bacillus subtilis genome project, we found that a mutant with inactivation of iolt (ydjk) exhibited a growth defect on myo-inositol as the sole carbon source. the putative product of iolt exhibits significant similarity with many bacterial sugar transporters in the databases. in b. subtilis, the iolabcdefghij and iolrs operons are known to be involved in inositol utilizatio ...	2002	11807058
sinorhizobium fredii hh103 has a truncated nolo gene due to a -1 frameshift mutation that is conserved among other geographically distant s. fredii strains.	strain svq121 is a mutant derivative of sinorhizobium fredii hh103 carrying a transposon tn5-lacz insertion into the nolo-coding region. sequence analysis of the wild-type gene revealed that it is homologous to that of rhizobium sp. ngr234, which is involved in the 3 (or 4)-o-carbamoylation of the nonreducing terminus of nod factors. downstream of nolo, as in rhizobium sp. ngr234, the noei gene responsible for methylation of the fucose moiety of nod factors was found. svq121 nod factors showed l ...	2002	11878319
[a study of the effects on the symbiotic nitrogen fixation of sinorhizobium fredii with the introduction of dctabd and nifa genes].	a recombinant plasmid phn307 containing c4-dicarboxylic acid transport genes (dctabd) from sinorhizobium meliloti, nifa genes from klebsiella pneumoniae and reporter genes luxab from pdb30 was constructed by using ptr102 as the vector. the phn307 was then introduced into the s. fredii hn01, yc4 and gr3 by tri-parental mating, and the stability of phn307 in the transconjugants under free-living and symbiotic condition was also investigated. the results of plant pot experiment indicated that the i ...	2002	11902003
identification of isolates from soybean nodules in xinjiang region as sinorhizobium xinjiangense and genetic differentiation of s. xinjiangense from sinorhizobium fredii.	eight fast-growing rhizobial isolates from xinjiang soils were identified as sinorhizobium xinjiangense by analyses of 16s rrna gene sequences, sds-page of proteins, intergenic spacer sequences and dna-dna hybridization. based on all of the results, these isolates and the reference strains for s. xinjiangense were a distinct genomic species, although the 16s rrna genes were closely related to that of sinorhizobium fredii.	2002	11931157
functional analysis of hrpf, a putative type iii translocon protein from xanthomonas campestris pv. vesicatoria.	type iii secretion systems (ttsss) are specialized protein transport systems in gram-negative bacteria which target effector proteins into the host cell. the ttss of the plant pathogen xanthomonas campestris pv. vesicatoria, encoded by the hrp (hypersensitive reaction and pathogenicity) gene cluster, is essential for the interaction with the plant. one of the secreted proteins is hrpf, which is required for pathogenicity but dispensable for type iii secretion of effector proteins in vitro, sugge ...	2002	11948151
conservation of plasmid-encoded traits among bean-nodulating rhizobium species.	rhizobium etli type strain cfn42 contains six plasmids. we analyzed the distribution of genetic markers from some of these plasmids in bean-nodulating strains belonging to different species (rhizobium etli, rhizobium gallicum, rhizobium giardinii, rhizobium leguminosarum, and sinorhizobium fredii). our results indicate that independent of geographic origin, r. etli strains usually share not only the psym plasmid but also other plasmids containing symbiosis-related genes, with a similar organizat ...	2002	11976134
key role of bacterial nh(4)(+) metabolism in rhizobium-plant symbiosis.	symbiotic nitrogen fixation is carried out in specialized organs, the nodules, whose formation is induced on leguminous host plants by bacteria belonging to the family rhizobiaceae: nodule development is a complex multistep process, which requires continued interaction between the two partners and thus the exchange of different signals and metabolites. nh(4)(+) is not only the primary product but also the main regulator of the symbiosis: either as ammonium and after conversion into organic compo ...	2002	12040124
sinorhizobium fredii isolates can be specifically identified by a 260 bp fragment from the nolxwbtuv locus.	a pair of primers homologous to the nolxwbtuv locus generated a 260 bp fragment by pcr only in the presence of sinorhizobium fredii template dna of different quality. this resulted in a fast and accurate method for the identification of s. fredii either from pure dna, whole bacterial cells or nodule extracts. by means of two pcr fragments, one specific for s. fredii (260-bp) and the other specific for bradyrhizobium japonicum (rsalpha), we found that s. fredii strain smh12 and b. japonicum e109 ...	2002	12111156
the diversity of phaseolus-nodulating rhizobial populations is altered by liming of acid soils planted with phaseolus vulgaris l. in brazil.	pcr-mediated restriction fragment length polymorphism (rflp) analysis of the 16s-23s rrna internally transcribed spacer (its) region and the 16s rrna gene indicated that the rhizobial populations isolated from common bean (phaseolus vulgaris l.) nodules in the unlimed soil from a series of five lime rates applied 6 years previously to plots of an acidic oxisol had less diversity than those from plots with higher rates of liming. isolates affiliated with rhizobium tropici iib and rhizobium legumi ...	2002	12147504
[study on the improvement of plasmid stability in soybean rhizobia].	by using luxab as the report genes, 3.2 kb parcba/de gene fragment from ptr102 was inserted into plafr3 which contained a 3.7 kb enhancing fragment and deleted its cos site. recombinant plasmids phn155 and phn156 were obtained. contrasted plasmids phn157 and phn158 which contained cos site were also constructed. these four plasmids were transferred into sinorhizobium fredii hn01 by tri-parental mating, and plasmid phn155 and phn158 were introduced into bradyrhizobium japonicum ta11 by two-parent ...	2000	12548995
[a sinorhizobium fredll strain that effectively nodulate medicago sativa].	sinorhizobium fredii 042bs was isolated from root nodules of alfalfa (medicago sativa) from xinjiang region. nodulation experiments showed that both soybean and alfalfa were nodulated by 042bs effectively. the 16s rdna pcr-rflp analysis was carried out by four restriction endonucleases, and the restriction maps of strain 042bs were identical with those of s. fredii usda205. the dna g + c mol% of strain 042bs was 60.0. the dna homology between 042bs and s. fredii usda205 and usda191 were 84.9% an ...	2001	12549015
[incompatibility among indigenous plasmids of sinorhizobium fredii strains and its application for plasmid curing].	the indigenous plasmids of s. frediii hn01 and wwg18 were labeled with tn5-mobsacb. those plasmids were cured on ty medium containing 10% sucrose to identify its function. the psymhn01b of hn01 was transferred into wwg18sr and c361sr. the results of plasmid detection, curing and pot plant experiment revealed that the incompatibility was existed between psym-hn01b and symbiotic plasmid of wwg18sr or the third plasmid of c361sr. but it was compatible with the nonsymbiotic plasmid of wwg18sr and sy ...	2001	12552908
