Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
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| complete genome sequence of bradyrhizobium japonicum j5, isolated from a soybean nodule in hokkaido, japan. | soybean bradyrhizobia form root nodules on soybean plants and symbiotically fix n2 strain j5 is phylogenetically far from well-known representatives within the bradyrhizobium japonicum linage. the complete genome showed the largest single chromosomal (10.1 mb) and symbiosis island (998 kb) among complete genomes of soybean bradyrhizobia. | 2017 | 28183772 |
| rna-seq analysis of nodule development at five different developmental stages of soybean (glycine max) inoculated with bradyrhizobium japonicum strain 113-2. | nodule development directly affects nitrogen fixation efficiency during soybean growth. although abundant genome-based information related to nodule development has been released and some studies have reported the molecular mechanisms that regulate nodule development, information on the way nodule genes operate in nodule development at different developmental stages of soybean is limited. in this report, notably different nodulation phenotypes in soybean roots inoculated with bradyrhizobium japo ... | 2017 | 28169364 |
| disparate response to microoxia and nitrogen oxides of the bradyrhizobium japonicum napedabc, nirk and norcbqd denitrification genes. | expression of the bradyrhizobium japonicum napedabc, nirk and norcbqd denitrification genes requires low oxygen (o2) tension and nitrate (no3(-)), through a regulatory network comprised of two coordinated cascades, fixlj-fixk2-nnrr and regsr-nifa. to precisely understand how these signals are integrated in the fixlj-fixk2-nnrr circuit, we analyzed β-galactosidase activities from nape-lacz, nirk-lacz and norc-lacz fusions, and performed analyses of napc and norc levels as well as periplasmic nitr ... | 2017 | 28167162 |
| proclat, a new bioinformatics tool for in silico protein reclassification: case study of drab, a protein coded from the dratgb operon in azospirillum brasilense. | azopirillum brasilense is a plant-growth promoting nitrogen-fixing bacteria that is used as bio-fertilizer in agriculture. since nitrogen fixation has a high-energy demand, the reduction of n2 to nh4(+) by nitrogenase occurs only under limiting conditions of nh4(+) and o2. moreover, the synthesis and activity of nitrogenase is highly regulated to prevent energy waste. in a. brasilense nitrogenase activity is regulated by the products of drag and drat. the product of the drab gene, located downst ... | 2016 | 28105917 |
| deciphering composition and function of the root microbiome of a legume plant. | diverse assemblages of microbes colonize plant roots and collectively function as a microbiome. earlier work has characterized the root microbiomes of numerous plant species, but little information is available for legumes despite their key role in numerous ecosystems including agricultural systems. legumes form a root nodule symbiosis with nitrogen-fixing rhizobia bacteria and thereby account for large, natural nitrogen inputs into soils. here, we describe the root bacteria microbiome of the le ... | 2017 | 28095877 |
| direct heme uptake by phytoplankton-associated roseobacter bacteria. | iron is an essential micronutrient and can limit the growth of both marine phytoplankton and heterotrophic bacterioplankton. in this study, we investigated the molecular basis of heme transport, an organic iron acquisition pathway, in phytoplankton-associated roseobacter bacteria and explored the potential role of bacterial heme uptake in the marine environment. we searched 153 roseobacter genomes and found that nearly half contained putative complete heme transport systems with nearly the same ... | 2017 | 28083564 |
| distribution of hydrogenases in cyanobacteria: a phylum-wide genomic survey. | microbial molecular hydrogen (h2) cycling plays an important role in several ecological niches. hydrogenases (h2ases), enzymes involved in h2 metabolism, are of great interest for investigating microbial communities, and producing bioh2. to obtain an overall picture of the genetic ability of cyanobacteria to produce h2ases, we conducted a phylum wide analysis of the distribution of the genes encoding these enzymes in 130 cyanobacterial genomes. the concomitant presence of the h2ase and genes inv ... | 2016 | 28083017 |
| comparative genomic analysis of bacillus amyloliquefaciens and bacillus subtilis reveals evolutional traits for adaptation to plant-associated habitats. | bacillus subtilis and its sister species b. amyloliquefaciens comprise an evolutionary compact but physiologically versatile group of bacteria that includes strains isolated from diverse habitats. many of these strains are used as plant growth-promoting rhizobacteria (pgpr) in agriculture and a plant-specialized subspecies of b. amyloliquefaciens-b. amyloliquefaciens subsp. plantarum, has recently been recognized, here we used 31 whole genomes [including two newly sequenced pgpr strains: b. amyl ... | 2016 | 28066362 |
| unsupervised statistical discovery of spaced motifs in prokaryotic genomes. | dna sequences contain repetitive motifs which have various functions in the physiology of the organism. a number of methods have been developed for discovery of such sequence motifs with a primary focus on detection of regulatory motifs and particularly transcription factor binding sites. most motif-finding methods apply probabilistic models to detect motifs characterized by unusually high number of copies of the motif in the analyzed sequences. | 2017 | 28056763 |
| natural and synthetic variants of the tricarboxylic acid cycle in cyanobacteria: introduction of the gaba shunt into synechococcus sp. pcc 7002. | for nearly half a century, it was believed that cyanobacteria had an incomplete tricarboxylic acid (tca) cycle, because 2-oxoglutarate dehydrogenase (2-ogdh) was missing. recently, a bypass route via succinic semialdehyde (ssa), which utilizes 2-oxoglutarate decarboxylase (ogda) and succinic semialdehyde dehydrogenase (ssad) to convert 2-oxoglutarate (2-og) into succinate, was identified, thus completing the tca cycle in most cyanobacteria. in addition to the recently characterized glyoxylate sh ... | 2016 | 28018308 |
| biotransformation of β-keto nitriles to chiral (s)-β-amino acids using nitrilase and ω-transaminase. | to enzymatically synthesize enantiomerically pure β-amino acids from β-keto nitriles using nitrilase and ω-transaminase. | 2017 | 28004208 |
| resilient microorganisms in dust samples of the international space station-survival of the adaptation specialists. | the international space station (iss) represents a unique biotope for the human crew but also for introduced microorganisms. microbes experience selective pressures such as microgravity, desiccation, poor nutrient-availability due to cleaning, and an increased radiation level. we hypothesized that the microbial community inside the iss is modified by adapting to these stresses. for this reason, we analyzed 8-12 years old dust samples from russian iss modules with major focus on the long-time sur ... | 2016 | 27998314 |
