Publications

phylogenomic analysis and predicted physiological role of the proton-translocating nadh:quinone oxidoreductase (complex i) across bacteria.	the proton-translocating nadh:quinone oxidoreductase (complex i) is a multisubunit integral membrane enzyme found in the respiratory chains of both bacteria and eukaryotic organelles. although much research has focused on the enzyme's central role in the mitochondrial respiratory chain, comparatively little is known about its role in the diverse energetic lifestyles of different bacteria. here, we used a phylogenomic approach to better understand the distribution of complex i across bacteria, th ...	2015	25873378
legume-rhizobia signal exchange: promiscuity and environmental effects.	although signal exchange between legumes and their rhizobia is among the best-known examples of this biological process, most of the more characterized data comes from just a few legume species and environmental stresses. although a relative wealth of information is available for some model legumes and some of the major pulses such as soybean, little is known about tropical legumes. this relative disparity in current knowledge is also apparent in the research on the effects of environmental stre ...	2015	26441880
nopc is a rhizobium-specific type 3 secretion system effector secreted by sinorhizobium (ensifer) fredii hh103.	sinorhizobium (ensifer) fredii hh103 is a broad host-range nitrogen-fixing bacterium able to nodulate many legumes, including soybean. in several rhizobia, root nodulation is influenced by proteins secreted through the type 3 secretion system (t3ss). this specialized secretion apparatus is a common virulence mechanism of many plant and animal pathogenic bacteria that delivers proteins, called effectors, directly into the eukaryotic host cells where they interfere with signal transduction pathway ...	2015	26569401
phylogeny of symbiotic genes and the symbiotic properties of rhizobia specific to astragalus glycyphyllos l.	the phylogeny of symbiotic genes of astragalus glycyphyllos l. (liquorice milkvetch) nodule isolates was studied by comparative sequence analysis of noda, nodc, nodh and nifh loci. in all these genes phylograms, liquorice milkvetch rhizobia (closely related to bacteria of three species, i.e. mesorhizobium amorphae, mesorhizobium septentrionale and mesorhizobium ciceri) formed one clearly separate cluster suggesting the horizontal transfer of symbiotic genes from a single ancestor to the bacteria ...	2015	26496493
the sinorhizobium (ensifer) fredii hh103 type 3 secretion system suppresses early defense responses to effectively nodulate soybean.	plants that interact with pathogenic bacteria in their natural environments have developed barriers to block or contain the infection. phytopathogenic bacteria have evolved mechanisms to subvert these defenses and promote infection. thus, the type 3 secretion system (t3ss) delivers bacterial effectors directly into the plant cells to alter host signaling and suppress defenses, providing an appropriate environment for bacterial multiplication. some rhizobial strains possess a symbiotic t3ss that ...	2015	25775271
the sinorhizobium fredii hh103 genome: a comparative analysis with s. fredii strains differing in their symbiotic behavior with soybean.	sinorhizobium fredii hh103 is a fast-growing rhizobial strain infecting a broad range of legumes including both american and asiatic soybeans. in this work, we present the sequencing and annotation of the hh103 genome (7.25 mb), consisting of one chromosome and six plasmids and representing the structurally most complex sinorhizobial genome sequenced so far. comparative genomic analyses of s. fredii hh103 with strains usda257 and ngr234 showed that the core genome of these three strains contains ...	2015	25675256
phenotypic heterogeneity affects stenotrophomonas maltophilia k279a colony morphotypes and β-lactamase expression.	phenotypic heterogeneity at the cellular level in response to various stresses, e.g., antibiotic treatment has been reported for a number of bacteria. in a clonal population, cell-to-cell variation may result in phenotypic heterogeneity that is a mechanism to survive changing environments including antibiotic therapy. stenotrophomonas maltophilia has been frequently isolated from cystic fibrosis patients, can cause numerous infections in other organs and tissues, and is difficult to treat due to ...	2015	26696982
the stress-related, rhizobial small rna rcsr1 destabilizes the autoinducer synthase encoding mrna sini in sinorhizobium meliloti.	quorum sensing is a cell density-dependent communication system of bacteria relying on autoinducer molecules. during the analysis of the post-transcriptional regulation of quorum sensing in the nitrogen fixing plant symbiont sinorhizobium meliloti, we predicted and verified a direct interaction between the 5'-utr of sini mrna encoding the autoinducer synthase and a small rna (srna), which we named rcsr1. in vitro, rcsr1 prevented cleavage in the 5'-utr of sini by rnase e and impaired sini transl ...	2015	26588798