[construction of a gfp broad-host-range promoter-probe vector and its application].	the 0.9 kb dna fragment was obtained by pcr and using a pair of special designed primers from the green fluorescent protein gene(gfp). it was then cloned into an expression vector pet-11c and named as phn115. a promoferless gfp vector with sd fragment was obtained from phn115 and subcloned into sk(+), pij 2925 and finally into ptr102. a broad-hast-range and visible promoter-probe vector, phn127 was constructed and used successfully for the identification of constitutive and inducible promoters f ...	1999	12555521
[the cloning and functional analysis of sinorhizobium fredii 042bs regulatory modulation genes].	the total dna of sinorhizobium fredii 042bs was digested by ecori for southern blotting with probes of nodd1 and nodd2 from s. fredii usda257. the 3 kb positive band hybrided with nodd1 probe and 6 kb positive band with nodd2 probe were found, respectively. partial gene library were constructed using puc18 as vector, and the clones with the nodd1 and nodd2 genes were obtained. the sequence of nodd1 and nodd2 of 042b showed that they are highly homologous with nodd1 and nodd2 of s. fredii. the fr ...	2002	12557345
soils of the chinese hubei province show a very high diversity of sinorhizobium fredii strains.	biodiversity studies of native soybean-nodulating rhizobia in soils from the chinese hubei province (honghu county; ph 8, alluvial soil) have been carried out. inoculation of an american (williams) and an asiatic (peking) soybean cultivar with eleven soil samples led to the isolation of 167 rhizobia strains. the ratio (%) of slow-/fast-growing isolates was different depending on the trap plant used. all isolates were able to nodulate both cultivars, although the n2-fixation efficiency (measured ...	2002	12583720
in silico pattern-based analysis of the human cytomegalovirus genome.	more than 200 open reading frames (orfs) from the human cytomegalovirus genome have been reported as potentially coding for proteins. we have used two pattern-based in silico approaches to analyze this set of putative viral genes. with the help of an objective annotation method that is based on the bio-dictionary, a comprehensive collection of amino acid patterns that describes the currently known natural sequence space of proteins, we have reannotated all of the previously reported putative gen ...	2003	12634390
discordant phylogenies within the rrn loci of rhizobia.	it is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of alpha-proteobacteria by sequencing analysis of three loci within their rrn operons. tree topologies generated with 16s rrna gene sequences were ...	2003	12730157
characterization of the xanthomonas axonopodis pv. glycines hrp pathogenicity island.	we sequenced an approximately 29-kb region from xanthomonas axonopodis pv. glycines that contained the hrp type iii secretion system, and we characterized the genes in this region by tn3-gus mutagenesis and gene expression analyses. from the region, hrp (hypersensitive response and pathogenicity) and hrc (hrp and conserved) genes, which encode type iii secretion systems, and hpa (hrp-associated) genes were identified. the characteristics of the region, such as the presence of many virulence gene ...	2003	12730176
citrate synthase mutants of sinorhizobium fredii usda257 form ineffective nodules with aberrant ultrastructure.	the tricarboxylic acid (tca) cycle plays an important role in generating the energy required by bacteroids to fix atmospheric nitrogen. citrate synthase is the first enzyme that controls the entry of carbon into the tca cycle. we cloned and determined the nucleotide sequence of the glta gene that encodes citrate synthase in sinorhizobium fredii usda257, a symbiont of soybeans (glycine max [l.] merr.) and several other legumes. the deduced citrate synthase protein has a molecular weight of 48,198 ...	2003	12788763
genetic diversity of fast-growing rhizobia that nodulate soybean ( glycine max l. merr).	the fast-growing rhizobium sp. strain ngr234, isolated from papua new guinea, and 13 strains of sinorhizobium fredii, isolated from china and vietnam, were fingerprinted by means of rapd, rep, eric and ardra. eric, rep and rapd markers revealed a considerable genetic diversity among fast-growing rhizobia. chinese isolates showed higher levels of diversity than those strains isolated from vietnam. ardra analysis revealed three different genotypes among fast-growing rhizobia that nodulate soybean, ...	2003	12802480
extracellular proteins involved in soybean cultivar-specific nodulation are associated with pilus-like surface appendages and exported by a type iii protein secretion system in sinorhizobium fredii usda257.	several gram-negative plant and animal pathogenic bacteria have evolved a type iii secretion system (ttss) to deliver effector proteins directly into the host cell cytosol. sinorhizobium fredii usda257, a symbiont of soybean and many other legumes, secretes proteins called nops (nodulation outer proteins) into the extracellular environment upon flavonoid induction. mutation analysis and the nucleotide sequence of a 31.2-kb symbiosis (sym) plasmid dna region of usda257 revealed the existence of a ...	2003	12848427
a purl mutant of sinorhizobium fredii hh103 is symbiotically defective and altered in its lipopolysaccharide.	the pleiotropic phenotype of an auxotrophic purl mutant (svq295) of sinorhizobium fredii hh103 has been investigated. svq295 forms colonies that are translucent, produce more slime and absorb less congo red than those of wild-type strain hh103. svq295 did not grow in minimal medium unless the culture was supplemented with thiamin and adenine or with thiamin and aica-riboside (5-aminoimidazole-4-carboxamide 1-beta-d-ribofuranoside), an intermediate of purine biosynthesis. bacterial cultures suppl ...	2003	12855732
nodd alleles of sinorhizobium fredii usda191 differentially influence soybean nodulation, nodc expression, and production of exopolysaccharides.	all rhizobium strains examined to date have one or multiple alleles of nodd. at least one copy of nodd and the presence of flavonoid exudates are required for nod gene induction and nodulation. sinorhizobium fredii usda191 has two copies of nodd. in this study, we demonstrate that inactivation of either copy of nodd caused a reduction in basal levels of expression of nodc. extra copies of nodd1 had no effect on the expression of nodc when compared with the wild type, but extra copies of nodd2 ab ...	2003	14506861
