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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 ...201627602024
nitrogen fixation and molecular oxygen: comparative genomic reconstruction of transcription regulation in alphaproteobacteria.biological nitrogen fixation plays a crucial role in the nitrogen cycle. an ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of bacteria and archaea. the transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the class alphaproteobacteria. this regulatory network includes the activator of nitrogen fixation nifa, working in tandem with the alternative sigma-factor rpon as well as oxygen-respons ...201627617010
new insights into nod factor biosynthesis: analyses of chitooligomers and lipo-chitooligomers of rhizobium sp. irbg74 mutants.soil-dwelling, nitrogen-fixing rhizobia signal their presence to legume hosts by secreting lipo-chitooligomers (lcos) that are decorated with a variety of chemical substituents. it has long been assumed, but never empirically shown, that the lco backbone is synthesized first by nodc, nodb, and noda, followed by addition of one or more substituents by other nod proteins. by analyzing a collection of in-frame deletion mutants of key nod genes in the bacterium rhizobium sp. irbg74 by mass spectrome ...201627623438
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.201627627803
mitigation of soil n2o emission by inoculation with a mixed culture of indigenous bradyrhizobium diazoefficiens.agricultural soil is the largest source of nitrous oxide (n2o), a greenhouse gas. soybean is an important leguminous crop worldwide. soybean hosts symbiotic nitrogen-fixing soil bacteria (rhizobia) in root nodules. in soybean ecosystems, n2o emissions often increase during decomposition of the root nodules. our previous study showed that n2o reductase can be used to mitigate n2o emission from soybean fields during nodule decomposition by inoculation with nosz++ strains [mutants with increased n2 ...201627633524
characterization of crude oil degrading bacteria isolated from contaminated soils surrounding gas stations.a total of twenty bacterial cultures were isolated from hydrocarbon contaminated soil. of the 20 isolates, ram03, ram06, ram13, and ram17 were specifically chosen based on their relatively higher growth on salt medium amended with 4 % crude oil, emulsion index, surface tension, and degradation percentage. these bacterial cultures had 16s rrna gene sequences that were most similar to ochrobactrum cytisi (ram03), ochrobactrum anthropi (ram06 and ram17), and sinorhizobium meliloti (ram13) with 96 % ...201627655077
rhizobial inoculation increases soil microbial functioning and gum arabic production of 13-year-old senegalia senegal (l.) britton, trees in the north part of senegal.rhizobial inoculation has been widely used in controlled conditions as a substitute for chemical fertilizers to increase plants growth and productivity. however, very little is known about such effects on mature trees in natural habitats. in this study, we investigated the effect of rhizobial inoculation on soil total microbial biomass, mineral nitrogen content, potential co2 respiration, fluorescein diacetate (fda), acid phosphatase activities, and gum arabic production by 13-year-old senegalia ...201627656192
titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers.soils are facing new environmental stressors, such as titanium dioxide nanoparticles (tio2-nps). while these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. here we report the response of the microbial community of an agricultural soil exposed over 90 days to tio2-nps (1 and 500 mg kg(-1) dry soil). to assess their impact on soil function, we focused on the nitrogen cycl ...201627659196
diverse bacteria with lignin degrading potentials isolated from two ranks of coal.taking natural coal as a "seed bank" of bacterial strains able to degrade lignin that is with molecular structure similar to coal components, we isolated 393 and 483 bacterial strains from a meager lean coal sample from hancheng coalbed and a brown coal sample from bayannaoer coalbed, respectively, by using different media. statistical analysis showed that isolates were significantly more site-specific than medium-specific. of the 876 strains belonging to 27 genera in actinobacteria, firmicutes, ...201627667989
structures of proline utilization a (puta) reveal the fold and functions of the aldehyde dehydrogenase superfamily domain of unknown function.aldehyde dehydrogenases (aldhs) catalyze the nad(p)(+)-dependent oxidation of aldehydes to carboxylic acids and are important for metabolism and detoxification. although the aldh superfamily fold is well established, some aldhs contain an uncharacterized domain of unknown function (duf) near the c terminus of the polypeptide chain. herein, we report the first structure of a protein containing the aldh superfamily duf. proline utilization a from sinorhizobium meliloti (smputa) is a 1233-residue b ...201627679491
bacterial multidrug efflux pumps: much more than antibiotic resistance determinants.bacterial multidrug efflux pumps are antibiotic resistance determinants present in all microorganisms. with few exceptions, they are chromosomally encoded and present a conserved organization both at the genetic and at the protein levels. in addition, most, if not all, strains of a given bacterial species present the same chromosomally-encoded efflux pumps. altogether this indicates that multidrug efflux pumps are ancient elements encoded in bacterial genomes long before the recent use of antibi ...201627681908
functional analysis of prka - a putative serine protein kinase from mesorhizobium alhagi ccnwxj12-2 - in stress resistance.serine/threonine protein kinases are highly conserved kinases with a wide distribution in microbes and with multiple functions. mesorhizobium alhagi ccnwxj12-2, a α-proteobacterium which could be able to form symbiosis with alhagi sparsifolia in northwest of china, contains a putative prka-family serine protein kinase, prka. in our previous study, the expression of prka was found to be downregulated in high-salt conditions. to elucidate the function of m. alhagi prka, a prka deletion mutant was ...201627686068
