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an aboveground pathogen inhibits belowground rhizobia and arbuscular mycorrhizal fungi in phaseolus vulgaris.induced aboveground plant defenses against pathogens can have negative effects on belowground microbial symbionts. while a considerable number of studies have utilized chemical elicitors to experimentally induce such defenses, there is surprisingly little evidence that actual aboveground pathogens affect root-associated microbes. we report here that an aboveground fungal pathogen of common bean (phaseolus vulgaris) induces a defense response that inhibits both the belowground formation of root n ...201425429887
cysteine protease and cystatin expression and activity during soybean nodule development and senescence.nodules play an important role in fixing atmospheric nitrogen for soybean growth. premature senescence of nodules can negatively impact on nitrogen availability for plant growth and, as such, we need a better understanding of nodule development and senescence. cysteine proteases are known to play a role in nodule senescence, but knowledge is still fragmented regarding the function their inhibitors (cystatins) during the development and senescence of soybean nodules. this study provides the first ...201425404209
complex two-component signaling regulates the general stress response in alphaproteobacteria.the general stress response (gsr) in alphaproteobacteria was recently shown to be controlled by a partner-switching mechanism that is triggered by phosphorylation of the response regulator phyr. activation of phyr ultimately results in release of the alternative extracytoplasmic function sigma factor σ(ecfg), which redirects transcription toward the gsr. little is known about the signal transduction pathway(s) controlling phyr phosphorylation. here, we identified the single-domain response regul ...201425404331
comprehensive characterization and rna-seq profiling of the hd-zip transcription factor family in soybean (glycine max) during dehydration and salt stress.the homeodomain leucine zipper (hd-zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. many hd-zip genes are characterized in arabidopsis (arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (oryza sativa), maize (zea mays), poplar (populus trichocarpa) and cucumber (cucmis sativus). findings in these species ...201425362847
dynamics of metabolic activities and gene expression in the roseobacter clade bacterium phaeobacter sp. strain med193 during growth with thiosulfate.metagenomic analyses of surface seawater reveal that genes for sulfur oxidation are widespread in bacterioplankton communities. however, little is known about the metabolic processes used to exploit the energy potentially gained from inorganic sulfur oxidation in oxic seawater. we therefore studied the sox gene system containing roseobacter clade isolate phaeobacter sp. strain med193 in acetate minimal medium with and without thiosulfate. the addition of thiosulfate enhanced the bacterial growth ...201425172867
physiological and biochemical responses of yarrowia lipolytica to dehydration induced by air-drying and freezing.organisms that can withstand anhydrobiosis possess the unique ability to temporarily and reversibly suspend their metabolism for the periods when they live in a dehydrated state. however, the mechanisms underlying the cell's ability to tolerate dehydration are far from being fully understood. the objective of this study was to highlight, for the first time, the cellular damage to yarrowia lipolytica as a result of dehydration induced by drying/rehydration and freezing/thawing. cellular response ...201425350121
symbiotic nitrogen fixation in legume nodules: metabolism and regulatory mechanisms.the special issue "symbiotic nitrogen fixation in legume nodules: metabolism and regulatory mechanisms" aims to investigate the physiological and biochemical advances in the symbiotic process with an emphasis on nodule establishment, development and functioning. the original research articles included in this issue provide important information regarding novel aspects of nodule metabolism and various regulatory pathways, which could have important future implications. this issue also included on ...201425347276
characterization of the bile and gall bladder microbiota of healthy pigs.bile is a biological fluid synthesized in the liver, stored and concentrated in the gall bladder (interdigestive), and released into the duodenum after food intake. the microbial populations of different parts of mammal's gastrointestinal tract (stomach, small and large intestine) have been extensively studied; however, the characterization of bile microbiota had not been tackled until now. we have studied, by culture-dependent techniques and a 16s rrna gene-based analysis, the microbiota presen ...201425336405
ectopic expression of mir156 represses nodulation and causes morphological and developmental changes in lotus japonicus.the effects of microrna156 overexpression on general plant architecture, branching, flowering time and nodulation were investigated in the model legume, lotus japonicus. we cloned an mir156 homolog, ljmir156a, from l. japonicus, and investigated its squamosa promoter binding protein like (spl) genes and its biological function at enhancing vegetative biomass yield, extending flowering time, and its impact on nodulation. thirteen potential targets for ljmir156 were identified in vitro and their e ...201425293935