| bradyrhizobium inoculants enhance grain yields of soybean and cowpea in northern ghana. | this study evaluated the symbiotic effectiveness and economic evaluation of rhizobium inoculants with the objective of recommending the most effective inoculant strain for soybean and cowpea production in northern ghana. field experiments were established in three locations using randomized complete block design with five blocks. a total of four treatments (legumefix, biofix, 100 kg n ha(-1) and uninoculated control for soybean and br 3267, br 3262, 100 kg n ha(-1) and uninoculated control for c ... | 2016 | 27965683 |
| conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone. | protein-protein interactions are fundamental for the proper functioning of the cell. as a result, protein interaction surfaces are subject to strong evolutionary constraints. recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. so far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compi ... | 2016 | 27965389 |
| structural basis for glutathione-mediated activation of the virulence regulatory protein prfa in listeria. | infection by the human bacterial pathogen listeria monocytogenes is mainly controlled by the positive regulatory factor a (prfa), a member of the crp/fnr family of transcriptional activators. published data suggest that prfa requires the binding of a cofactor for full activity, and it was recently proposed that glutathione (gsh) could fulfill this function. here we report the crystal structures of prfa in complex with gsh and in complex with gsh and its cognate dna, the hly operator prfa box mot ... | 2016 | 27930316 |
| the use of transposon insertion sequencing to interrogate the core functional genome of the legume symbiont rhizobium leguminosarum. | the free-living legume symbiont rhizobium leguminosarum is of significant economic value because of its ability to provide fixed nitrogen to globally important leguminous food crops, such as peas and lentils. discovery based research into the genetics and physiology of r. leguminosarum provides the foundational knowledge necessary for understanding the bacterium's complex lifestyle, necessary for augmenting its use in an agricultural setting. transposon insertion sequencing (inseq) facilitates h ... | 2016 | 27920770 |
| hydrogen overproducing nitrogenases obtained by random mutagenesis and high-throughput screening. | when produced biologically, especially by photosynthetic organisms, hydrogen gas (h2) is arguably the cleanest fuel available. an important limitation to the discovery or synthesis of better h2-producing enzymes is the absence of methods for the high-throughput screening of h2 production in biological systems. here, we re-engineered the natural h2 sensing system of rhodobacter capsulatus to direct the emission of lacz-dependent fluorescence in response to nitrogenase-produced h2. a lacz gene was ... | 2016 | 27910898 |
| construction of a miniaturized chromatic acclimation sensor from cyanobacteria with reversed response to a light signal. | cyanobacteria harbor unique photoreceptors, designated as cyanobacteriochromes (cbcrs). in this study, we attempted to engineer the chromatic acclimation sensor ccas, a cbcr derived from the cyanobacterium synechocystis sp. pcc 6803. the wild-type ccas induces gene expression under green light illumination and represses it under red light illumination. we focused on the domain structure of ccas, which consists of an n-terminal transmembrane helix; a gaf domain, which serves as the sensor domain; ... | 2016 | 27883080 |
| elucidation of gibberellin biosynthesis in bacteria reveals convergent evolution. | gibberellins (gas) are crucial phytohormones involved in many aspects of plant growth and development, including plant-microbe interactions, which has led to ga production by plant-associated fungi and bacteria as well. while the ga biosynthetic pathways in plants and fungi have been elucidated and found to have arisen independently through convergent evolution, little has been uncovered about ga biosynthesis in bacteria. some nitrogen-fixing, symbiotic, legume-associated rhizobia, including bra ... | 2017 | 27842068 |
| x-ray microanalytical studies of mineral elements in the tripartite symbiosis between lima bean, n2-fixing bacteria and mycorrhizal fungi. | the symbiosis between legumes, arbuscular mycorrhizal (am) fungi, and n2-fixing bacteria (nfb) provides mutual nutritional gains. however, assessing the nutritional status of the microorganisms is a difficult task. a methodology that could assess this status, in situ, could assist managing these organisms in agriculture. this study used x-ray microanalyses to quantify and locate mineral elements in structures formed in a tripartite symbiosis. lima bean (phaseolus lunatus l. walp) was cultivated ... | 2017 | 27838542 |
| structural characterization of the thermostable bradyrhizobium japonicumd-sorbitol dehydrogenase. | bradyrhizobium japonicum sorbitol dehydrogenase is nadh-dependent and is active at elevated temperatures. the best substrate is d-glucitol (a synonym for d-sorbitol), although l-glucitol is also accepted, giving it particular potential in industrial applications. crystallization led to a hexagonal crystal form, with crystals diffracting to 2.9 å resolution. in attempts to phase the data, a molecular-replacement solution based upon pdb entry 4nbu (33% identical in sequence to the target) was foun ... | 2016 | 27827356 |
| search for nodulation and nodule development-related cystatin genes in the genome of soybean (glycine max). | nodulation, nodule development and senescence directly affects nitrogen fixation efficiency, and previous studies have shown that inhibition of some cysteine proteases delay nodule senescence, so their nature inhibitors, cystatin genes, are very important in nodulation, nodule development, and senescence. although several cystatins are actively transcribed in soybean nodules, their exact roles and functional diversities in legume have not been well explored in genome-wide survey studies. in this ... | 2016 | 27826313 |
| tetrapyrrole signaling in plants. | tetrapyrroles make critical contributions to a number of important processes in diverse organisms. in plants, tetrapyrroles are essential for light signaling, the detoxification of reactive oxygen species, the assimilation of nitrate and sulfate, respiration, photosynthesis, and programed cell death. the misregulation of tetrapyrrole metabolism can produce toxic reactive oxygen species. thus, it is not surprising that tetrapyrrole metabolism is strictly regulated and that tetrapyrrole metabolism ... | 2016 | 27807442 |
| small open reading frames, non-coding rnas and repetitive elements in bradyrhizobium japonicum usda 110. | small open reading frames (sorfs) and genes for non-coding rnas are poorly investigated components of most genomes. our analysis of 1391 orfs recently annotated in the soybean symbiont bradyrhizobium japonicum usda 110 revealed that 78% of them contain less than 80 codons. twenty-one of these sorfs are conserved in or outside alphaproteobacteria and most of them are similar to genes found in transposable elements, in line with their broad distribution. stabilizing selection was demonstrated for ... | 2016 | 27788207 |