the is1111 family members is4321 and is5075 have subterminal inverted repeats and target the terminal inverted repeats of tn21 family transposons.	is5075 and is4321 are closely related (93.1% identical) members of the is1111 family that target a specific position in the 38-bp terminal inverted repeats of tn21 family transposons and that are inserted in only one orientation. they are 1,327 bp long and have identical ends consisting of short inverted repeats of 12 bp with an additional 7 bp (taatgag) or 6 bp (aatgag) to the left of the left inverted repeats and 3 bp (aga) or 4 bp (agat) to the right of the right inverted repeat. circular for ...	2003	14563872
[root colonization and nodulation of sinorhizobium fredii hn01dl in glycine max rhizosphere].	rhizobox-soil microcosms studies on the colonization, dispersal and nodulation of sinorhizobium fredii hn01dl marked with luxab gene in glycine max rhizosphere showed that the colonization dynamics and the density of hn01dl in non-sterilized rhizobox-soil microcosms were different from those in sterilized rhizobox-soil microcosms. the colonization density of the former reached the maximum (8.65 log cfu.g-1 root) 12 days after the coated seeds planted, and that of the latter decreased rapidly at ...	2003	14655359
the genus name ensifer casida 1982 takes priority over sinorhizobium chen et al. 1988, and sinorhizobium morelense wang et al. 2002 is a later synonym of ensifer adhaerens casida 1982. is the combination "sinorhizobium adhaerens" (casida 1982) willems et al. 2003 legitimate? request for an opinion.	the synonymy of the genera ensifer and sinorhizobium was recently reported, but it was proposed that the later-named genus, sinorhizobium, take priority in nomenclature. there is no justification in the international code of nomenclature of bacteria (prokaryotes) for this step; ensifer is the correct name of the genus, with ensifer adhaerens as the type species. species previously allocated to sinorhizobium are here proposed as the new combinations ensifer arboris, ensifer fredii, ensifer kostie ...	2003	14657154
molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity.	isolates belonging to six genera not previously known to oxidize co were obtained from enrichments with aquatic and terrestrial plants. dna from these and other isolates was used in pcr assays of the gene for the large subunit of carbon monoxide dehydrogenase (coxl). coxl and putative coxl fragments were amplified from known co oxidizers (e.g., oligotropha carboxidovorans and bradyrhizobium japonicum), from novel co-oxidizing isolates (e.g., aminobacter sp. strain cox, burkholderia sp. strain lu ...	2003	14660374
identification of fast and slow growing rhizobia nodulating soybean (glycine max [l.] merr) by a multiplex pcr reaction.	two dna fragments, a 730-bp and a 900-bp fragment, one homologous to host cultivar specificity genes nolbt of sinorhizobium fredii and the other one homologous to rsalpha, an insertion-like sequence present in bradyrhizobium japonicum, were generated by polymerase chain reaction (pcr) with two pairs of primers. the amount of each fragment generated by the multiplex pcr was proportional to the amount of template dna present. the amplification of the 900-bp rsalpha fragment was more sensitive, sin ...	2003	14680692
the effect of fita mutations on the symbiotic properties of sinorhizobium fredii varies in a chromosomal-background-dependent manner.	nodd1 of sinorhizobium fredii hh103, which is identical to that of s. fredii usda257 and usda191, repressed its own expression. spontaneous flavonoid-independent transcription activation (fita) mutants of s. fredii hh103 m (=hh103 rifr psym::tn 5-mob) showing constitutive expression of nod genes were isolated. no differences were found among soybean cultivar williams plants inoculated with fita mutants svq250 or svq253 or with the parental strain hh103m. soybean plants inoculated with mutant svq ...	2004	14689165
[effect of sinorhizobium fredii yc4 symbiotic plasmid amplification on nod factors and symbiotic n-fixation].	sinorhizobium fredii yc4 can form nitrogen-fixing nodules on soybean (glycine max) and wild soybean (g. soja). it can produce unique lipochitooligosaccharide nod factors (lcos), in comparison with the other four strains of s. fredii. the constitution of lcos produced by yc4 contained more hydrophobic substitutions detected by thin-layer chromatography (tlc) of 14c-labeled nod factors. a spontaneous mutant termed ysc3 amplified in the symbiotic plasmid was isolated from yc4, which can produce mor ...	2003	14733011
nolr regulates diverse symbiotic signals of sinorhizobium fredii hh103.	we have investigated in sinorhizobium fredii hh103-1 (=hh103 str(r)) the influence of the nolr gene on the production of three different bacterial symbiotic signals: nod factors, signal responsive (sr) proteins, and exopolysaccharide (eps). the presence of multiple copies of nolr (in plasmid pmus675) repressed the transcription of all the flavonoid-inducible genes analyzed: noda, nodd1, nolo, nolx, noel, rhcj, hesb, and y4pf. inactivation of nolr (mutant svq517) or its overexpression (presence o ...	2004	15195950
characterization of nopp, a type iii secreted effector of rhizobium sp. strain ngr234.	the type three secretion system (ttss) encoded by pngr234a, the symbiotic plasmid of rhizobium sp. strain ngr234, is responsible for the flavonoid- and nodd1-dependent secretion of nodulation outer proteins (nops). abolition of secretion of all or specific nops significantly alters the nodulation ability of ngr234 on many of its hosts. in the closely related strain rhizobium fredii usda257, inactivation of the ttss modifies the host range of the mutant so that it includes the improved glycine ma ...	2004	15231809
molecular aspects of soybean cultivar-specific nodulation by sinorhizobium fredii usda257.	sinorhizobium fredii usda257 forms nitrogen-fixing nodules in association with the primitive soybean cultivar 'peking' but fails to initiate nodules on many advanced soybean cultivars, including 'mccall'. this distinction is controlled by a set of nodulation genes termed nolxwbtuv. inactivation of any of these genes enables usda257 to nodulate mccall and many other improved soybean cultivars. mutation in the nolxwbtuv locus also alters the nod factor structure resulting in the production of a no ...	2003	15242277
analysis of rhizobium etli and of its symbiosis with wild phaseolus vulgaris supports coevolution in centers of host diversification.	common beans (phaseolus vulgaris) comprise three major geographic genetic pools, one in mexico, central america, and colombia, another in the southern andes, and a third in ecuador and northern peru. species rhizobium etli is the predominant rhizobia found symbiotically associated with beans in the americas. we have found polymorphism in the common nodulation gene nodc among r. etli strains from a wide range of geographical origins, which disclosed three nodc types. the different nodc alleles in ...	2004	15340138