the stress-related, rhizobial small rna rcsr1 destabilizes the autoinducer synthase encoding mrna sini in sinorhizobium meliloti.	quorum sensing is a cell density-dependent communication system of bacteria relying on autoinducer molecules. during the analysis of the post-transcriptional regulation of quorum sensing in the nitrogen fixing plant symbiont sinorhizobium meliloti, we predicted and verified a direct interaction between the 5'-utr of sini mrna encoding the autoinducer synthase and a small rna (srna), which we named rcsr1. in vitro, rcsr1 prevented cleavage in the 5'-utr of sini by rnase e and impaired sini transl ...	2015	26588798
effects of the joint exposure of decabromodiphenyl ether and tetrabromobisphenol a on soil bacterial community structure.	decabromodiphenyl ether (bde209) and tetrabromobisphenol a (tbbpa) are the main contaminants at electronic waste (e-waste) recycling sites (ewrss), and their potential toxicological effects have received extensive attention. however, the impact on soil microorganism of joint exposure to the two chemicals remains almost unknown. therefore, indoor incubation tests were performed on control and contaminated soil samples to determine the response of soil bacterial community structure in the joint pr ...	2015	25106514
efficient heterocyclisation by (di)terpene synthases.	while cyclic ether forming terpene synthases are known, the basis for such heterocyclisation is unclear. here it is reported that numerous (di)terpene synthases, particularly including the ancestral ent-kaurene synthase, efficiently produce isomers of manoyl oxide from the stereochemically appropriate substrate. accordingly, such heterocyclisation is easily accomplished by terpene synthases. indeed, the use of single residue changes to induce production of the appropriate substrate in the upstre ...	2015	26214384
evolution of intra-specific regulatory networks in a multipartite bacterial genome.	reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes. recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution. the evolution of such networks within and outside the species boundary is however still obscure. sinorhizobium meliloti is an ideal species for such study, having three large replicons, many genomes available and a signifi ...	2015	26340565
topological control of the caulobacter cell cycle circuitry by a polarized single-domain pas protein.	despite the myriad of different sensory domains encoded in bacteria, only a few types are known to control the cell cycle. here we use a forward genetic screen for caulobacter crescentus motility mutants to identify a conserved single-domain pas (per-arnt-sim) protein (mopj) with pleiotropic regulatory functions. mopj promotes re-accumulation of the master cell cycle regulator ctra after its proteolytic destruction is triggered by the divj kinase at the g1-s transition. mopj and ctra syntheses a ...	2015	25952018
the sinorhizobium meliloti syrm regulon: effects on global gene expression are mediated by syra and nodd3.	in sinorhizobium meliloti, three nodd transcriptional regulators activate bacterial nodulation (nod) gene expression. nodd1 and nodd2 require plant compounds to activate nod genes. the nodd3 protein does not require exogenous compounds to activate nod gene expression; instead, another transcriptional regulator, syrm, activates nodd3 expression. in addition, nodd3 can activate syrm expression. syrm also activates expression of another gene, syra, which when overexpressed causes a dramatic increas ...	2015	25777671
biofilm formation assessment in sinorhizobium meliloti reveals interlinked control with surface motility.	swarming motility and biofilm formation are opposite, but related surface-associated behaviors that allow various pathogenic bacteria to colonize and invade their hosts. in sinorhizobium meliloti, the alfalfa endosymbiont, these bacterial processes and their relevance for host plant colonization are largely unexplored. our previous work demonstrated distinct swarming abilities in two s. meliloti strains (rm1021 and gr4) and revealed that both environmental cues (iron concentration) and bacterial ...	2015	25887945
thermodynamic matchers for the construction of the cuckoo rna family.	rna family models describe classes of functionally related, non-coding rnas based on sequence and structure conservation. the most important method for modeling rna families is the use of covariance models, which are stochastic models that serve in the discovery of yet unknown, homologous rnas. however, the performance of covariance models in finding remote homologs is poor for rna families with high sequence conservation, while for families with high structure but low sequence conservation, the ...	2015	25779873
a novel family of integrases associated with prophages and genomic islands integrated within the trna-dihydrouridine synthase a (dusa) gene.	genomic islands play a key role in prokaryotic genome plasticity. genomic islands integrate into chromosomal loci such as transfer rna genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. a gene encoding a putative integrase was identified at a single site within the 5' end of the dusa gene in the genomes of over 200 bacteria. this integrase was discovered to be a component of numerous genomic islands, which appear to ...	2015	25883135
mercury reduction and methyl mercury degradation by the soil bacterium xanthobacter autotrophicus py2.	two previously uncharacterized potential broad-spectrum mercury (hg) resistance operons (mer) are present on the chromosome of the soil alphaproteobacteria xanthobacter autotrophicus py2. these operons, mer1 and mer2, contain two features which are commonly found in mer operons in the genomes of soil and marine alphaproteobacteria, but are not present in previously characterized mer operons: a gene for the mercuric reductase (mera) that encodes an alkylmercury lyase domain typical of those found ...	2015	26341208