multidrug efflux pumps at the crossroad between antibiotic resistance and bacterial virulence.multidrug efflux pumps can be involved in bacterial resistance to antibiotics at different levels. some efflux pumps are constitutively expressed at low levels and contribute to intrinsic resistance. in addition, their overexpression may allow higher levels of resistance. this overexpression can be transient, in the presence of an effector (phenotypic resistance), or constitutive when mutants in the regulatory elements of the expression of efflux pumps are selected (acquired resistance). efflux ...201627708632
regulation of fixlj by hfq controls symbiotically important genes in sinorhizobium meliloti.the rna-binding chaperone hfq plays critical roles in the establishment and functionality of the symbiosis between sinorhizobium meliloti and its legume hosts. a mutation in hfq reduces symbiotic efficiency resulting in a fix(-) phenotype, characterized by the inability of the bacterium to fix nitrogen. at least in part, this is due to the ability of hfq to regulate the fixlj operon, which encodes a sensor kinase-response regulator pair that controls expression of the nitrogenase genes. the abil ...201627712144
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 ...201727727485
functionality of in vitro reconstituted group ii intron rmint1-derived ribonucleoprotein particles.the functional unit of mobile group ii introns is a ribonucleoprotein particle (rnp) consisting of the intron-encoded protein (iep) and the excised intron rna. the iep has reverse transcriptase activity but also promotes rna splicing, and the rna-protein complex triggers site-specific dna insertion by reverse splicing, in a process called retrohoming. in vitro reconstituted ribonucleoprotein complexes from the lactococcus lactis group ii intron ll.ltrb, which produce a double strand break, have ...201627730127
interkingdom responses to bacterial quorum sensing signals regulate frequency and rate of nodulation in legume-rhizobia symbiosis.density-dependent phenotypic switching in bacteria, the phenomenon of quorum sensing (qs), is instrumental in many pathogenic and mutualistic behaviors. in many gram-negative bacteria, qs is regulated by n-acylated-l-homoserine lactones (ahls). synthetic analogues of these ahls hold significant promise for regulating qs at the host-symbiont interface. regulation depends on refined temporal and spatial models of quorums under native conditions. critical to this is an understanding of how the pres ...201627739645
plant drought tolerance enhancement by trehalose production of desiccation-tolerant microorganisms.a collection of desiccation-tolerant xeroprotectant-producing microorganisms was screened for their ability to protect plants against drought, and their role as plant growth-promoting rhizobacteria was investigated in two different crops (tomato and pepper). the most commonly described biochemical mechanisms for plant protection against drought by microorganisms including the production of phytohormones, antioxidants and xeroprotectants were analyzed. in particular, the degree of plant protectio ...201627746776
a proteomic atlas of the legume medicago truncatula and its nitrogen-fixing endosymbiont sinorhizobium meliloti.legumes are essential components of agricultural systems because they enrich the soil in nitrogen and require little environmentally deleterious fertilizers. a complex symbiotic association between legumes and nitrogen-fixing soil bacteria called rhizobia culminates in the development of root nodules, where rhizobia fix atmospheric nitrogen and transfer it to their plant host. here we describe a quantitative proteomic atlas of the model legume medicago truncatula and its rhizobial symbiont sinor ...201627748755
sinorhizobium meliloti chemotaxis to quaternary ammonium compounds is mediated by the chemoreceptor mcpx.the bacterium sinorhizobium meliloti is attracted to seed exudates of its host plant alfalfa (medicago sativa). since quaternary ammonium compounds (qacs) are exuded by germinating seeds, we assayed chemotaxis of s. meliloti towards betonicine, choline, glycine betaine, stachydrine and trigonelline. the wild type displayed a positive response to all qacs. using lc-ms, we determined that each germinating alfalfa seed exuded qacs in the nanogram range. compared to the closely related nonhost speci ...201727748981
matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity.sulfatases cleave sulfate groups from various molecules and constitute a biologically and industrially important group of enzymes. however, the number of sulfatases whose substrate has been characterized is limited in comparison to the huge diversity of sulfated compounds, yielding functional annotations of sulfatases particularly prone to flaws and misinterpretations. in the context of the explosion of genomic data, a classification system allowing a better prediction of substrate specificity a ...201627749924
surface properties of wild-type rhizobium leguminosarum bv. trifolii strain 24.2 and its derivatives with different extracellular polysaccharide content.rhizobium leguminosarum bv. trifolii is a soil bacterium able to establish symbiosis with agriculturally important legumes, i.e., clover plants (trifolium spp.). cell surface properties of rhizobia play an essential role in their interaction with both biotic and abiotic surfaces. physicochemical properties of bacterial cells are underpinned by the chemical composition of their envelope surrounding the cells, and depend on various environmental conditions. in this study, we performed a comprehens ...201627760230
a direct-sensing galactose chemoreceptor recently evolved in invasive strains of campylobacter jejuni.a rare chemotaxis receptor, tlp11, has been previously identified in invasive strains of campylobacter jejuni, the most prevalent cause of bacterial gastroenteritis worldwide. here we use glycan and small-molecule arrays, as well as surface plasmon resonance, to show that tlp11 specifically interacts with galactose. tlp11 is required for the chemotactic response of c. jejuni to galactose, as shown using wild type, allelic inactivation and addition mutants. the inactivated mutant displays reduced ...201627762269