| differential responses of dinitrogen fixation, diazotrophic cyanobacteria and ammonia oxidation reveal a potential warming-induced imbalance of the n-cycle in biological soil crusts. | n2 fixation and ammonia oxidation (ao) are the two most important processes in the nitrogen (n) cycle of biological soil crusts (bscs). we studied the short-term response of acetylene reduction assay (ara) rates, an indicator of potential n2 fixation, and ao rates to temperature (t, -5°c to 35°c) in bsc of different successional stages along the bsc ecological succession and geographic origin (hot chihuahuan and cooler great basin deserts). ara in all bscs increased with t until saturation occur ... | 2016 | 27776160 |
| deletion of the sacpd-c locus alters the symbiotic relationship between bradyrhizobium japonicum usda110 and soybean, resulting in elicitation of plant defense response and nodulation defects. | legumes form symbiotic associations with soil-dwelling bacteria collectively called rhizobia. this association results in the formation of nodules, unique plant-derived organs, within which the rhizobia are housed. rhizobia-encoded nitrogenase facilitates the conversion of atmospheric nitrogen into ammonia, which is utilized by the plants for its growth and development. fatty acids have been shown to play an important role in root nodule symbiosis. in this study, we have investigated the role of ... | 2016 | 27749147 |
| role of the tomato non-ripening mutation in regulating fruit quality elucidated using itraq protein profile analysis. | natural mutants of the non-ripening (nor) gene repress the normal ripening of tomato fruit. the molecular mechanism of fruit ripening regulation by the nor gene is unclear. to elucidate how the nor gene can affect ripening and fruit quality at the protein level, we used the fruits of nor mutants and wild-type ailsa craig (ac) to perform itraq (isobaric tags for relative and absolute quantitation) analysis. the nor mutation altered tomato fruit ripening and affected quality in various respects, i ... | 2016 | 27732677 |
| multidrug efflux pumps at the crossroad between antibiotic resistance and bacterial virulence. | multidrug efflux pumps can be involved in bacterial resistance to antibiotics at different levels. some efflux pumps are constitutively expressed at low levels and contribute to intrinsic resistance. in addition, their overexpression may allow higher levels of resistance. this overexpression can be transient, in the presence of an effector (phenotypic resistance), or constitutive when mutants in the regulatory elements of the expression of efflux pumps are selected (acquired resistance). efflux ... | 2016 | 27708632 |
| identification of unanticipated and novel n-acyl l-homoserine lactones (ahls) using a sensitive non-targeted lc-ms/ms method. | n-acyl l-homoserine lactones (ahls) constitute a predominant class of quorum-sensing signaling molecules used by gram-negative bacteria. here, we report a sensitive and non-targeted hplc-ms/ms method based on parallel reaction monitoring (prm) to identify and quantitate known, unanticipated, and novel ahls in microbial samples. using a hybrid quadrupole-high resolution mass analyzer, this method integrates ms scans and all-ion fragmentation ms/ms scans to allow simultaneous detection of ahl pare ... | 2016 | 27706219 |
| the response of soybean to nod factors and a bacteriocin. | microbe-to-plant signals can enhance the growth of a wide range of crops. the responses by soybean (glycine max var. 91m01) to 2 signal molecules were investigated: bradyrhizobium japonicum 532c lipo-chitooligosaccharide (nod bj v [c:18, mefuc]) (lco); and bacillus thuringiensis strain neb17 bacteriocin thuricin 17 (th17). the objective was to assess and quantify the response by soybean, in terms of factors that contribute to yield, to the experimental signal molecules in germination experiments ... | 2016 | 27700227 |
| phylogenetic identification, phenotypic variations, and symbiotic characteristics of the peculiar rhizobium, strain czr2, isolated from crotalaria zanzibarica in taiwan. | crotalaria zanzibarica is an exotic and widely distributed leguminous plant in taiwan. the relationship between c. zanzibarica and its rhizobial symbionts has been suggested to contribute to its successful invasion. a rhizobial strain (designed as czr2) isolated from the root nodules of c. zanzibarica and cultivated in standard yem medium displayed pleomorphism, with cells ranging between 2 and 10 μm in length and some branching. in the present study, we identified this rhizobial strain, investi ... | 2016 | 27682803 |
| bacterial multidrug efflux pumps: much more than antibiotic resistance determinants. | bacterial multidrug efflux pumps are antibiotic resistance determinants present in all microorganisms. with few exceptions, they are chromosomally encoded and present a conserved organization both at the genetic and at the protein levels. in addition, most, if not all, strains of a given bacterial species present the same chromosomally-encoded efflux pumps. altogether this indicates that multidrug efflux pumps are ancient elements encoded in bacterial genomes long before the recent use of antibi ... | 2016 | 27681908 |
| nickel availability in soil as influenced by liming and its role in soybean nitrogen metabolism. | nickel (ni) availability in soil varies as a function of ph. plants require ni in small quantities for normal development, especially in legumes due its role in nitrogen (n) metabolism. this study investigated the effect of soil base saturation, and ni amendments on ni uptake, n accumulation in the leaves and grains, as well as to evaluate organic acids changes in soybean. in addition, two n assimilation enzymes were assayed: nitrate reductase (nr) and ni-dependent urease. soybean plants inocula ... | 2016 | 27660633 |
| the diversity of sulfide oxidation and sulfate reduction genes expressed by the bacterial communities of the cariaco basin, venezuela. | qualitative expression of dissimilative sulfite reductase (dsra), a key gene in sulfate reduction, and sulfide:quinone oxidoreductase (sqr), a key gene in sulfide oxidation was investigated. neither of the two could be amplified from mrna retrieved with niskin bottles but were amplified from mrna retrieved by the deep sid. the sqr and sqr-like genes retrieved from the cariaco basin were related to the sqr genes from a bradyrhizobium sp., methylomicrobium alcaliphilum, sulfurovum sp. nbc37-1, sul ... | 2016 | 27651847 |
