Publications

secrets of soil survival revealed by the genome sequence of arthrobacter aurescens tc1.	arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils. member of the genus are metabolically and ecologically diverse and have the ability to survive in environmentally harsh conditions for extended periods of time. the genome of arthrobacter aurescens strain tc1, which was originally isolated from soil at an atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and two circular plasmids, ptc1 and p ...	2006	17194220
nopm and nopd are rhizobial nodulation outer proteins: identification using lc-maldi and lc-esi with a monolithic capillary column.	we have explored the potential of commercial polystyrene-divinylbenzene monolithic capillary nanolc-ms/ms for identifying sinorhizobium fredii hh103 nodulation outer proteins. monolithic nanolc with off-line maldi-tof/tof and on-line esi-q-otof is fast and robust, generating complementary data and offering high-confidence protein identifications from gel bands too weak for successful analysis using traditional approaches. this has allowed identification of two proteins not previously described a ...	2007	17249710
evidence of horizontal transfer of symbiotic genes from a bradyrhizobium japonicum inoculant strain to indigenous diazotrophs sinorhizobium (ensifer) fredii and bradyrhizobium elkanii in a brazilian savannah soil.	the importance of horizontal gene transfer (hgt) in the evolution and speciation of bacteria has been emphasized; however, most studies have focused on genes clustered in pathogenesis and very few on symbiosis islands. both soybean (glycine max [l.] merrill) and compatible bradyrhizobium japonicum and bradyrhizobium elkanii strains are exotic to brazil and have been massively introduced in the country since the early 1960s, occupying today about 45% of the cropped land. for the past 10 years, ou ...	2007	17308185
quorum-sensing regulation in rhizobia and its role in symbiotic interactions with legumes.	legume-nodulating bacteria (rhizobia) usually produce n-acyl homoserine lactones, which regulate the induction of gene expression in a quorum-sensing (or population-density)-dependent manner. there is significant diversity in the types of quorum-sensing regulatory systems that are present in different rhizobia and no two independent isolates worked on in detail have the same complement of quorum-sensing genes. the genes regulated by quorum sensing appear to be rather diverse and many are associa ...	2007	17360278
calcium regulates the production of nodulation outer proteins (nops) and precludes pili formation by sinorhizobium fredii usda257, a soybean symbiont.	sinorhizobium fredii usda257 forms nitrogen-fixing nodules on primitive soybean cultivars such as 'peking' but is unable to establish efficient symbiosis with north american cultivars. usda257 when grown in presence of genistein, a potent nodd-inducing isoflavonoid, secretes at least six nodulation outer proteins (nopx, nopb, nopl, nopp, nopa and nopc) to the extracellular milieu through a type iii secretion system. these proteins regulate legume nodulation in a host-specific manner. here, it is ...	2007	17391367
responses of rhizobia to desiccation in relation to osmotic stress, oxygen, and temperature.		2007	17400779
evidence for glycosylation on a dna-binding protein of salmonella enterica.	all organisms living under aerobic atmosphere have powerful mechanisms that confer their macromolecules protection against oxygen reactive species. microorganisms have developed biomolecule-protecting systems in response to starvation and/or oxidative stress, such as dna biocrystallization with dps (dna-binding protein from starved cells). dps is a protein that is produced in large amounts when the bacterial cell faces harm, which results in dna protection. in this work, we evaluated the glycosy ...	2007	17407574
identification of a gene cluster enabling lactobacillus casei bl23 to utilize myo-inositol.	genome analysis of lactobacillus casei bl23 revealed that, compared to l. casei atcc 334, it carries a 12.8-kb dna insertion containing genes involved in the catabolism of the cyclic polyol myo-inositol (mi). indeed, l. casei atcc 334 does not ferment mi, whereas strain bl23 is able to utilize this carbon source. the inserted dna consists of an iolr gene encoding a deor family transcriptional repressor and a divergently transcribed ioltabcdg1g2ejk operon, encoding a complete mi catabolic pathway ...	2007	17449687
characterization of symbiotic and endophytic bacteria isolated from root nodules of herbaceous legumes grown in qinghai-tibet plateau and in other zones of china.	qinghai-tibet plateau is the highest place in the world and the environment in that plateau is hard for animals and plants, with low temperature, low concentration of oxygen and high solar radiation. in this study, 61 root nodule isolates from vicia, oxytropis, medicago, melilotus and onobrychis species grown in qinghai-tibet plateau and in loess plateau were comparatively characterized. based upon the results of numerical taxonomy, ardra, aflp, dna-dna hybridization and 16s rdna sequencing, the ...	2007	17541555
genomes of the symbiotic nitrogen-fixing bacteria of legumes.		2007	17556525
metabolic reconstruction and modeling of nitrogen fixation in rhizobium etli.	rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants. this symbiotic relationship is crucial for the nitrogen cycle, and understanding symbiotic mechanisms is a scientific challenge with direct applications in agronomy and plant development. rhizobium etli is a bacteria which provides legumes with ammonia (among other chemical compounds), thereby stimulating plant growth. a genome-scale approach, integrating the biochemical information available for r. etli, constitutes an im ...	2007	17922569
protein-protein interactions within type iii secretion system-dependent pili of rhizobium sp. strain ngr234.	pili synthesized by the type iii secretion system of rhizobium species strain ngr234 are essential for protein secretion and thus for efficient symbiosis with many legumes. isolation and partial purification of these pili showed that they are composed of at least three proteins, nopa, nopb, and nopx. using biochemical assays, we show here that these proteins interact directly with one another.	2008	17981961
protein-protein interactions within type iii secretion system-dependent pili of rhizobium sp. strain ngr234.	pili synthesized by the type iii secretion system of rhizobium species strain ngr234 are essential for protein secretion and thus for efficient symbiosis with many legumes. isolation and partial purification of these pili showed that they are composed of at least three proteins, nopa, nopb, and nopx. using biochemical assays, we show here that these proteins interact directly with one another.	2008	17981961