genomic features separating ten strains of neorhizobium galegae with different symbiotic phenotypes.	the symbiotic phenotype of neorhizobium galegae, with strains specifically fixing nitrogen with either galega orientalis or g. officinalis, has made it a target in research on determinants of host specificity in nitrogen fixation. the genomic differences between representative strains of the two symbiovars are, however, relatively small. this introduced a need for a dataset representing a larger bacterial population in order to make better conclusions on characteristics typical for a subset of t ...	2015	25933608
the repabc plasmids with quorum-regulated transfer systems in members of the rhizobiales divide into two structurally and separately evolving groups.	the large repabc plasmids of the order rhizobiales with class i quorum-regulated conjugative transfer systems often define the nature of the bacterium that harbors them. these otherwise diverse plasmids contain a core of highly conserved genes for replication and conjugation raising the question of their evolutionary relationships. in an analysis of 18 such plasmids these elements fall into two organizational classes, group i and group ii, based on the sites at which cargo dna is located. cladog ...	2015	26590210
secretion systems and signal exchange between nitrogen-fixing rhizobia and legumes.	the formation of symbiotic nitrogen-fixing nodules on the roots and/or stem of leguminous plants involves a complex signal exchange between both partners. since many microorganisms are present in the soil, legumes and rhizobia must recognize and initiate communication with each other to establish symbioses. this results in the formation of nodules. rhizobia within nodules exchange fixed nitrogen for carbon from the legume. symbiotic relationships can become non-beneficial if one partner ceases t ...	2015	26191069
the absence of protein y4ys affects negatively the abundance of t3ss mesorhizobium loti secretin, rhcc2, in bacterial membranes.	mesorhizobium loti maff303099 has a functional type iii secretion system (t3ss) that is involved in the determination of nodulation competitiveness on lotus. the m. loti t3ss cluster contains gene y4ys (mlr8765) that codes for a protein of unknown function (y4ys). a mutation in the y4ys gene favors the m. loti symbiotic competitive ability on lotus tenuis cv. esmeralda and affects negatively the secretion of proteins through t3ss. here we localize y4ys in the bacterial membrane using a translati ...	2015	25688250
genome-guided insight into the methylotrophy of paracoccus aminophilus jcm 7686.	paracoccus aminophilus jcm 7686 (alphaproteobacteria) is a facultative, heterotrophic methylotroph capable of utilizing a wide range of c1 compounds as sole carbon and energy sources. analysis of the jcm 7686 genome revealed the presence of genes involved in the oxidation of methanol, methylamine, dimethylamine, trimethylamine, n,n-dimethylformamide, and formamide, as well as the serine cycle, which appears to be the only c1 assimilatory pathway in this strain. many of these genes are located in ...	2015	26347732
symbiotic potential and survival of native rhizobia kept on different carriers.	native rhizobia are ideal for use as commercial legume inoculants. the characteristics of the carrier used to store the inoculants are important for the survival and symbiotic potential of the rhizobia. the objective of this study was to investigate the effects of peat (peat), perlite sugarcane bagasse (psb), carboxymethyl cellulose plus starch (cmcs), and yeast extract mannitol supplemented with mannitol (yemm) on the survival, nodulation potential and n2 fixation capacity of the native strains ...	2015	26413054
systemic responses of barley to the 3-hydroxy-decanoyl-homoserine lactone producing plant beneficial endophyte acidovorax radicis n35.	quorum sensing auto-inducers of the n-acyl homoserine lactone (ahl) type produced by gram-negative bacteria have different effects on plants including stimulation on root growth and/or priming or acquirement of systemic resistance in plants. in this communication the influence of ahl production of the plant growth promoting endophytic rhizosphere bacterium acidovorax radicis n35 on barley seedlings was investigated. a. radicis n35 produces 3-hydroxy-c10-homoserine lactone (3-oh-c10-hsl) as the m ...	2016	28018401
exopolysaccharide production by sinorhizobium fredii hh103 is repressed by genistein in a nodd1-dependent manner.	in the rhizobia-legume symbiotic interaction, bacterial surface polysaccharides, such as exopolysaccharide (eps), lipopolysaccharide (lps), k-antigen polysaccharide (kps) or cyclic glucans (cg), appear to play crucial roles either acting as signals required for the progression of the interaction and/or preventing host defence mechanisms. the symbiotic significance of each of these polysaccharides varies depending on the specific rhizobia-legume couple. in this work we show that the production of ...	2016	27486751