negative regulation of ectoine uptake and catabolism in sinorhizobium meliloti: characterization of the ehur gene.ectoine has osmoprotective effects on sinorhizobium meliloti that differ from its effects in other bacteria. ectoine does not accumulate in s. meliloti cells; instead, it is degraded. the products of the ehuabcd-eutabcde operon were previously discovered to be responsible for the uptake and catabolism of ectoine in s. meliloti however, the mechanism by which ectoine is involved in the regulation of the ehuabcd-eutabcde operon remains unclear. the ehur gene, which is upstream of and oriented in t ...201727795315
the conserved dcw gene cluster of r. sphaeroides is preceded by an uncommonly extended 5' leader featuring the srna upsm.cell division and cell wall synthesis mechanisms are similarly conserved among bacteria. consequently some bacterial species have comparable sets of genes organized in the dcw (division and cell wall) gene cluster. dcw genes, their regulation and their relative order within the cluster are outstandingly conserved among rod shaped and gram negative bacteria to ensure an efficient coordination of growth and division. a well studied representative is the dcw gene cluster of e. coli. the first promo ...201627802301
comparative genomics of pseudomonas syringae pathovar tomato reveals novel chemotaxis pathways associated with motility and plant pathogenicity.the majority of bacterial foliar plant pathogens must invade the apoplast of host plants through points of ingress, such as stomata or wounds, to replicate to high population density and cause disease. how pathogens navigate plant surfaces to locate invasion sites remains poorly understood. many bacteria use chemical-directed regulation of flagellar rotation, a process known as chemotaxis, to move towards favorable environmental conditions. chemotactic sensing of the plant surface is a potential ...201627812402
reactive oxygen species generation-scavenging and signaling during plant-arbuscular mycorrhizal and piriformospora indica interaction under stress condition.a defined balance between the generation and scavenging of reactive oxygen species (ros) is essential to utilize ros as an adaptive defense response of plants under biotic and abiotic stress conditions. moreover, ros are not only a major determinant of stress response but also act as signaling molecule that regulates various cellular processes including plant-microbe interaction. in particular, rhizosphere constitutes the biologically dynamic zone for plant-microbe interactions which forms a mut ...201627818671
optical disassembly of cellular clusters by tunable 'tug-of-war' tweezers.bacterial biofilms underlie many persistent infections, posing major hurdles in antibiotic treatment. here we design and demonstrate 'tug-of-war' optical tweezers that can facilitate the assessment of cell-cell adhesion-a key contributing factor to biofilm development, thanks to the combined actions of optical scattering and gradient forces. with a customized optical landscape distinct from that of conventional tweezers, not only can such 'tug-of-war' tweezers stably trap and stretch a rod-shape ...201627818838
biological function of a polysaccharide degrading enzyme in the periplasm.carbohydrate polymers are industrially and medically important. for instance, a polysaccharide, alginate (from seaweed), is widely used in food, textile and pharmaceutical industries. certain bacteria also produce alginate through membrane spanning multi-protein complexes. using pseudomonas aeruginosa as a model organism, we investigated the biological function of an alginate degrading enzyme, algl, in alginate production and biofilm formation. we showed that algl negatively impacts alginate pro ...201627824067
microbial interactions: ecology in a molecular perspective.the microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. these interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. in addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial communi ...201627825606
crystal structure of bacterial haem importer complex in the inward-facing conformation.pathogenic bacteria remove iron from the haem of host tissues and use it as a catalytic center of many enzymes. haem uptake by pathogenic bacteria is facilitated by the membrane-integrated haem importer, which belongs to the type ii atp-binding cassette (abc) transporter. here we present crystal structures of burkholderia cenocepacia haem importer bhuuv complexed with the periplasmic haem-binding protein bhut and in the absence of bhut. the transmembrane helices of these structures show an inwar ...201627830695
identification of ybey-protein interactions involved in 16s rrna maturation and stress regulation in escherichia coli.ybey is part of a core set of rnases in escherichia coli and other bacteria. this highly conserved endoribonuclease has been implicated in several important processes such as 16s rrna 3' end maturation, 70s ribosome quality control, and regulation of mrnas and small noncoding rnas, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. thus, ybey likely interacts with numerous protein or rna partners that are involved in various aspects of cell ...201627834201
small regulatory rnas of rickettsia conorii.small regulatory rnas comprise critically important modulators of gene expression in bacteria, yet very little is known about their prevalence and functions in rickettsia species. r. conorii, the causative agent of mediterranean spotted fever, is a tick-borne pathogen that primarily infects microvascular endothelium in humans. we have determined the transcriptional landscape of r. conorii during infection of human microvascular endothelial cells (hmecs) by strand-specific rna sequencing to ident ...201627834404