widespread occurrence of a novel division of bacteria identified by 16s rrna gene sequences originally found in deep marine sediments.	phylogenetic analysis of 16s rrna gene sequences from deep marine sediments identified a deeply branching clade, designated candidate division js1. primers for pcr amplification of partial 16s rrna genes that target the js1 division were developed and used to detect js1 sequences in dna extracted from various sedimentary environments, including, for the first time, coastal marine and brackish sediments.	2004	15345467
involvement of exo5 in production of surface polysaccharides in rhizobium leguminosarum and its role in nodulation of vicia sativa subsp. nigra.	analysis of two exopolysaccharide-deficient mutants of rhizobium leguminosarum, rbl5808 and rbl5812, revealed independent tn5 transposon integrations in a single gene, designated exo5. as judged from structural and functional homology, this gene encodes a udp-glucose dehydrogenase responsible for the oxidation of udp-glucose to udp-glucuronic acid. a mutation in exo5 affects all glucuronic acid-containing polysaccharides and, consequently, all galacturonic acid-containing polysaccharides. exo5-d ...	2004	15375143
salt-tolerance genes involved in cation efflux and osmoregulation of sinorhizobium fredii rt19 detected by isolation and characterization of tn5 mutants.	salt-tolerance genes of sinorhizobium fredii rt19 were identified by the construction and screening of a transposon tn5-1063 library containing over 30,000 clones. twenty-one salt-sensitive mutants were obtained and five different genes were identified by sequencing. eight mutants were found with disruptions in the phaa2 gene, which encodes a cation efflux system protein, while mutations in genes encoding other cation effux system proteins were found in seven (phad2), two (phaf2) and two (phag2) ...	2004	15451112
unexpectedly diverse mesorhizobium strains and rhizobium leguminosarum nodulate native legume genera of new zealand, while introduced legume weeds are nodulated by bradyrhizobium species.	the new zealand native legume flora are represented by four genera, sophora, carmichaelia, clianthus, and montigena. the adventive flora of new zealand contains several legume species introduced in the 19th century and now established as serious invasive weeds. until now, nothing has been reported on the identification of the associated rhizobia of native or introduced legumes in new zealand. the success of the introduced species may be due, at least in part, to the nature of their rhizobial sym ...	2004	15466541
nopb, a soybean cultivar-specificity protein from sinorhizobium fredii usda257, is a type iii secreted protein.	the type iii secretion system (ttss) of plant- and animal-pathogenic bacteria is involved in translocation of virulence factors into the host cell cytosol where they modulate cellular processes. sinorhizobium fredii usda257 is a gram-negative soil bacterium that forms nitrogen-fixing nodules on specific soybean cultivars (glycine max (l.) merr.). this microsymbiont is known to secrete at least five nodulation outer proteins (nops) in response to flavonoid induction. some of these nops have been ...	2004	15553251
luxr homolog avhr in agrobacterium vitis affects the development of a grape-specific necrosis and a tobacco hypersensitive response.	the luxr homolog avir in agrobacterium vitis strain f2/5 was recently shown to be associated with induction of a hypersensitive response (hr) on tobacco and necrosis on grape plants, indicating that the responses are regulated by quorum sensing. we now report a second luxr homolog, avhr, whose disruption (mutant m1320) results in hr-negative and reduced grape necrosis phenotypes. the deduced avhr protein has characteristic autoinducer binding and dna binding domains and is unique among reported ...	2005	15601702
the hrpk operon of pseudomonas syringae pv. tomato dc3000 encodes two proteins secreted by the type iii (hrp) protein secretion system: hopb1 and hrpk, a putative type iii translocator.	pseudomonas syringae is a gram-negative bacterial plant pathogen that is dependent on a type iii protein secretion system (ttss) and the effector proteins it translocates into plant cells for pathogenicity. the p. syringae ttss is encoded by hrp-hrc genes that reside in a central region of a pathogenicity island (pai). flanking one side of this pai is the exchangeable effector locus (eel). we characterized the transcriptional expression of the open reading frames (orfs) within the eel of p. syri ...	2005	15629936
diversity of green-like and red-like ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbl) in differently managed agricultural soils.	a pcr-based approach was developed to detect ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) form i large-subunit genes (cbbl) as a functional marker of autotrophic bacteria that fix carbon dioxide via the calvin-benson-bassham cycle. we constructed two different primer sets, targeting the green-like and red-like phylogenetic groups of cbbl genes. the diversity of these cbbl genes was analyzed by the use of three differently managed agricultural soils from a long-term field experiment. ...	2005	15640185
protein domains and architectural innovation in plant-associated proteobacteria.	evolution of new complex biological behaviour tends to arise by novel combinations of existing building blocks. the functional and evolutionary building blocks of the proteome are protein domains, the function of a protein being dependent on its constituent domains. we clustered completely-sequenced proteomes of prokaryotes on the basis of their protein domain content, as defined by pfam (release 16.0). this revealed that, although there was a correlation between phylogeny and domain content, ot ...	2005	15715905
structural analysis of the capsular polysaccharide from sinorhizobium fredii hwg35.	we have determined the structure of a capsular polysaccharide from sinorhizobium fredii hwg35. this polysaccharide was isolated following the standard protocols applied for lipopolysaccharide isolation. on the basis of monosaccharide analysis, methylation analysis, mass spectrometric analysis, one-dimensional (1)h and (13)c nmr, and two-dimensional nmr experiments, the structure was shown to consist of a polymer having the following disaccharide repeating unit: -->6)-2,4-di-o-methyl-alpha-d-galp ...	2005	15877364
apparent incompatibility of plasmid psfryc4b of sinorhizobium fredii with two different plasmids in another strain.	sinorhizobium fredii yc4b is a spontaneous mutant derivative of strain yc4 that is unable to nodulate soybeans. the second-largest plasmid of strain yc4b, termed psfryc4b (810 kb), was transferred to s. fredii hn01sr, a strain which contains three large indigenous plasmids (psfrhn01a, psfrhn01b and psfrhn01c). surprisingly, two stable indigenous plasmids (psfrhn01a and psfrhn01b) of strain hn01sr were cured simultaneously by the introduction of psfryc4b. furthermore, a novel, unstable plasmid (p ...	2005	16010525
