Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| genomic basis of broad host range and environmental adaptability of rhizobium tropici ciat 899 and rhizobium sp. prf 81 which are used in inoculants for common bean (phaseolus vulgaris l.). | rhizobium tropici ciat 899 and rhizobium sp. prf 81 are α-proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. these strains are broadly used in commercial inoculants for application to common bean (phaseolus vulgaris) in south america and africa. both strains display intrinsic resistance to several abiotic stressful conditions such as low soil ph and high temperatures, which are common in tropical environments, and to several antimicrobials, including pesticides ... | 2012 | 23270491 |
| 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 |
| 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 |
| 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 |
| elucidation of the 3-o-deacylase gene, pagl, required for the removal of primary β-hydroxy fatty acid from the lipid a in the nitrogen-fixing endosymbiont rhizobium etli ce3. | until now, the gene responsible for the 3-o-deacylation of lipid a among nitrogen-fixing endosymbionts has not been characterized. several gram-negative animal pathogens such as salmonella enterica, pseudomonas aeruginosa, and bordetella bronchiseptica contain an outer membrane 3-o-deacylase (pagl) that has been implicated in host immune evasion. the role of 3-o-deacylated lipid a among nitrogen-fixing endosymbionts, plant endophytes, and plant pathogens has not been studied. however, d'haeze et ... | 2013 | 23511636 |
| 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 |
| rice and bean ahl-mimic quorum-sensing signals specifically interfere with the capacity to form biofilms by plant-associated bacteria. | many bacteria regulate their gene expression in response to changes in their population density in a process called quorum sensing (qs), which involves communication between cells mediated by small diffusible signal molecules termed autoinducers. n-acyl-homoserine-lactones (ahls) are the most common autoinducers in proteobacteria. qs-regulated genes are involved in complex interactions between bacteria of the same or different species and even with some eukaryotic organisms. eukaryotes, includin ... | 2013 | 23583723 |
| 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 |
| 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 |
| 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 |
| brucella bior regulator defines a complex regulatory mechanism for bacterial biotin metabolism. | the enzyme cofactor biotin (vitamin h or b7) is an energetically expensive molecule whose de novo biosynthesis requires 20 atp equivalents. it seems quite likely that diverse mechanisms have evolved to tightly regulate its biosynthesis. unlike the model regulator bira, a bifunctional biotin protein ligase with the capability of repressing the biotin biosynthetic pathway, bior has been recently reported by us as an alternative machinery and a new type of gntr family transcriptional factor that ca ... | 2013 | 23729648 |
| 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 |
| 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 |
| new players in the same old game: a system level in silico study to predict type iii secretion system and effector proteins in bacterial genomes reveals common themes in t3ss mediated pathogenesis. | type iii secretion system (t3ss) plays an important role in virulence or symbiosis of many pathogenic or symbiotic bacteria [chm 2:291-294, 2007; physiology (bethesda) 20:326-339, 2005]. t3ss acts like a tunnel between a bacterium and its host through which the bacterium injects 'effector' proteins into the latter [nature 444:567-573, 2006; cosb 18:258-266, 2008]. the effectors spatially and temporally modify the host signalling pathways [fems microbiol rev 35:1100-1125, 2011; cell host microbe5 ... | 2013 | 23890184 |
| catalytic mechanism of 5-chlorohydroxyhydroquinone dehydrochlorinase from the ycii superfamily of largely unknown function. | tftg, 5-chloro-2-hydroxyhydroquinone (5-chq) dehydrochlorinase, is involved in the biodegradation of 2,4,5-trichlorophenoxyacetate by burkholderia phenoliruptrix ac1100. it belongs to the ycii superfamily, a group of proteins with largely unknown function. in this work, we utilized structural and functional studies, including the apo-form and 2,5-dihydroxybenzoquinone binary complex crystal structures, computational analysis, and site-directed mutagenesis, to determine the dehydrochlorination me ... | 2013 | 23955343 |