ectopic expression of mir156 represses nodulation and causes morphological and developmental changes in lotus japonicus.the effects of microrna156 overexpression on general plant architecture, branching, flowering time and nodulation were investigated in the model legume, lotus japonicus. we cloned an mir156 homolog, ljmir156a, from l. japonicus, and investigated its squamosa promoter binding protein like (spl) genes and its biological function at enhancing vegetative biomass yield, extending flowering time, and its impact on nodulation. thirteen potential targets for ljmir156 were identified in vitro and their e ...201425293935
streptomyces coelicolor sco4226 is a nickel binding protein.the open reading frame sco4226 of streptomyces coelicolor a3(2) encodes an 82-residue hypothetical protein. biochemical assays revealed that each sco4226 dimer binds four nickel ions. to decipher the molecular function, we solved the crystal structures of sco4226 in both apo- and nickel-bound (ni-sco4226) forms at 1.30 and 2.04 å resolution, respectively. each subunit of sco4226 dimer adopts a canonical ferredoxin-like fold with five β-strands flanked by two α-helices. in the structure of ni-sco ...201425285530
coregulated genes link sulfide:quinone oxidoreductase and arsenic metabolism in synechocystis sp. strain pcc6803.although the biogeochemistry of the two environmentally hazardous compounds arsenic and sulfide has been extensively investigated, the biological interference of these two toxic but potentially energy-rich compounds has only been hypothesized and indirectly proven. here we provide direct evidence for the first time that in the photosynthetic model organism synechocystis sp. strain pcc6803 the two metabolic pathways are linked by coregulated genes that are involved in arsenic transport, sulfide o ...201425022856
structure, function and inhibition of ent-kaurene synthase from bradyrhizobium japonicum.we report the first x-ray crystal structure of ent-kaur-16-ene synthase from bradyrhizobium japonicum, together with the results of a site-directed mutagenesis investigation into catalytic activity. the structure is very similar to that of the α domains of modern plant terpene cyclases, a result that is of interest since it has been proposed that many plant terpene cyclases may have arisen from bacterial diterpene cyclases. the ent-copalyl diphosphate substrate binds to a hydrophobic pocket near ...201425269599
a mur regulator protein in the extremophilic bacterium deinococcus radiodurans.ferric uptake regulator (fur) is a transcriptional regulator that controls the expression of genes involved in the uptake of iron and manganese, as well as vital nutrients, and is essential for intracellular redox cycling. we identified a unique fur homolog (dr0865) from deinococcus radiodurans, which is known for its extreme resistance to radiation and oxidants. a dr0865 mutant (mt-0865) showed a higher sensitivity to manganese stress, hydrogen peroxide, gamma irradiation and ultraviolet (uv) i ...201425243898
rna-seq analysis of the multipartite genome of rhizobium etli ce3 shows different replicon contributions under heat and saline shock.regulation of transcription is essential for any organism and rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. this bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (phaseolus vulgaris) in a symbiotic relationship. abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of r. etli and therefore its symbiotic interaction with p. vulgaris. however, it is still unc ...201425201548
differing courses of genetic evolution of bradyrhizobium inoculants as revealed by long-term molecular tracing in acacia mangium plantations.introducing nitrogen-fixing bacteria as an inoculum in association with legume crops is a common practice in agriculture. however, the question of the evolution of these introduced microorganisms remains crucial, both in terms of microbial ecology and agronomy. we explored this question by analyzing the genetic and symbiotic evolution of two bradyrhizobium strains inoculated on acacia mangium in malaysia and senegal 15 and 5 years, respectively, after their introduction. based on typing of sever ...201425002434
rna sequencing analysis of the broad-host-range strain sinorhizobium fredii ngr234 identifies a large set of genes linked to quorum sensing-dependent regulation in the background of a trai and ngri deletion mutant.the alphaproteobacterium sinorhizobium fredii ngr234 has an exceptionally wide host range, as it forms nitrogen-fixing nodules with more legumes than any other known microsymbiont. within its 6.9-mbp genome, it encodes two n-acyl-homoserine-lactone synthase genes (i.e., trai and ngri) involved in the biosynthesis of two distinct autoinducer i-type molecules. here, we report on the construction of an ngr234-δtrai and an ngr234-δngri mutant and their genome-wide transcriptome analysis. a high-reso ...201425002423
bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in canada.sixteen strains of symbiotic bacteria from root nodules of glycine max grown in ottawa, canada, were previously characterized and placed in a novel group within the genus bradyrhizobium. to verify their taxonomic status, these strains were further characterized using a polyphasic approach. all strains possessed identical 16s rrna gene sequences that were 99.79 % similar to the closest relative, bradyrhizobium liaoningense lmg 18230(t). phylogenetic analysis of concatenated atpd, glnii, reca, gyr ...201424969302