a pyrf auxotrophic mutant of sinorhizobium fredii hh103 impaired in its symbiotic interactions with soybean and other legumes.	transposon tn5-mob mutagenesis allowed the selection of a sinorhizobium fredii hh103 mutant derivative (svq 292) that requires the presence of uracil to grow in minimal media. the mutated gene, pyrf, codes for an orotidine-5 - monophosphate decarboxylase (ec 4.1.1.23). mutant svq 292 and its parental prototrophic mutant hh103 showed similar nod-factor and lipopolysaccharide profiles. the symbiotic properties of mutant svq 292 were severely impaired with all legumes tested. mutant svq 292 formed ...	2007	18075998
advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus ensifer (including former sinorhizobium).	there is a need for easy, practical, reliable and robust techniques for the identification and classification of bacterial isolates to the species level as alternatives to 16s rrna gene sequence analysis and dna-dna hybridization. here, we demonstrate that multilocus sequence analysis (mlsa) of housekeeping genes is a valuable alternative technique. an mlsa study of 10 housekeeping genes (atpd, dnak, gap, glna, glta, gyrb, pnp, reca, rpob and thrc) was performed on 34 representatives of the genu ...	2008	18175710
structure of the o-antigen of the main lipopolysaccharide isolated from sinorhizobium fredii smh12.	the lipopolysaccharide of sinorhizobium fredii smh12, a wide-range host bacterium isolated from nodulated soybean plants growing in vietnam, has been studied. isolation of lipopolysaccharide by the phenol-water method leads to a mixture of two polysaccharides; polyacrylamide gel electrophoresis indicates that both are possibly lipopolysaccharides. the structures of the o-antigen of the main lipopolysaccharide and its deacetylated form are determined by sugar and methylation analysis, partial hyd ...	2008	18208318
requirement of a plasmid-encoded catalase for survival of rhizobium etli cfn42 in a polyphenol-rich environment.	nitrogen-fixing bacteria collectively called rhizobia are adapted to live in polyphenol-rich environments. the mechanisms that allow these bacteria to overcome toxic concentrations of plant polyphenols have not been clearly elucidated. we used a crude extract of polyphenols released from the seed coat of the black bean to simulate a polyphenol-rich environment and analyze the response of the bean-nodulating strain rhizobium etli cfn42. our results showed that the viability of the wild type as we ...	2008	18310436
isolation and characterization of an operon involved in sulfate and sulfite metabolism in sinorhizobium fredii.	a gene cluster orfabcd from a sinorhizobium fredii hn01 mutant strain hsmralpha was isolated. we showed that it was an operon involved in sulfur metabolism. functional studies revealed that, except for orfb, the three genes orfa, orfc and orfd were involved in sulfite reduction. orfa and orfc were similar to the cysg and cysi from sinorhizobium meliloti 1021 and rhizobium etli cfn 42, respectively. orfd encodes a conserved hypothetical protein in other bacteria. we demonstrate here, for the firs ...	2008	18336549
ttsi regulates symbiotic genes in rhizobium species ngr234 by binding to tts boxes.	infection of legumes by rhizobium sp. ngr234 and subsequent development of nitrogen-fixing nodules are dependent on the coordinated actions of nod factors, proteins secreted by a type iii secretion system (t3ss) and modifications to surface polysaccharides. the production of these signal molecules is dependent on plant flavonoids which trigger a regulatory cascade controlled by the transcriptional activators nodd1, nodd2, syrm2 and ttsi. ttsi is known to control the genes responsible for t3ss fu ...	2008	18363648
symbiosis-promoting and deleterious effects of nopt, a novel type 3 effector of rhizobium sp. strain ngr234.	establishment of symbiosis between certain host plants and nitrogen-fixing bacteria ("rhizobia") depends on type 3 effector proteins secreted via the bacterial type 3 secretion system (t3ss). here, we report that the open reading frame y4zc of strain ngr234 encodes a novel rhizobial type 3 effector, termed nopt (for nodulation outer protein t). analysis of secreted proteins from ngr234 and t3ss mutants revealed that nopt is secreted via the t3ss. nopt possessed autoproteolytic activity when expr ...	2008	18487326
characterization of a symbiotically effective rhizobium resistant to arsenic: isolated from the root nodules of vigna mungo (l.) hepper grown in an arsenic-contaminated field.	bacteria were isolated from the root nodules of vigna mungo (l.) hepper, grown in an arsenic-contaminated field and the strain was selected by its nodulation ability as well as better arsenic tolerant capacity compared to others. the selected strain was identified as rhizobium by 16s rdna sequencing and designated as vma301. phylogenetic analysis of the gene sequences showed its close relatedness with sinorhizobium fredii. lc(50) value of arsenate for the bacteria as determined by flow cytometry ...	2008	18497483
regulation and symbiotic significance of nodulation outer proteins secretion in sinorhizobium fredii hh103.	in this work we show that the sinorhizobium fredii hh103 ttsi gene is essential for the expression of the tts genes and secretion of nodulation outer proteins (nops). moreover, we demonstrate for the first time, to our knowledge, that the nod box preceding ttsi is necessary for nops secretion. ttsi is responsible for the transcriptional activation of nopx, nopa, rhcj and rhcq. we confirm that the s. fredii hh103 ttsi gene is activated by nodd1 and repressed by nolr. in contrast, nodd2 is not inv ...	2008	18524937
bradyrhizobium elkanii, bradyrhizobium yuanmingense and bradyrhizobium japonicum are the main rhizobia associated with vigna unguiculata and vigna radiata in the subtropical region of china.	cowpea (vigna unguiculata) and mung bean (vigna radiata) are important legume crops yet their rhizobia have not been well characterized. in the present study, 62 rhizobial strains isolated from the root nodules of these plants grown in the subtropical region of china were analyzed via a polyphasic approach. the results showed that 90% of the analyzed strains belonged to or were related to bradyrhizobium japonicum, bradyrhizobium liaoningense, bradyrhizobium yuanmingense and bradyrhizobium elkani ...	2008	18564340
genetic diversity of native bradyrhizobia isolated from soybeans (glycine max l.) in different agricultural-ecological-climatic regions of india.	fifty isolates from root nodules of soybean plants sampled in five agricultural-ecological-climatic regions of india were analyzed by pcr-restriction fragment length polymorphism analysis of the 16s rrna gene, the intergenic spacer region between the 16s and 23s rrna genes (igs), and the nifh and nodc genes. eight haplotypes assigned to the bradyrhizobium genus were identified, and the genetic diversity was conserved across regions. sequence analyses of the igs and the dnak, glnii, reca, and nif ...	2008	18676699