transcriptional responses of the bacterium burkholderia terrae bs001 to the fungal host lyophyllum sp. strain karsten under soil-mimicking conditions.in this study, the mycosphere isolate burkholderia terrae bs001 was confronted with the soil fungus lyophyllum sp. strain karsten on soil extract agar plates in order to examine its transcriptional responses over time. at the initial stages of the experiment (t1-day 3; t2-day 5), contact between both partner organisms was absent, whereas in the final stage (t3-day 8), the two populations made intimate physical contact. overall, a strong modulation of the strain bs001 gene expression patterns was ...201627844108
transcriptional responses of the bacterium burkholderia terrae bs001 to the fungal host lyophyllum sp. strain karsten under soil-mimicking conditions.in this study, the mycosphere isolate burkholderia terrae bs001 was confronted with the soil fungus lyophyllum sp. strain karsten on soil extract agar plates in order to examine its transcriptional responses over time. at the initial stages of the experiment (t1-day 3; t2-day 5), contact between both partner organisms was absent, whereas in the final stage (t3-day 8), the two populations made intimate physical contact. overall, a strong modulation of the strain bs001 gene expression patterns was ...201627844108
introducing a clustering step in a consensus approach for the scoring of protein-protein docking models.correctly scoring protein-protein docking models to single out native-like ones is an open challenge. it is also an object of assessment in capri (critical assessment of predicted interactions), the community-wide blind docking experiment. we introduced in the field the first pure consensus method, consrank, which ranks models based on their ability to match the most conserved contacts in the ensemble they belong to. in capri, scorers are asked to evaluate a set of available models and select th ...201627846259
characterisation of a new family of carboxyl esterases with an osmc domain.proteins in the serine esterase family are widely distributed in bacterial phyla and display activity against a range of biologically produced and chemically synthesized esters. a serine esterase from the psychrophilic bacterium pseudoalteromonas arctica with a c-terminal osmc-like domain was recently characterized; here we report on the identification and characterization of further putative esterases with osmc-like domains constituting a new esterase family that is found in a variety of bacter ...201627851780
the evolution of symbiont preference traits in the model legume medicago truncatula.many hosts preferentially associate with or reward better symbionts, but how these symbiont preference traits evolve is an open question. legumes often form more nodules with or provide more resources to rhizobia that fix more nitrogen (n), but they also acquire n from soil via root foraging. it is unclear whether root responses to abiotically and symbiotically derived n evolve independently. here, we measured root foraging and both preferential allocation of root resources to and preferential a ...201727864973
a developmental and molecular view of formation of auxin-induced nodule-like structures in land plants.several studies have shown that plant hormones play important roles during legume-rhizobia symbiosis. for instance, auxins induce the formation of nodule-like structures (nlss) on legume roots in the absence of rhizobia. furthermore, these nls can be colonized by nitrogen-fixing bacteria, which favor nitrogen fixation compared to regular roots and subsequently increase plant yield. interestingly, auxin also induces similar nls in cereal roots. while several genetic studies have identified plant ...201627891144
bacillus subtilis early colonization of arabidopsis thaliana roots involves multiple chemotaxis receptors.colonization of plant roots by bacillus subtilis is mutually beneficial to plants and bacteria. plants can secrete up to 30% of their fixed carbon via root exudates, thereby feeding the bacteria, and in return the associated b. subtilis bacteria provide the plant with many growth-promoting traits. formation of a biofilm on the root by matrix-producing b. subtilis is a well-established requirement for long-term colonization. however, we observed that cells start forming a biofilm only several hou ...201627899502
methods for the isolation of genes encoding novel pha metabolism enzymes from complex microbial communities.development of different phas as alternatives to petrochemically derived plastics can be facilitated by mining metagenomic libraries for diverse pha cycle genes that might be useful for synthesis of bio-plastics. the specific phenotypes associated with mutations of the pha synthesis pathway genes in sinorhizobium meliloti and pseudomonas putida, allows the use of powerful selection and screening tools to identify complementing novel pha synthesis genes. identification of novel genes through thei ...201727900694
dna double-strand break repair is involved in desiccation resistance of sinorhizobium meliloti, but is not essential for its symbiotic interaction with medicago truncatula.the soil bacterium sinorhizobium meliloti, a nitrogen-fixing symbiont of legume plants, is exposed to numerous stress conditions in nature, some of which cause the formation of harmful dna double-strand breaks (dsbs). in particular, the reactive oxygen species (ros) and the reactive nitrogen species (rns) produced during symbiosis, and the desiccation occurring in dry soils, are conditions which induce dsbs. two major systems of dsb repair are known in s. meliloti: homologous recombination (hr) ...201727902438
discovery and structural characterisation of new fold type iv-transaminases exemplify the diversity of this enzyme fold.transaminases are useful biocatalysts for the production of amino acids and chiral amines as intermediates for a broad range of drugs and fine chemicals. here, we describe the discovery and characterisation of new transaminases from microorganisms which were enriched in selective media containing (r)-amines as sole nitrogen source. while most of the candidate proteins were clearly assigned to known subgroups of the fold iv family of plp-dependent enzymes by sequence analysis and characterisation ...201627905516