abundance and diversity of soybean-nodulating rhizobia in black soil are impacted by land use and crop management.to investigate the effects of land use and crop management on soybean rhizobial communities, 280 nodule isolates were trapped from 7 fields with different land use and culture histories. besides the known bradyrhizobium japonicum, three novel genospecies were isolated from these fields. grassland (gl) maintained a higher diversity of soybean bradyrhizobia than the other cultivation systems. two genospecies (bradyrhizobium spp. i and iii) were distributed widely in all treatments, while bradyrhiz ...201424951780
transcriptional regulator lsrb of sinorhizobium meliloti positively regulates the expression of genes involved in lipopolysaccharide biosynthesis.rhizobia induce nitrogen-fixing nodules on host legumes, which is important in agriculture and ecology. lipopolysaccharide (lps) produced by rhizobia is required for infection or bacteroid survival in host cells. genes required for lps biosynthesis have been identified in several rhizobium species. however, the regulation of their expression is not well understood. here, sinorhizobium meliloti lsrb, a member of the lysr family of transcriptional regulators, was found to be involved in lps biosyn ...201424951786
the symbiotic biofilm of sinorhizobium fredii smh12, necessary for successful colonization and symbiosis of glycine max cv osumi, is regulated by quorum sensing systems and inducing flavonoids via nodd1.bacterial surface components, especially exopolysaccharides, in combination with bacterial quorum sensing signals are crucial for the formation of biofilms in most species studied so far. biofilm formation allows soil bacteria to colonize their surrounding habitat and survive common environmental stresses such as desiccation and nutrient limitation. this mode of life is often essential for survival in bacteria of the genera mesorhizobium, sinorhizobium, bradyrhizobium, and rhizobium. the role of ...201425166872
the mismetallation of enzymes during oxidative stress.mononuclear iron enzymes can tightly bind non-activating metals. how do cells avoid mismetallation? the model bacterium escherichia coli may control its metal pools so that thermodynamics favor the correct metallation of each enzyme. this system is disrupted, however, by superoxide and hydrogen peroxide. these species oxidize ferrous iron and thereby displace it from many iron-dependent mononuclear enzymes. ultimately, zinc binds in its place, confers little activity, and imposes metabolic bottl ...201425160623
evidence that the c-terminal domain of a type b puta protein contributes to aldehyde dehydrogenase activity and substrate channeling.proline utilization a (puta) is a bifunctional enzyme that catalyzes the oxidation of proline to glutamate. structures of type a putas have revealed the catalytic core consisting of proline dehydrogenase (prodh) and δ(1)-pyrroline-5-carboxylate dehydrogenase (p5cdh) modules connected by a substrate-channeling tunnel. type b putas also have a c-terminal domain of unknown function (ctduf) that is absent in type a putas. small-angle x-ray scattering (saxs), mutagenesis, and kinetics are used to det ...201425137435
identification of cold-responsive mirnas and their target genes in nitrogen-fixing nodules of soybean.as a warm climate species, soybean is highly sensitive to chilling temperatures. exposure to chilling temperatures causes a significant reduction in the nitrogen fixation rate in soybean plants and subsequent yield loss. however, the molecular basis for the sensitivity of soybean to chilling is poorly understood. in this study, we identified cold-responsive mirnas in nitrogen-fixing nodules of soybean. upon chilling, the expression of gma-mir397a, gma-mir166u and gma-mir171p was greatly upregula ...201425100171
proteomic analysis of free-living bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis.strain cpac 7 (=semia 5080) was recently reclassified into the new species bradyrhizobium diazoefficiens; due to its outstanding efficiency in fixing nitrogen, it has been used in commercial inoculants for application to crops of soybean [glycine max (l.) merr.] in brazil and other south american countries. although the efficiency of b. diazoefficiens inoculant strains is well recognized, few data on their protein expression are available.201425086822
structural insights into the catalytic mechanism of synechocystis magnesium protoporphyrin ix o-methyltransferase (chlm).magnesium protoporphyrin ix o-methyltransferase (chlm) catalyzes transfer of the methyl group from s-adenosylmethionine to the carboxyl group of the c13 propionate side chain of magnesium protoporphyrin ix. this reaction is the second committed step in chlorophyll biosynthesis from protoporphyrin ix. here we report the crystal structures of chlm from the cyanobacterium synechocystis sp. pcc 6803 in complex with s-adenosylmethionine and s-adenosylhomocysteine at resolutions of 1.6 and 1.7 å, resp ...201425077963