mutation in the cobo gene generates auxotrophy for cobalamin and methionine and impairs the symbiotic properties of sinorhizobium fredii hh103 with soybean and other legumes.	we report here the isolation of a methionine and cobalamin mutant strain (svq336) of sinorhizobium fredii hh103 obtained by tn5-lacz mutagenesis. sequence analysis showed that the transposon was inserted into a gene homologous to cobo. this gene codes for a cobalamin adenosyltransferase which is involved in the biosynthesis of vitamin b12. another hh103 cobo mutant (strain svq524), was constructed by the insertion of omega interposon. both cobo mutants required the addition of methionine because ...	2009	18719891
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
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
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
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
rhizobia from lanzarote, the canary islands, that nodulate phaseolus vulgaris have characteristics in common with sinorhizobium meliloti isolates from mainland spain.	the stable, low-molecular-weight (lmw) rna fractions of several rhizobial isolates of phaseolus vulgaris grown in the soil of lanzarote, an island of the canary islands, were identical to a less-common pattern found within sinorhizobium meliloti (assigned to group ii) obtained from nodules of alfalfa and alfalfa-related legumes grown in northern spain. the p. vulgaris isolates and the group ii lmw rna s. meliloti isolates also were distinguishable in that both had two conserved inserts of 20 and ...	2009	19218416
infection by heterodera glycines elevates isoflavonoid production and influences soybean nodulation.	high-performance liquid chromatography and sinorhizobium fredii usda191 nodc-lacz gene fusion were used to monitor changes in the isoflavonoid content of soybean roots infected with heterodera glycines isolate tn1. isoflavonoid concentrations in infected roots of both h. glycines-resistant hartwig and susceptible essex soybean were two to four-fold higher than those of uninfected roots 2 and 3 days after inoculation. the isoflavonoids produced activated the transcription of nodc-lacz fusion. the ...	1999	19270906
sinorhizobium fredii hh103 cgs mutants are unable to nodulate determinate- and indeterminate nodule-forming legumes and overproduce an altered eps.	sinorhizobium fredii hh103 produces cyclic beta glucans (cg) composed of 18 to 24 glucose residues without or with 1-phosphoglycerol as the only substituent. the s. fredii hh103-rifr cgs gene (formerly known as ndvb) was sequenced and mutated with the lacz-gentamicin resistance cassette. mutant svq562 did not produce cg, was immobile, and grew more slowly in the hypoosmotic gym medium, but its survival in distilled water was equal to that of hh103-rifr. lipopolysaccharides and k-antigen polysacc ...	2009	19348575
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
effects of the purl gene expression level on the competitive nodulation ability of sinorhizobium fredii.	purine pathway in rhizobium is important during the nodulation processes. the purl gene in sinorhizobium fredii (s. fredii) has been identified to be required for the whole establishment of a nitrogen-fixing nodule. to get a better understanding of the purl gene's impacts on rhizobium-plant interaction, the competitive nodulation abilities of s. fredii containing different purl expression plasmids were studied. several kinds of coinoculations were performed, including using different bacterial c ...	2009	19459004
rhizobium leguminosarum biovar viciae 3841, deficient in 27-hydroxyoctacosanoate-modified lipopolysaccharide, is impaired in desiccation tolerance, biofilm formation and motility.	the lipopolysaccharide (lps) of the gram-negative legume symbiont rhizobium leguminosarum biovar viciae 3,841 contains several unique modifications, including the addition of a 27-hydroxyoctacosanoic acid (27ohc28 : 0), also termed the very long chain fatty acid (vlcfa), attached at the 2' position of lipid a. a transposon mutant that lacks expression of two putative 3-oxo-acyl [acyl-carrier protein] synthase ii genes, fabf1 and fabf2, from the vlcfa biosynthetic cluster, was isolated and charac ...	2009	19460825
the symbiosis interactome: a computational approach reveals novel components, functional interactions and modules in sinorhizobium meliloti.	rhizobium-legume symbiosis is an attractive biological process that has been studied for decades because of its importance in agriculture. however, this system has undergone extensive study and although many of the major factors underpinning the process have been discovered using traditional methods, much remains to be discovered.	2009	19531251
bradyrhizobium spp. and sinorhizobium fredii are predominant in root nodules of vigna angularis, a native legume crop in the subtropical region of china.	adzuki bean (vigna angularis) is an important legume crop native to china, but its rhizobia have not been well characterized. in the present study, a total of 60 rhizobial strains isolated from eight provinces of china were analyzed with amplified 16s rrna gene rflp, igs-rflp, and sequencing analyses of 16s rrna, atpd, reca, and nodc genes. these strains were identified as genomic species within rhizobium, sinorhizobium, mesorhizobium, bradyrhizobium, and ochrobactrum. the most abundant groups w ...	2009	19557346
different species and symbiotic genotypes of field rhizobia can nodulate phaseolus vulgaris in tunisian soils.	abstract a collection of 160 isolates of rhizobia nodulating phaseolus vulgaris in three geographical regions in tunisia was characterized by restriction fragment length polymorphism analysis of polymerase chain reaction (pcr)-amplified 16s rdna, nifh and nodc genes. nine groups of rhizobia were delineated: rhizobium gallicum biovar (bv.) gallicum, rhizobium leguminosarum bv. phaseoli and bv. viciae, rhizobium etli bv. phaseoli, rhizobium giardinii bv. giardinii, and four groups related to speci ...	2002	19709241
identification of direct transcriptional target genes of exos/chvi two-component signaling in sinorhizobium meliloti.	the sinorhizobium meliloti exos/chvi two-component signaling pathway is required for the development of a nitrogen-fixing symbiosis between s. meliloti and its plant hosts. exos/chvi also has important roles in regulating succinoglycan production, biofilm formation, motility, nutrient utilization, and the viability of free-living bacteria. previous microarray experiments with an exos96::tn5 mutant indicated that exos/chvi influences the expression of a few hundred genes, complicating the investi ...	2009	19749054