symbiotic nitrogen fixation and the challenges to its extension to nonlegumes.	access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. there are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation ...	2016	27084023
the effect of root exudate 7,4'-dihydroxyflavone and naringenin on soil bacterial community structure.	our goal was to investigate how root exudate flavonoids influence the soil bacterial community structure and to identify members of the community that change their relative abundance in response to flavonoid exudation. using a model system that approximates flavonoid exudation of medicago sativa roots, we treated a soil with 7,4'-dihydroxyflavone and naringenin in two separate experiments using three different rates: medium (equivalent to the exudation rate of 7,4'-dihydroxyflavone from m. sativ ...	2016	26752410
microsymbiont diversity and phylogeny of native bradyrhizobia associated with soybean (glycine max l. merr.) nodulation in south african soils.	the genetic diversity and identification of slow- and fast-growing soybean root nodule bacterial isolates from different agro-climatic regions in mpumalanga, limpopo and gauteng provinces of south africa were evaluated. the 16s-rdna-rflp analysis of 100 rhizobial isolates and eight reference type strains placed the isolates into six major clusters, and revealed their site-dependent genomic diversity. sequence analysis of single and concatenated housekeeping genes (atpd, glnii and gyrb), as well ...	2016	27324571
rna-seq analysis of differential gene expression responding to different rhizobium strains in soybean (glycine max) roots.	the root nodule symbiosis (rns) between legume plants and rhizobia is the most efficient and productive source of nitrogen fixation, and has critical importance in agriculture and mesology. soybean (glycine max), one of the most important legume crops in the world, establishes a nitrogen-fixing symbiosis with different types of rhizobia, and the efficiency of symbiotic nitrogen fixation in soybean greatly depends on the symbiotic host-specificity. although, it has been reported that rhizobia use ...	2016	27303417
modification of bacterial effector proteins inside eukaryotic host cells.	pathogenic bacteria manipulate their hosts by delivering a number of virulence proteins -called effectors- directly into the plant or animal cells. recent findings have shown that such effectors can suffer covalent modifications inside the eukaryotic cells. here, we summarize the recent reports where effector modifications by the eukaryotic machinery have been described. we restrict our focus on proteins secreted by the type iii or type iv systems, excluding other bacterial toxins. we describe t ...	2016	27489796
the absence of the n-acyl-homoserine-lactone autoinducer synthase genes trai and ngri increases the copy number of the symbiotic plasmid in sinorhizobium fredii ngr234.	plant-released flavonoids induce the transcription of symbiotic genes in rhizobia and one of the first bacterial responses is the synthesis of so called nod factors. they are responsible for the initial root hair curling during onset of root nodule development. this signal exchange is believed to be essential for initiating the plant symbiosis with rhizobia affiliated with the alphaproteobacteria. here, we provide evidence that in the broad host range strain sinorhizobium fredii ngr234 the compl ...	2016	27917168
biochemical and molecular mechanisms of plant-microbe-metal interactions: relevance for phytoremediation.	plants and microbes coexist or compete for survival and their cohesive interactions play a vital role in adapting to metalliferous environments, and can thus be explored to improve microbe-assisted phytoremediation. plant root exudates are useful nutrient and energy sources for soil microorganisms, with whom they establish intricate communication systems. some beneficial bacteria and fungi, acting as plant growth promoting microorganisms (pgpms), may alleviate metal phytotoxicity and stimulate p ...	2016	27446148
succinyl-coa synthetase: new antigen candidate of bartonella bacilliformis.	bartonella bacilliformis is the causative agent of carrion's disease, a neglected illness with mortality rates of 40-85% in the absence of treatment. the lack of a diagnostic technique to overcome misdiagnosis and treat asymptomatic carriers is of note. this study aimed to identify new b. bacilliformis antigenic candidates that could lead to a new diagnostic tool able to be implemented in endemic rural areas.	2016	27627803
crispr-cas defense system and potential prophages in cyanobacteria associated with the coral black band disease.	understanding how pathogens maintain their virulence is critical to developing tools to mitigate disease in animal populations. we sequenced and assembled the first draft genome of roseofilum reptotaenium ao1, the dominant cyanobacterium underlying pathogenicity of the virulent coral black band disease (bbd), and analyzed parts of the bbd-associated geitlerinema sp. bbd_1991 genome in silico. both cyanobacteria are equipped with an adaptive, heritable clustered regularly interspaced short palind ...	2016	28066391