transcriptome-based identification of the sinorhizobium meliloti nodd1 regulon.	the nodd1 regulon of sinorhizobium meliloti was determined through the analysis of the s. meliloti transcriptome in response to the plant flavone luteolin and the overexpression of nodd1. nine new genes regulated by both nodd1 and luteolin were identified, demonstrating that nodd1 controls few functions behind nodulation in s. meliloti.	2005	16085895
domain structure of hrpe, the hrp pilus subunit of xanthomonas campestris pv. vesicatoria.	the plant-pathogenic bacterium xanthomonas campestris pv. vesicatoria possesses a type iii secretion (tts) system necessary for pathogenicity in susceptible hosts and induction of the hypersensitive response in resistant plants. this specialized protein transport system is encoded by a 23-kb hrp (hypersensitive response and pathogenicity) gene cluster. x. campestris pv. vesicatoria produces filamentous structures, hrp pili, at the cell surface under hrp-inducing conditions. the hrp pilus acts as ...	2005	16109959
sinorhizobium fredii usda257 releases a 22-kda outer membrane protein (omp22) to the extracellular milieu when grown in calcium-limiting conditions.	calcium, which regulates a wide variety of cellular functions, plays an important role in rhizobium-legume interactions. we investigated the effect of calcium on surface appendages of sinorhizobium fredii usda257. cold-field emission scanning electron microscopy observation of usda257 grown in calcium-limiting conditions revealed cells with unusual shape and size. transmission electron microscopy observation revealed intact flagella were present only when usda257 cells were grown in calcium-suff ...	2005	16134893
symbiotic abilities of sinorhizobium fredii with modified expression of purl.	previous reports showed that a transposon-induced purl- mutant of sinorhizobium fredii induced pseudonodules on glycine max and the addition of 5-aminoimidazole-4-carboxamide-riboside or adenine to the plant could not restore the mutant to establish effective symbiosis. to gain a better understanding of the impact of the purl gene on symbiosis formation, we measured the effect of modified expression of this gene on the symbiotic abilities of s. fredii on soybean (g. max). a 1.98-kb in-frame dele ...	2006	16228203
sini- and expr-dependent quorum sensing in sinorhizobium meliloti.	quorum sensing (qs) in sinorhizobium meliloti, the n-fixing bacterial symbiont of medicago host plants, involves at least half a dozen different n-acyl homoserine lactone (ahl) signals and perhaps an equal number of ahl receptors. the accumulation of 55 proteins was found to be dependent on sini, the ahl synthase, and/or on expr, one of the ahl receptors. gas chromatography-mass spectrometry and electrospray ionization tandem mass spectrometry identified 3-oxo-c(14)-homoserine lactone (3-oxo-c(1 ...	2005	16291666
diversity and structure of bacterial chemolithotrophic communities in pine forest and agroecosystem soils.	obligate lithotrophs (e.g., ammonia oxidizers) and facultative lithotrophs (e.g., co and hydrogen oxidizers) collectively comprise a phylogenetically diverse functional group that contributes significantly to carbon and nitrogen cycles in soils and plays important roles in trace gas dynamics (e.g., carbon monoxide and nitrous and nitric oxides) that affect tropospheric chemistry and radiative forcing. in spite of their diverse physiologies, facultative and obligate lithotrophs typically possess ...	2005	16332829
effect of sym plasmid curing on symbiotic effectiveness in rhizobium fredii.	a mutant, usda 206c, of rhizobium fredii usda 206 was obtained by passage on acridine plates. this mutant was cured of its 197-megadalton sym plasmid but retained its symbiotic effectiveness. multiple plasmid and chromosomally borne nif gene copies have previously been shown in r. fredii usda 206. hindiii and ecori restriction enzyme digests of plasmid and total dna showed that at least two nif gene copies are probably missing in usda 206c. to compare the symbiotic effectiveness of usda 206 and ...	1985	16346803
symbiotic effectiveness and host-strain interactions of rhizobium fredii usda 191 on different soybean cultivars.	nodulation, acetylene reduction activity, dry matter accumulation, and total nitrogen accumulation by nodulated plants growing in a nitrogen-free culture system were used to compare the symbiotic effectiveness of the fast-growing rhizobium fredii usda 191 with that of the slow-growing bradyrhizobium japonicum usda 110 in symbiosis with five soybean (glycine max (l.) merr.) cultivars. measurement of the amount of nitrogen accumulated during a 20-day period of vegetative growth (28 to 48 days afte ...	1986	16347066
growth of fast- and slow-growing rhizobia on ethanol.	free-living soybean rhizobia and bradyrhizobium spp. (lupine) have the ability to catabolize ethanol. of the 30 strains of rhizobia examined, only the fast- and slow-growing soybean rhizobia and the slow-growing bradyrhizobium sp. (lupine) were capable of using ethanol as a sole source of carbon and energy for growth. two strains from each of the other rhizobium species examined (r. meliloti, r. loti, and r. leguminosarum biovars phaseoli, trifolii, and viceae) failed to grow on ethanol. one rhi ...	1986	16347190
serological relatedness of rhizobium fredii to other rhizobia and to the bradyrhizobia.	several isolates of rhizobium fredii were examined for their serological relatedness to each other, to bradyrhizobium japonicum, and to other fast- and slow-growing rhizobia. immunofluorescence, agglutination, and immunodiffusion analyses indicated that r. fredii contains at least three separate somatic serogroups, usda 192, usda 194, and usda 205. there was no cross-reaction between any of the r. fredii isolates and 13 of the 14 b. japonicum somatic serogroups tested. cross-reactions were obtai ...	1987	16347404
conservation of a symbiotic dna region in soybean root nodule bacteria.	bradyrhizobium japonicum usda 3i1b110 contains a dna region in which symbiotic genes and many repeated sequences are closely linked. hybridization analysis revealed that this region was highly conserved in some b. japonicum strains (usda 24, usda 122, usda 123, atcc 10324, 61a24) but not in others (usda 76, 61a76, 61a101). the genomic presence of multiple copies of one of the repeated sequences (rsalpha) appeared to be specifically characteristic for soybean root nodule bacteria, including the f ...	1987	16347446
induction of symbiotically defective auxotrophic mutants of rhizobium fredii hh303 by transposon mutagenesis.	symbiotically defective auxotrophic mutants were isolated by transposon tn5 mutagenesis of rhizobium fredii hh303, a fast-growing microsymbiont of north american commercial soybean cultivars such as glycine max cv. williams. three different tn5-carrying suicide vectors, pblk1-2, psup1011, and pgs9, were used for mutagenesis with transposition frequencies of 4 x 10, 3 x 10, and 1 x 10, respectively, while the frequency of background mutation resistant to 500 mug of kanamycin per ml was 1 x 10. fr ...	1988	16347555