the absence of nops secretion in sinorhizobium fredii hh103 increases gmpr1 expression in williams soybean.	sinorhizobium fredii hh103 secretes through the type iii secretion system at least eight nodulation outer proteins (nops), including the effector nopp. these proteins are necessary for an effective nodulation of soybean. in this work, we show that expression of the nopp gene depended on flavonoids and on the transcriptional regulators nodd1 and ttsi. inactivation of nopp led to an increase in the symbiotic capacity of s. fredii hh103 to nodulate williams soybean. in addition, we studied whether ...	2009	19810813
characterization of a gene family of outer membrane proteins (ropb) in rhizobium leguminosarum bv. viciae vf39sm and the role of the sensor kinase chvg in their regulation.	the outer membrane of gram-negative bacteria represents the interface between the bacterium and its external environment. it has a critical role as a protective barrier against harmful substances and is also important in host-bacteria interactions representing the initial physical point of contact between the host cell and bacterial cell. ropb is a previously identified outer membrane protein from rhizobium leguminosarum bv. viciae that is present in free-living cells but absent in bacteroids (h ...	2010	20023026
characterization of a gene family of outer membrane proteins (ropb) in rhizobium leguminosarum bv. viciae vf39sm and the role of the sensor kinase chvg in their regulation.	the outer membrane of gram-negative bacteria represents the interface between the bacterium and its external environment. it has a critical role as a protective barrier against harmful substances and is also important in host-bacteria interactions representing the initial physical point of contact between the host cell and bacterial cell. ropb is a previously identified outer membrane protein from rhizobium leguminosarum bv. viciae that is present in free-living cells but absent in bacteroids (h ...	2010	20023026
computational prediction of type iii secreted proteins from gram-negative bacteria.	type iii secretion system (t3ss) is a specialized protein delivery system in gram-negative bacteria that injects proteins (called effectors) directly into the eukaryotic host cytosol and facilitates bacterial infection. for many plant and animal pathogens, t3ss is indispensable for disease development. recently, t3ss has also been found in rhizobia and plays a crucial role in the nodulation process. although a great deal of efforts have been done to understand type iii secretion, the precise mec ...	2010	20122221
a persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations.	acute exacerbations of chronic obstructive pulmonary disease (copd) are a major source of morbidity and contribute significantly to healthcare costs. although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in copd airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. the aim of this study was to comprehensively profile airway bacterial com ...	2010	20141328
translocation of nopp by sinorhizobium fredii usda257 into vigna unguiculata root nodules.	sinorhizobium fredii is a nitrogen-fixing legume symbiont that stimulates the formation of root nodules. s. fredii nodulation of roots is influenced by nop proteins, which are secreted through a type iii secretion system (t3ss). we demonstrate that s. fredii injects nopp into vigna unguiculata nodules in a t3ss-dependent manner.	2010	20382805
disruption of the glycine cleavage system enables sinorhizobium fredii usda257 to form nitrogen-fixing nodules on agronomically improved north american soybean cultivars.	the symbiosis between sinorhizobium fredii usda257 and soybean [glycine max (l.) merr.] exhibits a high degree of cultivar specificity. usda257 nodulates primitive soybean cultivars but fails to nodulate agronomically improved cultivars such as mccall. in this study we provide evidence for the involvement of a new genetic locus that controls soybean cultivar specificity. this locus was identified in usda257 by tn5 transposon mutagenesis followed by nodulation screening on mccall soybean. we have ...	2010	20453144
single-cell genomics reveals the lifestyle of poribacteria, a candidate phylum symbiotically associated with marine sponges.	in this study, we present a single-cell genomics approach for the functional characterization of the candidate phylum poribacteria, members of which are nearly exclusively found in marine sponges. the microbial consortia of the mediterranean sponge aplysina aerophoba were singularized by fluorescence-activated cell sorting, and individual microbial cells were subjected to phi29 polymerase-mediated 'whole-genome amplification'. pyrosequencing of a single amplified genome (sag) derived from a memb ...	2010	20613790
single-cell genomics reveals the lifestyle of poribacteria, a candidate phylum symbiotically associated with marine sponges.	in this study, we present a single-cell genomics approach for the functional characterization of the candidate phylum poribacteria, members of which are nearly exclusively found in marine sponges. the microbial consortia of the mediterranean sponge aplysina aerophoba were singularized by fluorescence-activated cell sorting, and individual microbial cells were subjected to phi29 polymerase-mediated 'whole-genome amplification'. pyrosequencing of a single amplified genome (sag) derived from a memb ...	2010	20613790
evolutionary dynamics of insertion sequences in relation to the evolutionary histories of the chromosome and symbiotic plasmid genes of rhizobium etli populations.	insertion sequences (is) are mobile genetic elements that are distributed in many prokaryotes. in particular, in the genomes of the symbiotic nitrogen-fixing bacteria collectively known as rhizobia, is are fairly abundant in plasmids or chromosomal islands that carry the genes needed for symbiosis. here, we report an analysis of the distribution and genetic conservation of the is found in the genome of rhizobium etli cfn42 in a collection of 87 rhizobium strains belonging to populations with dif ...	2010	20675442
pyruvate is synthesized by two pathways in pea bacteroids with different efficiencies for nitrogen fixation.	nitrogen fixation in legume bacteroids is energized by the metabolism of dicarboxylic acids, which requires their oxidation to both oxaloacetate and pyruvate. in alfalfa bacteroids, production of pyruvate requires nad+ malic enzyme (dme) but not nadp+ malic enzyme (tme). however, we show that rhizobium leguminosarum has two pathways for pyruvate formation from dicarboxylates catalyzed by dme and by the combined activities of phosphoenolpyruvate (pep) carboxykinase (pcka) and pyruvate kinase (pyk ...	2010	20675477
the rkpu gene of sinorhizobium fredii hh103 is required for bacterial k-antigen polysaccharide production and for efficient nodulation with soybean but not with cowpea.	in this work, the role of the rkpu and rkpj genes in the production of the k-antigen polysaccharides (kps) and in the symbiotic capacity of sinorhizobium fredii hh103, a broad host-range rhizobial strain able to nodulate soybean and many other legumes, was studied. the rkpj- and rkpu-encoded products are orthologous to escherichia coli proteins involved in capsule export. s. fredii hh103 mutant derivatives were contructed in both genes. to our knowledge, this is the first time that the role of r ...	2010	20688828