phylogenetic distribution and evolutionary pattern of an α-proteobacterial small rna gene that controls polyhydroxybutyrate accumulation in sinorhizobium meliloti.	it has become clear that srnas play relevant regulatory functions in bacteria. however, a comprehensive understanding of their biological roles considering evolutionary aspects has not been achieved for most of them. thus, we have characterized the evolutionary and phylogenetic aspects of the sinorhizobium meliloti mmgr gene encoding the small rna mmgr, which has been recently reported to be involved in the regulation of polyhydroxybutyrate accumulation in this bacterium. we constructed a covari ...	2016	27033949
computational approach to predict species-specific type iii secretion system (t3ss) effectors using single and multiple genomes.	many gram-negative bacteria use type iii secretion systems (t3sss) to translocate effector proteins into host cells. t3ss effectors can give some bacteria a competitive edge over others within the same environment and can help bacteria to invade the host cells and allow them to multiply rapidly within the host. therefore, developing efficient methods to identify effectors scattered in bacterial genomes can lead to a better understanding of host-pathogen interactions and ultimately to important m ...	2016	27993130
phylogenetic diversity of ammopiptanthus rhizobia and distribution of rhizobia associated with ammopiptanthus mongolicus in diverse regions of northwest china.	aiming to investigate the diversity and distribution of rhizobia associated with ammopiptanthus, an endangered evergreen legume widely distributed in deserts, we characterized a total of 219 nodule isolates from nine sampling sites in northwest china with different soil characteristics based upon restriction fragment length polymorphism (rflp) analysis of 16s ribosomal rna (rrna) and symbiotic genes (nodc and nifh). ten isolates representing different 16s rrna-rflp types were selected for furthe ...	2016	27079453
the regulatory protein rosr affects rhizobium leguminosarum bv. trifolii protein profiles, cell surface properties, and symbiosis with clover.	rhizobium leguminosarum bv. trifolii is capable of establishing a symbiotic relationship with plants from the genus trifolium. previously, a regulatory protein encoded by rosr was identified and characterized in this bacterium. rosr possesses a cys2-his2-type zinc finger motif and belongs to ros/mucr family of rhizobial transcriptional regulators. transcriptome profiling of the rosr mutant revealed a role of this protein in several cellular processes, including the synthesis of cell-surface comp ...	2016	27602024
a transcriptomic analysis of the effect of genistein on sinorhizobium fredii hh103 reveals novel rhizobial genes putatively involved in symbiosis.	sinorhizobium fredii hh103 is a rhizobial soybean symbiont that exhibits an extremely broad host-range. flavonoids exuded by legume roots induce the expression of rhizobial symbiotic genes and activate the bacterial protein nodd, which binds to regulatory dna sequences called nod boxes (nb). nb drive the expression of genes involved in the production of molecular signals (nod factors) as well as the transcription of ttsi, whose encoded product binds to tts boxes (tb), inducing the secretion of p ...	2016	27539649
quorum sensing and the use of quorum quenchers as natural biocides to inhibit sulfate-reducing bacteria.	sulfate-reducing bacteria (srb) are one of the main protagonist groups of biocorrosion in the seawater environment. given their principal role in biocorrosion, it remains a crucial task to develop strategies to reduce the abundance of srbs. conventional approaches include the use of biocides and antibiotics, which can impose health, safety, and environmental concerns. this review examines an alternative approach to this problem. this is achieved by reviewing the role of quorum sensing (qs) in sr ...	2016	27983678
novel cupriavidus strains isolated from root nodules of native uruguayan mimosa species.	the large legume genus mimosa is known to be associated with both alphaproteobacterial and betaproteobacterial symbionts, depending on environment and plant taxonomy, e.g., brazilian species are preferentially nodulated by burkholderia, whereas those in mexico are associated with alphaproteobacterial symbionts. little is known, however, about the symbiotic preferences of mimosa spp. at the southern subtropical limits of the genus. in the present study, rhizobia were isolated from field-collected ...	2016	26994087
rna-seq analysis of the rhizobium tropici ciat 899 transcriptome shows similarities in the activation patterns of symbiotic genes in the presence of apigenin and salt.	rhizobium tropici strain ciat 899 establishes effective symbioses with several legume species, including phaseolus vulgaris and leucaena leucocephala. this bacterium synthesizes a large variety of nodulation factors in response to nod-gene inducing flavonoids and, surprisingly, also under salt stress conditions. the aim of this study was to identify differentially expressed genes in the presence of both inducer molecules, and analyze the promoter regions located upstream of these genes.	2016	26951045
genome sequence of shinella sp. strain dd12, isolated from homogenized guts of starved daphnia magna.	shinella sp. strain dd12, a novel phosphite assimilating bacterium, has been isolated from homogenized guts of 4 days starved zooplankton daphnia magna. here we report the draft genome of this bacterium, which comprises 7,677,812 bp and 7505 predicted protein-coding genes.	2016	26865909