| proteomic studies on the effects of lipo-chitooligosaccharide and thuricin 17 under unstressed and salt stressed conditions in arabidopsis thaliana. | plants, being sessile organisms, are exposed to widely varying environmental conditions throughout their life cycle. compatible plant-microbe interactions favor plant growth and development, and help plants deal with these environmental challenges. microorganisms produce a diverse range of elicitor molecules to establish symbiotic relationships with the plants they associate with, in a given ecological niche. lipo-chitooligosaccharide (lco) and thuricin 17 (th17) are two such compounds shown to ... | 2016 | 27625672 |
| nitrogen fixation and molecular oxygen: comparative genomic reconstruction of transcription regulation in alphaproteobacteria. | biological nitrogen fixation plays a crucial role in the nitrogen cycle. an ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of bacteria and archaea. the transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the class alphaproteobacteria. this regulatory network includes the activator of nitrogen fixation nifa, working in tandem with the alternative sigma-factor rpon as well as oxygen-respons ... | 2016 | 27617010 |
| 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 |
| from the lab to the farm: an industrial perspective of plant beneficial microorganisms. | any successful strategy aimed at enhancing crop productivity with microbial products ultimately relies on the ability to scale at regional to global levels. microorganisms that show promise in the lab may lack key characteristics for widespread adoption in sustainable and productive agricultural systems. this paper provides an overview of critical considerations involved with taking a strain from discovery to the farmer's field. in addition, we review some of the most effective microbial product ... | 2016 | 27540383 |
| 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 |
| the role of flavonoids in nodulation host-range specificity: an update. | flavonoids are crucial signaling molecules in the symbiosis between legumes and their nitrogen-fixing symbionts, the rhizobia. the primary function of flavonoids in the interaction is to induce transcription of the genes for biosynthesis of the rhizobial signaling molecules called nod factors, which are perceived by the plant to allow symbiotic infection of the root. many legumes produce specific flavonoids that only induce nod factor production in homologous rhizobia, and therefore act as impor ... | 2016 | 27529286 |
| phytotoxicity attenuation in vigna radiata under heavy metal stress at the presence of biochar and n fixing bacteria. | this study assesses the effect of n-fixing bacteria and biochar synergism on plant growth and development of vigna mungo under heavy metal stress (hm). heavy metal stress is a worldwide problem, which causes critical effects on plant life due to oxidative stress. application of biochar is a recent biological remediation technique, which often leads to an immobilization of heavy metals in soil. . synergism of bacteria and biochar is a novel aspect to enhance plant growth under heavy metal stress. ... | 2017 | 27527669 |
| 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 |
| genome of rhizobium leucaenae strains cfn 299(t) and cpao 29.8: searching for genes related to a successful symbiotic performance under stressful conditions. | common bean (phaseolus vulgaris l.) is the most important legume cropped worldwide for food production and its agronomic performance can be greatly improved if the benefits from symbiotic nitrogen fixation are maximized. the legume is known for its high promiscuity in nodulating with several rhizobium species, but those belonging to the rhizobium tropici "group" are the most successful and efficient in fixing nitrogen in tropical acid soils. rhizobium leucaenae belongs to this group, which is ab ... | 2016 | 27485828 |
| region 4 of rhizobium etli primary sigma factor (siga) confers transcriptional laxity in escherichia coli. | sigma factors are rna polymerase subunits engaged in promoter recognition and dna strand separation during transcription initiation in bacteria. primary sigma factors are responsible for the expression of housekeeping genes and are essential for survival. rpod, the primary sigma factor of escherichia coli, a γ-proteobacteria, recognizes consensus promoter sequences highly similar to those of some α-proteobacteria species. despite this resemblance, rpod is unable to sustain transcription from mos ... | 2016 | 27468278 |
| origin and evolution of nitrogen fixation genes on symbiosis islands and plasmid in bradyrhizobium. | the nitrogen fixation (nif) genes of nodule-forming bradyrhizobium strains are generally located on symbiosis islands or symbiosis plasmids, suggesting that these genes have been transferred laterally. the nif genes of rhizobial and non-rhizobial bradyrhizobium strains were compared in order to infer the evolutionary histories of nif genes. based on all codon positions, the phylogenetic tree of concatenated nifd and nifk sequences showed that nifdk on symbiosis islands formed a different clade f ... | 2016 | 27431195 |
| genetic codes with no dedicated stop codon: context-dependent translation termination. | the prevailing view of the nuclear genetic code is that it is largely frozen and unambiguous. flexibility in the nuclear genetic code has been demonstrated in ciliates that reassign standard stop codons to amino acids, resulting in seven variant genetic codes, including three previously undescribed ones reported here. surprisingly, in two of these species, we find efficient translation of all 64 codons as standard amino acids and recognition of either one or all three stop codons. how, therefore ... | 2016 | 27426948 |
| the novel regulatory ncrna, nfis, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifk mrna in pseudomonas stutzeri a1501. | unlike most pseudomonas, the root-associated bacterium pseudomonas stutzeri a1501 fixes nitrogen after the horizontal acquisition of a nitrogen-fixing (nif) island. a genome-wide search for small noncoding rnas (ncrnas) in p. stutzeri a1501 identified the novel p. stutzeri-specific ncrna nfis in the core genome, whose synthesis was significantly induced under nitrogen fixation or sorbitol stress conditions. the expression of nfis was rna chaperone hfq-dependent and activated by the sigma factor ... | 2016 | 27407147 |
| characterization of iron-sulfur clusters in flavin-containing opine dehydrogenase. | flavin-containing opine dehydrogenase from bradyrhizobium japonicum forms a heterooligomeric α4β4γ4 enzyme complex. an electron paramagnetic resonance spectroscopy analysis using wild-type and site-directed mutants revealed that [4fe-4s] and [2fe-2s] clusters bind to two different types of [fe-s] binding sites in the γ- and α-subunits, respectively. the latter was found to be important for structural folding and enzyme catalysis. | 2016 | 27388263 |
| redox-dependent dynamics in heme-bound bacterial iron response regulator (irr) protein. | the iron response regulator (irr) protein from bradyrhizobium japonicum mediates iron-dependent regulation of heme biosynthesis. irr degrades in response to heme availability through a process that involves the binding of heme to cys-29 in the heme regulatory motif (hrm) in the presence of molecular oxygen. in this work, we assessed the dynamics of one-electron reduction of heme-bound irr by monitoring the formation of transient intermediates by pulse radiolysis. hydrated electrons generated by ... | 2016 | 27379473 |