| evolutionary diversification and characterization of the eubacterial gene family encoding dxr type ii, an alternative isoprenoid biosynthetic enzyme. | isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. in most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosphate (mep) pathway. the production of mep is usually catalyzed by deoxyxylulose 5-phosphate reductoisomerase (dxr-i) but a few organisms use an alternative dxr-like enzyme (dxr-ii). | 2013 | 24004839 |
| poly β-hydroxybutyrate production by bacillus subtilis ng220 using sugar industry waste water. | the production of poly β-hydroxybutyrate (phb) by bacillus subtilis ng220 was observed utilizing the sugar industry waste water supplemented with various carbon and nitrogen sources. at a growth rate of 0.14 g h(-1) l(-1), using sugar industry waste water was supplemented with maltose (1% w/v) and ammonium sulphate (1% w/v); the isolate produced 5.297 g/l of poly β-hydroxybutyrate accumulating 51.8% (w/w) of biomass. the chemical nature of the polymer was confirmed with nuclear magnetic resonanc ... | 2013 | 24027767 |
| characterization of indigenous rhizobia from caatinga. | the aim of this study was to characterize rhizobial isolates from cratylia mollis mart. ex benth, calliandra depauperata benth. and mimosa tenuiflora (willd.) poir. by means of rhizobial colonies morphology and restriction analysis of the 16s ribosomal gene (16s rdna-ardra). nodules were collected in the field and from plants cultivated in a greenhouse experiment using caatinga soil samples. sixty seven isolates were described by morphological analysis. forty seven representative isolates were u ... | 2010 | 24031482 |
| 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 |
| prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment. | the commercial availability of next generation sequencing (ngs) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with ngs technologies. studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which m ... | 2013 | 24046766 |
| 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 |
| functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter. | targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. the overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknow ... | 2013 | 24062736 |
| 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 |
| purine biosynthesis-deficient burkholderia mutants are incapable of symbiotic accommodation in the stinkbug. | the riptortus-burkholderia symbiotic system represents a promising experimental model to study the molecular mechanisms involved in insect-bacterium symbiosis due to the availability of genetically manipulated burkholderia symbiont. using transposon mutagenesis screening, we found a symbiosis-deficient mutant that was able to colonize the host insect but failed to induce normal development of host's symbiotic organ. the disrupted gene was identified as purl involved in purine biosynthesis. in vi ... | 2013 | 24088627 |
| purine biosynthesis-deficient burkholderia mutants are incapable of symbiotic accommodation in the stinkbug. | the riptortus-burkholderia symbiotic system represents a promising experimental model to study the molecular mechanisms involved in insect-bacterium symbiosis due to the availability of genetically manipulated burkholderia symbiont. using transposon mutagenesis screening, we found a symbiosis-deficient mutant that was able to colonize the host insect but failed to induce normal development of host's symbiotic organ. the disrupted gene was identified as purl involved in purine biosynthesis. in vi ... | 2013 | 24088627 |
| 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 |
| a nopa deletion mutant of sinorhizobium fredii usda257, a soybean symbiont, is impaired in nodulation. | sinorhizobium fredii usda257 employs type iii secretion system (t3ss) to deliver effector proteins into the host cells through pili. the nopa protein is the major component of usda257 pili. the promoter region of usda257 nopa possesses a well conserved tts box. serial deletion analysis revealed that the tts box is absolutely essential for flavonoid induction of nopa. deletion of nopa drastically lowered the number of nodules formed by usda257 on cowpea and soybean cultivar peking. in contrast to ... | 2014 | 24121614 |
| 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 |
| nitrate and periplasmic nitrate reductases. | the nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. in this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. many bacteria readily reduce nitrate to nit ... | 2014 | 24141308 |
| 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 |
| 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 |
| 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 |