the sinorhizobium fredii hh103 mucr1 global regulator is connected with the nod regulon and is required for efficient symbiosis with lotus burttii and glycine max cv. williams.	sinorhizobium fredii hh103 is a rhizobial strain showing a broad host range of nodulation. in addition to the induction of bacterial nodulation genes, transition from a free-living to a symbiotic state requires complex genetic expression changes with the participation of global regulators. we have analyzed the role of the zinc-finger transcriptional regulator mucr1 from s. fredii hh103 under both free-living conditions and symbiosis with two hh103 host plants, glycine max and lotus burttii. inac ...	2016	27482821
ensifer glycinis sp. nov., a rhizobial species associated with species of the genus glycine.	rhizobial strains from root nodules of astragalus mongholicus and soybean (glycine max) were characterized phylogenetically as members of the genus ensifer (formerly named sinorhizobium), based on 16s rrna gene sequence comparisons. results based upon concatenated sequence analysis of three housekeeping genes (reca, atpd and glnii, ≤ 93.8 % similarities to known species) and average nucleotide identity (ani) values of whole genome sequence comparisons (ranging from 89.6 % to 83.4 % to ensifer fr ...	2016	27125987
improvement in nitrogen fixation capacity could be part of the domestication process in soybean.	biological nitrogen fixation (bnf) in soybeans is a complex process involving the interplay between the plant host and the symbiotic rhizobia. as nitrogen supply has a crucial role in growth and development, higher nitrogen fixation capacity would be important to achieve bigger plants and larger seeds, which were important selection criteria during plant domestication by humans. to test this hypothesis, we monitored the nitrogen fixation-related performance in 31 cultivated and 17 wild soybeans ...	2016	27118154
mucr is required for transcriptional activation of conserved ion transporters to support nitrogen fixation of sinorhizobium fredii in soybean nodules.	to achieve effective symbiosis with legume, rhizobia should fine-tune their background regulation network in addition to activating key genes involved in nodulation (nod) and nitrogen fixation (nif). here, we report that an ancestral zinc finger regulator, mucr1, other than its paralog, mucr2, carrying a frameshift mutation, is essential for supporting nitrogen fixation of sinorhizobium fredii ccbau45436 within soybean nodules. in contrast to the chromosomal mucr1, mucr2 is located on symbiosis ...	2016	26883490
genomic resources for identification of the minimal n2 -fixing symbiotic genome.	the lack of an appropriate genomic platform has precluded the use of gain-of-function approaches to study the rhizobium-legume symbiosis, preventing the establishment of the genes necessary and sufficient for symbiotic nitrogen fixation (snf) and potentially hindering synthetic biology approaches aimed at engineering this process. here, we describe the development of an appropriate system by reverse engineering sinorhizobium meliloti. using a novel in vivo cloning procedure, the enga-trna-rmlc ( ...	2016	26768651
sinorhizobium fredii hh103 bacteroids are not terminally differentiated and show altered o-antigen in nodules of the inverted repeat-lacking clade legume glycyrrhiza uralensis.	in rhizobial species that nodulate inverted repeat-lacking clade (irlc) legumes, such as the interaction between sinorhizobium meliloti and medicago, bacteroid differentiation is driven by an endoreduplication event that is induced by host nodule-specific cysteine rich (ncr) antimicrobial peptides and requires the participation of the bacterial protein baca. we have studied bacteroid differentiation of sinorhizobium fredii hh103 in three host plants: glycine max, cajanus cajan and the irlc legum ...	2016	26521863
construction and pilot screening of a signature-tagged mutant library of sinorhizobium fredii.	sinorhizobium fredii is well known for its ability to establish symbiosis with diverse legumes such as glycine max (soybean, determinate nodules) and cajanus cajan (pigeon pea, indeterminate nodules). in order to make screening of s. fredii genes related to symbiosis cost-effective, we constructed a large tn5 insertion mutant library of s. fredii ccbau45436 using the signature-tagged mutagenesis (stm) technique. this stm library contains a total of 25,500 independent mutants distributed in 17 su ...	2016	26472206
sinorhizobium fredii hh103 invades lotus burttii by crack entry in a nod factor-and surface polysaccharide-dependent manner.	sinorhizobium fredii hh103-rif(r), a broad host range rhizobial strain, induces nitrogen-fixing nodules in lotus burttii but ineffective nodules in l. japonicus. confocal microscopy studies showed that mesorhizobium loti maff303099 and s. fredii hh103-rif(r) invade l. burttii roots through infection threads or epidermal cracks, respectively. infection threads in root hairs were not observed in l. burttii plants inoculated with s. fredii hh103-rif(r). a s. fredii hh103-rif(r) noda mutant failed t ...	2016	27827003
bacterial β-kdo glycosyltransferases represent a new glycosyltransferase family (gt99).	kdo (3-deoxy-d-manno-oct-2-ulosonic acid) is an eight-carbon sugar mostly confined to gram-negative bacteria. it is often involved in attaching surface polysaccharides to their lipid anchors. α-kdo provides a bridge between lipid a and the core oligosaccharide in all bacterial lpss, whereas an oligosaccharide of β-kdo residues links "group 2" capsular polysaccharides to (lyso)phosphatidylglycerol. β-kdo is also found in a small number of other bacterial polysaccharides. the structure and functio ...	2016	27199480