| nod factor effects on root hair-specific transcriptome of medicago truncatula: focus on plasma membrane transport systems and reactive oxygen species networks. | root hairs are involved in water and nutrient uptake, and thereby in plant autotrophy. in legumes, they also play a crucial role in establishment of rhizobial symbiosis. to obtain a holistic view of medicago truncatula genes expressed in root hairs and of their regulation during the first hours of the engagement in rhizobial symbiotic interaction, a high throughput rna sequencing on isolated root hairs from roots challenged or not with lipochitooligosaccharides nod factors (nf) for 4 or 20 h was ... | 2016 | 27375649 |
| 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 |
| rnaifold2t: constraint programming design of thermo-ires switches. | rna thermometers (rnats) are cis-regulatory elements that change secondary structure upon temperature shift. often involved in the regulation of heat shock, cold shock and virulence genes, rnats constitute an interesting potential resource in synthetic biology, where engineered rnats could prove to be useful tools in biosensors and conditional gene regulation. | 2016 | 27307638 |
| rhizobial gibberellin negatively regulates host nodule number. | in legume-rhizobia symbiosis, the nodule number is controlled to ensure optimal growth of the host. in lotus japonicus, the nodule number has been considered to be tightly regulated by host-derived phytohormones and glycopeptides. however, we have discovered a symbiont-derived phytohormonal regulation of nodule number in mesorhizobium loti. in this study, we found that m. loti synthesized gibberellic acid (ga) under symbiosis. hosts inoculated with a ga-synthesis-deficient m. loti mutant formed ... | 2016 | 27307029 |
| 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 |
| inoculant of arbuscular mycorrhizal fungi (rhizophagus clarus) increase yield of soybean and cotton under field conditions. | nutrient availability is an important factor in crop production, and regular addition of chemical fertilizers is the most common practice to improve yield in agrosystems for intensive crop production. the use of some groups of microorganisms that have specific activity providing nutrients to plants is a good alternative, and arbuscular mycorrhizal fungi (amf) enhance plant nutrition by providing especially phosphorus, improving plant growth and increasing crop production. unfortunately, the use ... | 2016 | 27303367 |
| the bradyrhizobium japonicum ferrous iron transporter feoab is required for ferric iron utilization in free living aerobic cells and for symbiosis. | the bacterium bradyrhizobium japonicum usda110 does not synthesize siderophores for iron utilization in aerobic environments, and the mechanism of iron uptake within symbiotic soybean root nodules is unknown. an mbfa bfr double mutant defective in iron export and storage activities cannot grow aerobically in very high iron medium. here, we found that this phenotype was suppressed by loss of function mutations in the feoab operon encoding ferrous (fe(2+)) iron uptake proteins. expression of the f ... | 2016 | 27288412 |
| synthetic lethality of the bfr and mbfa genes reveals a functional relationship between iron storage and iron export in managing stress responses in bradyrhizobium japonicum. | an mbfa mutant of bradyrhizobium japonicum defective in iron export is sensitive to short term exposure to high levels iron or h2o2. here, we found that the mbfa strain grown in elevated iron media (100 μm) became resistant to those treatments, suggesting a stress response adaptation. the bfr gene encodes the iron storage protein bacterioferritin, and its expression is derepressed by iron. an mbfa bfr double mutant showed a loss of stress adaptation, and had a severe growth phenotype in high iro ... | 2016 | 27285822 |
| regulation of small rnas and corresponding targets in nod factor-induced phaseolus vulgaris root hair cells. | a genome-wide analysis identified the set of small rnas (srnas) from the agronomical important legume phaseolus vulgaris (common bean), including novel p. vulgaris-specific micrornas (mirnas) potentially important for the regulation of the rhizobia-symbiotic process. generally, novel mirnas are difficult to identify and study because they are very lowly expressed in a tissue- or cell-specific manner. in this work, we aimed to analyze srnas from common bean root hairs (rh), a single-cell model, i ... | 2016 | 27271618 |
| the role of proteus mirabilis cell wall features in biofilm formation. | biofilms formed by proteus mirabilis strains are a serious medical problem, especially in the case of urinary tract infections. early stages of biofilm formation, such as reversible and irreversible adhesion, are essential for bacteria to form biofilm and avoid eradication by antibiotic therapy. adhesion to solid surfaces is a complex process where numerous factors play a role, where hydrophobic and electrostatic interactions with solid surface seem to be substantial. cell surface hydrophobicity ... | 2016 | 27262948 |
| the structure of legume-rhizobium interaction networks and their response to tree invasions. | establishing mutualistic interactions in novel environments is important for the successful establishment of some non-native plant species. these associations may, in turn, impact native species interaction networks as non-natives become dominant in their new environments. using phylogenetic and ecological interaction network approaches we provide the first report of the structure of belowground legume-rhizobium interaction networks and how they change along a gradient of invasion (uninvaded, se ... | 2016 | 27255514 |
| identification and characterization of a novel (+)-γ-lactamase from microbacterium hydrocarbonoxydans. | 2-azabicyclo[2.2.1]hept-5-en-3-one (γ-lactam) is an important precursor of many carbocyclic nucleoside analogs and pharmaceuticals. (-)-γ-lactam has attracted much attention because of its role as an intermediate of antiviral drugs such as abacavir and carbovir. (+)-γ-lactamase can be used for the kinetic resolution of γ-lactam to obtain (-)-γ-lactam. in this study, a novel (+)-γ-lactamase (mh33h4-5540) was discovered from the gene library of microbacterium hydrocarbonoxydans based on a colorime ... | 2016 | 27255489 |
| rhizobium strains differ considerably in outer membrane permeability and polymyxin b resistance. | six rhizobium (rhizobium leguminosarum bv. trifolii ta1, sinorhizobium meliloti 1021, mesorhizobium huakuii ifo 15243(t), ochrobactrum lupini lup 21(t), bradyrhizobium japonicum usda110 and b. elkanii usda 76) and two escherichia coli strains (e. coli atcc 25922 and e. coli hb 101) were compared in respect to polymyxin b and edta resistance, as well as bacterial outer membrane (om) permeability to a fluorescent hydrophobic agent (n-phenyl-1-naphthylamine - npn). tem (transmission electron micros ... | 2016 | 27253495 |
