| bacterial-induced calcium oscillations are common to nitrogen-fixing associations of nodulating legumes and nonlegumes. | plants that form root-nodule symbioses are within a monophyletic 'nitrogen-fixing' clade and associated signalling processes are shared with the arbuscular mycorrhizal symbiosis. central to symbiotic signalling are nuclear-associated oscillations in calcium ions (ca(2+) ), occurring in the root hairs of several legume species in response to the rhizobial nod factor signal. in this study we expanded the species analysed for activation of ca(2+) oscillations, including nonleguminous species within ... | 2015 | 26010117 |
| genome analysis of a novel bradyrhizobium sp. doa9 carrying a symbiotic plasmid. | bradyrhizobium sp. doa9 isolated from the legume aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the bradyrhizobiaceae. genome analysis of doa9 revealed that its genome comprised a single chromosome of 7.1 mbp and a plasmid of 0.7 mbp. the chromosome showed highest similarity with that of the nod gene-harboring soybean symbiont b. japonicum usda110, whereas the plasmid showed highest similarity with pbbta01 of the nod gene-l ... | 2015 | 25710540 |
| 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 |
| 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 |
| stressed by a lov triangle. | | 2012 | 22447905 |
| the sinorhizobium fredii hh103 lipopolysaccharide is not only relevant at early soybean nodulation stages but also for symbiosome stability in mature nodules. | in this work we have characterised the sinorhizobium fredii hh103 grea lpsb lpscde genetic region and analysed for the first time the symbiotic performance of sinorhizobium fredii lps mutants on soybean. the organization of the s. fredii hh103 grea, lpsb, and lpscde genes was equal to that of sinorhizobium meliloti 1021. s. fredii hh103 grea, lpsb, and lpse mutant derivatives produced altered lps profiles that were characteristic of the gene mutated. in addition, s. fredii hh103 grea mutants sho ... | 2013 | 24098345 |
| phylogenetic analysis of erythritol catabolic loci within the rhizobiales and proteobacteria. | the ability to use erythritol as a sole carbon source is not universal among the rhizobiaceae. based on the relatedness to the catabolic genes in brucella it has been suggested that the eryabcd operon may have been horizontally transferred into rhizobium. during work characterizing a locus necessary for the transport and catabolism of erythritol, adonitol and l-arabitol in sinorhizobium meliloti, we became interested in the differences between the erythritol loci of s. meliloti and r. leguminosa ... | 2013 | 23432981 |
| the trnaarg gene and enga are essential genes on the 1.7-mb psymb megaplasmid of sinorhizobium meliloti and were translocated together from the chromosome in an ancestral strain. | bacterial genomes with two (or more) chromosome-like replicons are known, and these appear to be particularly frequent in alphaproteobacteria. the genome of the n(2)-fixing alfalfa symbiont sinorhizobium meliloti 1021 contains a 3.7-mb chromosome and 1.4-mb (psyma) and 1.7-mb (psymb) megaplasmids. in this study, the trna(arg) and enga genes, located on the psymb megaplasmid, are shown to be essential for growth. these genes could be deleted from psymb when copies were previously integrated into ... | 2013 | 23123907 |
| molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. | the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ... | 2014 | 25492513 |
| molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. | the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ... | 2014 | 25492513 |
| molecular characterization of a novel temperate sinorhizobium bacteriophage, фlm21, encoding dna methyltransferase with ccrm-like specificity. | φlm21 is a temperate phage isolated from sinorhizobium sp. strain lm21 (alphaproteobacteria). genomic analysis and electron microscopy suggested that φlm21 is a member of the family siphoviridae. the phage has an isometric head and a long noncontractile tail. the genome of φlm21 has 50,827 bp of linear double-stranded dna encoding 72 putative proteins, including proteins responsible for the assembly of the phage particles, dna packaging, transcription, replication, and lysis. virion proteins wer ... | 2014 | 25187538 |
| 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 |
| 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 |
| 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 |
| plant growth promotion potential is equally represented in diverse grapevine root-associated bacterial communities from different biopedoclimatic environments. | plant-associated bacteria provide important services to host plants. environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. however, whether these environmental factors may influence the plant growth promoting (pgp) potential of the root-associated bacteria is not widely understood. to address this issue, the diversity and pgp potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three medit ... | 2013 | 23878810 |