structure of the virulence-associated protein vapd from the intracellular pathogen rhodococcus equi.rhodococcus equi is a multi-host pathogen that infects a range of animals as well as immune-compromised humans. equine and porcine isolates harbour a virulence plasmid encoding a homologous family of virulence-associated proteins associated with the capacity of r. equi to divert the normal processes of endosomal maturation, enabling bacterial survival and proliferation in alveolar macrophages. to provide a basis for probing the function of the vap proteins in virulence, the crystal structure of ...201425084333
kinetic and structural characterization of tunnel-perturbing mutants in bradyrhizobium japonicum proline utilization a.proline utilization a from bradyrhizobium japonicum (bjputa) is a bifunctional flavoenzyme that catalyzes the oxidation of proline to glutamate using fused proline dehydrogenase (prodh) and δ(1)-pyrroline-5-carboxylate dehydrogenase (p5cdh) domains. recent crystal structures and kinetic data suggest an intramolecular channel connects the two active sites, promoting substrate channeling of the intermediate δ(1)-pyrroline-5-carboxylate/glutamate-γ-semialdehyde (p5c/gsa). in this work, the structur ...201425046425
genome-based analysis of the transcriptome from mature chickpea root nodules.symbiotic nitrogen fixation (snf) in root nodules of grain legumes such as chickpea is a highly complex process that drastically affects the gene expression patterns of both the prokaryotic as well as eukaryotic interacting cells. a successfully established symbiotic relationship requires mutual signaling mechanisms and a continuous adaptation of the metabolism of the involved cells to varying environmental conditions. although some of these processes are well understood today many of the molecu ...201425071808
identification of a dominant gene in medicago truncatula that restricts nodulation by sinorhizobium meliloti strain rm41.leguminous plants are able to form a root nodule symbiosis with nitrogen-fixing soil bacteria called rhizobia. this symbiotic association shows a high level of specificity. beyond the specificity for the legume family, individual legume species/genotypes can only interact with certain restricted group of bacterial species or strains. specificity in this system is regulated by complex signal exchange between the two symbiotic partners and thus multiple genetic mechanisms could be involved in the ...201424934080
the effect of colloidal solution of molybdenum nanoparticles on the microbial composition in rhizosphere of cicer arietinum l.the use of colloidal solutions of metals as micronutrients enhances plant resistance to unfavorable environmental conditions and ensures high yields of food crops due to the active penetration of nanoelements into the plant cells. microbiological examination of rhizosphere soil have revealed that combined use of colloidal solution of nanoparticles of molybdenum (csnm, 8 mg/l), and microbial preparation for pre-sowing inoculation of chickpea seeds stimulates the development of 'agronomically valu ...201425024677
whole-genome sequencing of mesorhizobium huakuii 7653r provides molecular insights into host specificity and symbiosis island dynamics.evidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between mesorhizobium strain maff303099 and m. huakuii. to define underlying causes for the rather striking difference in host specificity between m. huakuii strain 7653r and maff303099, several probable determinants also require comparison at the genomic level. an improved understanding of mobile genetic elements that can be integrated into the main chromosomes of mesorhizobium to form genomic island ...201424906389
comparative genomics of bradyrhizobium japonicum cpac 15 and bradyrhizobium diazoefficiens cpac 7: elite model strains for understanding symbiotic performance with soybean.the soybean-bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. b. japonicum cpac 15 (=semia 5079) is outstanding in its saprophytic capacity and competitiveness, whereas b. diazoefficiens cpac 7 (=semia 5080) is known for its high efficiency in fixing nitrogen. both are well ada ...201424888481
genetic basis for denitrification in ensifer meliloti.denitrification is defined as the dissimilatory reduction of nitrate or nitrite to nitric oxide (no), nitrous oxide (n2o), or dinitrogen gas (n2). n2o is a powerful atmospheric greenhouse gas and cause of ozone layer depletion. legume crops might contribute to n2o production by providing nitrogen-rich residues for decomposition or by associating with rhizobia that are able to denitrify under free-living and symbiotic conditions. however, there are limited direct empirical data concerning n2o pro ...201424888981
deletions of the sacpd-c locus elevate seed stearic acid levels but also result in fatty acid and morphological alterations in nitrogen fixing nodules.soybean (glycine max) seeds are the primary source of edible oil in the united states. despite its widespread utility, soybean oil is oxidatively unstable. until recently, the majority of soybean oil underwent chemical hydrogenation, a process which also generates trans fats. an alternative to chemical hydrogenation is genetic modification of seed oil through identification and introgression of mutant alleles. one target for improvement is the elevation of a saturated fat with no negative cardio ...201424886084