comparative analysis of myxococcus predation on soil bacteria.	predator-prey relationships among prokaryotes have received little attention but are likely to be important determinants of the composition, structure, and dynamics of microbial communities. many species of the soil-dwelling myxobacteria are predators of other microbes, but their predation range is poorly characterized. to better understand the predatory capabilities of myxobacteria in nature, we analyzed the predation performance of numerous myxococcus isolates across 12 diverse species of bact ...	2010	20802074
comparing symbiotic efficiency between swollen versus nonswollen rhizobial bacteroids.	symbiotic rhizobia differentiate physiologically and morphologically into nitrogen-fixing bacteroids inside legume host nodules. the differentiation is apparently terminal in some legume species, such as peas (pisum sativum) and peanuts (arachis hypogaea), likely due to extreme cell swelling induced by the host. in other legume species, such as beans (phaseolus vulgaris) and cowpeas (vigna unguiculata), differentiation into bacteroids, which are similar in size and shape to free-living rhizobia, ...	2010	20837702
ensifer (sinorhizobium) sojae sp. nov., isolated from root nodules of glycine max grown in saline-alkaline soils in hebei province of china.	thirteen bacterial strains isolated from root nodules of soybean grown in saline-alkaline soils in the chinese province of hebei were identified as a unique group in genus ensifer (sinorhizobium) based upon box-pcr patterns, sequencing analyses of 16s rrna and housekeeping genes, and dna-dna hybridization. phenotypically, positive acid production and negative reduction in litmus milk and sensitivity to 50 µg ml(1) of amplicillin, as well as some other features could differentiate the novel group ...	2010	20851917
proteobactin and a yersiniabactin-related siderophore mediate iron acquisition in proteus mirabilis.	proteus mirabilis causes complicated urinary tract infections (utis). while the urinary tract is an iron-limiting environment, iron acquisition remains poorly characterized for this uropathogen. microarray analysis of p. mirabilis hi4320 cultured under iron limitation identified 45 significantly upregulated genes (p ≤ 0.05) that represent 21 putative iron-regulated systems. two gene clusters, pmi0229-0239 and pmi2596-2605, encode putative siderophore systems. pmi0229-0239 encodes a non-ribosomal ...	2010	20923418
r gene-controlled host specificity in the legume-rhizobia symbiosis.	leguminous plants can enter into root nodule symbioses with nitrogen-fixing soil bacteria known as rhizobia. an intriguing but still poorly understood property of the symbiosis is its host specificity, which is controlled at multiple levels involving both rhizobial and host genes. it is widely believed that the host specificity is determined by specific recognition of bacterially derived nod factors by the cognate host receptor(s). here we describe the positional cloning of two soybean genes rj2 ...	2010	20937853
molecular mechanisms of persistence of mutualistic bacteria photorhabdus in the entomopathogenic nematode host.	symbioses between microbes and animals are ubiquitous, yet little is known about the intricate mechanisms maintaining such associations. in an emerging mutualistic model system, insect-pathogenic bacteria photorhabdus and their insect-parasitic nematode partner heterorhabditis, we found that the bacteria undergo major transcriptional reshaping in the nematode intestine. besides general starvation mechanisms, the bacteria induce cellular acidification to slow down growth, switch to pentose phosph ...	2010	20957199
diverse rhizobia associated with sophora alopecuroides grown in different regions of loess plateau in china.	a total of seventy-five symbiotic bacterial strains isolated from root nodules of wild sophora alopecuroides grown in different regions of china's loess plateau were characterized. based on the combined rflp patterns, thirty-five genotypes were defined among the rhizobia and they were classified into nine genomic species, including mesorhizobium alhagi and m. gobiense as the main groups, as well as agrobacterium tumefaciens, m. amorphae, phyllobacterium trifolii, rhizobium giardinii, r. indigofe ...	2010	20965680
auxin and plant-microbe interactions.	microbial synthesis of the phytohormone auxin has been known for a long time. this property is best documented for bacteria that interact with plants because bacterial auxin can cause interference with the many plant developmental processes regulated by auxin. auxin biosynthesis in bacteria can occur via multiple pathways as has been observed in plants. there is also increasing evidence that indole-3-acetic acid (iaa), the major naturally occurring auxin, is a signaling molecule in microorganism ...	2011	21084388
the aspergillus fumigatus sialidase is a 3-deoxy-d-glycero-d-galacto-2-nonulosonic acid hydrolase (kdnase): structural and mechanistic insights.	aspergillus fumigatus is a filamentous fungus that can cause severe respiratory disease in immunocompromised individuals. a putative sialidase from a. fumigatus was recently cloned and shown to be relatively poor in cleaving n-acetylneuraminic acid (neu5ac) in comparison with bacterial sialidases. here we present the first crystal structure of a fungal sialidase. when the apo structure was compared with bacterial sialidase structures, the active site of the aspergillus enzyme suggested that neu5 ...	2011	21247893
genetic diversity of nodulating and non-nodulating rhizobia associated with wild soybean (glycine soja sieb. & zucc.) in different ecoregions of china.	a total of 99 bacterial isolates that originated from root nodules of glycine soja were characterized with restriction analyses of amplified 16s ribosomal dna and 16s-23s rdna intergenic spacers (its), and sequence analyses of 16s rrna, rpob, atpd, reca and nodc genes. when tested for nodulation of g. soja, 72 of the isolates were effective symbionts, and these belonged to five species: bradyrhizobium japonicum, bradyrhizobium elkanii, bradyrhizobium yuanmingense, bradyrhizobium liaoningense and ...	2011	21303397
glyceollin, a soybean phytoalexin with medicinal properties.	this review covers the biosynthesis of glyceollin and its biological activities including antiproliferative/antitumor action (toward b16 melanoma cells, lncap prostate cancer cells, and bg-1 ovarian cancer cells), anti-estrogenic action (through estrogen receptors a- and ß-), antibacterial action (toward erwinia carotovora, escherichia coli, bradyrhizobium japonicum, sinorhizobium fredii ), antinematode activity, and antifungal activity (toward fusarium solani, phakospora pachyrhizi, diaporthe p ...	2011	21336922