defining substrate specificities for lipase and phospholipase candidates.microorganisms produce a wide spectrum of (phospho)lipases that are secreted in order to make external substrates available for the organism. alternatively, other (phospho)lipases may be physically associated with the producing organism causing a turnover of intrinsic lipids and frequently giving rise to a remodeling of the cellular membranes. although potential (phospho)lipases can be predicted with a number of algorithms when the gene/protein sequence is available, experimental proof of the en ...201627911408
the interaction between plants and bacteria in the remediation of petroleum hydrocarbons: an environmental perspective.widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (phcs) has generated a need for remediation and, given that many phcs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. this review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore phc polluted sites. plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacter ...201627917161
type iv effector proteins involved in the medicago-sinorhizobium symbiosis.in this study, we investigated genetic elements of the type iv secretion system (t4ss) found in sinorhizobium spp. and the role they play in symbiosis. sinorhizobium meliloti and s. medicae each contain a putative t4ss similar to that used by agrobacterium tumefaciens during pathogenesis. the cre reporter assay for translocation system was used to validate potential effector proteins. both s. meliloti and s. medicae contained the effector protein tfea, which was translocated into the host plant. ...201727918247
the use of transposon insertion sequencing to interrogate the core functional genome of the legume symbiont rhizobium leguminosarum.the free-living legume symbiont rhizobium leguminosarum is of significant economic value because of its ability to provide fixed nitrogen to globally important leguminous food crops, such as peas and lentils. discovery based research into the genetics and physiology of r. leguminosarum provides the foundational knowledge necessary for understanding the bacterium's complex lifestyle, necessary for augmenting its use in an agricultural setting. transposon insertion sequencing (inseq) facilitates h ...201627920770
sinorhizobium meliloti ybey is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation.structural and biochemical features suggest that the almost ubiquitous bacterial ybey protein may serve catalytic and/or hfq-like protective functions central to small rna (srna)-mediated regulation and rna metabolism. we have biochemically and genetically characterized the ybey ortholog of the legume symbiont sinorhizobium meliloti (smybey). co-immunoprecipitation (coip) with a flag-tagged smybey yielded a poor enrichment in rna species, compared to hfq coip-rna uncovered previously by a simila ...201627923992
functional characterization of aconitase x as a cis-3-hydroxy-l-proline dehydratase.in the aconitase superfamily, which includes the archetypical aconitase, homoaconitase, and isopropylmalate isomerase, only aconitase x is not functionally annotated. the corresponding gene (lhpi) was often located within the bacterial gene cluster involved in l-hydroxyproline metabolism. screening of a library of (hydroxy)proline analogues revealed that this protein catalyzes the dehydration of cis-3-hydroxy-l-proline to δ(1)-pyrroline-2-carboxylate. furthermore, electron paramagnetic resonance ...201627929065
evolution of a multi-step phosphorelay signal transduction system in ensifer: recruitment of the sigma factor rpon and a novel enhancer-binding protein triggers acid-activated gene expression.most ensifer strains are comparatively acid sensitive, compromising their persistence in low ph soils. in the acid-tolerant strain ensifer medicae wsm419, the acid-activated expression of lpia is essential for enhancing survival in lethal acidic conditions. here we characterise a multi-step phosphorelay signal transduction pathway consisting of tcsa, tcra, fsrr, rpon and its cognate enhancer-binding protein ebpa, which is required for the induction of lpia and the downstream acvb gene. the fsrr, ...201727935141
a kinase-phosphatase switch transduces environmental information into a bacterial cell cycle circuit.the bacterial cell cycle has been extensively studied under standard growth conditions. how it is modulated in response to environmental changes remains poorly understood. here, we demonstrate that the freshwater bacterium caulobacter crescentus blocks cell division and grows to filamentous cells in response to stress conditions affecting the cell membrane. our data suggest that stress switches the membrane-bound cell cycle kinase ccka to its phosphatase mode, leading to the rapid dephosphorylat ...201627941972
multiple and variable nhej-like genes are involved in resistance to dna damage in streptomyces ambofaciens.non-homologous end-joining (nhej) is a double strand break (dsb) repair pathway which does not require any homologous template and can ligate two dna ends together. the basic bacterial nhej machinery involves two partners: the ku protein, a dna end binding protein for dsb recognition and the multifunctional ligd protein composed a ligase, a nuclease and a polymerase domain, for end processing and ligation of the broken ends. in silico analyses performed in the 38 sequenced genomes of streptomyce ...201627965636
interaction between nitrogen and phosphate stress responses in sinorhizobium meliloti.bacteria have developed various stress response pathways to improve their assimilation and allocation of limited nutrients, such as nitrogen and phosphate. while both the nitrogen stress response (nsr) and phosphate stress response (psr) have been studied individually, there are few experiments reported that characterize effects of multiple stresses on one or more pathways in sinorhizobium meliloti, a facultatively symbiotic, nitrogen-fixing bacteria. the pii proteins, glnb and glnk, regulate th ...201627965651