| growth and survival of mesorhizobium loti inside acanthamoeba enhanced its ability to develop more nodules on lotus corniculatus. | the importance of protozoa as environmental reservoirs of pathogens is well recognized, while their impact on survival and symbiotic properties of rhizobia has not been explored. the possible survival of free-living rhizobia inside amoebae could influence bacterial abundance in the rhizosphere of legume plants and the nodulation competitiveness of microsymbionts. two well-characterized strains of mesorhizobium: mesorhizobium loti nzp2213 and mesorhizobium huakuii symbiovar loti maff303099 were a ... | 2015 | 25779926 |
| 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 |
| identification of genes and pathways related to phenol degradation in metagenomic libraries from petroleum refinery wastewater. | two fosmid libraries, totaling 13,200 clones, were obtained from bioreactor sludge of petroleum refinery wastewater treatment system. the library screening based on pcr and biological activity assays revealed more than 400 positive clones for phenol degradation. from these, 100 clones were randomly selected for pyrosequencing in order to evaluate the genetic potential of the microorganisms present in wastewater treatment plant for biodegradation, focusing mainly on novel genes and pathways of ph ... | 2013 | 23637911 |
| south african papilionoid legumes are nodulated by diverse burkholderia with unique nodulation and nitrogen-fixation loci. | the root-nodule bacteria of legumes endemic to the cape floristic region are largely understudied, even though recent reports suggest the occurrence of nodulating burkholderia species unique to the region. in this study, we considered the diversity and evolution of nodulating burkholderia associated with the endemic papilionoid tribes hypocalypteae and podalyrieae. we identified distinct groups from verified rhizobial isolates by phylogenetic analyses of the 16s rrna and reca housekeeping gene r ... | 2013 | 23874611 |
| genome-wide rna sequencing analysis of quorum sensing-controlled regulons in the plant-associated burkholderia glumae pg1 strain. | burkholderia glumae pg1 is a soil-associated motile plant-pathogenic bacterium possessing a cell density-dependent regulation system called quorum sensing (qs). its genome contains three genes, here designated bgai1 to bgai3, encoding distinct autoinducer-1 (ai-1) synthases, which are capable of synthesizing qs signaling molecules. here, we report on the construction of b. glumae pg1 δbgai1, δbgai2, and δbgai3 mutants, their phenotypic characterization, and genome-wide transcriptome analysis usi ... | 2015 | 26362987 |
| 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 |
| structural insights into a novel interkingdom signaling circuit by cartography of the ligand-binding sites of the homologous quorum sensing luxr-family. | recent studies have identified a novel interkingdom signaling circuit, via plant signaling molecules, and a bacterial sub-family of luxr proteins, bridging eukaryotes and prokaryotes. indeed pivotal plant-bacteria interactions are regulated by the so called plant associated bacteria (pab) luxr solo regulators that, although closely related to the quorum sensing (qs) luxr family, do not bind or respond to canonical quorum sensing n-acyl homoserine lactones (ahls), but only to specific host plant ... | 2013 | 24132148 |
| sociomicrobiome of wood decay in a tropical rain forest: unraveling complexity. | given that microbial interactions in nature are very complex, we propose that quorum-sensing, as well as quorum-quenching, phenazine and secondary metabolite production, resistance and toxin-antitoxin systems within a microbial community should all comprise the battery of processes involving the study of what we would define as the "sociomicrobiome". in the present study the genes/molecules, subsystems and taxonomic breakup of the mentioned processes were identified in decaying tropical wood fro ... | 2013 | 24052931 |
| production, purification and characterization of a novel thermotolerant endoglucanase (cmcase) from bacillus strain isolated from cow dung. | in an attempt to screen out cellulase producing bacteria from herbivorous animal fecal matter it was possible to isolate a potent bacterium from cow dung. the bacterium was identified as bacillus sp. using 16s rdna based molecular phylogenetic approach. the effect of different agricultural wastes, paper wastes and carboxymethyl cellulose on endoglucanase production was tested and was found to produce maximally at 8% carboxymethyl cellulose. the endoglucanase was precipitated by ammonium sulfate ... | 2013 | 23519129 |
| structure and biological roles of sinorhizobium fredii hh103 exopolysaccharide. | here we report that the structure of the sinorhizobium fredii hh103 exopolysaccharide (eps) is composed of glucose, galactose, glucuronic acid, pyruvic acid, in the ratios 5∶2∶2∶1 and is partially acetylated. a s. fredii hh103 exoa mutant (svq530), unable to produce eps, not only forms nitrogen fixing nodules with soybean but also shows increased competitive capacity for nodule occupancy. mutant svq530 is, however, less competitive to nodulate vigna unguiculata. biofilm formation was reduced in ... | 2014 | 25521500 |
| cell cycle constraints on capsulation and bacteriophage susceptibility. | despite the crucial role of bacterial capsules in pathogenesis, it is still unknown if systemic cues such as the cell cycle can control capsule biogenesis. in this study, we show that the capsule of the synchronizable model bacterium caulobacter crescentus is cell cycle regulated and we unearth a bacterial transglutaminase homolog, hvya, as restriction factor that prevents capsulation in g1-phase cells. this capsule protects cells from infection by a generalized transducing caulobacter phage (φc ... | 2014 | 25421297 |