| biochemical and functional characterization of spda, a 2', 3'cyclic nucleotide phosphodiesterase from sinorhizobium meliloti. | 3', 5'camp signaling in sinorhizobium meliloti was recently shown to contribute to the autoregulation of legume infection. in planta, three adenylate cyclases cyad1, cyad2 and cyak, synthesizing 3', 5'camp, together with the crp-like transcriptional regulator clr and smc02178, a gene of unknown function, are involved in controlling plant infection. | 2013 | 24279347 |
| replicon-dependent differentiation of symbiosis-related genes in sinorhizobium strains nodulating glycine max. | in order to investigate the genetic differentiation of sinorhizobium strains nodulating glycine max and related microevolutionary mechanisms, three housekeeping genes (smc00019, trua, and thra) and 16 symbiosis-related genes on the chromosome (7 genes), psyma (6 genes), and psymb (3 genes) were analyzed. five distinct species were identified among the test strains by calculating the average nucleotide identity (ani) of smc00019-trua-thra: sinorhizobium fredii, sinorhizobium sojae, sinorhizobium ... | 2014 | 24317084 |
| characterization of rhizobium grahamii extrachromosomal replicons and their transfer among rhizobia. | rhizobium grahamii belongs to a new phylogenetic group of rhizobia together with rhizobium mesoamericanum and other species. r. grahamii has a broad-host-range that includes leucaena leucocephala and phaseolus vulgaris, although it is a poor competitor for p. vulgaris nodulation in the presence of rhizobium etli or rhizobium phaseoli strains. this work analyzed the genome sequence and transfer properties of r. grahamii plasmids. | 2014 | 24397311 |
| genes conferring copper resistance in sinorhizobium meliloti ccnwsx0020 also promote the growth of medicago lupulina in copper-contaminated soil. | sinorhizobium meliloti ccnwsx0020, isolated from root nodules of medicago lupulina growing in gold mine tailings in the northwest of china, displayed both copper resistance and growth promotion of leguminous plants in copper-contaminated soil. nevertheless, the genetic and biochemical mechanisms responsible for copper resistance in s. meliloti ccnwsx0020 remained uncharacterized. to investigate genes involved in copper resistance, an s. meliloti ccnwsx0020 tn5 insertion library of 14,000 mutants ... | 2014 | 24441157 |
| 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 |
| bradyrhizobium ganzhouense sp. nov., an effective symbiotic bacterium isolated from acacia melanoxylon r. br. nodules. | three slow-growing rhizobial strains, designated ritf806(t), ritf807 and ritf211, isolated from root nodules of acacia melanoxylon grown in ganzhou city, jiangxi province, china, had been previously defined, based on amplified 16s rrna gene restriction analysis, as a novel group within the genus bradyrhizobium. to clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. according to 16s rrna gene se ... | 2014 | 24585376 |
| the growth of steroidobacter agariperforans sp. nov., a novel agar-degrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to rhizobiales. | an agar-degrading bacterium was isolated from soil collected in a vegetable cropping field. the growth of this isolate was enhanced by supplying culture supernatants of bacteria belonging to the order rhizobiales. phylogenetic analysis based on 16s rrna gene sequences indicated the novel bacterium, strain ka5-b(t), belonged to the genus steroidobacter in gammaproteobacteria, but differed from its closest relative, steroidobacter denitrificans fs(t), at the species level with 96.5% similarity. st ... | 2014 | 24621511 |
| 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 |
| the genetics of symbiotic nitrogen fixation: comparative genomics of 14 rhizobia strains by resolution of protein clusters. | the symbiotic relationship between legumes and nitrogen fixing bacteria is critical for agriculture, as it may have profound impacts on lowering costs for farmers, on land sustainability, on soil quality, and on mitigation of greenhouse gas emissions. however, despite the importance of the symbioses to the global nitrogen cycling balance, very few rhizobial genomes have been sequenced so far, although there are some ongoing efforts in sequencing elite strains. in this study, the genomes of fourt ... | 2012 | 24704847 |
| 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 |
| 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 |
| phenotypic characterization of astragalus glycyphyllos symbionts and their phylogeny based on the 16s rdna sequences and rflp of 16s rrna gene. | in this study, the nitrogen fixing astragalus glycyphyllos symbionts were characterized by phenotypic properties, restriction fragment length polymorphism (rflp), and sequences of 16s rdna. the generation time of a. glycyphyllos rhizobia in yeast extract mannitol medium was in the range 4-6 h. the studied isolates exhibited a low resistance to antibiotics, a moderate tolerance to nacl, assimilated di- and trisaccharides, and produced acid in medium containing mannitol as a sole carbon source. in ... | 2014 | 24710996 |
