Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
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| effect of arsenic on tolerance mechanisms of two plant growth-promoting bacteria used as biological inoculants. | bacterial ability to colonize the rhizosphere of plants in arsenic (as) contaminated soils is highly important for symbiotic and free-living plant growth-promoting rhizobacteria (pgpr) used as inoculants, since they can contribute to enhance plant as tolerance and limit metalloid uptake by plants. the aim of this work was to study the effect of as on growth, exopolysaccharide (eps) production, biofilm formation and motility of two strains used as soybean inoculants, bradyrhizobium japonicum e109 ... | 2015 | 26141894 |
| photoreceptor engineering. | sensory photoreceptors not only control diverse adaptive responses in nature, but as light-regulated actuators they also provide the foundation for optogenetics, the non-invasive and spatiotemporally precise manipulation of cellular events by light. novel photoreceptors have been engineered that establish control by light over manifold biological processes previously inaccessible to optogenetic intervention. recently, photoreceptor engineering has witnessed a rapid development, and light-regulat ... | 2015 | 26137467 |
| npk macronutrients and microrna homeostasis. | macronutrients are essential elements for plant growth and development. in natural, non-cultivated systems, the availability of macronutrients is not a limiting factor of growth, due to fast recycling mechanisms. however, their availability might be an issue in modern agricultural practices, since soil has been frequently over exploited. from a crop management perspective, the nitrogen (n), phosphorus (p), and potassium (k) are three important limiting factors and therefore frequently added as f ... | 2015 | 26136763 |
| mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator. | ferric uptake regulator (fur) plays a key role in the iron homeostasis of prokaryotes, such as bacterial pathogens, but the molecular mechanisms and structural basis of fur-dna binding remain incompletely understood. here, we report high-resolution structures of magnetospirillum gryphiswaldense msr-1 fur in four different states: apo-fur, holo-fur, the fur-feoab1 operator complex and the fur-pseudomonas aeruginosa fur box complex. apo-fur is a transition metal ion-independent dimer whose binding ... | 2015 | 26134419 |
| the origin of specificity and insight into recognition between an aminoacyl carrier protein and its partner ligase. | acyl carrier proteins (acps) are among the most promiscuous proteins in terms of protein-protein interactions and it is quite puzzling how acps select the correct partner between many possible upstream and downstream binding proteins. to address this question, we performed molecular dynamics simulations on dimeric bradyrhizobium japonicum gly:cp ligase 1 to inspect the origin of its selectivity towards the three types of carrier proteins, namely holocp, apocp, and holocp-gly, which only differ i ... | 2015 | 26129823 |
| structural characterization of the fla2 flagellum of rhodobacter sphaeroides. | rhodobacter sphaeroides is a free-living alphaproteobacterium that contains two clusters of functional flagellar genes in its genome: one acquired by horizontal gene transfer (fla1) and one that is endogenous (fla2). we have shown that the fla2 system is normally quiescent and under certain conditions produces polar flagella, while the fla1 system is always active and produces a single flagellum at a nonpolar position. in this work we purified and characterized the structure and analyzed the com ... | 2015 | 26124240 |
| ohr protects corynebacterium glutamicum against organic hydroperoxide induced oxidative stress. | ohr, a bacterial protein encoded by the organic hydroperoxide resistance (ohr) gene, plays a critical role in resistance to organic hydroperoxides. in the present study, we show that the cys-based thiol-dependent ohr of corynebacterium glutamicum decomposes organic hydroperoxides more efficiently than hydrogen peroxide. replacement of either of the two cys residues of ohr by a ser residue resulted in drastic loss of activity. the electron donors supporting regeneration of the peroxidase activity ... | 2015 | 26121694 |
| a comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight. | rice is a major crop worldwide. bacterial blight (bb) caused by xanthomonas oryzae pv. oryzae (xoo) has become one of the most devastating diseases for rice. it has been clear that phosphorylation plays essential roles in plant disease resistance. however, the role of phosphorylation is poorly understood in rice-xoo system. here, we report the first study on large scale enrichment of phosphopeptides and identification of phosphosites in rice before and 24 h after xoo infection. | 2015 | 26112675 |
| diversity of the epsilonproteobacteria dsb (disulfide bond) systems. | the bacterial proteins of the dsb family-important components of the post-translational protein modification system-catalyze the formation of disulfide bridges, a process that is crucial for protein structure stabilization and activity. dsb systems play an essential role in the assembly of many virulence factors. recent rapid advances in global analysis of bacteria have thrown light on the enormous diversity among bacterial dsb systems. while the escherichia coli disulfide bond-forming system is ... | 2015 | 26106374 |
| nitrite-oxidizing bacterium nitrobacter winogradskyi produces n-acyl-homoserine lactone autoinducers. | nitrobacter winogradskyi is a chemolithotrophic bacterium that plays a role in the nitrogen cycle by oxidizing nitrite to nitrate. here, we demonstrate a functional n-acyl-homoserine lactone (acyl-hsl) synthase in this bacterium. the n. winogradskyi genome contains genes encoding a putative acyl-hsl autoinducer synthase (nwi0626, nwii) and a putative acyl-hsl autoinducer receptor (nwi0627, nwir) with amino acid sequences 38 to 78% identical to those in rhodopseudomonas palustris and other rhizob ... | 2015 | 26092466 |
| a putative type iii secretion system effector encoded by the ma20_12780 gene in bradyrhizobium japonicum is-34 causes incompatibility with rj4 genotype soybeans. | the nodulation of bradyrhizobium japonicum is-34 is restricted by rj4 genotype soybeans (glycine max). to identify the genes responsible for this incompatibility, tn5 mutants of b. japonicum is-34 that were able to overcome this nodulation restriction were obtained. analysis of the tn5 mutants revealed that tn5 was inserted into a region containing the ma20_12780 gene. in addition, direct disruption of this gene using marker exchange overcame the nodulation restriction by rj4 genotype soybeans. ... | 2015 | 26092458 |
| endosymbiosis in trypanosomatid protozoa: the bacterium division is controlled during the host cell cycle. | mutualism is defined as a beneficial relationship for the associated partners and usually assumes that the symbiont number is controlled. some trypanosomatid protozoa co-evolve with a bacterial symbiont that divides in coordination with the host in a way that results in its equal distribution between daughter cells. the mechanism that controls this synchrony is largely unknown, and its comprehension might provide clues to understand how eukaryotic cells evolved when acquiring symbionts that late ... | 2015 | 26082757 |