| alfalfa snakin-1 prevents fungal colonization and probably coevolved with rhizobia. | the production of antimicrobial peptides is a common defense strategy of living cells against a wide range of pathogens. plant snakin peptides inhibit bacterial and fungal growth at extremely low concentrations. however, little is known of their molecular and ecological characteristics, including origin, evolutionary equivalence, specific functions and activity against beneficial microbes. the aim of this study was to identify and characterize snakin-1 from alfalfa (mssn1). | 2014 | 25227589 |
| commonalities and differences of t3sss in rhizobia and plant pathogenic bacteria. | plant pathogenic bacteria and rhizobia infect higher plants albeit the interactions with their hosts are principally distinct and lead to completely different phenotypic outcomes, either pathogenic or mutualistic, respectively. bacterial protein delivery to plant host plays an essential role in determining the phenotypic outcome of plant-bacteria interactions. the involvement of type iii secretion systems (t3sss) in mediating animal- and plant-pathogen interactions was discovered in the mid-80's ... | 2014 | 24723933 |
| identification of bradyrhizobium elkanii genes involved in incompatibility with soybean plants carrying the rj4 allele. | symbioses between leguminous plants and soil bacteria known as rhizobia are of great importance to agricultural production and nitrogen cycling. while these mutualistic symbioses can involve a wide range of rhizobia, some legumes exhibit incompatibility with specific strains, resulting in ineffective nodulation. the formation of nodules in soybean plants (glycine max) is controlled by several host genes, which are referred to as rj genes. the soybean cultivar barc2 carries the rj4 gene, which re ... | 2015 | 26187957 |
| involvement of aph(3')-iia in the formation of mosaic aminoglycoside resistance genes in natural environments. | intragenic recombination leading to mosaic gene formation is known to alter resistance profiles for particular genes and bacterial species. few studies have examined to what extent aminoglycoside resistance genes undergo intragenic recombination. we screened the genbank database for mosaic gene formation in homologs of the aph(3')-iia (nptii) gene. aph(3')-iia inactivates important aminoglycoside antibiotics. the gene is widely used as a selectable marker in biotechnology and enters the environm ... | 2015 | 26042098 |
| widespread occurrence of a novel division of bacteria identified by 16s rrna gene sequences originally found in deep marine sediments. | phylogenetic analysis of 16s rrna gene sequences from deep marine sediments identified a deeply branching clade, designated candidate division js1. primers for pcr amplification of partial 16s rrna genes that target the js1 division were developed and used to detect js1 sequences in dna extracted from various sedimentary environments, including, for the first time, coastal marine and brackish sediments. | 2004 | 15345467 |
| responses of rhizobia to desiccation in relation to osmotic stress, oxygen, and temperature. | | 2007 | 17400779 |
| identification and phylogenetic characterization of cobalamin biosynthetic genes of ensifer adhaerens. | ensifer adhaerens csba was screened as a cobalamin producer. the draft genome sequence revealed that the strain possesses 22 cobalamin biosynthetic genes (cob genes). the cob gene arrangement on the genome of e. adhaerens csba was similar to that of other ensifer species, and most similar to that of pseudomonas denitrificans sc510. the cobn sequence phylogeny was generally congruent with that of the 16s rrna gene, and it is suggeted that e. adhaerens csba might have inherited the cob genes from ... | 2012 | 23257908 |
| identification and phylogenetic characterization of cobalamin biosynthetic genes of ensifer adhaerens. | ensifer adhaerens csba was screened as a cobalamin producer. the draft genome sequence revealed that the strain possesses 22 cobalamin biosynthetic genes (cob genes). the cob gene arrangement on the genome of e. adhaerens csba was similar to that of other ensifer species, and most similar to that of pseudomonas denitrificans sc510. the cobn sequence phylogeny was generally congruent with that of the 16s rrna gene, and it is suggeted that e. adhaerens csba might have inherited the cob genes from ... | 2012 | 23257908 |
| a novel (s)-6-hydroxynicotine oxidase gene from shinella sp. strain hzn7. | nicotine is an important environmental toxicant in tobacco waste. shinella sp. strain hzn7 can metabolize nicotine into nontoxic compounds via variations of the pyridine and pyrrolidine pathways. however, the catabolic mechanism of this variant pathway at the gene or enzyme level is still unknown. in this study, two 6-hydroxynicotine degradation-deficient mutants, n7-m9 and n7-w3, were generated by transposon mutagenesis. the corresponding mutant genes, designated nctb and tnp2, were cloned and ... | 2014 | 25002425 |