| 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 |
| genomic analysis of cyclic-di-gmp-related genes in rhizobial type strains and functional analysis in rhizobium etli. | rhizobia are soil bacteria that can fix nitrogen in symbiosis with leguminous plants or exist free living in the rhizosphere. crucial to their complex lifestyle is the ability to sense and respond to diverse environmental stimuli, requiring elaborate signaling pathways. in the majority of bacteria, the nucleotide-based second messenger cyclic diguanosine monophosphate (c-di-gmp) is involved in signal transduction. surprisingly, little is known about the importance of c-di-gmp signaling in rhizob ... | 2014 | 24728599 |
| structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein nolr. | the symbiosis between rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. as part of the transcriptional machinery for nodulation and symbiosis across a range of rhizobium, nolr serves as a global regulatory protein. here, we present the x-ray crystal structures of nolr in the unliganded form and complexed with two different 22-base pair (bp) double-stranded operator sequences (oligos at and aa). structu ... | 2014 | 24733893 |
| atmospheric n deposition increases bacterial laccase-like multicopper oxidases: implications for organic matter decay. | anthropogenic release of biologically available nitrogen (n) has increased dramatically over the last 150 years, which can alter the processes controlling carbon (c) storage in terrestrial ecosystems. in a northern hardwood forest ecosystem located in michigan in the united states, nearly 20 years of experimentally increased atmospheric n deposition has reduced forest floor decay and increased soil c storage. this change occurred concomitantly with compositional changes in basidiomycete fungi an ... | 2014 | 24837374 |
| 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 |
| quorum quenching agents: resources for antivirulence therapy. | the continuing emergence of antibiotic-resistant pathogens is a concern to human health and highlights the urgent need for the development of alternative therapeutic strategies. quorum sensing (qs) regulates virulence in many bacterial pathogens, and thus, is a promising target for antivirulence therapy which may inhibit virulence instead of cell growth and division. this means that there is little selective pressure for the evolution of resistance. many natural quorum quenching (qq) agents have ... | 2014 | 24886865 |
| effect of sinorhizobium fredii strain sneb183 on the biological control of soybean cyst nematode in soybean. | the soybean cyst nematode (scn; heterodera glycines) is a major detriment to soybean production. the endophytic bacterium sinorhizobium fredii strain sneb183 is known to inhibit the activity of scn. in the present study, soybean seedlings were inoculated with sneb183, to study the penetration juveniles, and their development inside the roots. the number of cysts in the soybean roots was also examined. the induced systemic resistance in soybean was also examined through the split-root system. our ... | 2014 | 24912826 |
| 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 |
| cell cycle transition from s-phase to g1 in caulobacter is mediated by ancestral virulence regulators. | zinc-finger domain transcriptional regulators regulate a myriad of functions in eukaryotes. interestingly, ancestral versions (mucr) from alpha-proteobacteria control bacterial virulence/symbiosis. whether virulence regulators can also control cell cycle transcription is unknown. here we report that mucr proteins implement a hitherto elusive primordial s→g1 transcriptional switch. after charting g1-specific promoters in the cell cycle model caulobacter crescentus by comparative chip-seq, we use ... | 2014 | 24939058 |
| 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 |
| dna topoisomerase viii: a novel subfamily of type iib topoisomerases encoded by free or integrated plasmids in archaea and bacteria. | type ii dna topoisomerases are divided into two families, iia and iib. types iia and iib enzymes share homologous b subunits encompassing the atp-binding site, but have non-homologous a subunits catalyzing dna cleavage. type iia topoisomerases are ubiquitous in bacteria and eukarya, whereas members of the iib family are mostly present in archaea and plants. here, we report the detection of genes encoding type iib enzymes in which the a and b subunits are fused into a single polypeptide. these pr ... | 2014 | 24990376 |
| 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 |