influence of glycine spp. on competitiveness of bradyrhizobium japonicum and rhizobium fredii.	the displacement of indigenous bradyrhizobium japonicum in soybean nodules with more effective strains offers the possibility of enhanced n(2) fixation in soybean (glycine max (l.) merr.). our objective was to determine whether the wild soybean (g. soja sieb. & zucc.) genotype pi 468397 would cause reduced competitiveness of important indigenous b. japonicum strains usda 31, 76, and 123 and thereby permit nodulation by rhizobium fredii, the fast-growing microsymbiont of soybean. in an initial ex ...	1988	16347589
nodulation and nitrogen fixation efficacy of rhizobium fredii with phaseolus vulgaris genotypes.	phaseolus plant introduction (pi) genotypes (consisting of 684 p. vulgaris, 26 p. acutifolius, 39 p. lunatus, and 5 p. coccineus accessions) were evaluated for their ability to form effective symbioses with strains of six slow-growing (bradyrhizobium) and four fast-growing (rhizobium fredii) soybean rhizobia. of the 684 p. vulgaris genotypes examined, three pis were found to form effective nitrogen-fixing symbioses with the r. fredii strains. while none of the bradyrhizobium strains nodulated an ...	1988	16347705
relationship of the presence and copy number of plasmids to exopolysaccharide production and symbiotic effectiveness in rhizobium fredii usda 206.	rhizobium fredii usda 206 harbors four large plasmids, one of which carries nodulation and nitrogen fixation genes. previously isolated groups of plasmid-cured derivatives of strain usda 206 were compared with each other to determine possible plasmid functions. mutant strain 206cans was isolated as a nonmucoid (muc) derivative of strain 206ca, a mutant that was cured of two plasmids. the muc phenotype of 206cans was only expressed when the strain was grown on certain media, particularly those wi ...	1989	16347890
exopolysaccharide-deficient mutants of rhizobium fredii hh303 which are symbiotically effective.	nineteen tn5-induced mutants of rhizobium fredii hh303 defective in acidic exopolysaccharide synthesis were isolated by screening for lack of calcofluor fluorescence. they were grouped by complementation analysis by using rhizobium meliloti cosmids carrying exo genes. all of the 19 mutants were symbiotically effective or partially effective, indicating that the major bacterial acidic exopolysaccharide of this strain of r. fredii may not be required for symbiotic development in the soybean.	1989	16347980
cadmium resistance screening in nitrilotriacetate-buffered minimal media.	media used to determine the mics of heavy metals for bacteria are unreliable because organic components in the media bind or chelate most of the metal being studied. to define specific metal activity in media and to maintain metal activity at a constant level, hepes-mes [n-2-hydroxyethylpiperazine-n' -2-ethanesulfonic acid-2-(n-morpholine)ethanesulfonic acid] salts medium with arabinose medium was modified, and the modified medium was used to examine the mic of cadmium for rhizobium fredii usda ...	1989	16348000
transfer of the pea symbiotic plasmid pjb5ji in nonsterile soil.	transfer of the pea (pisum sativum l.) symbiotic plasmid pjb5ji between strains of rhizobia was examined in sterile and nonsterile silt loam soil. sinorhizobium fredii usda 201 and hh003 were used as plasmid donors, and symbiotic plasmid-cured rhizobium leguminosarum 6015 was used as the recipient. the plasmid was carried but not expressed in s. fredii strains, whereas transfer of the plasmid to r. leguminosarum 6015 rendered the recipient capable of nodulating pea plants. confirmation of plasmi ...	1991	16348589
effects of ph and osmotic stress on cellular polyamine contents in the soybean rhizobia rhizobium fredii p220 and bradyrhizobium japonicum a1017.	homospermidine is a polyamine present in its highest concentrations in root nodule bacteria. by using the soybean rhizobia rhizobium fredii p220 and bradyrhizobium japonicum a1017, the effects of the ph and osmolarity of the medium on rhizobial growth and cellular polyamine contents were investigated. elevation of medium ph repressed the growth of slowly growing b. japonicum a1017 and resulted in a slight increase in cellular putrescine, while homospermidine content was not significantly affecte ...	1993	16348911
tellurium and selenium resistance in rhizobia and its potential use for direct isolation of rhizobium meliloti from soil.	forty-eight rhizobium and bradyrhizobium strains were screened for resistance to tellurite, selenite, and selenate. high levels of resistance to the metals were observed only in rhizobium meliloti and rhizobium fredii strains; the mics were 2 to 8 mm for te(iv), >200 mm for se(vi), and 50 to 100 mm for se(iv). incorporation of se and te into growth media permitted us to directly isolate r. meliloti strains from soil. mutant strains of rhizobia having decreased levels of se and te resistance were ...	1994	16349263
effects of ionic and osmotic strength on the glucosyltransferase of rhizobium meliloti responsible for cyclic beta-(1,2)-glucan biosynthesis.	the cyclic beta-(1,2)-glucans of rhizobium meliloti and agrobacterium tumefaciens play an important role during hypoosmotic adaptation, and the synthesis of these compounds is osmoregulated. glucosyltransferase, the enzyme responsible for cyclic beta-(1,2)-glucan biosynthesis, is present constitutively, suggesting that osmotic regulation of the biosynthesis of these glucans occurs through modulation of enzyme activity. in this study, we examined regulation of cyclic glucan biosynthesis in vitro ...	1998	16349538
sinorhizobium fredii hh103 mutants affected in capsular polysaccharide (kps) are impaired for nodulation with soybean and cajanus cajan.	the sinorhizobium fredii hh103 rkp-1 region, which is involved in capsular polysaccharides (kps) production, was isolated and sequenced. the organization of the s. fredii genes identified, rkpuaghij and kpsf3, was identical to that described for s. meliloti 1021 but different from that of s. meliloti ak631. the long rkpa gene (7.5 kb) of s. fredii hh103 and s. meliloti 1021 appears as a fusion of six clustered ak631 genes, rkpabcdef. s. fredii hh103-rif(r) mutants affected in rkph or rkpg were c ...	2006	16404952
catabolism of 1,5-anhydro-d-fructose in sinorhizobium morelense s-30.7.5: discovery, characterization, and overexpression of a new 1,5-anhydro-d-fructose reductase and its application in sugar analysis and rare sugar synthesis.	the bacterium sinorhizobium morelense s-30.7.5 was isolated by a microbial screening using the sugar 1,5-anhydro-d-fructose (af) as the sole carbon source. this strain metabolized af by a novel pathway involving its reduction to 1,5-anhydro-d-mannitol (am) and the further conversion of am to d-mannose by c-1 oxygenation. growth studies showed that the af metabolizing capability is not confined to s. morelense s-30.7.5 but is a more common feature among the rhizobiaceae. the af reducing enzyme wa ...	2006	16461673