| vascular sap proteomics: providing insight into long-distance signaling during stress. | the plant vascular system, composed of the xylem and phloem, is important for the transport of water, mineral nutrients, and photosynthate throughout the plant body. the vasculature is also the primary means by which developmental and stress signals move from one organ to another. due to practical and technological limitations, proteomics analysis of xylem and phloem sap has been understudied in comparison to accessible sample types such as leaves and roots. however, recent advances in sample co ... | 2016 | 27242852 |
| regulation of the regulators: post-translational modifications, subcellular, and spatiotemporal distribution of plant 14-3-3 proteins. | 14-3-3 proteins bind to and modulate the activity of phosphorylated proteins that regulate a variety of metabolic processes in eukaryotes. multiple 14-3-3 isoforms are expressed in most organisms and display redundancy in both sequence and function. plants contain the largest number of 14-3-3 isoforms. for example, arabidopsis thaliana contains thirteen 14-3-3 genes, each of which is expressed. interest in the plant 14-3-3 field has swelled over the past decade, largely due to the vast number of ... | 2016 | 27242818 |
| metabolomic profiling of bradyrhizobium diazoefficiens-induced root nodules reveals both host plant-specific and developmental signatures. | bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. our previous studies described b. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. in order to further characterize nodule metabolism, we here determine by flow injection-time-of-flight mass spectrometry analysis the metabolome of (i) nodules and roots fr ... | 2016 | 27240350 |
| regulation of the cobalt/nickel efflux operon dmerf in agrobacterium tumefaciens and a link between the iron-sensing regulator rira and cobalt/nickel resistance. | the agrobacterium tumefaciens c58 genome harbors an operon containing the dmer (atu0890) and dmef (atu0891) genes, which encode a transcriptional regulatory protein belonging to the rcnr/csor family and a metal efflux protein belonging to the cation diffusion facilitator (cdf) family, respectively. the dmerf operon is specifically induced by cobalt and nickel, with cobalt being the more potent inducer. promoter-lacz transcriptional fusion, an electrophoretic mobility shift assay, and dnase i foo ... | 2016 | 27235438 |
| root exudates drive interspecific facilitation by enhancing nodulation and n2 fixation. | plant diversity in experimental systems often enhances ecosystem productivity, but the mechanisms causing this overyielding are only partly understood. intercropping faba beans (vicia faba l.) and maize (zea mays l.) result in overyielding and also, enhanced nodulation by faba beans. by using permeable and impermeable root barriers in a 2-y field experiment, we show that root-root interactions between faba bean and maize significantly increase both nodulation and symbiotic n2 fixation in intercr ... | 2016 | 27217575 |
| 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 |
| evolution of a sigma factor: an all-in-one of gene duplication, horizontal gene transfer, purifying selection, and promoter differentiation. | sigma factors are an essential part of bacterial gene regulation and have been extensively studied as far as their molecular mechanisms and protein structure are concerned. however, their molecular evolution, especially for the alternative sigma factors, is poorly understood. here, we analyze the evolutionary forces that have shaped the rpoh sigma factors within the alphaproteobacteria. we found that an ancient duplication gave rise to two major groups of rpoh sigma factors and that after this e ... | 2016 | 27199915 |
| characterization and biological activities of cyclic (1 → 3, 1 → 6)-β-glucans from bradyrhizobium japonicum. | to isolate cyclic (1 → 3, 1 → 6)-β-glucan from bradyrhizobium japonicum mtcc120, to characterize its structure and to study its biological activities. | 2016 | 27193761 |
| 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 recognition of hydrolyzed carbapenems and inhibitors by subclass b3 metallo-β-lactamase smb-1. | metallo-β-lactamases (mbls) confer resistance to carbapenems, and their increasing global prevalence is a growing clinical concern. to elucidate the mechanisms by which these enzymes recognize and hydrolyze carbapenems, we solved 1.4 to 1.6 å crystal structures of smb-1 (serratia metallo-β-lactamase 1), a subclass b3 mbl, bound to hydrolyzed carbapenems (doripenem, meropenem, and imipenem). in these structures, smb-1 interacts mainly with the carbapenem core structure via elements in the active ... | 2016 | 27161644 |
| the control of auxin transport in parasitic and symbiotic root-microbe interactions. | most field-grown plants are surrounded by microbes, especially from the soil. some of these, including bacteria, fungi and nematodes, specifically manipulate the growth and development of their plant hosts, primarily for the formation of structures housing the microbes in roots. these developmental processes require the correct localization of the phytohormone auxin, which is involved in the control of cell division, cell enlargement, organ development and defense, and is thus a likely target fo ... | 2015 | 27135343 |
| genome-wide transcription start site mapping of bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation. | differential rna-sequencing (drna-seq) is indispensable for determination of primary transcriptomes. however, using drna-seq data to map transcriptional start sites (tsss) and promoters genome-wide is a bioinformatics challenge. we performed drna-seq of bradyrhizobium japonicum usda 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map tsss and promoters. | 2016 | 27107716 |
| function of the borrelia burgdorferi ftsh homolog is essential for viability both in vitro and in vivo and independent of hflk/c. | in many bacteria, the ftsh protease and its modulators, hflk and hflc, form a large protein complex that contributes to both membrane protein quality control and regulation of the cellular response to environmental stress. both activities are crucial to the lyme disease pathogen borrelia burgdorferi, which depends on membrane functions, such as motility, protein transport, and cell signaling, to respond to rapid changes in its environment. using an inducible system, we demonstrate that ftsh prod ... | 2016 | 27094329 |
| reactive oxygen species and nitric oxide control early steps of the legume - rhizobium symbiotic interaction. | the symbiotic interaction between legumes and nitrogen-fixing rhizobium bacteria leads to the formation of a new organ, the nodule. early steps of the interaction are characterized by the production of bacterial nod factors, the reorientation of root-hair tip growth, the formation of an infection thread (it) in the root hair, and the induction of cell division in inner cortical cells of the root, leading to a nodule primordium formation. reactive oxygen species (ros) and nitric oxide (no) have b ... | 2016 | 27092165 |