| anoxic growth of ensifer meliloti 1021 by n2o-reduction, a potential mitigation strategy. | denitrification in agricultural soils is a major source of n2o. legume crops enhance n2o emission by providing n-rich residues, thereby stimulating denitrification, both by free-living denitrifying bacteria and by the symbiont (rhizobium) within the nodules. however, there are limited data concerning n2o production and consumption by endosymbiotic bacteria associated with legume crops. it has been reported that the alfalfa endosymbiont ensifer meliloti strain 1021, despite possessing and express ... | 2015 | 26074913 |
| nodulation characterization and proteomic profiling of bradyrhizobium liaoningense ccbau05525 in response to water-soluble humic materials. | the lignite biodegradation procedure to produce water-soluble humic materials (wshm) with a penicillium stain was established by previous studies in our laboratory. this study researched the effects of wshm on the growth of bradyrhizobium liaoningense ccbau05525 and its nodulation on soybean. results showed that wshm enhanced the cell density of ccbau05525 in culture, and increased the nodule number, nodule fresh weight and nitrogenase activity of the inoculated soybean plants. then the chemical ... | 2015 | 26054030 |
| genome wide transcriptional profiling of herbaspirillum seropedicae smr1 grown in the presence of naringenin. | herbaspirillum seropedicae is a diazotrophic bacterium which associates endophytically with economically important gramineae. flavonoids such as naringenin have been shown to have an effect on the interaction between h. seropedicae and its host plants. we used a high-throughput sequencing based method (rna-seq) to access the influence of naringenin on the whole transcriptome profile of h. seropedicae. three hundred and four genes were downregulated and seventy seven were upregulated by naringeni ... | 2015 | 26052319 |
| survival and competitiveness of bradyrhizobium japonicum strains 20 years after introduction into field locations in poland. | it was previously demonstrated that there are no indigenous strains of bradyrhizobium japonicum forming nitrogen-fixing root nodule symbioses with soybean plants in arable field soils in poland. however, bacteria currently classified within this species are present (together with bradyrhizobium canariense) as indigenous populations of strains specific for nodulation of legumes in the genisteae tribe. these rhizobia, infecting legumes such as lupins, are well established in polish soils. the stud ... | 2015 | 26048934 |
| system approaches to study root hairs as a single cell plant model: current status and future perspectives. | our current understanding of plant functional genomics derives primarily from measurements of gene, protein and/or metabolite levels averaged over the whole plant or multicellular tissues. these approaches risk diluting the response of specific cells that might respond strongly to the treatment but whose signal is diluted by the larger proportion of non-responding cells. for example, if a gene is expressed at a low level, does this mean that it is indeed lowly expressed or is it highly expressed ... | 2015 | 26042143 |
| stable fluorescent and enzymatic tagging of bradyrhizobium diazoefficiens to analyze host-plant infection and colonization. | bradyrhizobium diazoefficiens usda 110 (formerly named bradyrhizobium japonicum) can fix dinitrogen when living as an endosymbiont in root nodules of soybean and some other legumes. formation of a functional symbiosis relies on a defined developmental program mediated by controlled gene expression in both symbiotic partners. in contrast to other well-studied rhizobium-legume model systems that have been thoroughly examined by means of genetically tagged strains, analysis of b. diazoefficiens hos ... | 2015 | 26035130 |
| symbiotic effectiveness of inoculation with bradyrhizobium isolates on soybean [glycine max (l.) merrill] genotypes with different maturities. | the influence of soybean genotypes with different maturity groups on the symbiotic effectiveness of bradyrhizobium spp under high native soil n is not well known. therefore, the objective of this work was to evaluate the influence of maturity time of soybean genotypes on the symbiotic effectiveness of bradyrhizobium spp. at higher soil n. three isolates of bradyrhizobium spp. (uk-isolate, tal-379 isolate and local-isolate) and six soybean genotypes, three late maturing (wogayen, tgx-1336424 and ... | 2014 | 26034703 |
| arbuscular mycorrhizal fungi and rhizobium facilitate nitrogen uptake and transfer in soybean/maize intercropping system. | the tripartite symbiosis between legumes, rhizobia and mycorrhizal fungi are generally considered to be beneficial for the nitrogen (n) uptake of legumes, but the facilitation of symbiosis in legume/non-legume intercropping systems is not clear. therefore, the aims of the research are as follows: (1) to verify if the dual inoculation can facilitate the n uptake and n transfer in maize/soybean intercropping systems and (2) to calculate how much n will be transferred from soybean to maize. a pot e ... | 2015 | 26029236 |
| trehalose promotes rhodococcus sp. strain yyl colonization in activated sludge under tetrahydrofuran (thf) stress. | few studies have focused on the role of compatible solutes in changing the microbial community structure in bioaugmentation systems. in this study, we investigated the influence of trehalose as a biostimulant on the microbial community in tetrahydrofuran (thf)-treated wastewater bioaugmentation systems with rhodococcus sp. yyl. functional gene profile changes were used to study the variation in the microbial community. soluble di-iron monooxygenases (sdimo), particularly group-5 sdimos (i.e., te ... | 2015 | 26029182 |
| dna microarray-based identification of genes regulated by ntrc in bradyrhizobium japonicum. | the bradyrhizobium japonicum ntrbc two-component system is a critical regulator of cellular nitrogen metabolism, including the acquisition and catabolism of nitrogenous compounds. to better define the roles of this system, genome-wide transcriptional profiling was performed to identify the ntrc regulon during the response to nitrogen limitation. upon cells perceiving low intracellular nitrogen, they stimulate the phosphorylation of ntrc, which induces genes responsible for alteration of the core ... | 2015 | 26025905 |
| inoculation with an enhanced n2 -fixing bradyrhizobium japonicum strain (usda110) does not alter soybean (glycine max merr.) response to elevated [co2 ]. | this study tested the hypothesis that inoculation of soybean (glycine max merr.) with a bradyrhizobium japonicum strain (usda110) with greater n2 fixation rates would enhance soybean response to elevated [co2 ]. in field experiments at the soybean free air co2 enrichment facility, inoculation of soybean with usda110 increased nodule occupancy from 5% in native soil to 54% in elevated [co2 ] and 34% at ambient [co2 ]. despite this success, inoculation with usda110 did not result in greater photos ... | 2015 | 26012898 |