rhizobial exopolysaccharides: genetic control and symbiotic functions.	specific complex interactions between soil bacteria belonging to rhizobium, sinorhizobium, mesorhizobium, phylorhizobium, bradyrhizobium and azorhizobium commonly known as rhizobia, and their host leguminous plants result in development of root nodules. nodules are new organs that consist mainly of plant cells infected with bacteroids that provide the host plant with fixed nitrogen. proper nodule development requires the synthesis and perception of signal molecules such as lipochitooligosacchari ...	2006	16483356
transformation of rhizobia with broad-host-range plasmids by using a freeze-thaw method.	several species of rhizobia were successfully transformed with broad-host-range plasmids of different replicons by using a modified freeze-thaw method. a generic binary vector (ppzp211) was maintained in mesorhizobium loti without selection and stably inherited during nodulation. the method could extend the potential of rhizobia as a vehicle for plant transformation.	2006	16517691
induction of bradyrhizobium japonicum common nod genes by isoflavones isolated from glycine max.	the early events in legume nodulation by rhizobium spp. involve a conserved gene cluster known as the common nod region. a broad-host-range plasmid (pea2-21) containing a bradyrhizobium japonicum noddabc-lacz translational fusion was constructed and used to monitor nod gene expression in response to soybean root extract. two inducing compounds were isolated and identified. analysis using ultraviolet absorption spectra, proton nuclear magnetic resonance, and mass spectrometry showed that the two ...	1987	16593884
synthesis of poly (3-hydroxybutyrate-co-3-hydroxyoctanoate) by a sinorhizobium fredii strain.	the potential of a sinorhizobium fredii strain to produce a copolymer from glucose and sodium dodecanoate substrates was investigated.	2006	16599986
the genome of rhizobium leguminosarum has recognizable core and accessory components.	rhizobium leguminosarum is an alpha-proteobacterial n2-fixing symbiont of legumes that has been the subject of more than a thousand publications. genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. we have sequenced the genome of r. leguminosarum biovar viciae strain 3841.	2006	16640791
two indirect methods for detecting ureide synthesis by nodulated legumes.	two methods were developed for the detection of altered ureide metabolism in legume nodules. both techniques are based on the positive correlation between the presence of high xanthine dehydrogenase (ec 1.2.1.37) specific activity in nodules and the ability of those nodules to produce the ureides, allantoin and allantoic acid. in the first method, nodulated legumes are treated for 2 weeks with a soil drench of allopurinol. after allopurinol treatment, leaves of n(2)-fed, ureide-producing legumes ...	1986	16664857
regulation of nodulation in the soybean-rhizobium symbiosis : strain and cultivar variability.	double inoculation (15 h apart) of the soybean cultivar williams with bradyrhizobium japonicum i-110ars reveals a rapid regulatory plant response that inhibits nodulation of distal portions of the primary root (m pierce, wd bauer 1984 plant physiol 73: 286-290). only living, homologous rhizobia elicit the response. we conducted similar double inoculation experiments to test the hypothesis that this is a universal phenomenon in soybean symbioses. we investigated interactions of the cultivar mccal ...	1987	16665616
modulation of host gene expression during initiation and early growth of nodules in cowpea, vigna unguiculata (l.) walp.	inoculation of 2-day-old cowpea (vigna unguiculata [l.] walp.) seedlings with rhizobium fredii usda257 results in proficient nodulation of the tap root. the most abundant nodulation occurs in a region roughly corresponding to the position of the root tip at the time of inoculation. we have examined plant gene expression in this region, after inoculation with either usda257 or a nonnodulating mutant, 257b3. after isolation of mrna and in vitro translation, the protein products were separated by t ...	1990	16667410
nodulation of soybean by a transposon-mutant of rhizobium fredii usda257 is subject to competitive nodulation blocking by other rhizobia.	rhizobium fredii usda257 fails to nodulate the improved soybean [glycine max (l.)merr.] cultivar mccall in plastic growth pouches. mutant 257dh4, which was derived from usda257 by transposon mutagenesis, forms nitrogen fixing nodules under these conditions. if usda257 is present in inocula containing the mutant, most infections are arrested prior to organization of the nodule meristem, and nodule number is reduced by 95%. the improved cultivars essex, harosoy, hodgson 78, and viçoja, as well as ...	1990	16667829
cultivar-specific interactions of soybean with rhizobium fredii are regulated by the genotype of the root.	rhizobium fredii usda257 forms nitrogen-fixing nodules on soybean cultivar peking, but not on cultivar mccall. this pattern of nodulation persists when mccall and peking seedlings are cultivated together in plastic growth pouches. reciprocal grafting experiments confirm that the root genotype, and not that of the shoot, regulates such cultivar specificity. when peking roots are grafted onto mccall seedlings, the nodulation responses of roots similarly remain unaffected. transposon-mutant 257dh4, ...	1990	16667934
factors affecting the attachment of rhizospheric bacteria to bean and soybean roots.	the plant rhizosphere is an important soil ecological environment for plant-microorganism interactions, which include colonization by a variety of microorganisms in and around the roots that may result in symbiotic, endophytic, associative, or parasitic relationships within the plant, depending on the type of microorganisms, soil nutrient status, and soil environment. rhizosphere competence may be attributable to the differences in the extent of bacterial attachment to the root surface. we prese ...	2006	16684104
highly efficient chemoenzymatic synthesis of naturally occurring and non-natural alpha-2,6-linked sialosides: a p. damsela alpha-2,6-sialyltransferase with extremely flexible donor-substrate specificity.		2006	16721893
y4xp, an open reading frame located in a type iii protein secretion system locus of sinorhizobium fredii usda257 and usda191, encodes cysteine synthase.	sinorhizobium fredii usda257, a soybean symbiont, exports several nodulation outer proteins (nops) into the rhizosphere. these proteins, which are exported by a type iii secretion system (ttss), have a pivotal role in host-specific nodulation. the entire ttss of s. fredii lies within a 31-kb region that includes conserved genes that code for secretion machinery proteins, nops, and several open reading frames (orf) of unknown function. identifying the functions of these orf is essential to unders ...	2006	16776297