| screening of metagenomic and genomic libraries reveals three classes of bacterial enzymes that overcome the toxicity of acrylate. | acrylate is produced in significant quantities through the microbial cleavage of the highly abundant marine osmoprotectant dimethylsulfoniopropionate, an important process in the marine sulfur cycle. acrylate can inhibit bacterial growth, likely through its conversion to the highly toxic molecule acrylyl-coa. previous work identified an acrylyl-coa reductase, encoded by the gene acui, as being important for conferring on bacteria the ability to grow in the presence of acrylate. however, some bac ... | 2014 | 24848004 |
| 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 |
| 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 |
| the type 3 protein secretion system of cupriavidus taiwanensis strain lmg19424 compromises symbiosis with leucaena leucocephala. | cupriavidus taiwanensis forms proficient symbioses with a few mimosa species. inactivation of a type iii protein secretion system (t3ss) had no effect on mimosa pudica but allowed c. taiwanensis to establish chronic infections and fix nitrogen in leucaena leucocephala. unlike what was observed for other rhizobia, glutamate rather than plant flavonoids mediated transcriptional activation of this atypical t3ss. | 2012 | 22865066 |
| robust markers reflecting phylogeny and taxonomy of rhizobia. | genomic ani (average nucleotide identity) has been found to be able to replace dna-dna hybridization in prokaryote taxonomy. the ani of each of the core genes that has a phylogeny congruent with the reference species tree of rhizobia was compared to the genomic ani. this allowed us to identify three housekeeping genes (smc00019-trua-thra) whose ani reflected the intraspecies and interspecies genomic ani among rhizobial strains, revealing an ani gap (≥2%) between the inter- and intra-species comp ... | 2012 | 23028691 |
| a support vector machine based method to distinguish proteobacterial proteins from eukaryotic plant proteins. | members of the phylum proteobacteria are most prominent among bacteria causing plant diseases that result in a diminution of the quantity and quality of food produced by agriculture. to ameliorate these losses, there is a need to identify infections in early stages. recent developments in next generation nucleic acid sequencing and mass spectrometry open the door to screening plants by the sequences of their macromolecules. such an approach requires the ability to recognize the organismal origin ... | 2012 | 23046503 |
| functional analysis of nopm, a novel e3 ubiquitin ligase (nel) domain effector of rhizobium sp. strain ngr234. | type 3 effector proteins secreted via the bacterial type 3 secretion system (t3ss) are not only virulence factors of pathogenic bacteria, but also influence symbiotic interactions between nitrogen-fixing nodule bacteria (rhizobia) and leguminous host plants. in this study, we characterized nopm (nodulation outer protein m) of rhizobium sp. strain ngr234, which shows sequence similarities with novel e3 ubiquitin ligase (nel) domain effectors from the human pathogens shigella flexneri and salomone ... | 2012 | 22615567 |
| 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 |
| methylation--an uncommon modification of glycans. | a methyl (me) group on a sugar residue is a rarely reported event. until now, this type of modification has been found in the animal kingdom only in worms and molluscs, whereas it is more frequently present in some species of bacteria, fungi, algae and plants, but not in mammals. the monosaccharides involved as well as the positions of the me groups on the sugar vary with species. methylation appears to play a role in some recognition events, but details are still unknown. this review summarises ... | 2012 | 22944672 |
| mutualistic co-evolution of type iii effector genes in sinorhizobium fredii and bradyrhizobium japonicum. | two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. in one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. in the opposing model, conflicts between mutualist and host are largely resolved and the interaction is characterized by evolutionary stasis. we tested these opposing frameworks in two line ... | 2013 | 23468637 |
| the kiwifruit emerging pathogen pseudomonas syringae pv. actinidiae does not produce ahls but possesses three luxr solos. | pseudomonas syringae pv. actinidiae (psa) is an emerging phytopathogen causing bacterial canker disease in kiwifruit plants worldwide. quorum sensing (qs) gene regulation plays important roles in many different bacterial plant pathogens. in this study we analyzed the presence and possible role of n-acyl homoserine lactone (ahl) quorum sensing in psa. it was established that psa does not produce ahls and that a typical complete luxi/r qs system is absent in psa strains. psa however possesses thre ... | 2014 | 24498215 |
| functional conservation of the capacity for ent-kaurene biosynthesis and an associated operon in certain rhizobia. | bacterial interactions with plants are accompanied by complex signal exchange processes. previously, the nitrogen-fixing symbiotic (rhizo)bacterium bradyrhizobium japonicum was found to carry adjacent genes encoding two sequentially acting diterpene cyclases that together transform geranylgeranyl diphosphate to ent-kaurene, the olefin precursor to the gibberellin plant hormones. species from the three other major genera of rhizobia were found to have homologous terpene synthase genes. cloning an ... | 2014 | 24142247 |