| cropping systems modulate the rate and magnitude of soil microbial autotrophic co2 fixation in soil. | the effect of different cropping systems on co2 fixation by soil microorganisms was studied by comparing soils from three exemplary cropping systems after 10 years of agricultural practice. studied cropping systems included: continuous cropping of paddy rice (rice-rice), rotation of paddy rice and rapeseed (rice-rapeseed), and rotated cropping of rapeseed and corn (rapeseed-corn). soils from different cropping systems were incubated with continuous (14)c-co2 labeling for 110 days. the co2-fixing ... | 2015 | 26005435 |
| lov histidine kinase modulates the general stress response system and affects the virb operon expression in brucella abortus. | brucella is the causative agent of the zoonotic disease brucellosis, and its success as an intracellular pathogen relies on its ability to adapt to the harsh environmental conditions that it encounters inside the host. the brucella genome encodes a sensor histidine kinase containing a lov domain upstream from the kinase, lovhk, which plays an important role in light-regulated brucella virulence. in this report we study the intracellular signaling pathway initiated by the light sensor lovhk using ... | 2015 | 25993430 |
| multiple chaperonins in bacteria--novel functions and non-canonical behaviors. | chaperonins are a class of molecular chaperones that assemble into a large double ring architecture with each ring constituting seven to nine subunits and enclosing a cavity for substrate encapsulation. the well-studied escherichia coli chaperonin groel binds non-native substrates and encapsulates them in the cavity thereby sequestering the substrates from unfavorable conditions and allowing the substrates to fold. using this mechanism, groel assists folding of about 10-15 % of cellular proteins ... | 2015 | 25986150 |
| comparative analysis of denitrifying activities of hyphomicrobium nitrativorans, hyphomicrobium denitrificans, and hyphomicrobium zavarzinii. | hyphomicrobium spp. are commonly identified as major players in denitrification systems supplied with methanol as a carbon source. however, denitrifying hyphomicrobium species are poorly characterized, and very few studies have provided information on the genetic and physiological aspects of denitrification in pure cultures of these bacteria. this is a comparative study of three denitrifying hyphomicrobium species, h. denitrificans atcc 51888, h. zavarzinii zv622, and a newly described species, ... | 2015 | 25979892 |
| identification and functional characterization of soybean root hair micrornas expressed in response to bradyrhizobium japonicum infection. | three soybean [glycine max (l) merr.] small rna libraries were generated and sequenced using the illumina platform to examine the role of mirnas during soybean nodulation. the small rna libraries were derived from root hairs inoculated with bradyrhizobium japonicum (in_rh) or mock-inoculated with water (un_rh), as well as from the comparable inoculated stripped root samples (i.e. inoculated roots with the root hairs removed). sequencing of these libraries identified a total of 114 mirnas, includ ... | 2016 | 25973713 |
| transcriptional activity of the giant barrel sponge, xestospongia muta holobiont: molecular evidence for metabolic interchange. | compared to our understanding of the taxonomic composition of the symbiotic microbes in marine sponges, the functional diversity of these symbionts is largely unknown. furthermore, the application of genomic, transcriptomic, and proteomic techniques to functional questions on sponge host-symbiont interactions is in its infancy. in this study, we generated a transcriptome for the host and a metatranscriptome of its microbial symbionts for the giant barrel sponge, xestospongia muta, from the carib ... | 2015 | 25972851 |
| novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich peptide and methionine sulfoxide reductase. | reactive chlorine species (rcs) defense mechanisms are important for bacterial fitness in diverse environments. in addition to the anthropogenic use of rcs in the form of bleach, these compounds are also produced naturally through photochemical reactions of natural organic matter and in vivo by the mammalian immune system in response to invading microorganisms. to gain insight into bacterial rcs defense mechanisms, we investigated azospira suillum strain ps, which produces periplasmic rcs as an ... | 2015 | 25968643 |
| enhanced oxygen consumption in herbaspirillum seropedicae fnr mutants leads to increased nifa mediated transcriptional activation. | orthologous proteins of the crp/fnr family have been previously implicated in controlling expression and/or activity of the nifa transcriptional activator in some diazotrophs. this study aimed to address the role of three fnr-like proteins from h. seropedicae smr1 in controlling nifa activity and consequent nifa-mediated transcription activation. | 2015 | 25947294 |
| microrna167-directed regulation of the auxin response factors gmarf8a and gmarf8b is required for soybean nodulation and lateral root development. | legume root nodules convert atmospheric nitrogen gas into ammonium through symbiosis with a prokaryotic microsymbiont broadly called rhizobia. auxin signaling is required for determinant nodule development; however, the molecular mechanism of auxin-mediated nodule formation remains largely unknown. here, we show in soybean (glycine max) that the microrna mir167 acts as a positive regulator of lateral root organs, namely nodules and lateral roots. mir167c expression was up-regulated in the vascul ... | 2015 | 25941314 |
| structural basis for carbapenem-hydrolyzing mechanisms of carbapenemases conferring antibiotic resistance. | carbapenems (imipenem, meropenem, biapenem, ertapenem, and doripenem) are β-lactam antimicrobial agents. because carbapenems have the broadest spectra among all β-lactams and are primarily used to treat infections by multi-resistant gram-negative bacteria, the emergence and spread of carbapenemases became a major public health concern. carbapenemases are the most versatile family of β-lactamases that are able to hydrolyze carbapenems and many other β-lactams. according to the dependency of dival ... | 2015 | 25938965 |
| genomic features separating ten strains of neorhizobium galegae with different symbiotic phenotypes. | the symbiotic phenotype of neorhizobium galegae, with strains specifically fixing nitrogen with either galega orientalis or g. officinalis, has made it a target in research on determinants of host specificity in nitrogen fixation. the genomic differences between representative strains of the two symbiovars are, however, relatively small. this introduced a need for a dataset representing a larger bacterial population in order to make better conclusions on characteristics typical for a subset of t ... | 2015 | 25933608 |
| secondary structural entropy in rna switch (riboswitch) identification. | rna regulatory elements play a significant role in gene regulation. riboswitches, a widespread group of regulatory rnas, are vital components of many bacterial genomes. these regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in rna. riboswitch-mediated mechanisms are ubiquitous across bacterial genomes. a typical class of riboswitch has its own unique structural and biological complexity, m ... | 2015 | 25928324 |