modeling rice metabolism: from elucidating environmental effects on cellular phenotype to guiding crop improvement.crop productivity is severely limited by various biotic and abiotic stresses. thus, it is highly needed to understand the underlying mechanisms of environmental stress response and tolerance in plants, which could be addressed by systems biology approach. to this end, high-throughput omics profiling and in silico modeling can be considered to explore the environmental effects on phenotypic states and metabolic behaviors of rice crops at the systems level. especially, the advent of constraint-bas ...201627965696
an adenylyl cyclase with a phosphodiesterase domain in basal plants with a motile sperm system.adenylyl cyclase (ac), which produces the signalling molecule camp, has numerous important cellular functions in diverse organisms from prokaryotes to eukaryotes. here we report the identification and characterization of an ac gene from the liverwort marchantia polymorpha. the encoded protein has both a c-terminal ac catalytic domain similar to those of class iii acs and an n-terminal cyclic nucleotide phosphodiesterase (pde) domain that degrades cyclic nucleotides, thus we designated the gene m ...201627982074
mtnf-ya1, a central transcriptional regulator of symbiotic nodule development, is also a determinant of medicago truncatula susceptibility toward a root pathogen.plant nf-y transcription factors control a wide array of biological functions enabling appropriate reproductive and developmental processes as well as adaptation to various abiotic and biotic environments. in medicago truncatula, mtnf-ya1 was previously identified as a key determinant for nodule development and establishment of rhizobial symbiosis. here, we highlight a new role for this protein in compatibility to aphanomyces euteiches, a root pathogenic oomycete. the mtnf-ya1-1 mutant plants sh ...201627994614
cell cycle constraints and environmental control of local dna hypomethylation in α-proteobacteria.heritable dna methylation imprints are ubiquitous and underlie genetic variability from bacteria to humans. in microbial genomes, dna methylation has been implicated in gene transcription, dna replication and repair, nucleoid segregation, transposition and virulence of pathogenic strains. despite the importance of local (hypo)methylation at specific loci, how and when these patterns are established during the cell cycle remains poorly characterized. taking advantage of the small genomes and the ...201627997543
using transposition to introduce egfp fusions in sinorhizobium meliloti: a tool to analyze protein localization patterns in bacteria.conventional methods used for the in vivo analysis of subcellular protein localizations and their spatio-temporal dynamics in prokaryotes are based on either the engineering of n(amino)- or c(carboxy)-terminal fusions of fluorescent proteins with the protein of interest, or involved probing internal sites for tag integration. in addition, the use of inducible or constitutive promoters for the expression of fluorescent fusion proteins can lead to overexpression and result in localization artifact ...201628007516
regulation of differentiation of nitrogen-fixing bacteria by microsymbiont targeting of plant thioredoxin s1.legumes associate with rhizobia to form nitrogen (n2)-fixing nodules, which is important for plant fitness [1, 2]. medicago truncatula controls the terminal differentiation of sinorhizobium meliloti into n2-fixing bacteroids by producing defensin-like nodule-specific cysteine-rich peptides (ncrs) [3, 4]. the redox state of ncrs influences some biological activities in free-living bacteria, but the relevance of redox regulation of ncrs in planta is unknown [5, 6], although redox regulation plays ...201728017611
identification and network-enabled characterization of auxin response factor genes in medicago truncatula.the auxin response factor (arf) family of transcription factors is an important regulator of environmental response and symbiotic nodulation in the legume medicago truncatula. while previous studies have identified members of this family, a recent spurt in gene expression data coupled with genome update and reannotation calls for a reassessment of the prevalence of arf genes and their interaction networks in m. truncatula. we performed a comprehensive analysis of the m. truncatula genome and tra ...201628018393
agrobacterium tumefaciens estc, encoding an enzyme containing esterase activity, is regulated by estr, a regulator in the marr family.analysis of the a. tumefaciens genome revealed estc, which encodes an esterase located next to its transcriptional regulator estr, a regulator of esterase in the marr family. inactivation of estc results in a small increase in the resistance to organic hydroperoxides, whereas a high level of expression of estc from an expression vector leads to a reduction in the resistance to organic hydroperoxides and menadione. the estc gene is transcribed divergently from its regulator, estr. expression anal ...201628036400
quorum-quenching limits quorum-sensing exploitation by signal-negative invaders.some bacteria produce and perceive quorum-sensing (qs) signals that coordinate several behaviours, including the costly processes that are exoenzyme production and plasmid transfer. in the case of plasmid transfer, the emergence of qs signal-altered invaders and their policing are poorly documented. in agrobacterium tumefaciens, the virulence ti-plasmid encodes both synthesis and sensing of qs-signals, which promote its transfer from a donor to a recipient cell. here, we reported that qs-altered ...201728054641
functional analysis of the two cyclophilin isoforms of sinorhizobium meliloti.the nitrogen fixing sinorhizobium meliloti possesses two genes, ppia and ppib, encoding two cyclophilin isoforms which belong to the superfamily of peptidyl prolyl cis/trans isomerases (ppiase, ec: 5.2.1.8). here, we functionally characterize the two proteins and we demonstrate that both recombinant cyclophilins are able to isomerise the suc-aapf-pna synthetic peptide but neither of them displays chaperone function in the citrate synthase thermal aggregation assay. furthermore, we observe that t ...201728058638