diversity and biogeography of rhizobia isolated from root nodules of glycine max grown in hebei province, china.	a total of 215 rhizobial strains were isolated and analyzed with 16s rrna gene, 16s-23s intergenic spacer, housekeeping genes atpd, reca, and glnii, and symbiotic genes nifh and nodc to understand the genetic diversity of soybean rhizobia in hebei province, china. all the strains except one were symbiotic bacteria classified into nine genospecies in the genera of bradyrhizobium and sinorhizobium. surveys on the distribution of these rhizobia in different regions showed that bradyrhizobium japoni ...	2011	21340735
characterization of root-nodulating bacteria associated to prosopis farcta growing in the arid regions of tunisia.	diversity of 50 bacterial isolates recovered from root nodules of prosopis farcta grown in different arid soils in tunisia, was investigated. characterization of isolates was assessed using a polyphasic approach including phenotypic characteristics, 16s rrna gene pcr--rflp and sequencing, noda gene sequencing and mlsa. it was found that most of isolates are tolerant to high temperature (40°c) and salinity (3%). genetic characterization emphasizes that isolates were assigned to the genus ensifer ...	2011	21359955
multilocus sequence-based analysis delineates a clonal population of agrobacterium (rhizobium) radiobacter (agrobacterium tumefaciens) of human origin.	the genus agrobacterium includes plant-associated bacteria and opportunistic human pathogens. taxonomy and nomenclature within the genus remain controversial. in particular, isolates of human origin were all affiliated with the species agrobacterium (rhizobium) radiobacter, while phytopathogenic strains were designated under the synonym denomination agrobacterium tumefaciens. in order to study the relative distribution of agrobacterium strains according to their origins, we performed a multilocu ...	2011	21398532
symbiotic properties and first analyses of the genomic sequence of the fast growing model strain sinorhizobium fredii hh103 nodulating soybean.	glycine max (soybean) plants can be nodulated by fast-growing rhizobial strains of the genus sinorhizobium as well as by slow-growing strains clustered in the genus bradyrhizobium. fast-growing rhizobia strains with different soybean cultivar specificities have been isolated from chinese soils and from other geographical regions. most of these strains have been clustered into the species sinorhizobium fredii. the s. fredii strain hh103 was isolated from soils of hubei province, central china and ...	2011	21458507
exploring the symbiotic pangenome of the nitrogen-fixing bacterium sinorhizobium meliloti.	abstract: background: sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. an extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. ak83 and bl225c are two nodule-isolated strains with diverse symbiotic phenotypes; bl225c is more efficient in promoting growth of the medicago sativa plants than strain ak83. in order to investigate the genetic ...	2011	21569405
nodulation-gene-inducing flavonoids increase overall production of autoinducers and expression of n-acyl homoserine lactone synthesis genes in rhizobia.	legume-nodulating rhizobia use n-acyl homoserine lactones (ahls) to regulate several physiological traits related to the symbiotic plant-microbe interaction. in this work, we show that sinorhizobium fredii smh12, rhizobium etli isp42 and rhizobium sullae is123, three rhizobial strains with different nodulation ranges, produced a similar pattern of ahl molecules, sharing, in all cases, production of n-octanoyl homoserine lactone and its 3-oxo and/or 3-hydroxy derivatives. interestingly, productio ...	2011	21600980
maldi-tof mass spectrometry is a fast and reliable platform for identification and ecological studies of species from family rhizobiaceae.	family rhizobiaceae includes fast growing bacteria currently arranged into three genera, rhizobium, ensifer and shinella, that contain pathogenic, symbiotic and saprophytic species. the identification of these species is not possible on the basis of physiological or biochemical traits and should be based on sequencing of several genes. therefore alternative methods are necessary for rapid and reliable identification of members from family rhizobiaceae. in this work we evaluated the suitability o ...	2011	21655291
the conjugative plasmid of a bean-nodulating sinorhizobium fredii strain is assembled from sequences of two rhizobium plasmids and the chromosome of a sinorhizobium strain.	abstract:	2011	21702991
functional analysis of the nifqdcta1y4vghij operon of sinorhizobium fredii strain ngr234 using a transposon with a nifa-dependent read-out promoter.	rhizobia are a disparate collection of soil bacteria capable of reducing atmospheric nitrogen in symbiosis with legumes (fix phenotype). synthesis of the nitrogenase and its accessory components is under the transcriptional control of the key regulator nifa and generally restricted to the endosymbiotic forms of rhizobia known as bacteroids. amongst studied rhizobia, sinorhizobium fredii strain ngr234 has the remarkable ability to fix nitrogen in association with more than 130 species in 73 legum ...	2011	21719545
single-cell genomics: unravelling the genomes of unculturable microorganisms.		2011	21733126
sinorhizobium fredii hh103 does not strictly require kps and/or eps to nodulate glycyrrhiza uralensis, an indeterminate nodule-forming legume.	the sinorhizobium fredii hh103 rkp-1 region, which is involved in capsular polysaccharide (kps) biosynthesis, is constituted by the rkpu, rkpaghij, and kpsf3 genes. two mutants in this region affecting the rkpa (svq536) and rkpi (svq538) genes were constructed. polyacrylamide gel electrophoresis and (1)h-nmr analyses did not detect kps in these mutants. rt-pcr experiments indicated that, most probably, the rkpaghi genes are cotranscribed. glycine max cultivars (cvs.) williams and peking inoculat ...	2011	21761170
sinorhizobium fredii usda257 and s. fredii usda191, cultivar-specific and non-specific symbionts of soybean, produce distinct cell surface appendages.	sinorhizobium fredii usda257 and s. fredii usda191 are fast-growing rhizobia that form nitrogen-fixing nodules on soybean roots. in contrast to usda191, usda257 exhibits cultivar specificity and can form nodules only on primitive soybean cultivars. in response to flavonoids released from soybean roots these two rhizobia secrete nodulation outer proteins (nop) to the extracellular milieu through a type iii secretion system. in spite of the fact that nop proteins are known to regulate legume nodul ...	2011	21764962