| nitrogenase diversity and activity in the gastrointestinal tract of the wood-eating catfish panaque nigrolineatus. | the amazonian catfish, panaque nigrolineatus, consume large amounts of wood in their diets. the nitrogen-fixing community within the gastrointestinal (gi) tract of these catfish was found to include nifh phylotypes that are closely related to clostridium sp., alpha and gammaproteobacteria, and sequences associated with gi tracts of lower termites. fish fed a diet of sterilized palm wood were found to contain nifh messenger rna within their gi tracts, displaying high sequence similarity to the ni ... | 2015 | 25909976 |
| genomic signature of selective sweeps illuminates adaptation of medicago truncatula to root-associated microorganisms. | medicago truncatula is a model legume species used to investigate plant-microorganism interactions, notably root symbioses. massive population genomic and transcriptomic data now available for this species open the way for a comprehensive investigation of genomic variations associated with adaptation of m. truncatula to its environment. here we performed a fine-scale genome scan of selective sweep signatures in m. truncatula using more than 15 million single nucleotide polymorphisms identified o ... | 2015 | 25901015 |
| manganese homeostasis and utilization in pathogenic bacteria. | manganese (mn) is a required cofactor for all forms of life. given the importance of mn to bacteria, the host has devised strategies to sequester mn from invaders. in the macrophage phagosome, nramp1 removes mn and other essential metals to starve intracellular pathogens; in the extracellular space, calprotectin chelates mn and zn. calprotectin-mediated mn sequestration is a newly appreciated host defense mechanism, and recent findings are highlighted herein. in order to acquire mn when extracel ... | 2015 | 25898914 |
| the role of transition metal transporters for iron, zinc, manganese, and copper in the pathogenesis of yersinia pestis. | yersinia pestis, the causative agent of bubonic, septicemic and pneumonic plague, encodes a multitude of fe transport systems. some of these are defective due to frameshift or is element insertions, while others are functional in vitro but have no established role in causing infections. indeed only 3 fe transporters (ybt, yfe and feo) have been shown to be important in at least one form of plague. the yersiniabactin (ybt) system is essential in the early dermal/lymphatic stages of bubonic plague ... | 2015 | 25891079 |
| distribution in microbial genomes of genes similar to loda and goxa which encode a novel family of quinoproteins with amino acid oxidase activity. | l-amino acid oxidases (laos) have been generally described as flavoproteins that oxidize amino acids releasing the corresponding ketoacid, ammonium and hydrogen peroxide. the generation of hydrogen peroxide gives to these enzymes antimicrobial characteristics. they are involved in processes such as biofilm development and microbial competition. laos are of great biotechnological interest in different applications such as the design of biosensors, biotransformations and biomedicine. the marine ba ... | 2015 | 25886995 |
| regulatory nodd1 and nodd2 genes of rhizobium tropici strain ciat 899 and their roles in the early stages of molecular signaling and host-legume nodulation. | nodulation and symbiotic nitrogen fixation are mediated by several genes, both of the host legume and of the bacterium. the rhizobial regulatory nodd gene plays a critical role, orchestrating the transcription of the other nodulation genes. rhizobium tropici strain ciat 899 is an effective symbiont of several legumes-with an emphasis on common bean (phaseolus vulgaris)-and is unusual in carrying multiple copies of nodd, the roles of which remain to be elucidated. | 2015 | 25880529 |
| metcap: a bioinformatics probe design pipeline for large-scale targeted metagenomics. | massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. alternative approaches such as t ... | 2015 | 25880302 |
| a comprehensive genomic, transcriptomic and proteomic analysis of a hyperosmotic stress sensitive α-proteobacterium. | with the aim of remaining viable, bacteria must deal with changes in environmental conditions, including increases in external osmolarity. while studies concerning bacterial response to this stress condition have focused on soil, marine and enteric species, this report is about caulobacter crescentus, a species inhabiting freshwater oligotrophic habitats. | 2015 | 25879753 |
| identification of a novel afipia species isolated from an indian flying fox. | an old world fruit bat pteropus giganteus, held in captivity and suffering from necrosis of its wing digits, failed to respond to antibiotic therapy and succumbed to the infection. samples submitted to the national centre for foreign animal disease were tested for viral infection. vero e6 cells exhibited minor but unique cytopathic effects on second blind passage, and full cpe by passage four. utilizing an unbiased random amplification technique from cell culture supernatant, we identified a bac ... | 2015 | 25874801 |
| the plant growth-promoting bacteria azospirillum amazonense: genomic versatility and phytohormone pathway. | the rhizosphere bacterium azospirillum amazonense associates with plant roots to promote plant growth. variation in replicon numbers and rearrangements is common among azospirillum strains, and characterization of these naturally occurring differences can improve our understanding of genome evolution. we performed an in silico comparative genomic analysis to understand the genomic plasticity of a. amazonense. the number of a. amazonense-specific coding sequences was similar when compared with th ... | 2015 | 25866821 |
| quantitative hopanoid analysis enables robust pattern detection and comparison between laboratories. | hopanoids are steroid-like lipids from the isoprenoid family that are produced primarily by bacteria. hopanes, molecular fossils of hopanoids, offer the potential to provide insight into environmental transitions on the early earth, if their sources and biological functions can be constrained. semiquantitative methods for mass spectrometric analysis of hopanoids from cultures and environmental samples have been developed in the last two decades. however, the structural diversity of hopanoids, an ... | 2015 | 25865768 |
| symbiosis island shuffling with abundant insertion sequences in the genomes of extra-slow-growing strains of soybean bradyrhizobia. | extra-slow-growing bradyrhizobia from root nodules of field-grown soybeans harbor abundant insertion sequences (iss) and are termed highly reiterated sequence-possessing (hrs) strains. we analyzed the genome organization of hrs strains with the focus on is distribution and symbiosis island structure. using pulsed-field gel electrophoresis, we consistently detected several plasmids (0.07 to 0.4 mb) in the hrs strains (nk5, nk6, usda135, 2281, usda123, and t2), whereas no plasmids were detected in ... | 2015 | 25862225 |