| identification of two nickel ion-induced genes, nci16 and pcgst1, in paramecium caudatum. | here, we describe the isolation of two nickel-induced genes in paramecium caudatum, nci16 and pcgst1, by subtractive hybridization. nci16 encoded a predicted four-transmembrane domain protein (∼16 kda) of unknown function, and pcgst1 encoded glutathione s-transferase (gst; ∼25 kda) with gst and glutathione peroxidase (gpx) activities. exposing cells to cobalt chloride also caused the moderate upregulation of nci16 and pcgst1 mrnas. both nickel sulfate and cobalt chloride dose dependently induced ... | 2014 | 25001407 |
| 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 |
| 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 |
| nitrogen-fixing rhizobial strains isolated from common bean seeds: phylogeny, physiology, and genome analysis. | rhizobial bacteria are commonly found in soil but also establish symbiotic relationships with legumes, inhabiting the root nodules, where they fix nitrogen. endophytic rhizobia have also been reported in the roots and stems of legumes and other plants. we isolated several rhizobial strains from the nodules of noninoculated bean plants and looked for their provenance in the interiors of the seeds. nine isolates were obtained, covering most known bean symbiont species, which belong to the rhizobiu ... | 2014 | 25002426 |
| evidence of autoinducer-dependent and -independent heterogeneous gene expression in sinorhizobium fredii ngr234. | populations of genetically identical sinorhizobium fredii ngr234 cells differ significantly in their expression profiles of autoinducer (ai)-dependent and ai-independent genes. promoter fusions of the ngr234 ai synthase genes trai and ngri showed high levels of phenotypic heterogeneity during growth in ty medium on a single-cell level. however, adding very high concentrations of n-(3-oxooctanoyl-)-l-homoserine lactone resulted in a more homogeneous expression profile. similarly, the lack of inte ... | 2014 | 25002427 |
| riboregulation in plant-associated α-proteobacteria. | the symbiotic α-rhizobia sinorhizobium meliloti, bradyrhizobium japonicum, rhizobium etli and the related plant pathogen agrobacterium tumefaciens are important model organisms for studying plant-microbe interactions. these metabolically versatile soil bacteria are characterized by complex lifestyles and large genomes. here we summarize the recent knowledge on their small non-coding rnas (srnas) including conservation, function, and interaction of the srnas with the rna chaperone hfq. in each of ... | 2014 | 25003187 |
| 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 |
| distribution and diversity of rhizobia associated with wild soybean (glycine soja sieb. & zucc.) in northwest china. | a total of 155 nodule isolates that originated from seven sites in northwest china were characterized by pcr-rflp of the 16s rrna gene and sequence analysis of multiple core genes (16s rrna, reca, atpd, and glnii) in order to investigate the diversity and biogeography of glycine soja-nodulating rhizobia. among the isolates, 80 were ensifer fredii, 19 were ensifer morelense, 49 were rhizobium radiobacter, and 7 were putative novel rhizobium species. the phylogenies of e. fredii and e. morelense i ... | 2014 | 25052953 |
| effects of the joint exposure of decabromodiphenyl ether and tetrabromobisphenol a on soil bacterial community structure. | decabromodiphenyl ether (bde209) and tetrabromobisphenol a (tbbpa) are the main contaminants at electronic waste (e-waste) recycling sites (ewrss), and their potential toxicological effects have received extensive attention. however, the impact on soil microorganism of joint exposure to the two chemicals remains almost unknown. therefore, indoor incubation tests were performed on control and contaminated soil samples to determine the response of soil bacterial community structure in the joint pr ... | 2015 | 25106514 |
| characterization of a class ii 5-enopyruvylshikimate-3-phosphate synthase with high tolerance to glyphosate from sinorhizobium fredii. | 5-enopyruvylshikimate-3-phosphate synthase (epsp synthase) is an important enzyme in the shikimate pathway mediating the biosynthesis of aromatic compounds in plants and microorganisms. a novel class ii epsp synthase aroa s. fredii from sinorhizobium fredii ngr234 was overexpressed in escherichia coli bl21. it was purified to homogeneity and its catalytic properties were studied. the enzyme exhibited optimum catalytic activity at ph 8.0 and 50 °c. it was stable below 40 °c, and over a broad rang ... | 2014 | 25151150 |
| 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 |