fixj: a major regulator of the oxygen limitation response and late symbiotic functions of sinorhizobium meliloti.	sinorhizobium meliloti exists either in a free-living state in the soil or in symbiosis within legume nodules, where the bacteria differentiate into nitrogen-fixing bacteroids. expression of genes involved in nitrogen fixation and associated respiration is governed by two intermediate regulators, nifa and fixk, respectively, which are controlled by a two-component regulatory system fixlj in response to low-oxygen conditions. in order to identify the fixlj regulon, gene expression profiles were d ...	2006	16788198
popf1 and popf2, two proteins secreted by the type iii protein secretion system of ralstonia solanacearum, are translocators belonging to the hrpf/nopx family.	ralstonia solanacearum gmi1000 is a gram-negative plant pathogen which contains an hrp gene cluster which codes for a type iii protein secretion system (ttss). we identified two novel hrp-secreted proteins, called popf1 and popf2, which display similarity to one another and to putative ttss translocators, hrpf and nopx, from xanthomonas spp. and rhizobia, respectively. they also show similarities with ttss translocators of the yopb family from animal-pathogenic bacteria. both popf1 and popf2 bel ...	2006	16788199
inactivation of the sinorhizobium fredii hh103 rhcj gene abolishes nodulation outer proteins (nops) secretion and decreases the symbiotic capacity with soybean.	it has been postulated that nodulation outer proteins (nops) avoid effective nodulation of sinorhizobium fredii usda257 to nodulate with american soybeans. s. fredii hh103 naturally nodulates with both asiatic (non-commercial) and american (commercial) soybeans. inactivation of the s. fredii hh103 gene rhcj, which belongs to the tts (type iii secretion) cluster, abolished nop secretion and decreased its symbiotic capacity with the two varieties of soybeans. s. fredii strains hh103 and usda257, t ...	2006	16835843
diverse flavonoids stimulate nodd1 binding to nod gene promoters in sinorhizobium meliloti.	nodd1 is a member of the nodd family of lysr-type transcriptional regulators that mediates the expression of nodulation (nod) genes in the soil bacterium sinorhizobium meliloti. each species of rhizobia establishes a symbiosis with a limited set of leguminous plants. this host specificity results in part from a nodd-dependent upregulation of nod genes in response to a cocktail of flavonoids in the host plant's root exudates. to demonstrate that nodd is a key determinant of host specificity, we e ...	2006	16855231
phylogeny of 16s rrna, ribulose 1,5-bisphosphate carboxylase/oxygenase, and adenosine 5'-phosphosulfate reductase genes from gamma- and alphaproteobacterial symbionts in gutless marine worms (oligochaeta) from bermuda and the bahamas.	gutless oligochaetes are small marine worms that live in obligate associations with bacterial endosymbionts. while symbionts from several host species belonging to the genus olavius have been described, little is known of the symbionts from the host genus inanidrilus. in this study, the diversity of bacterial endosymbionts in inanidrilus leukodermatus from bermuda and inanidrilus makropetalos from the bahamas was investigated using comparative sequence analysis of the 16s rrna gene and fluoresce ...	2006	16885306
the pha2 gene cluster involved in na+ resistance and adaption to alkaline ph in sinorhizobium fredii rt19 encodes a monovalent cation/proton antiporter.	sinorhizobium fredii rt19 can tolerate up to 0.6 m nacl, whereas all its pha2-disrupted mutants, constructed by tn5 mutagenesis, failed to grow in even the presence of 0.1 m nacl. no growth difference was detected in pha2 mutants at a ph<7.5 in the presence or absence of k+, but growth reduction was observed in the presence of k+ when ph>7.5. the pha2 gene cluster was able to completely restore the growth of the pha2 mutants of s. fredii rt19 in 0.6 m nacl. measurement of monovalent cation intra ...	2006	16923072
exo-oligosaccharides of rhizobium sp. strain ngr234 are required for symbiosis with various legumes.	rhizobia are nitrogen-fixing bacteria that establish endosymbiotic associations with legumes. nodule formation depends on various bacterial carbohydrates, including lipopolysaccharides, k-antigens, and exopolysaccharides (eps). an acidic eps from rhizobium sp. strain ngr234 consists of glucosyl (glc), galactosyl (gal), glucuronosyl (glca), and 4,6-pyruvylated galactosyl (pvgal) residues with beta-1,3, beta-1,4, beta-1,6, alpha-1,3, and alpha-1,4 glycoside linkages. here we examined the role of n ...	2006	16923883
characterization of myo-inositol utilization by corynebacterium glutamicum: the stimulon, identification of transporters, and influence on l-lysine formation.	although numerous bacteria possess genes annotated iol in their genomes, there have been very few studies on the possibly associated myo-inositol metabolism and its significance for the cell. we found that corynebacterium glutamicum utilizes myo-inositol as a carbon and energy source, enabling proliferation with a high maximum rate of 0.35 h-1. whole-genome dna microarray analysis revealed that 31 genes respond to myo-inositol utilization, with 21 of them being localized in two clusters of >14 k ...	2006	16997948
identification of a functional 2-keto-myo-inositol dehydratase gene of sinorhizobium fredii usda191 required for myo-inositol utilization.	sinorhizobium fredii usda191 is a gram-negative bacterium capable of forming nitrogen-fixing nodules on soybean roots. the usda191 idha gene encoding myo-inositol dehydrogenase, an enzyme necessary for myo-inositol utilization, is known to be involved in competitive nodulation and nitrogen fixation. in bacillus subtilis, myo-inositol dehydrogenase catalyzes the first step of the myo-inositol catabolic pathway. recently iole was identified as the gene encoding 2-keto-myo-inositol dehydratase, whi ...	2006	17151471
identification of novel sinorhizobium meliloti mutants compromised for oxidative stress protection and symbiosis.	employing a novel two-part screen, we identified sinorhizobium meliloti mutants that were both sensitive to hydrogen peroxide and symbiotically defective on the host plant medicago sativa. the mutations affect a wide variety of cellular processes and represent both novel and previously identified genes important in symbiosis.	2007	17172326
identification of novel sinorhizobium meliloti mutants compromised for oxidative stress protection and symbiosis.	employing a novel two-part screen, we identified sinorhizobium meliloti mutants that were both sensitive to hydrogen peroxide and symbiotically defective on the host plant medicago sativa. the mutations affect a wide variety of cellular processes and represent both novel and previously identified genes important in symbiosis.	2007	17172326