| rpon1, but not rpon2, is required for twitching motility, natural competence, growth on nitrate, and virulence of ralstonia solanacearum. | the plant pathogen ralstonia solanacearum has two genes encoding for the sigma factor σ(54): rpon1, located in the chromosome and rpon2, located in a distinct "megaplasmid" replicon. in this study, individual mutants as well as a double mutant of rpon were created in r. solanacearum strain gmi1000 in order to determine the extent of functional overlap between these two genes. by virulence assay we observed that rpon1 is required for virulence whereas rpon2 is not. in addition rpon1 controls othe ... | 2015 | 25852679 |
| redox markers for drought-induced nodule senescence, a process occurring after drought-induced senescence of the lowest leaves in soybean (glycine max). | water is an increasingly scarce resource that limits crop productivity in many parts of the world, and the frequency and severity of drought are predicted to increase as a result of climate change. improving tolerance to drought stress is therefore important for maximizing future crop yields. the aim of this study was to compare the effects of drought on soybean (glycine max) leaves and nodules in order to define phenotypic markers and changes in cellular redox state that characterize the stress ... | 2015 | 25851140 |
| the pseudomonas aeruginosa antimetabolite l -2-amino-4-methoxy-trans-3-butenoic acid (amb) is made from glutamate and two alanine residues via a thiotemplate-linked tripeptide precursor. | the pseudomonas aeruginosa toxin l-2-amino-4-methoxy-trans-3-butenoic acid (amb) is a non-proteinogenic amino acid which is toxic for prokaryotes and eukaryotes. production of amb requires a five-gene cluster encoding a putative lyse-type transporter (amba), two non-ribosomal peptide synthetases (ambb and ambe), and two iron(ii)/α-ketoglutarate-dependent oxygenases (ambc and ambd). bioinformatics analysis predicts one thiolation (t) domain for ambb and two t domains (t1 and t2) for ambe, suggest ... | 2015 | 25814981 |
| the intracellular scots pine shoot symbiont methylobacterium extorquens dsm13060 aggregates around the host nucleus and encodes eukaryote-like proteins. | endophytes are microbes that inhabit plant tissues without any apparent signs of infection, often fundamentally altering plant phenotypes. while endophytes are typically studied in plant roots, where they colonize the apoplast or dead cells, methylobacterium extorquens strain dsm13060 is a facultatively intracellular symbiont of the meristematic cells of scots pine (pinus sylvestris l.) shoot tips. the bacterium promotes host growth and development without the production of known plant growth-st ... | 2015 | 25805725 |
| the class iii cyclobutane pyrimidine dimer photolyase structure reveals a new antenna chromophore binding site and alternative photoreduction pathways. | photolyases are proteins with an fad chromophore that repair uv-induced pyrimidine dimers on the dna in a light-dependent manner. the cyclobutane pyrimidine dimer class iii photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. here we present the crystal structure of a class iii photolyase termed photolyase-related protein a (phra) of agrobacterium tumefaciens at 1.67-å resolution. phra contains 5,10-methenyltetrahydrofolate (m ... | 2015 | 25784552 |
| 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 |
| the escherichia coli small protein mnts and exporter mntp optimize the intracellular concentration of manganese. | escherichia coli does not routinely import manganese, but it will do so when iron is unavailable, so that manganese can substitute for iron as an enzyme cofactor. when intracellular manganese levels are low, the cell induces the mnth manganese importer plus mnts, a small protein of unknown function; when manganese levels are high, the cell induces the mntp manganese exporter and reduces expression of mnth and mnts. the role of mnts has not been clear. previous work showed that forced mnts synthe ... | 2015 | 25774656 |
| the dual nature of trehalose in citrus canker disease: a virulence factor for xanthomonas citri subsp. citri and a trigger for plant defence responses. | xanthomonas citri subsp. citri (xcc) is a bacterial pathogen that causes citrus canker in susceptible citrus spp. the xcc genome contains genes encoding enzymes from three separate pathways of trehalose biosynthesis. expression of genes encoding trehalose-6-phosphate synthase (otsa) and trehalose phosphatase (otsb) was highly induced during canker development, suggesting that the two-step pathway of trehalose biosynthesis via trehalose-6-phosphate has a function in pathogenesis. this pathway was ... | 2015 | 25770587 |
| pgprs and nitrogen-fixing legumes: a perfect team for efficient cd phytoremediation? | cadmium (cd) is a toxic, biologically non-essential and highly mobile metal that has become an increasingly important environmental hazard to both wildlife and humans. in contrast to conventional remediation technologies, phytoremediation based on legume-rhizobia symbiosis has emerged as an inexpensive decontamination alternative which also revitalize contaminated soils due to the role of legumes in nitrogen cycling. in recent years, there is a growing interest in understanding symbiotic legume- ... | 2015 | 25763004 |
| tetrapyrrole-based drought stress signalling. | tetrapyrroles such as chlorophyll and heme play a vital role in primary plant metabolic processes such as photosynthesis and respiration. over the past decades, extensive genetic and molecular analyses have provided valuable insights into the complex regulatory network of the tetrapyrrole biosynthesis. however, tetrapyrroles are also implicated in abiotic stress tolerance, although the mechanisms are largely unknown. with recent reports demonstrating that modified tetrapyrrole biosynthesis in pl ... | 2015 | 25756609 |
| hfq plays important roles in virulence and stress adaptation in cronobacter sakazakii atcc 29544. | cronobacter spp. are opportunistic pathogens that cause neonatal meningitis and sepsis with high mortality in neonates. despite the peril associated with cronobacter infection, the mechanisms of pathogenesis are still being unraveled. hfq, which is known as an rna chaperone, participates in the interaction with bacterial small rnas (srnas) to regulate posttranscriptionally the expression of various genes. recent studies have demonstrated that hfq contributes to the pathogenesis of numerous speci ... | 2015 | 25754196 |
| structural characterisation of the virulence-associated protein vapg from the horse pathogen rhodococcus equi. | virulence and host range in rhodococcus equi depends on the variable pathogenicity island of their virulence plasmids. notable gene products are a family of small secreted virulence-associated proteins (vaps) that are critical to intramacrophagic proliferation. equine-adapted strains, which cause severe pyogranulomatous pneumonia in foals, produce a cell-associated vapa that is necessary for virulence, alongside five other secreted homologues. in the absence of biochemical insight, attention has ... | 2015 | 25746683 |
| metagenomic analysis of the bacterial community associated with the taproot of sugar beet. | we analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (beta vulgaris l.) in order to investigate the genes involved in plant growth-promoting traits (pgpts), namely 1-aminocyclopropane-1-carboxylic acid (acc) deaminase, indole acetic acid (iaa), n2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. the most frequently detected gene among the pgpt c ... | 2015 | 25740621 |