| isolation and characterization of a gene associated with sulfate assimilation in sinorhizobium fredii wgf03. | sulfur is an essential element for rhizobia, such as sulfated modified nod factors and nitrogenase. to investigate the role of sulfur metabolism in rhizobium-soybean symbiosis, a transponson random insertional mutants' library was constructed and a sulfur assimilation-related gene was isolated and characterized. a mutant strain unable to utilized sulfate was screened from 11,000 random insertional mutants of sinorhizobium fredii wgf03. sequencing analysis showed that a sulfate assimilation-relat ... | 2014 | 25182128 |
| 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 |
| 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 |
| cloning, expression, purification and preliminary x-ray analysis of estn2, a novel archaeal α/β-hydrolase from candidatus nitrososphaera gargensis. | estn2 is a novel α/β-hydrolase originating from the ammonia-oxidizing thaumarchaeon candidatus nitrososphaera gargensis. the genome of the organism was sequenced and genes conferring putative lipolytic activity were amplified and cloned into escherichia coli as a heterologous host. through function-based screening, esterase and lipase activity was detected. a recombinant enzyme designated estn2 was successfully expressed, purified and crystallized. the crystals belonged to space group i2, with o ... | 2014 | 25286947 |
| differentiating indigenous soybean bradyrhizobium and rhizobium spp. of indian soils. | soybean is extensively cultivated worldwide and is the largest source of biologically fixed nitrogen among legumes. it is nodulated by both slow and fast growing rhizobia. indigenous soybean rhizobia in vertisols of central india were assessed for utilization of 35 carbon sources and intrinsic resistance to 19 antibiotics. there was greater utilization of trehalose and raffinose by fast growers (87 and 73 % by fast vs. 35 and 30 % by slow growers); but slow growers had higher ability to utilize ... | 2013 | 25320421 |
| differentiating indigenous soybean bradyrhizobium and rhizobium spp. of indian soils. | soybean is extensively cultivated worldwide and is the largest source of biologically fixed nitrogen among legumes. it is nodulated by both slow and fast growing rhizobia. indigenous soybean rhizobia in vertisols of central india were assessed for utilization of 35 carbon sources and intrinsic resistance to 19 antibiotics. there was greater utilization of trehalose and raffinose by fast growers (87 and 73 % by fast vs. 35 and 30 % by slow growers); but slow growers had higher ability to utilize ... | 2013 | 25320421 |
| evidence for methionine-sulfoxide-reductase gene transfer from alphaproteobacteria to the transcriptionally active (macro)nucleus of the ciliate, euplotes raikovi. | deleterious phenomena of protein oxidation affect every aerobic organism and methionine residues are their elective targets. the reduction of methionine sulfoxides back to methionines is catalyzed by methionine-sulfoxide reductases (msrs), enzymes which are particularly active in microorganisms because of their unique nature of individual cells directly exposed to environmental oxidation. | 2014 | 25420622 |
| 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 |
| optimization of pretreatment and fermentation conditions for production of extracellular cellulase complex using sugarcane bagasse. | sugarcane bagasse (scb), a lignocellulosic byproduct of juice extraction from sugarcane, is rich in cellulose (40-42%). this could be used as a substrate for the production of cellulase complex. fermentation conditions were optimized for production of cellulase complex (cmcase, cellulobiase and fpase) by wild type trichoderma sp. using sugarcane bagasse as sole carbon source. alkaline treatment (2% naoh) of bagasse (alscb) was found suitable for the production of reducing sugar over the acidic p ... | 2014 | 25489168 |
| 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 |
| 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 |
| 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 |
| genes encoding conserved hypothetical proteins localized in the conjugative transfer region of plasmid pret42a from rhizobium etli cfn42 participate in modulating transfer and affect conjugation from different donors. | among sequenced genomes, it is common to find a high proportion of genes encoding proteins that cannot be assigned a known function. in bacterial genomes, genes related to a similar function are often located in contiguous regions. the presence of genes encoding conserved hypothetical proteins (chp) in such a region may suggest that they are related to that particular function. plasmid pret42a from rhizobium etli cfn42 is a conjugative plasmid containing a segment of approximately 30 kb encoding ... | 2014 | 25642223 |