molecular detection and environment-specific diversity of glycosyl hydrolase family 1 β-glucosidase in different habitats.	β-glucosidase is a crucial element of the microbial cellulose multienzyme complex since it is responsible for the regulation of the entire cellulose hydrolysis process. therefore, the aim of the present work was to explore the diversity and distribution of glycosyl hydrolase family 1 β-glucosidase genes in three different environmental niches including, himalayan soil, cow dung and compost by metagenomic approach. preliminary evaluation through metabolic profiling using biolog based utilization ...	2016	27790196
high-quality permanent draft genome sequence of ensifer sp. pc2, isolated from a nitrogen-fixing root nodule of the legume tree (khejri) native to the thar desert of india.	ensifer sp. pc2 is an aerobic, motile, gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume p. cineraria (l.) druce (khejri), which is a keystone species that grows in arid and semi-arid regions of the indian thar desert. strain pc2 exists as a dominant saprophyte in alkaline soils of western rajasthan. it is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as speci ...	2016	27340511
bacterial molecular signals in the sinorhizobium fredii-soybean symbiosis.	sinorhizobium (ensifer) fredii (s. fredii) is a rhizobial species exhibiting a remarkably broad nodulation host-range. thus, s. fredii is able to effectively nodulate dozens of different legumes, including plants forming determinate nodules, such as the important crops soybean and cowpea, and plants forming indeterminate nodules, such as glycyrrhiza uralensis and pigeon-pea. this capacity of adaptation to different symbioses makes the study of the molecular signals produced by s. fredii strains ...	2016	27213334
genetic analysis reveals the essential role of nitrogen phosphotransferase system components in sinorhizobium fredii ccbau 45436 symbioses with soybean and pigeonpea plants.	the nitrogen phosphotransferase system (pts(ntr)) consists of ei(ntr), npr, and eiia(ntr). the active phosphate moiety derived from phosphoenolpyruvate is transferred through ei(ntr) and npr to eiia(ntr). sinorhizobium fredii can establish a nitrogen-fixing symbiosis with the legume crops soybean (as determinate nodules) and pigeonpea (as indeterminate nodules). in this study, s. fredii strains with mutations in ptsp and ptso (encoding ei(ntr) and npr, respectively) formed ineffective nodules on ...	2016	26682851
estimating divergence times and substitution rates in rhizobia.	accurate estimation of divergence times of soil bacteria that form nitrogen-fixing associations with most leguminous plants is challenging because of a limited fossil record and complexities associated with molecular clocks and phylogenetic diversity of root nodule bacteria, collectively called rhizobia. to overcome the lack of fossil record in bacteria, divergence times of host legumes were used to calibrate molecular clocks and perform phylogenetic analyses in rhizobia. the 16s rrna gene and i ...	2016	27168719
swimming performance of bradyrhizobium diazoefficiens is an emergent property of its two flagellar systems.	many bacterial species use flagella for self-propulsion in aqueous media. in the soil, which is a complex and structured environment, water is found in microscopic channels where viscosity and water potential depend on the composition of the soil solution and the degree of soil water saturation. therefore, the motility of soil bacteria might have special requirements. an important soil bacterial genus is bradyrhizobium, with species that possess one flagellar system and others with two different ...	2016	27053439
evolutionary switches between two serine codon sets are driven by selection.	serine is the only amino acid that is encoded by two disjoint codon sets so that a tandem substitution of two nucleotides is required to switch between the two sets. previously published evidence suggests that, for the most evolutionarily conserved serines, the codon set switch occurs by simultaneous substitution of two nucleotides. here we report a genome-wide reconstruction of the evolution of serine codons in triplets of closely related species from diverse prokaryotes and eukaryotes. the res ...	2016	27799560
the novel regulatory ncrna, nfis, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifk mrna in pseudomonas stutzeri a1501.	unlike most pseudomonas, the root-associated bacterium pseudomonas stutzeri a1501 fixes nitrogen after the horizontal acquisition of a nitrogen-fixing (nif) island. a genome-wide search for small noncoding rnas (ncrnas) in p. stutzeri a1501 identified the novel p. stutzeri-specific ncrna nfis in the core genome, whose synthesis was significantly induced under nitrogen fixation or sorbitol stress conditions. the expression of nfis was rna chaperone hfq-dependent and activated by the sigma factor ...	2016	27407147