| proteomic analysis of the soybean symbiosome identifies new symbiotic proteins. | legumes form a symbiosis with rhizobia in which the plant provides an energy source to the rhizobia bacteria that it uses to fix atmospheric nitrogen. this nitrogen is provided to the legume plant, allowing it to grow without the addition of nitrogen fertilizer. as part of the symbiosis, the bacteria in the infected cells of a new root organ, the nodule, are surrounded by a plant-derived membrane, the symbiosome membrane, which becomes the interface between the symbionts. fractions containing th ... | 2015 | 25724908 |
| an integrated approach to reconstructing genome-scale transcriptional regulatory networks. | transcriptional regulatory networks (trns) program cells to dynamically alter their gene expression in response to changing internal or environmental conditions. in this study, we develop a novel workflow for generating large-scale trn models that integrates comparative genomics data, global gene expression analyses, and intrinsic properties of transcription factors (tfs). an assessment of this workflow using benchmark datasets for the well-studied γ-proteobacterium escherichia coli showed that ... | 2015 | 25723545 |
| preferential association of endophytic bradyrhizobia with different rice cultivars and its implications for rice endophyte evolution. | plant colonization by bradyrhizobia is found not only in leguminous plants but also in nonleguminous species such as rice. to understand the evolution of the endophytic symbiosis of bradyrhizobia, the effect of the ecosystems of rice plantations on their associations was investigated. samples were collected from various rice (oryza sativa) tissues and crop rotational systems. the rice endophytic bradyrhizobia were isolated on the basis of oligotrophic properties, selective medium, and nodulation ... | 2015 | 25710371 |
| dephosphorylated npr is involved in an envelope stress response of escherichia coli. | besides the canonical phosphoenolpyruvate-dependent phosphotransferase system (pts) for carbohydrate transport, most proteobacteria possess the so-called nitrogen pts (pts(ntr)) that transfers a phosphate group from phosphoenolpyruvate (pep) over enzyme i(ntr) (ei(ntr)) and npr to enzyme iia(ntr) (eiia(ntr)). the pts(ntr) lacks membrane-bound components and functions exclusively in a regulatory capacity. while eiia(ntr) has been implicated in a variety of cellular processes such as potassium hom ... | 2015 | 25701731 |
| genome sequence of bradyrhizobium japonicum e109, one of the most agronomically used nitrogen-fixing rhizobacteria in argentina. | we present here the complete genome sequence of bradyrhizobium japonicum strain e109, one of the most used rhizobacteria for soybean inoculation in argentina since the 1970s. the genome consists of a 9.22-mbp single chromosome and contains several genes related to nitrogen fixation, phytohormone biosynthesis, and a rhizospheric lifestyle. | 2015 | 25700406 |
| rhizobia and their bio-partners as novel drivers for functional remediation in contaminated soils. | environmental pollutants have received considerable attention due to their serious effects on human health. there are physical, chemical, and biological means to remediate pollution; among them, bioremediation has become increasingly popular. the nitrogen-fixing rhizobia are widely distributed in the soil and root ecosystems and can increase legume growth and production by supplying nitrogen, resulting in the reduced need for fertilizer applications. rhizobia also possess the biochemical and eco ... | 2015 | 25699064 |
| 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 |
| plants coping abiotic and biotic stresses: a tale of diligent management. | 2015 | 25685808 | |
| dt2008: a promising new genetic resource for improved drought tolerance in soybean when solely dependent on symbiotic n2 fixation. | water deficit is one of the major constraints for soybean production in vietnam. the soybean breeding research efforts conducted at the agriculture genetics institute (agi) of vietnam resulted in the development of promising soybean genotypes, suitable for the drought-stressed areas in vietnam and other countries. such a variety, namely, dt2008, was recommended by agi and widely used throughout the country. the aim of this work was to assess the growth of shoots, roots, and nodules of dt2008 ver ... | 2015 | 25685802 |
| a genomic encyclopedia of the root nodule bacteria: assessing genetic diversity through a systematic biogeographic survey. | root nodule bacteria are free-living soil bacteria, belonging to diverse genera within the alphaproteobacteria and betaproteobacteria, that have the capacity to form nitrogen-fixing symbioses with legumes. the symbiosis is specific and is governed by signaling molecules produced from both host and bacteria. sequencing of several model rnb genomes has provided valuable insights into the genetic basis of symbiosis. however, the small number of sequenced rnb genomes available does not currently ref ... | 2015 | 25685260 |
| multiple steps control immunity during the intracellular accommodation of rhizobia. | medicago truncatula belongs to the legume family and forms symbiotic associations with nitrogen fixing bacteria, the rhizobia. during these interactions, the plants develop root nodules in which bacteria invade the plant cells and fix nitrogen for the benefit of the plant. despite massive infection, legume nodules do not develop visible defence reactions, suggesting a special immune status of these organs. some factors influencing rhizobium maintenance within the plant cells have been previously ... | 2015 | 25682610 |
| a first line of stress defense: small heat shock proteins and their function in protein homeostasis. | small heat shock proteins (shsps) are virtually ubiquitous molecular chaperones that can prevent the irreversible aggregation of denaturing proteins. shsps complex with a variety of non-native proteins in an atp-independent manner and, in the context of the stress response, form a first line of defense against protein aggregation in order to maintain protein homeostasis. in vertebrates, they act to maintain the clarity of the eye lens, and in humans, shsp mutations are linked to myopathies and n ... | 2015 | 25681016 |
| soybean (glycine max l. merr.) sprouts germinated under red light irradiation induce disease resistance against bacterial rotting disease. | specific wavelengths of light can exert various physiological changes in plants, including effects on responses to disease incidence. to determine whether specific light wavelength had effects on rotting disease caused by pseudomonas putida 229, soybean sprouts were germinated under a narrow range of wavelengths from light emitting diodes (leds), including red (650-660), far red (720-730) and blue (440-450 nm) or broad range of wavelength from daylight fluorescence bulbs. the controls were compo ... | 2015 | 25679808 |