biodiversity and biogeography of rhizobia associated with soybean plants grown in the north china plain.	as the putative center of origin for soybean and the second largest region of soybean production in china, the north china plain covers temperate and subtropical regions with diverse soil characteristics. however, the soybean rhizobia in this plain have not been sufficiently studied. in order to investigate the biodiversity and biogeography of soybean rhizobia in this plain, a total of 309 isolates of symbiotic bacteria from the soybean nodules collected from 16 sampling sites were studied with ...	2011	21784912
effect of rj-genotype and cultivation temperature on the community structure of soybean-nodulating bradyrhizobia.	the nodulation tendency and community structure of indigenous bradyrhizobia on rj-genotype soybean cultivars at cultivation temperatures of 33/28°c, 28/23°c and 23/18°c, 16/8 h (day/night degrees, hours) were investigated using 780 bradyrhizobial dna samples from an andosol with 13 soybean cultivars of four rj-genotypes (non-rj, rj(2)rj(3), rj(4) and rj(2)rj(3)rj(4)). a dendrogram was constructed based on restriction fragment length polymorphism of the polymerase chain reaction products (pcr-rfl ...	2011	22156423
a novel cold-active beta-d-galactosidase from the paracoccus sp. 32d - gene cloning, purification and characterization.	abstract: background: beta-d-galactosidases (ec 3.2.1.23) catalyze the hydrolysis of terminal non-reducing beta-d-galactose residues in beta-d-galactosides. cold-active beta-d-galactosidases have recently become a focus of attention of researchers and dairy product manufactures owing to theirs ability to: (i) eliminate of lactose from refrigerated milk for people afflicted with lactose intolerance, (ii) convert lactose to glucose and galactose which increase the sweetness of milk and decreases ...	2011	22166118
Environmental signals and regulatory pathways that influence exopolysaccharide production in rhizobia.	Rhizobia are Gram-negative bacteria that can exist either as free-living bacteria or as nitrogen-fixing symbionts inside root nodules of leguminous plants. The composition of the rhizobial outer surface, containing a variety of polysaccharides, plays a significant role in the adaptation of these bacteria in both habitats. Among rhizobial polymers, exopolysaccharide (EPS) is indispensable for the invasion of a great majority of host plants which form indeterminate-type nodules. Various functions ...	2011	22174640
Identification of a novel gene for biosynthesis of a bacteroid-specific electron carrier menaquinone.	Ubiquinone (UQ) has been considered as an electron mediator in electron transfer that generates ATP in Rhizobium under both free-living and symbiosis conditions. When mutated, the dmtH gene has a symbiotic phenotype of forming ineffective nodules on Astragalus sinicus. The gene was isolated from a Mesorhizobium huakuii 7653R transposon-inserted mutant library. The DNA sequence and conserved protein domain analyses revealed that dmtH encodes demethylmenaquinone (DMK) methyltransferase, which cata ...	2011	22194970
new beta rhizobial strains able to efficiently nodulate parapiptadenia rigida (benth.) brenan.	among the leguminous trees natives to uruguay parapiptadenia rigida (angico), a mimosoideae legume, is one of the most promising species for agroforestry. like many other legumes, it is able to establish symbiotic associations with rhizobia and belongs to the group known as "nitrogen fixing trees", which are major components of agroforestry systems. information about rhizobial symbionts for this genus is scarce, and thus the aim of this work was to identify and characterize rhizobia associated w ...	2012	22226956
characterisation of the burkholderia pseudomallei k96243 cps i coding region.	burkholderia pseudomallei is the causative agent of melioidosis, a disease endemic to regions of southeast asia and northern australia. both humans and a range of other animal species are susceptible to melioidosis and the production of a group 3 polysaccharide capsule in b. pseudomallei is essential for virulence. this b. pseudomallei capsular polysaccharide (cps) i comprises unbranched manno-heptopyranose residues and is encoded by a 34.5 kb locus on chromosome 1. despite the importance of thi ...	2012	22252864
genome sequence of the soybean symbiont sinorhizobium fredii hh103.	sinorhizobium fredii hh103 is a fast-growing rhizobial strain that is able to nodulate legumes that develop determinate nodules, e.g., soybean, and legumes that form nodules of the indeterminate type. here we present the genome of hh103, which consists of one chromosome and five plasmids with a total size of 7.22 mb.	2012	22374952
sinorhizobium fredii hh103 rkp-3 genes are required for k-antigen polysaccharide biosynthesis, affect lipopolysaccharide structure and are essential for infection of legumes forming determinate nodules.	the sinorhizobium fredii hh103 rkp-3 region has been isolated and sequenced. based on the similarities between the s. fredii hh103 rkpl, rkpm, rkpn, rkpo, rkpp, and rkpq genes and their corresponding orthologues in helicobacter pylori, we propose a possible pathway for the biosynthesis of the s. fredii hh103 k-antigen polysaccharide (kps) repeating unit. three rkp-3 genes (rkpm, rkpp, and rkpq) involved in the biosynthesis of the hh103 kps repeating unit (a derivative of the pseudaminic acid) ha ...	2012	22397406
stressed by a lov triangle.		2012	22447905
the ruegeria pomeroyi acui gene has a role in dmsp catabolism and resembles yhdh of e. coli and other bacteria in conferring resistance to acrylate.	the escherichia coli yhdh polypeptide is in the mdr012 sub-group of medium chain reductase/dehydrogenases, but its biological function was unknown and no phenotypes of yhdh(-) mutants had been described. we found that an e. coli strain with an insertional mutation in yhdh was hyper-sensitive to inhibitory effects of acrylate, and, to a lesser extent, to those of 3-hydroxypropionate. close homologues of yhdh occur in many bacterial taxa and at least two animals. the acrylate sensitivity of yhdh(- ...	2012	22563425
comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations.	the rhizobium-legume symbiosis has been widely studied as the model of mutualistic evolution and the essential component of sustainable agriculture. extensive genetic and recent genomic studies have led to the hypothesis that many distinct strategies, regardless of rhizobial phylogeny, contributed to the varied rhizobium-legume symbiosis. we sequenced 26 genomes of sinorhizobium and bradyrhizobium nodulating soybean to test this hypothesis. the bradyrhizobium core genome is disproportionally enr ...	2012	22586130
functional analysis of nopm, a novel e3 ubiquitin ligase (nel) domain effector of rhizobium sp. strain ngr234.	type 3 effector proteins secreted via the bacterial type 3 secretion system (t3ss) are not only virulence factors of pathogenic bacteria, but also influence symbiotic interactions between nitrogen-fixing nodule bacteria (rhizobia) and leguminous host plants. in this study, we characterized nopm (nodulation outer protein m) of rhizobium sp. strain ngr234, which shows sequence similarities with novel e3 ubiquitin ligase (nel) domain effectors from the human pathogens shigella flexneri and salomone ...	2012	22615567