| 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 |
| genetic diversity of rhizobia isolates from amazon soils using cowpea (vigna unguiculata) as trap plant. | the aim of this work was to characterize rhizobia isolated from the root nodules of cowpea (vigna unguiculata) plants cultivated in amazon soils samples by means of ardra (amplified rdna restriction analysis) and sequencing analysis, to know their phylogenetic relationships. the 16s rrna gene of rhizobia was amplified by pcr (polymerase chain reaction) using universal primers y1 and y3. the amplification products were analyzed by the restriction enzymes hinfi, mspi and ddei and also sequenced wi ... | 2012 | 24031880 |
| genome sequence of ensifer adhaerens ov14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes. | recently it has been shown that ensifer adhaerens can be used as a plant transformation technology, transferring genes into several plant genomes when equipped with a ti plasmid. for this study, we have sequenced the genome of ensifer adhaerens ov14 (ov14) and compared it with those of agrobacterium tumefaciens c58 (c58) and sinorhizobium meliloti 1021 (1021); the latter of which has also demonstrated a capacity to genetically transform crop genomes, albeit at significantly reduced frequencies. | 2014 | 24708309 |
| 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 |
| the calcium-stimulated lipid a 3-o deacylase from rhizobium etli is not essential for plant nodulation. | the lipid a component of lipopolysaccharide from the nitrogen-fixing plant endosymbiont, rhizobium etli, is structurally very different from that found in most enteric bacteria. the lipid a from free-living r. etli is structurally heterogeneous and exists as a mixture of species which are either pentaacylated or tetraacylated. in contrast, the lipid a from r. etli bacteroids is reported to consist exclusively of tetraacylated lipid a species. the tetraacylated lipid a species in both cases lack ... | 2013 | 23583844 |
| the use of fosmid metagenomic libraries in preliminary screening for various biological activities. | it is generally believed that there are many natural sources of as yet unknown bioactive compounds with a high biotechnological potential. however, the common method based on the use of cell extracts in the preliminary screening for particular molecules or activities is problematic as amounts of obtained compounds may be low, and such experiments are hardly reproducible. therefore, the aim of this work was to test whether a novel strategy to search for previously unknown biological activities ca ... | 2014 | 25048369 |
| 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 |
| 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 |
| draft genome sequence of the nitrogen-fixing symbiotic bacterium bradyrhizobium elkanii 587. | the draft sequence of the genome of bradyrhizobium elkanii 587 is presented. this was obtained using illumina next-gen dna sequencing combined with sanger sequencing. genes for the pathways involved in biological nitrogen fixation (the nif gene cluster), nod genes including nodabc, and genes for the type iii protein secretion system (t3ss) are present. | 2012 | 22689236 |
| in situ identification of plant-invasive bacteria with maldi-tof mass spectrometry. | rhizobia form a disparate collection of soil bacteria capable of reducing atmospheric nitrogen in symbiosis with legumes. the study of rhizobial populations in nature involves the collection of large numbers of nodules found on roots or stems of legumes, and the subsequent typing of nodule bacteria. to avoid the time-consuming steps of isolating and cultivating nodule bacteria prior to genotyping, a protocol of strain identification based on the comparison of maldi-tof ms spectra was established ... | 2012 | 22615938 |
| genome sequence of the soybean symbiont sinorhizobium fredii hh103. | sinorhizobium fredii hh103 is a fast-growing rhizobial strain that is able to nodulate legumes that develop determinate nodules, e.g., soybean, and legumes that form nodules of the indeterminate type. here we present the genome of hh103, which consists of one chromosome and five plasmids with a total size of 7.22 mb. | 2012 | 22374952 |
| mathematical ecology analysis of geographical distribution of soybean-nodulating bradyrhizobia in japan. | we characterized the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia from weakly acidic soils in japan and their geographical distribution in an ecological study of indigenous soybean rhizobia. we isolated bradyrhizobia from three kinds of rj-genotype soybeans. their genetic diversity and community structure were analyzed by pcr-rflp analysis of the 16s-23s rrna gene internal transcribed spacer (its) region with 11 bradyrhizobium usda strains as referenc ... | 2013 | 24240318 |
| hijacking of leguminous nodulation signaling by the rhizobial type iii secretion system. | root-nodule symbiosis between leguminous plants and nitrogen-fixing bacteria (rhizobia) involves molecular communication between the two partners. key components for the establishment of symbiosis are rhizobium-derived lipochitooligosaccharides (nod factors; nfs) and their leguminous receptors (nfrs) that initiate nodule development and bacterial entry. here we demonstrate that the soybean microsymbiont bradyrhizobium elkanii uses the type iii secretion system (t3ss), which is known for its deli ... | 2013 | 24082124 |