genetic characterization of soybean rhizobia isolated from different ecological zones in north-eastern afghanistan.	seventy rhizobial isolates were obtained from the root nodules of two soybean (glycine max) cultivars: japanese cultivar enrei and usa cultivar stine3300, which were inoculated with different soil samples from afghanistan. in order to study the genetic properties of the isolates, the dna sequences of the 16s rrna gene and symbiotic genes (nodd1 and nifd) were elucidated. furthermore, the isolates were inoculated into the roots of two soybean cultivars, and root nodule numbers and nitrogen fixati ...	2017	28321006
the overproduction of indole-3-acetic acid (iaa) in endophytes upregulates nitrogen fixation in both bacterial cultures and inoculated rice plants.	endophytic bacteria from roots and leaves of rice plants were isolated and identified in order to select the diazotrophs and improve their nitrogen-fixing abilities. the nitrogen-fixing endophytes were identified by pcr amplification of the nifh gene fragment. for this purpose, two isolates, enterobacter cloacae rca25 and klebsiella variicola rca26, and two model bacteria (herbaspirillum seropedicae z67 and sinorhizobium fredii ngr234) were transformed to increase the biosynthesis of the main pl ...	2017	28197647
high-quality draft genome sequence of rhizobium mesoamericanum strain stm6155, a mimosa pudica microsymbiont from new caledonia.	rhizobium mesoamericanum stm6155 (inscd = atyy01000000) is an aerobic, motile, gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume mimosa pudica l.. stm6155 was isolated in 2009 from a nodule of the trap host m. pudica grown in nickel-rich soil collected near mont dore, new caledonia. r. mesoamericanum stm6155 was selected as part of the doe joint genome institute 2010 genomic encyclopedia for bacteria and archae ...	2017	28116041
a novel symbiovar (aegeanense) of the genus ensifer nodulates vigna unguiculata.	cowpea (vigna unguiculata) forms nitrogen-fixing root nodules with diverse symbiotic bacteria, mainly slow-growing rhizobial species belonging to the genus bradyrhizobium, although a few studies have reported the isolation of fast-growing rhizobia under laboratory and field conditions. although much research has been done on cowpea-nodulating bacteria in various countries around the world, very limited information is available on cowpea rhizobia in european soils. the aim of this study was to st ...	2017	28220509
ensifer shofinae sp. nov., a novel rhizobial species isolated from root nodules of soybean (glycine max).	two bacterial strains isolated from root nodules of soybean were characterized phylogenetically as members of a distinct group in the genus ensifer based on 16s rrna gene comparisons. they were also verified as a separated group by the concatenated sequence analyses of reca, atpd and glnii (with similarities ≤93.9% to the type strains for defined species), and by the average nucleotide identities (ani) between the whole genome sequence of the representative strain ccbau 251167(t) and those of th ...	2017	28209394
elucidation of gibberellin biosynthesis in bacteria reveals convergent evolution.	gibberellins (gas) are crucial phytohormones involved in many aspects of plant growth and development, including plant-microbe interactions, which has led to ga production by plant-associated fungi and bacteria as well. while the ga biosynthetic pathways in plants and fungi have been elucidated and found to have arisen independently through convergent evolution, little has been uncovered about ga biosynthesis in bacteria. some nitrogen-fixing, symbiotic, legume-associated rhizobia, including bra ...	2017	27842068
the sinorhizobium (ensifer) fredii hh103 nodulation outer protein nopi is a determinant for efficient nodulation of soybean and cowpea plants.	the type iii secretion system (t3ss) is a specialized secretion apparatus that is commonly used by many plant and animal pathogenic bacteria to deliver proteins, termed effectors, to the interior of the host cells. these effectors suppress host defenses and interfere with signal transduction pathways to promote infection. some rhizobial strains possess a functional t3ss, which is involved in the suppression of host defense responses, host range determination, and symbiotic efficiency. the analys ...	2017	27986730
a putative 3-hydroxyisobutyryl-coa hydrolase is required for efficient symbiotic nitrogen fixation in sinorhizobium meliloti and sinorhizobium fredii ngr234.	we report that the smb20752 gene of the alfalfa symbiont sinorhizobium meliloti is a novel symbiotic gene required for full n2 -fixation. deletion of smb20752 resulted in lower nitrogenase activity and smaller nodules without impacting overall nodule morphology. orthologs of smb20752 were present in all alpha and beta rhizobia, including the ngr_b20860 gene of sinorhizobium fredii ngr234. a ngr_b20860 mutant formed fix(-) determinate nodules that developed normally to a late stage of the symbios ...	2017	27727485
genomic characterization of ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from asian, african and american deserts.	nitrogen fixing bacteria isolated from hot arid areas in asia, africa and america but from diverse leguminous plants have been recently identified as belonging to a possible new species of ensifer (sinorhizobium). in this study, 6 strains belonging to this new clade were compared with ensifer species at the genome-wide level. their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined.	2017	28088165