| decipher the molecular response of plant single cell types to environmental stresses. | the analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single ... | 2016 | 27088086 |
| 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 |
| nitrous oxide reduction kinetics distinguish bacteria harboring clade i nosz from those harboring clade ii nosz. | bacteria capable of reduction of nitrous oxide (n2o) to n2 separate into clade i and clade ii organisms on the basis of nos operon structures and nosz sequence features. to explore the possible ecological consequences of distinct nos clusters, the growth of bacterial isolates with either clade i (pseudomonas stutzeri strain dcp-ps1, shewanella loihica strain pv-4) or clade ii (dechloromonas aromatica strain rcb, anaeromyxobacter dehalogenans strain 2cp-c) nosz with n2o was examined. growth curve ... | 2016 | 27084012 |
| process optimization and kinetic modelling of cyclic (1→3, 1→6)-β-glucans production from bradyrhizobium japonicum mtcc120. | cyclic (1→3, 1→6)-β-glucans are water soluble, biocompatible polymers with potential applications in food and pharmaceutical industries but have not yet been exploited due to their poor yield. in the present study statistical experimental design methodology was employed to improve their production. initial screening indicated arabinose and peptone as best carbon and nitrogen source respectively, for glucan production. arabinose and osmolyte concentrations as well as ph significantly contributed ... | 2016 | 27046066 |
| polysaccharide-based bioflocculant template of a diazotrophic bradyrhizobium japonicum 36 for controlled assembly of agcl nanoparticles. | a simple and green method was developed for the biosynthesis of silver chloride nanoparticles, free from silver nanoparticles, using polysaccharide-based bioflocculant of a diazotrophic rhizobacteria bradyrhizobium japonicum 36 strain. the synthesized silver chloride nanoparticles were characterized by uv-vis, xrd, ft-ir and tem. the concentration-dependent and controllable method for silver chloride nanoparticles was developed. the biosynthesized silver chloride nanoparticles exhibited strong a ... | 2016 | 27039118 |
| comparison of cultures and 16s rrna sequencing for identification of bacteria in two-stage revision arthroplasties: preliminary report. | the use of a prefabricated spacer in two-stage revision arthroplasty remains one of the few surgery strategies for infected-joint arthroplasty treatment, despite the many unidentified microorganisms in the infected joint replacements reported in some recent studies. the aim of this prospective survey was to investigate if the sonication followed by polymerase chain reaction (pcr) can improve bacterial identification on the surfaces of prefabricated spacers and if the systemic laboratory mediator ... | 2016 | 27015812 |
| site-directed mutagenesis from arg195 to his of a microalgal putatively chloroplastidial glycerol-3-phosphate acyltransferase causes an increase in phospholipid levels in yeast. | to analyze the contribution of glycerol-3-phosphate acyltransferase (gpat) to the first acylation of glycerol-3-phosphate (g-3-p), the present study focused on a functional analysis of the gpat gene from lobosphaera incisa (designated as ligpat). a full-length cdna of ligpat consisting of a 1,305-bp orf, a 1,652-bp 5'-utr, and a 354-bp 3'-utr, was cloned. the orf encoded a 434-amino acid peptide, of which 63 residues at the n-terminus defined a chloroplast transit peptide. multiple sequence alig ... | 2016 | 27014309 |
| metal-specific control of gene expression mediated by bradyrhizobium japonicum mur and escherichia coli fur is determined by the cellular context. | bradyrhizobium japonicum mur and escherichia coli fur are manganese- and iron-responsive transcriptional regulators, respectively, that belong to the same protein family. here, we show that neither mur nor fur discriminate between fe(2+) and mn(2+) in vitro nor is there a metal preference for conferral of dna-binding activity on the purified proteins. when expressed in e. coli, b. japonicum mur responded to iron, but not manganese, as determined by in vivo promoter occupancy and transcriptional ... | 2016 | 26998998 |
| h2-saturation of high affinity h2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups. | soil microbial communities are continuously exposed to h2 diffusing into the soil from the atmosphere. n2-fixing nodules represent a peculiar microniche in soil where h2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). in this study, we investigated the impact of h2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil h2 exposure from the atmosphere and n2-fixing nodules. biphasic kinetic parameters governing ... | 2016 | 26989620 |
| complete genome sequence of bradyrhizobium sp. strain ccge-la001, isolated from field nodules of the enigmatic wild bean phaseolus microcarpus. | we present the complete genome sequence of bradyrhizobium sp. strain ccge-la001, a nitrogen-fixing bacterium isolated from nodules of phaseolus microcarpus. strain ccge-la001 represents the first sequenced bradyrhizobial strain obtained from a wild phaseolus sp. its genome revealed a large and novel symbiotic island. | 2016 | 26988045 |
| horizontal transfer of β-carbonic anhydrase genes from prokaryotes to protozoans, insects, and nematodes. | horizontal gene transfer (hgt) is a movement of genetic information occurring outside of normal mating activities. it is especially common between prokaryotic endosymbionts and their protozoan, insect, and nematode hosts. although beta carbonic anhydrase (β-ca) plays a crucial role in metabolic functions of many living organisms, the origin of β-ca genes in eukaryotic species remains unclear. | 2016 | 26983858 |
| molecular evidence for sediment nitrogen fixation in a temperate new england estuary. | primary production in coastal waters is generally nitrogen (n) limited with denitrification outpacing nitrogen fixation (n2-fixation). however, recent work suggests that we have potentially underestimated the importance of heterotrophic sediment n2-fixation in marine ecosystems. we used clone libraries to examine transcript diversity of nifh (a gene associated with n2-fixation) in sediments at three sites in a temperate new england estuary (waquoit bay, massachusetts, usa) and compared our resul ... | 2016 | 26977375 |
| draft genome sequence of mesorhizobium sp. ufla 01-765, a multitolerant, efficient symbiont and plant growth-promoting strain isolated from zn-mining soil using leucaena leucocephala as a trap plant. | we report the 7.4-mb draft genome sequence of mesorhizobium sp. strain ufla 01-765, a gram-negative bacterium of the phyllobacteriaceae isolated from zn-mining soil in minas gerais, brazil. this strain promotes plant growth, efficiently fixes n2 in symbiosis with leucaena leucocephala on multicontaminated soil, and has potential for application in bioremediation of marginal lands. | 2016 | 26966214 |