| relevance of fucose-rich extracellular polysaccharides produced by rhizobium sullae strains nodulating hedysarum coronarium l. legumes. | specific and complex interactions between soil bacteria, known as rhizobia, and their leguminous host plants result in the development of root nodules. this process implies a complex dialogue between the partners. rhizobia synthesize different classes of polysaccharides: exopolysaccharides (eps), kdo-rich capsular polysaccharides, lipopolysaccharides, and cyclic β-(1,2)-glucans. these polymers are actors of a successful symbiosis with legumes. we focus here on studying the eps produced by rhizob ... | 2013 | 23183977 |
| comparative genomics of the core and accessory genomes of 48 sinorhizobium strains comprising five genospecies. | the sinorhizobia are amongst the most well studied members of nitrogen-fixing root nodule bacteria and contribute substantial amounts of fixed nitrogen to the biosphere. while the alfalfa symbiont sinorhizobium meliloti rm 1021 was one of the first rhizobial strains to be completely sequenced, little information is available about the genomes of this large and diverse species group. | 2013 | 23425606 |
| the type iii secretion system of bradyrhizobium japonicum usda122 mediates symbiotic incompatibility with rj2 soybean plants. | the rhcj and ttsi mutants of bradyrhizobium japonicum usda122 for the type iii protein secretion system (t3ss) failed to secrete typical effector proteins and gained the ability to nodulate rj2 soybean plants (hardee), which are symbiotically incompatible with wild-type usda122. this suggests that effectors secreted via the t3ss trigger incompatibility between these two partners. | 2013 | 23204412 |
| rna sequencing analysis of the broad-host-range strain sinorhizobium fredii ngr234 identifies a large set of genes linked to quorum sensing-dependent regulation in the background of a trai and ngri deletion mutant. | the alphaproteobacterium sinorhizobium fredii ngr234 has an exceptionally wide host range, as it forms nitrogen-fixing nodules with more legumes than any other known microsymbiont. within its 6.9-mbp genome, it encodes two n-acyl-homoserine-lactone synthase genes (i.e., trai and ngri) involved in the biosynthesis of two distinct autoinducer i-type molecules. here, we report on the construction of an ngr234-δtrai and an ngr234-δngri mutant and their genome-wide transcriptome analysis. a high-reso ... | 2014 | 25002423 |
| abundance and diversity of soybean-nodulating rhizobia in black soil are impacted by land use and crop management. | to investigate the effects of land use and crop management on soybean rhizobial communities, 280 nodule isolates were trapped from 7 fields with different land use and culture histories. besides the known bradyrhizobium japonicum, three novel genospecies were isolated from these fields. grassland (gl) maintained a higher diversity of soybean bradyrhizobia than the other cultivation systems. two genospecies (bradyrhizobium spp. i and iii) were distributed widely in all treatments, while bradyrhiz ... | 2014 | 24951780 |
| transcriptional regulator lsrb of sinorhizobium meliloti positively regulates the expression of genes involved in lipopolysaccharide biosynthesis. | rhizobia induce nitrogen-fixing nodules on host legumes, which is important in agriculture and ecology. lipopolysaccharide (lps) produced by rhizobia is required for infection or bacteroid survival in host cells. genes required for lps biosynthesis have been identified in several rhizobium species. however, the regulation of their expression is not well understood. here, sinorhizobium meliloti lsrb, a member of the lysr family of transcriptional regulators, was found to be involved in lps biosyn ... | 2014 | 24951786 |
| the symbiotic biofilm of sinorhizobium fredii smh12, necessary for successful colonization and symbiosis of glycine max cv osumi, is regulated by quorum sensing systems and inducing flavonoids via nodd1. | bacterial surface components, especially exopolysaccharides, in combination with bacterial quorum sensing signals are crucial for the formation of biofilms in most species studied so far. biofilm formation allows soil bacteria to colonize their surrounding habitat and survive common environmental stresses such as desiccation and nutrient limitation. this mode of life is often essential for survival in bacteria of the genera mesorhizobium, sinorhizobium, bradyrhizobium, and rhizobium. the role of ... | 2014 | 25166872 |
| identification of a dominant gene in medicago truncatula that restricts nodulation by sinorhizobium meliloti strain rm41. | leguminous plants are able to form a root nodule symbiosis with nitrogen-fixing soil bacteria called rhizobia. this symbiotic association shows a high level of specificity. beyond the specificity for the legume family, individual legume species/genotypes can only interact with certain restricted group of bacterial species or strains. specificity in this system is regulated by complex signal exchange between the two symbiotic partners and thus multiple genetic mechanisms could be involved in the ... | 2014 | 24934080 |