| a globin domain in a neuronal transmembrane receptor of caenorhabditis elegans and ascaris suum: molecular modeling and functional properties. | we report the structural and biochemical characterization of glb-33, a putative neuropeptide receptor that is exclusively expressed in the nervous system of the nematode caenorhabditis elegans. this unique chimeric protein is composed of a 7-transmembrane domain (7tm), glb-33 7tm, typical of a g-protein-coupled receptor, and of a globin domain (gd), glb-33 gd. comprehensive sequence similarity searches in the genome of the parasitic nematode, ascaris suum, revealed a chimeric protein that is sim ... | 2015 | 25666609 |
| predominant populations of indigenous soybean-nodulating bradyrhizobium japonicum strains obtained from organic farming systems in minnesota. | bradyrhizobium from organic fields in minnesota were isolated and genotyped to assess diversity of soybean-bradyrhizobia in organic farming systems that can be used to improve soybean productivity. | 2015 | 25660818 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| ccer and akgr regulate central carbon and energy metabolism in alphaproteobacteria. | many pathways of carbon and energy metabolism are conserved across the phylogeny, but the networks that regulate their expression or activity often vary considerably among organisms. in this work, we show that two previously uncharacterized transcription factors (tfs) are direct regulators of genes encoding enzymes of central carbon and energy metabolism in the alphaproteobacterium rhodobacter sphaeroides. the laci family member ccer (rsp_1663) directly represses genes encoding enzymes in the en ... | 2015 | 25650399 |
| identification of ferredoxin ii as a major calcium binding protein in the nitrogen-fixing symbiotic bacterium mesorhizobium loti. | legumes establish with rhizobial bacteria a nitrogen-fixing symbiosis which is of the utmost importance for both plant nutrition and a sustainable agriculture. calcium is known to act as a key intracellular messenger in the perception of symbiotic signals by both the host plant and the microbial partner. regulation of intracellular free ca(2+) concentration, which is a fundamental prerequisite for any ca(2+)-based signalling system, is accomplished by complex mechanisms including ca(2+) binding ... | 2015 | 25648224 |
| identification of bacterial guanylate cyclases. | the ability of bacteria to use cgmp as a second messenger has been controversial for decades. recently, nucleotide cyclases from rhodospirillum centenum, gcya, and xanthomonas campestris, guax, have been shown to possess guanylate cyclase activities. enzymatic activities of these guanylate cyclases measured in vitro were low, which makes interpretation of the assays ambiguous. protein sequence analysis at present is insufficient to distinguish between bacterial adenylate and guanylate cyclases, ... | 2015 | 25645367 |
| metabolite profiling reveals abiotic stress tolerance in tn5 mutant of pseudomonas putida. | pseudomonas is an efficient plant growth-promoting rhizobacteria (pgpr); however, intolerance to drought and high temperature limit its application in agriculture as a bioinoculant. transposon 5 (tn5) mutagenesis was used to generate a stress tolerant mutant from a pgpr pseudomonas putida nbri1108 isolated from chickpea rhizosphere. a mutant nbri1108t, selected after screening of nearly 10,000 transconjugants, exhibited significant tolerance towards high temperature and drought. southern hybridi ... | 2015 | 25629312 |
| mutualism-parasitism paradigm synthesized from results of root-endophyte models. | plant tissues host a variety of fungi. one important group is the dark septate endophytes (dses) that colonize plant roots and form characteristic intracellular structures - melanized hyphae and microsclerotia. the dse associations are common and frequently observed in various biomes and plant taxa. reviews suggest that the proportion of plant species colonized by dse equal that colonized by am and microscopic studies show that the proportion of the root system colonized by fungi dse can equal, ... | 2014 | 25628615 |
| mutualism-parasitism paradigm synthesized from results of root-endophyte models. | plant tissues host a variety of fungi. one important group is the dark septate endophytes (dses) that colonize plant roots and form characteristic intracellular structures - melanized hyphae and microsclerotia. the dse associations are common and frequently observed in various biomes and plant taxa. reviews suggest that the proportion of plant species colonized by dse equal that colonized by am and microscopic studies show that the proportion of the root system colonized by fungi dse can equal, ... | 2014 | 25628615 |
| revision of the taxonomic status of the species rhizobium lupini and reclassification as bradyrhizobium lupini comb. nov. | the species rhizobium lupini was isolated from lupinus nodules and included in the approved lists of bacterial names in 1980. nevertheless, on the basis of the analysis of the type strain of this species available in dsmz, dsm 30140(t), whose 16s rrna gene was identical to that of the type strain of bradyrhizobium japonicum , r. lupini was considered a later synonym of this species. in this study we confirmed that the strain dsm 30140(t) belongs to the species b. japonicum , but also that it can ... | 2015 | 25609676 |
| leghemoglobin is nitrated in functional legume nodules in a tyrosine residue within the heme cavity by a nitrite/peroxide-dependent mechanism. | protein tyrosine (tyr) nitration is a post-translational modification yielding 3-nitrotyrosine (no2 -tyr). formation of no2 -tyr is generally considered as a marker of nitro-oxidative stress and is involved in some human pathophysiological disorders, but has been poorly studied in plants. leghemoglobin (lb) is an abundant hemeprotein of legume nodules that plays an essential role as an o2 transporter. liquid chromatography coupled to tandem mass spectrometry was used for a targeted search and qu ... | 2015 | 25603991 |
| structural basis for the facilitative diffusion mechanism by semisweet transporter. | sweet family proteins mediate sugar transport across biological membranes and play crucial roles in plants and animals. the sweets and their bacterial homologues, the semisweets, are related to the pq-loop family, which is characterized by highly conserved proline and glutamine residues (pq-loop motif). although the structures of the bacterial semisweets were recently reported, the conformational transition and the significance of the conserved motif in the transport cycle have remained elusive. ... | 2015 | 25598322 |
| association mapping of qtls for sclerotinia stem rot resistance in a collection of soybean plant introductions using a genotyping by sequencing (gbs) approach. | sclerotinia stem rot (ssr) is the most important soybean disease in eastern canada. the development of resistant cultivars represents the most cost-effective means of limiting the impact of this disease. in view of ensuring durable resistance, it is imperative to identify germplasm harbouring different resistance loci and to provide breeders with closely linked molecular markers to facilitate breeding. with this end in view, we assessed resistance using a highly reproducible artificial inoculati ... | 2015 | 25595526 |