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.201728088165
a conserved tlr5 binding and activation hot spot on flagellin.flagellin is a bacterial protein that polymerizes into the flagellar filament and is essential for bacterial motility. when flagellated bacteria invade the host, flagellin is recognized by toll-like receptor 5 (tlr5) as a pathogen invasion signal and eventually evokes the innate immune response. here, we provide a conserved structural mechanism by which flagellins from gram-negative γ-proteobacteria and gram-positive firmicutes bacteria bind and activate tlr5. the comparative structural analysis ...201728106112
the role of strigolactones and their potential cross-talk under hostile ecological conditions in plants.the changing environment always questions the survival mechanism of life on earth. the plant being special in the sense of their sessile habit need to face many of these environmental fluctuations as they have a lesser escape option. to counter these adverse conditions, plants have developed efficient sensing, signaling, and response mechanism. among them the role of phytohormones in the management of hostile ecological situations is remarkable. the strigolactone, a newly emerged plant hormone h ...201628119634
the role of strigolactones and their potential cross-talk under hostile ecological conditions in plants.the changing environment always questions the survival mechanism of life on earth. the plant being special in the sense of their sessile habit need to face many of these environmental fluctuations as they have a lesser escape option. to counter these adverse conditions, plants have developed efficient sensing, signaling, and response mechanism. among them the role of phytohormones in the management of hostile ecological situations is remarkable. the strigolactone, a newly emerged plant hormone h ...201628119634
genome sequence of the symbiotic type strain rhizobium tibeticum ccbau85039t.rhizobium tibeticum was originally isolated from root nodules of trigonella archiducis-nicolai grown in tibet, china. this species is also able to nodulate medicago sativa and phaseolus vulgaris the whole-genome sequence of the type strain, r. tibeticum ccbau85039(t), is reported in this study.201728126941
pretreatment of vinasse from the sugar refinery industry under non-sterile conditions by trametes versicolor in a fluidized bed bioreactor and its effect when coupled to an uasb reactor.during hydrous ethanol production from the sugar refinery industry in mexico, vinasse is generated. phenolic compounds and melanoidins contribute to its color and make degradation of the vinasse a difficult task. although anaerobic digestion (ad) is feasible for vinasse treatment, the presence of recalcitrant compounds can be toxic or inhibitory for anaerobic microorganism. therefore, this study presents new data on the coupled of the fbr (fluidized bed bioreactor) to the uasb (upflow anaerobic ...201728127398
rnase e and rnase j are needed for s-adenosylmethionine homeostasis in sinorhizobium meliloti.the ribonucleases (rnases) e and j play major roles in escherichia coli and bacillus subtilis, respectively, and co-exist in sinorhizobium meliloti. we analyzed s. meliloti 2011 mutants with mini-tn5 insertions in the corresponding genes rne and rnj and found many overlapping effects. we observed similar changes in mrna levels including lower mrna levels of the motility and chemotaxis related genes flaa, flgb, and cher and higher levels of ndva (important for glucan export). the acyl-homoserine ...201728141492
regulation of polyhydroxybutyrate accumulation in sinorhizobium meliloti by the trans-encoded small rna mmgr.riboregulation has a major role in the fine-tuning of multiple bacterial processes. among the rna players, trans-encoded untranslated small rnas (srnas) regulate complex metabolic networks by tuning expression from multiple target genes in response to numerous signals. in sinorhizobium meliloti, over 400 srnas are expressed under different stimuli. the srna mmgr (standing for makes more granules regulator) has been of particular interest to us since its sequence and structure are highly conserve ...201728167519
sinorhizobium meliloti ybey is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation. 201728180335
role and regulation of acc deaminase gene in sinorhizobium meliloti: is it a symbiotic, rhizospheric or endophytic gene?plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (acc) deaminase (acds) is one of the most diffused. this gene is supposed to be involved in the cleaving of plant-produced acc, the precursor of the plant stress-hormone ethylene toning down the plant respon ...201728194158
alkalinity of lanzarote soils is a factor shaping rhizobial populations with sinorhizobium meliloti being the predominant microsymbiont of lotus lancerottensis.lotus lancerottensis is an endemic species that grows widely throughout lanzarote island (canary is.). characterization of 48 strains isolated from root nodules of plants growing in soils from eleven locations on the island showed that 38 isolates (79.1%) belonged to the species sinorhizobium meliloti, whereas only six belonged to mesorhizobium sp., the more common microsymbionts for the lotus. other genotypes containing only one isolate were classified as pararhizobium sp., sinorhizobium sp., p ...201728216096
a comprehensive phylogenetic analysis of copper transporting p1b atpases from bacteria of the rhizobiales order uncovers multiplicity, diversity and novel taxonomic subtypes.the ubiquitous cytoplasmic membrane copper transporting p1b-1 and p1b-3 -type atpases pump out cu(+) and cu(2+) , respectively, to prevent cytoplasmic accumulation and avoid toxicity. the presence of five copies of cu-atpases in the symbiotic nitrogen-fixing bacteria sinorhizobium meliloti is remarkable; it is the largest number of cu(+) -transporters in a bacterial genome reported to date. since the prevalence of multiple cu-atpases in members of the rhizobiales order is unknown, we performed a ...201728217917