| genetic divergence of bradyrhizobium strains nodulating soybeans as revealed by multilocus sequence analysis of genes inside and outside the symbiosis island. | the genus bradyrhizobium has been considered to be a taxonomically difficult group. in this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among bradyrhizobium strains nodulating soybeans in china. eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (smc00019, thra, and trua). this was also supported by analyses of eight genes outside the symbiosis island ("off-island" genes; smc00019, thra, trua, ... | 2014 | 24632260 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 3-hydroxybutyrate oligomer hydrolase and 3-hydroxybutyrate dehydrogenase participate in intracellular polyhydroxybutyrate and polyhydroxyvalerate degradation in paracoccus denitrificans. | genes encoding 3-hydroxybutyrate oligomer hydrolase (phazc) and 3-hydroxybutyrate dehydrogenase (hbd) were isolated from paracoccus denitrificans. phazc and hbd were overproduced as his-tagged proteins in escherichia coli and purified by affinity and gel filtration chromatography. purified his-tagged proteins had molecular masses of 31 kda and 120 kda (a tetramer of 29-kda subunits). the his-tagged phazc hydrolyzed not only 3-hydroxybutyrate oligomers but also 3-hydroxyvalerate oligomers. the hi ... | 2014 | 24271169 |
| denitrifying bacterial communities affect current production and nitrous oxide accumulation in a microbial fuel cell. | the biocathodic reduction of nitrate in microbial fuel cells (mfcs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. in this paper the community composition of denitrifiers in the cathode of a mfc is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. the num ... | 2013 | 23717427 |
| transcriptome analysis of "candidatus liberibacter solanacearum" in its psyllid vector, bactericera cockerelli. | "candidatus liberibacter solanacearum" (lso) is an emergent pathogen of carrots in europe and solanaceous plants in north and central america and new zealand. this bacterium is closely related to other pathogenic candidatus liberibacter spp., all vectored by psyllids. in order to understand the molecular interaction of this pathogen and its psyllid vector, bactericera cockerelli, illumina sequencing of psyllid harboring lso was performed to determine if this approach could be used to assess the ... | 2014 | 24992557 |
| 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 |
| microbial diversity and abundance in the xinjiang luliang long-term water-flooding petroleum reservoir. | microbial populations associated with microbial enhanced oil recovery (meor) and their abundance in the xinjiang luliang water-flooding petroleum reservoir were investigated using 16s rrna, nitrate reductases, dissimilatory sulfate reductase, and methyl coenzyme-m reductase-encoded genes to provide ecological information for the potential application of meor. 16s rrna gene miseq sequencing revealed that this reservoir harbored large amounts of taxa, including 155 bacterial and 7 archeal genera. ... | 2015 | 25641701 |
| prokaryotic diversity in zostera noltii-colonized marine sediments. | the diversity of microorganisms present in a sediment colonized by the phanerogam zostera noltii has been analyzed. microbial dna was extracted and used for constructing two 16s rdna clone libraries for bacteria and archaea. bacterial diversity was very high in these samples, since 57 different sequences were found among the 60 clones analyzed. eight major lineages of the domain bacteria were represented in the library. the most frequently retrieved bacterial group (36% of the clones) was delta- ... | 2000 | 10742267 |
| characterization of root-nodulating bacteria associated to prosopis farcta growing in the arid regions of tunisia. | diversity of 50 bacterial isolates recovered from root nodules of prosopis farcta grown in different arid soils in tunisia, was investigated. characterization of isolates was assessed using a polyphasic approach including phenotypic characteristics, 16s rrna gene pcr--rflp and sequencing, noda gene sequencing and mlsa. it was found that most of isolates are tolerant to high temperature (40°c) and salinity (3%). genetic characterization emphasizes that isolates were assigned to the genus ensifer ... | 2011 | 21359955 |
| a novel cold-active beta-d-galactosidase from the paracoccus sp. 32d - gene cloning, purification and characterization. | abstract: background: beta-d-galactosidases (ec 3.2.1.23) catalyze the hydrolysis of terminal non-reducing beta-d-galactose residues in beta-d-galactosides. cold-active beta-d-galactosidases have recently become a focus of attention of researchers and dairy product manufactures owing to theirs ability to: (i) eliminate of lactose from refrigerated milk for people afflicted with lactose intolerance, (ii) convert lactose to glucose and galactose which increase the sweetness of milk and decreases ... | 2011 | 22166118 |