in situ identification of plant-invasive bacteria with maldi-tof mass spectrometry.	rhizobia form a disparate collection of soil bacteria capable of reducing atmospheric nitrogen in symbiosis with legumes. the study of rhizobial populations in nature involves the collection of large numbers of nodules found on roots or stems of legumes, and the subsequent typing of nodule bacteria. to avoid the time-consuming steps of isolating and cultivating nodule bacteria prior to genotyping, a protocol of strain identification based on the comparison of maldi-tof ms spectra was established ...	2012	22615938
a set of lotus japonicus gifu x lotus burttii recombinant inbred lines facilitates map-based cloning and qtl mapping.	model legumes such as lotus japonicus have contributed significantly to the understanding of symbiotic nitrogen fixation. this insight is mainly a result of forward genetic screens followed by map-based cloning to identify causal alleles. the l. japonicus ecotype 'gifu' was used as a common parent for inter-accession crosses to produce f2 mapping populations either with other l. japonicus ecotypes, mg-20 and funakura, or with the related species l. filicaulis. these populations have all been use ...	2012	22619310
selenium distribution and speciation in the hyperaccumulator astragalus bisulcatus and associated ecological partners.	the goal of this study was to investigate how plant selenium (se) hyperaccumulation may affect ecological interactions and whether associated partners may affect se hyperaccumulation. the se hyperaccumulator astragalus bisulcatus was collected in its natural seleniferous habitat, and x-ray fluorescence mapping and x-ray absorption near-edge structure spectroscopy were used to characterize se distribution and speciation in all organs as well as in encountered microbial symbionts and herbivores. s ...	2012	22645068
draft genome sequence of the nitrogen-fixing symbiotic bacterium bradyrhizobium elkanii 587.	the draft sequence of the genome of bradyrhizobium elkanii 587 is presented. this was obtained using illumina next-gen dna sequencing combined with sanger sequencing. genes for the pathways involved in biological nitrogen fixation (the nif gene cluster), nod genes including nodabc, and genes for the type iii protein secretion system (t3ss) are present.	2012	22689236
comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, gujarat, india.	soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to co2 dynamics in soil. in this study, we used culture dependent and independent methods to assess the community structure and diversity of chemolithoautotrophs in agricultural and coastal barren saline soils (low and high salinity). we studied the composition and distribution of chemolithoautotrophs by means of functional marker gene cbbl encoding large subunit of ribulo ...	2012	22834535
complete genome sequence of the broad-host-range strain sinorhizobium fredii usda257.	here we announce the complete genome sequence of the symbiotic and nitrogen-fixing bacterium sinorhizobium fredii usda257. the genome shares a high degree of sequence similarity with the closely related broad-host-range strains s. fredii ngr234 and hh103. most strikingly, the usda257 genome encodes a wealth of secretory systems.	2012	22843606
the type 3 protein secretion system of cupriavidus taiwanensis strain lmg19424 compromises symbiosis with leucaena leucocephala.	cupriavidus taiwanensis forms proficient symbioses with a few mimosa species. inactivation of a type iii protein secretion system (t3ss) had no effect on mimosa pudica but allowed c. taiwanensis to establish chronic infections and fix nitrogen in leucaena leucocephala. unlike what was observed for other rhizobia, glutamate rather than plant flavonoids mediated transcriptional activation of this atypical t3ss.	2012	22865066
methylation--an uncommon modification of glycans.	a methyl (me) group on a sugar residue is a rarely reported event. until now, this type of modification has been found in the animal kingdom only in worms and molluscs, whereas it is more frequently present in some species of bacteria, fungi, algae and plants, but not in mammals. the monosaccharides involved as well as the positions of the me groups on the sugar vary with species. methylation appears to play a role in some recognition events, but details are still unknown. this review summarises ...	2012	22944672
rhizobia species: a boon for "plant genetic engineering".	since past three decades new discoveries in plant genetic engineering have shown remarkable potentials for crop improvement. agrobacterium ti plasmid based dna transfer is no longer the only efficient way of introducing agronomically important genes into plants. recent studies have explored a novel plant genetic engineering tool, rhizobia sp., as an alternative to agrobacterium, thereby expanding the choice of bacterial species in agricultural plant biotechnology. rhizobia sp. serve as an open l ...	2011	23024417
robust markers reflecting phylogeny and taxonomy of rhizobia.	genomic ani (average nucleotide identity) has been found to be able to replace dna-dna hybridization in prokaryote taxonomy. the ani of each of the core genes that has a phylogeny congruent with the reference species tree of rhizobia was compared to the genomic ani. this allowed us to identify three housekeeping genes (smc00019-trua-thra) whose ani reflected the intraspecies and interspecies genomic ani among rhizobial strains, revealing an ani gap (≥2%) between the inter- and intra-species comp ...	2012	23028691
a support vector machine based method to distinguish proteobacterial proteins from eukaryotic plant proteins.	members of the phylum proteobacteria are most prominent among bacteria causing plant diseases that result in a diminution of the quantity and quality of food produced by agriculture. to ameliorate these losses, there is a need to identify infections in early stages. recent developments in next generation nucleic acid sequencing and mass spectrometry open the door to screening plants by the sequences of their macromolecules. such an approach requires the ability to recognize the organismal origin ...	2012	23046503
use of proteomic analysis to elucidate the role of calcium in acetone-butanol-ethanol fermentation by clostridium beijerinckii ncimb 8052.	calcium carbonate increases growth, substrate utilization, and acetone-butanol-ethanol (abe) fermentation by clostridium beijerinckii ncimb 8052. toward an understanding of the basis for these pleiotropic effects, we profiled changes in the c. beijerinckii ncimb 8052 proteome that occur in response to the addition of caco(3). we observed increases in the levels of different heat shock proteins (grpe and dnak), sugar transporters, and proteins involved in dna synthesis, repair, recombination, and ...	2013	23104411