| genes encoding conserved hypothetical proteins localized in the conjugative transfer region of plasmid pret42a from rhizobium etli cfn42 participate in modulating transfer and affect conjugation from different donors. | among sequenced genomes, it is common to find a high proportion of genes encoding proteins that cannot be assigned a known function. in bacterial genomes, genes related to a similar function are often located in contiguous regions. the presence of genes encoding conserved hypothetical proteins (chp) in such a region may suggest that they are related to that particular function. plasmid pret42a from rhizobium etli cfn42 is a conjugative plasmid containing a segment of approximately 30 kb encoding ... | 2014 | 25642223 |
| the sinorhizobium fredii hh103 genome: a comparative analysis with s. fredii strains differing in their symbiotic behavior with soybean. | sinorhizobium fredii hh103 is a fast-growing rhizobial strain infecting a broad range of legumes including both american and asiatic soybeans. in this work, we present the sequencing and annotation of the hh103 genome (7.25 mb), consisting of one chromosome and six plasmids and representing the structurally most complex sinorhizobial genome sequenced so far. comparative genomic analyses of s. fredii hh103 with strains usda257 and ngr234 showed that the core genome of these three strains contains ... | 2015 | 25675256 |
| the absence of protein y4ys affects negatively the abundance of t3ss mesorhizobium loti secretin, rhcc2, in bacterial membranes. | mesorhizobium loti maff303099 has a functional type iii secretion system (t3ss) that is involved in the determination of nodulation competitiveness on lotus. the m. loti t3ss cluster contains gene y4ys (mlr8765) that codes for a protein of unknown function (y4ys). a mutation in the y4ys gene favors the m. loti symbiotic competitive ability on lotus tenuis cv. esmeralda and affects negatively the secretion of proteins through t3ss. here we localize y4ys in the bacterial membrane using a translati ... | 2015 | 25688250 |
| genome 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 |
| the sinorhizobium (ensifer) fredii hh103 type 3 secretion system suppresses early defense responses to effectively nodulate soybean. | plants that interact with pathogenic bacteria in their natural environments have developed barriers to block or contain the infection. phytopathogenic bacteria have evolved mechanisms to subvert these defenses and promote infection. thus, the type 3 secretion system (t3ss) delivers bacterial effectors directly into the plant cells to alter host signaling and suppress defenses, providing an appropriate environment for bacterial multiplication. some rhizobial strains possess a symbiotic t3ss that ... | 2015 | 25775271 |
| the sinorhizobium meliloti syrm regulon: effects on global gene expression are mediated by syra and nodd3. | in sinorhizobium meliloti, three nodd transcriptional regulators activate bacterial nodulation (nod) gene expression. nodd1 and nodd2 require plant compounds to activate nod genes. the nodd3 protein does not require exogenous compounds to activate nod gene expression; instead, another transcriptional regulator, syrm, activates nodd3 expression. in addition, nodd3 can activate syrm expression. syrm also activates expression of another gene, syra, which when overexpressed causes a dramatic increas ... | 2015 | 25777671 |
| 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 |
| 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 |
| 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 |
| [symbiotic matching between soybean cultivar luhuang no. 1 and different rhizobia]. | soybean plants could establish symbiosis and fix nitrogen with different rhizobial species in the genera of sinorhizobium and bradyrhizobium. studies on the symbiotic matching between soybean cultivars and different rhizobial species are theoretically and practically important for selecting effective strains used to inoculate the plants and improve the soybean production and quality. a total of 27 strains were isolated and purified from a soil sample of huanghuaihai area by using the soybean cul ... | 2014 | 25876410 |
| 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 |
| biofilm formation assessment in sinorhizobium meliloti reveals interlinked control with surface motility. | swarming motility and biofilm formation are opposite, but related surface-associated behaviors that allow various pathogenic bacteria to colonize and invade their hosts. in sinorhizobium meliloti, the alfalfa endosymbiont, these bacterial processes and their relevance for host plant colonization are largely unexplored. our previous work demonstrated distinct swarming abilities in two s. meliloti strains (rm1021 and gr4) and revealed that both environmental cues (iron concentration) and bacterial ... | 2015 | 25887945 |