| single-cell genomics reveals the lifestyle of poribacteria, a candidate phylum symbiotically associated with marine sponges. | in this study, we present a single-cell genomics approach for the functional characterization of the candidate phylum poribacteria, members of which are nearly exclusively found in marine sponges. the microbial consortia of the mediterranean sponge aplysina aerophoba were singularized by fluorescence-activated cell sorting, and individual microbial cells were subjected to phi29 polymerase-mediated 'whole-genome amplification'. pyrosequencing of a single amplified genome (sag) derived from a memb ... | 2010 | 20613790 |
| single-cell genomics reveals the lifestyle of poribacteria, a candidate phylum symbiotically associated with marine sponges. | in this study, we present a single-cell genomics approach for the functional characterization of the candidate phylum poribacteria, members of which are nearly exclusively found in marine sponges. the microbial consortia of the mediterranean sponge aplysina aerophoba were singularized by fluorescence-activated cell sorting, and individual microbial cells were subjected to phi29 polymerase-mediated 'whole-genome amplification'. pyrosequencing of a single amplified genome (sag) derived from a memb ... | 2010 | 20613790 |
| 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 |
| phylogeny of 16s rrna, ribulose 1,5-bisphosphate carboxylase/oxygenase, and adenosine 5'-phosphosulfate reductase genes from gamma- and alphaproteobacterial symbionts in gutless marine worms (oligochaeta) from bermuda and the bahamas. | gutless oligochaetes are small marine worms that live in obligate associations with bacterial endosymbionts. while symbionts from several host species belonging to the genus olavius have been described, little is known of the symbionts from the host genus inanidrilus. in this study, the diversity of bacterial endosymbionts in inanidrilus leukodermatus from bermuda and inanidrilus makropetalos from the bahamas was investigated using comparative sequence analysis of the 16s rrna gene and fluoresce ... | 2006 | 16885306 |
| conservation and occurrence of trans-encoded srnas in the rhizobiales. | post-transcriptional regulation by trans-encoded srnas, for example via base-pairing with target mrnas, is a common feature in bacteria and influences various cell processes, e.g., response to stress factors. several studies based on computational and rna-seq approaches identified approximately 180 trans-encoded srnas in sinorhizobium meliloti. the initial point of this report is a set of 52 trans-encoded srnas derived from the former studies. sequence homology combined with structural conservat ... | 2011 | 24710299 |
| single-cell genomics: unravelling the genomes of unculturable microorganisms. | | 2011 | 21733126 |
| draft genome sequence of the bean-nodulating sinorhizobium fredii strain gr64. | sinorhizobium fredii gr64 is a peculiar strain that is able to effectively nodulate bean but not soybean, the common host of s. fredii. here we present the draft genome of s. fredii gr64. this information will contribute to a better understanding of the symbiotic rhizobium-plant interaction and of rhizobial evolution. | 2012 | 23209231 |
| complete genome sequence of the broad-host-range strain sinorhizobium fredii usda257. | here we announce the complete genome sequence of the symbiotic and nitrogen-fixing bacterium sinorhizobium fredii usda257. the genome shares a high degree of sequence similarity with the closely related broad-host-range strains s. fredii ngr234 and hh103. most strikingly, the usda257 genome encodes a wealth of secretory systems. | 2012 | 22843606 |
| selenium distribution and speciation in the hyperaccumulator astragalus bisulcatus and associated ecological partners. | the goal of this study was to investigate how plant selenium (se) hyperaccumulation may affect ecological interactions and whether associated partners may affect se hyperaccumulation. the se hyperaccumulator astragalus bisulcatus was collected in its natural seleniferous habitat, and x-ray fluorescence mapping and x-ray absorption near-edge structure spectroscopy were used to characterize se distribution and speciation in all organs as well as in encountered microbial symbionts and herbivores. s ... | 2012 | 22645068 |
| a set of lotus japonicus gifu x lotus burttii recombinant inbred lines facilitates map-based cloning and qtl mapping. | model legumes such as lotus japonicus have contributed significantly to the understanding of symbiotic nitrogen fixation. this insight is mainly a result of forward genetic screens followed by map-based cloning to identify causal alleles. the l. japonicus ecotype 'gifu' was used as a common parent for inter-accession crosses to produce f2 mapping populations either with other l. japonicus ecotypes, mg-20 and funakura, or with the related species l. filicaulis. these populations have all been use ... | 2012 | 22619310 |
| the ruegeria pomeroyi acui gene has a role in dmsp catabolism and resembles yhdh of e. coli and other bacteria in conferring resistance to acrylate. | the escherichia coli yhdh polypeptide is in the mdr012 sub-group of medium chain reductase/dehydrogenases, but its biological function was unknown and no phenotypes of yhdh(-) mutants had been described. we found that an e. coli strain with an insertional mutation in yhdh was hyper-sensitive to inhibitory effects of acrylate, and, to a lesser extent, to those of 3-hydroxypropionate. close homologues of yhdh occur in many bacterial taxa and at least two animals. the acrylate sensitivity of yhdh(- ... | 2012 | 22563425 |