massive parallel insertion site sequencing of an arrayed sinorhizobium meliloti signature-tagged mini-tn 5 transposon mutant library.transposon mutagenesis in conjunction with identification of genomic transposon insertion sites is a powerful tool for gene function studies. we have implemented a protocol for parallel determination of transposon insertion sites by illumina sequencing involving a hierarchical barcoding method that allowed for tracking back insertion sites to individual clones of an arrayed signature-tagged transposon mutant library. this protocol was applied to further characterize a signature-tagged mini-tn 5 ...201728235609
a family of single copy repabc-type shuttle vectors stably maintained in the alpha-proteobacterium sinorhizobium meliloti.a considerable share of bacterial species maintains segmented genomes. plant symbiotic α-proteobacterial rhizobia contain up to six repabc-type replicons in addition to the primary chromosome. these low or unit-copy replicons, classified as secondary chromosomes, chromids, or megaplasmids, are exclusively found in α-proteobacteria. replication and faithful partitioning of these replicons to the daughter cells is mediated by the repabc region. the importance of α-rhizobial symbiotic nitrogen fixa ...201728264559
functional metagenomics reveals novel β-galactosidases not predictable from gene sequences.the techniques of metagenomics have allowed researchers to access the genomic potential of uncultivated microbes, but there remain significant barriers to determination of gene function based on dna sequence alone. functional metagenomics, in which dna is cloned and expressed in surrogate hosts, can overcome these barriers, and make important contributions to the discovery of novel enzymes. in this study, a soil metagenomic library carried in an incp cosmid was used for functional complementatio ...201728273103
biogeography of a novel clade of ensifer meliloti associated with the australian legume trigonella suavissima.here we describe a novel clade within ensifer meliloti and consider how geographic and ecological isolation contributed to the limited distribution of this group. members of the genus ensifer are best known for their ability to form nitrogen-fixing symbioses with forage legumes of three related genera, medicago l., melilotus mill., and trigonella l., which are members of the tribe trifoleae. they have a natural distribution extending from the mediterranean basin through west asia, where there is ...201728283520
high yield production of rhizobium nodb chitin deacetylase and its use for in vitro synthesis of lipo-chitinoligosaccharide precursors.lipo-chitinoligosaccharides (lcos) are key molecules for the establishment of plant-microorganisms symbiosis. interactions of leguminous crops with nitrogen-fixing rhizobial bacteria involve nod factors, while myc-lcos improve the association of most plants with arbuscular mycorrhizal fungi. both nod factors and myc-lcos are composed of a chitinoligosaccharide fatty acylated at the non-reducing end accompanied with various substituting groups. one straightforward way to access lcos is starting f ...201728284052
two-component regulatory system acts/actr is required for sinorhizobium meliloti adaptation to oxidative stress.the two-component system acts/actr plays important roles in bacterial adaptation to abiotic stress, including acid tolerance and oxidant resistance. however, the underlying regulatory mechanism is not clear. in this study, we found that the acts/actr system is required for adaptation to oxidative stress by regulating the transcription of the genes actr, katb, gsha and gshb1. the acts and actr mutants were sensitive to low ph and oxidants such as h2o2, oxidized glutathione (gssg) and sodium nitro ...201728285657
rhizobial symbiosis alleviates polychlorinated biphenyls-induced systematic oxidative stress via brassinosteroids signaling in alfalfa.the role of symbiotic rhizobia in the alleviation of polychlorinated biphenyl (pcb)-induced phytotoxicity in alfalfa and the brassinosteroid (br) hormone signaling involved were investigated during phytoremediation. the association between alfalfa and sinorhizobium meliloti was adopted as a remediation model. phytotoxicity due to pcb 77 (3,3',4,4'-tetrachlorobiphenyl) exerted adverse impacts on plant performance (biomass accumulation and photosynthesis) and elicited cellular oxidative stress (ov ...201728314132
characterization of a gene encoding a membrane protein that affects exopolysaccharide production and intracellular mg2+ concentrations in ensifer meliloti.exopolysaccharides play an important role in the physiology of a bacterial cell. ensifer meliloti is capable of producing at least two types of exopolysaccharides (eps); succinoglycan, and galactoglucan. in e. meliloti exopolysaccharides are best known for their role in mediating interaction with its symbiotic hosts. it was previously shown that high concentrations of mg 2+ or k + were capable of suppressing the mucoid phenotype associated with galactoglucan production in an expr+ derivative of ...201728333317
specificity in legume-rhizobia symbioses.most species in the leguminosae (legume family) can fix atmospheric nitrogen (n₂) via symbiotic bacteria (rhizobia) in root nodules. here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. the leguminosae was divided into three sub-families, the caesalpinioideae, mimosoideae and papilionoideae. bradyrhizobium spp. were the exclusive rhizobial symbionts of species i ...201728346361
the underlying process of early ecological and genetic differentiation in a facultative mutualistic sinorhizobium meliloti population.the question of how genotypic and ecological units arise and spread in natural microbial populations remains controversial in the field of evolutionary biology. here, we investigated the early stages of ecological and genetic differentiation in a highly clonal sympatric sinorhizobium meliloti population. whole-genome sequencing revealed that a large dna region of the symbiotic plasmid psymb was replaced in some isolates with a similar synteny block carrying densely clustered snps and displaying ...201728386109
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