| hydrazidase, a novel amidase signature enzyme that hydrolyzes acylhydrazides. | the degradation mechanisms of natural and artificial hydrazides have been elucidated. here we screened and isolated bacteria that utilize the acylhydrazide 4-hydroxybenzoic acid 1-phenylethylidene hydrazide (hbph) from soils. physiological and phylogenetic studies identified one bacterium as microbacterium sp. strain hm58-2, from which we purified intracellular hydrazidase, cloned its gene, and prepared recombinant hydrazidase using an escherichia coli expression system. the microbacterium sp. h ... | 2015 | 25583978 |
| transport processes of the legume symbiosome membrane. | the symbiosome membrane (sm) is a physical barrier between the host plant and nitrogen-fixing bacteria in the legume:rhizobia symbiosis, and represents a regulated interface for the movement of solutes between the symbionts that is under plant control. the primary nutrient exchange across the sm is the transport of a carbon energy source from plant to bacteroid in exchange for fixed nitrogen. at a biochemical level two channels have been implicated in movement of fixed nitrogen across the sm and ... | 2014 | 25566274 |
| the dam replacing gene product enhances neisseria gonorrhoeae fa1090 viability and biofilm formation. | many neisseriaceae do not exhibit dam methyltransferase activity and, instead of the dam gene, possess drg (dam replacing gene) inserted in the leus/dam locus. the drg locus in neisseria gonorrhoeae fa1090 has a lower gc-pairs content (40.5%) compared to the whole genome of n. gonorrhoeae fa1090 (52%). the gonococcal drg gene encodes a dna endonuclease drg, with gmeatc specificity. disruption of drg or insertion of the dam gene in gonococcal genome changes the level of expression of genes as sho ... | 2014 | 25566225 |
| soybean mir172c targets the repressive ap2 transcription factor nnc1 to activate enod40 expression and regulate nodule initiation. | micrornas are noncoding rnas that act as master regulators to modulate various biological processes by posttranscriptionally repressing their target genes. repression of their target mrna(s) can modulate signaling cascades and subsequent cellular events. recently, a role for mir172 in soybean (glycine max) nodulation has been described; however, the molecular mechanism through which mir172 acts to regulate nodulation has yet to be explored. here, we demonstrate that soybean mir172c modulates bot ... | 2014 | 25549672 |
| identification of new metabolites of bacterial transformation of indole by gas chromatography-mass spectrometry and high performance liquid chromatography. | arthrobacter sp. spg transformed indole completely in the presence of an additional carbon source. high performance liquid chromatography and gas chromatography-mass spectrometry detected indole-3-acetic acid, indole-3-glyoxylic acid, and indole-3-aldehyde as biotransformation products. this is the first report of the formation of indole-3-acetic acid, indole-3-glyoxylic acid, and indole-3-aldehyde from indole by any bacterium. | 2014 | 25548566 |
| genome-wide expression analysis of soybean nf-y genes reveals potential function in development and drought response. | nuclear factor-y (nf-y), a heterotrimeric transcription factor, is composed of nf-ya, nf-yb and nf-yc proteins. in plants, there are usually more than 10 genes for each family and their members have been identified to be key regulators in many developmental and physiological processes controlling gametogenesis, embryogenesis, nodule development, seed development, abscisic acid (aba) signaling, flowering time, primary root elongation, blue light responses, endoplasmic reticulum (er) stress respon ... | 2014 | 25542200 |
| genome-wide expression analysis of soybean nf-y genes reveals potential function in development and drought response. | nuclear factor-y (nf-y), a heterotrimeric transcription factor, is composed of nf-ya, nf-yb and nf-yc proteins. in plants, there are usually more than 10 genes for each family and their members have been identified to be key regulators in many developmental and physiological processes controlling gametogenesis, embryogenesis, nodule development, seed development, abscisic acid (aba) signaling, flowering time, primary root elongation, blue light responses, endoplasmic reticulum (er) stress respon ... | 2014 | 25542200 |
| whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (phacs) from japan trench and nankai trough seawater. | special features of the japanese ocean include its ranges of latitude and depth. this study is the first to examine the diversity of class i and ii pha synthases (phac) in dna samples from pelagic seawater taken from the japan trench and nankai trough from a range of depths from 24 m to 5373 m. phac is the key enzyme in microorganisms that determines the types of monomer units that are polymerized into polyhydroxyalkanoate (pha) and thus affects the physicochemical properties of this thermoplast ... | 2014 | 25539583 |
| the root hair "infectome" of medicago truncatula uncovers changes in cell cycle genes and reveals a requirement for auxin signaling in rhizobial infection. | nitrogen-fixing rhizobia colonize legume roots via plant-made intracellular infection threads. genetics has identified some genes involved but has not provided sufficient detail to understand requirements for infection thread development. therefore, we transcriptionally profiled medicago truncatula root hairs prior to and during the initial stages of infection. this revealed changes in the responses to plant hormones, most notably auxin, strigolactone, gibberellic acid, and brassinosteroids. sev ... | 2014 | 25527707 |
| draft genome sequence of bradyrhizobium japonicum is-34, which is incompatible with rj4 genotype soybeans. | we report here the draft genome sequence of bradyrhizobium japonicum is-34, which is incompatible with rj4 genotype soybeans. a candidate gene involved in this incompatibility was found to be present in this genome. | 2014 | 25523773 |
| 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 |
| bradhyrhizobium japonicum hydrogen-ubiquinone oxidoreductase activity: quinone specificity, inhibition by quinone analogs, and evidence for separate sites of electron acceptor reactivity. | the purified h2-uptake hydrogenase of bradyrhizobium japonicum, containing no cytochrome b, catalyzed efficient h2-ubiquinone oxidoreductase activity. hydrogen-oxidizing membranes also catalyzed h₂-ubiquinone oxidoreductase activity, and the site of ubiquinone reduction was localized to the he-quinone oxidoreductase complex based on comparative antimycin a and hqno titrations of both h₂-ubiquinone-1 oxidoreductase and ubiquinol-1 oxidase activities. a variety of quinones could function as electr ... | 1995 | 25507405 |
| atmospheric hydrogen scavenging: from enzymes to ecosystems. | we have known for 40 years that soils can consume the trace amounts of molecular hydrogen (h2) found in the earth’s atmosphere.this process is predicted to be the most significant term in the global hydrogen cycle. however, the organisms and enzymes responsible for this process were only recently identified. pure culture experiments demonstrated that several species of actinobacteria, including streptomycetes and mycobacteria, can couple the oxidation of atmospheric h2 to the reduction of ambien ... | 2015 | 25501483 |