| development of a microemulsion formulation for antimicrobial seca inhibitors. | in our previous study, we have identified five antimicrobial small molecules via structure based design, which inhibit seca of candidatus liberibacter asiaticus (las). seca is a critical protein translocase atpase subunit and is involved in pre-protein translocation across and integration into the cellular membrane in bacteria. in this study, eleven compounds were identified using similarity search method based on the five lead seca inhibitors identified previously. the identified seca inhibitor ... | 2016 | 26963811 |
| sulfur fertilization changes the community structure of rice root-, and soil- associated bacteria. | under paddy field conditions, biological sulfur oxidation occurs in the oxidized surface soil layer and rhizosphere, in which oxygen leaks from the aerenchyma system of rice plants. in the present study, we examined community shifts in sulfur-oxidizing bacteria associated with the oxidized surface soil layer and rice roots under different sulfur fertilization conditions based on the 16s ribosomal rna (rrna) gene in order to explore the existence of oligotrophic sulfur-oxidizing bacteria in the p ... | 2016 | 26947443 |
| versatile vectors for efficient mutagenesis of bradyrhizobium diazoefficiens and other alphaproteobacteria. | analysis of bacterial gene function commonly relies on gene disruption or replacement followed by phenotypic characterization of the resulting mutant strains. deletion or replacement of targeted regions is commonly achieved via two homologous recombination (hr) events between the bacterial genome and a nonreplicating plasmid carrying dna fragments flanking the region to be deleted. the counterselection of clones that have integrated the entire plasmid in their genome via a single hr event is cru ... | 2016 | 26921431 |
| seasonal variation in nifh abundance and expression of cyanobacterial communities associated with boreal feather mosses. | dinitrogen (n2)-fixation by cyanobacteria living in symbiosis with pleurocarpous feather mosses (for example, pleurozium schreberi and hylocomium splendens) represents the main pathway of biological n input into n-depleted boreal forests. little is known about the role of the cyanobacterial community in contributing to the observed temporal variability of n2-fixation. using specific nifh primers targeting four major cyanobacterial clusters and quantitative pcr, we investigated how community comp ... | 2016 | 26918665 |
| hmus and hmuq of ensifer/sinorhizobium meliloti degrade heme in vitro and participate in heme metabolism in vivo. | ensifer meliloti is a nitrogen-fixing symbiont of the alfalfa legume able to use heme as an iron source. the transport mechanism involved in heme acquisition in e. meliloti has been identified and characterized, but the fate of heme once inside the cell is not known. in silico analysis of e. meliloti 1021 genome revealed no canonical heme oxygenases although two genes encoding putative heme degrading enzymes, smc01518 and hmus, were identified. smc01518 is similar to hmuq of bradyrhizobium japon ... | 2016 | 26906560 |
| contributions of sinorhizobium meliloti transcriptional regulator dksa to bacterial growth and efficient symbiosis with medicago sativa. | the stringent response, mediated by the (p)ppgpp synthetase rela and the rna polymerase-binding protein dksa, is triggered by limiting nutrient conditions. for some bacteria, it is involved in regulation of virulence. we investigated the role of two dksa-like proteins from the gram-negative nitrogen-fixing symbiont sinorhizobium meliloti in free-living culture and in interaction with its host plant medicago sativa the two paralogs, encoded by the genes smc00469 and smc00049, differ in the consti ... | 2016 | 26883825 |
| structural and transcriptional characterization of a novel member of the soybean urease gene family. | in plants, ureases have been related to urea degradation, to defense against pathogenic fungi and phytophagous insects, and to the soybean-bradyrhizobium japonicum symbiosis. two urease isoforms have been described for soybean: the embryo-specific, encoded by eu1 gene, and the ubiquitous urease, encoded by eu4. a third urease-encoding locus exists in the completed soybean genome. the gene was designated eu5 and the putative product of its orf as sbu-iii. phylogenetic analysis shows that 41 plant ... | 2016 | 26874294 |
| the effector candidate repertoire of the arbuscular mycorrhizal fungus rhizophagus clarus. | arbuscular mycorrhizal fungi (amf) form an ecologically important symbiosis with more than two thirds of studied land plants. recent studies of plant-pathogen interactions showed that effector proteins play a key role in host colonization by controlling the plant immune system. we hypothesise that also for symbiotic-plant interactions the secreted effectome of the fungus is a major component of communication and the conservation level of effector proteins between amf species may be indicative wh ... | 2016 | 26861502 |
| comprehensive comparative genomic and transcriptomic analyses of the legume genes controlling the nodulation process. | nitrogen is one of the most essential plant nutrients and one of the major factors limiting crop productivity. having the goal to perform a more sustainable agriculture, there is a need to maximize biological nitrogen fixation, a feature of legumes. to enhance our understanding of the molecular mechanisms controlling the interaction between legumes and rhizobia, the symbiotic partner fixing and assimilating the atmospheric nitrogen for the plant, researchers took advantage of genetic and genomic ... | 2016 | 26858743 |
| functional analysis of alternative transcripts of the soybean rj2 gene that restricts nodulation with specific rhizobial strains. | the rj2 gene is a tir-nbs-lrr-type resistance gene in soybean (glycine max) that restricts root nodule symbiosis with a group of bradyrhizobium japonicum strains including usda122. rj2 generates two distinct transcript variants in its expression profile through alternative splicing. alternative splicing of rj2 is caused by the retention of the 86-bp intron 4. inclusion of intron 4 in mature mrna introduces an in-frame stop codon; as such, the alternative transcript is predicted to encode a trunc ... | 2016 | 26848549 |
| do soybeans select specific species of bradyrhizobium during growth? | soybean is an important crop, with processed soybeans being the second largest source of vegetable oil and the largest source of animal protein feed in the world. nodules on soybean roots are responsible for symbiotic nitrogen fixation, enabling soybean plants to obtain sufficient nitrogen for growth and seed production. because nitrogen is an essential, but often limiting, nutrient for plant growth, improvements in nitrogen fixation are highly required in agriculture. we recently reported a com ... | 2015 | 26841977 |