stress-induced remodeling of the bacterial proteome.microorganisms live in fluctuating environments, requiring stress response pathways to resist environmental insults and stress. these pathways dynamically monitor cellular status, and mediate adaptive changes by remodeling the proteome, largely accomplished by remodeling transcriptional networks and protein degradation. the complementarity of fast, specific proteolytic degradation and slower, broad transcriptomic changes gives cells the mechanistic repertoire to dynamically adjust cellular proce ...201424845675
role of the vira histidine autokinase of agrobacterium tumefaciens in the initial steps of pathogenesis.histidine kinases serve as critical environmental sensing modules, and despite their designation as simple two-component modules, their functional roles are remarkably diverse. in agrobacterium tumefaciens pathogenesis, vira serves with virg as the initiating sensor/transcriptional activator for inter-kingdom gene transfer and transformation of higher plants. through responses to three separate signal inputs, low ph, sugars, and phenols, a. tumefaciens commits to pathogenesis in virtually all fl ...201424860585
high-level soluble expression of the hema gene from rhodobacter capsulatus and comparative study of its enzymatic properties.the rhodobacter capsulatus hema gene, which encodes 5-aminolevulinic acid synthase (alas), was expressed in escherichia coli rosetta (de3) and the enzymatic properties of the purified recombinant alas (rc-alas) were studied. compared with alass encoded by hema genes from agrobacterium radiobacter (ar-alas) and rhodobacter sphaeroides (rs-alas), the specific activity of rc-alas reached 198.2 u/mg, which was about 31.2% and 69.5% higher than those of ar-alas (151.1 u/mg) and rs-alas (116.9 u/mg), ...201424793767
genetic divergence of bradyrhizobium strains nodulating soybeans as revealed by multilocus sequence analysis of genes inside and outside the symbiosis island.the genus bradyrhizobium has been considered to be a taxonomically difficult group. in this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among bradyrhizobium strains nodulating soybeans in china. eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (smc00019, thra, and trua). this was also supported by analyses of eight genes outside the symbiosis island ("off-island" genes; smc00019, thra, trua, ...201424632260
the role of symbiotic nitrogen fixation in sustainable production of biofuels.with the ever-increasing population of the world (expected to reach 9.6 billion by 2050), and altered life style, comes an increased demand for food, fuel and fiber. however, scarcity of land, water and energy accompanied by climate change means that to produce enough to meet the demands is getting increasingly challenging. today we must use every avenue from science and technology available to address these challenges. the natural process of symbiotic nitrogen fixation, whereby plants such as l ...201424786096
symbiotic activity of pea (pisum sativum) after application of nod factors under field conditions.growth and symbiotic activity of legumes are mediated by nod factors (lco, lipo-chitooligosaccharides). to assess the effects of application of nod factors on symbiotic activity and yield of pea, a two-year field experiment was conducted on a haplic luvisol developed from loess. nod factors were isolated from rhizobium leguminosarum bv. viciae strain gr09. pea seeds were treated with the nod factors (10⁻¹¹ m) or water (control) before planting. symbiotic activity was evaluated by measurements of ...201424786094
reduction of selenite to red elemental selenium by rhodopseudomonas palustris strain n.the trace metal selenium is in demand for health supplements to human and animal nutrition. we studied the reduction of selenite (seo₃⁻²) to red elemental selenium by rhodopseudomonas palustris strain n. this strain was cultured in a medium containing seo₃⁻² and the particles obtained from cultures were analyzed using transmission electron microscopy (tem), energy dispersive microanalysis (edx) and x ray diffraction analysis (xrd). our results showed the strain n could reduce seo₃⁻² to red eleme ...201424759917
diterpene synthases and their responsible cyclic natural products.this review provides an overview of diterpene synthases which were initially identified via genetic and/or biochemical means, traversing all organisms researched to date.201424858310
rnathermsw: direct temperature simulations for predicting the location of rna thermometers.the mechanism of rna thermometers is a subject of growing interest. also known as rna thermosensors, these temperature-sensitive segments of the mrna regulate gene expression by changing their secondary structure in response to temperature fluctuations. the detection of rna thermometers in various genes of interest is valuable as it could lead to the discovery of new thermometers participating in fundamental processes such as preferential translation during heat-shock. rnathermsw is a user-frien ...201424718440
a link between arabinose utilization and oxalotrophy in bradyrhizobium japonicum.rhizobia have a versatile catabolism that allows them to compete successfully with other microorganisms for nutrients in the soil and in the rhizosphere of their respective host plants. in this study, bradyrhizobium japonicum usda 110 was found to be able to utilize oxalate as the sole carbon source. a proteome analysis of cells grown in minimal medium containing arabinose suggested that oxalate oxidation extends the arabinose degradation branch via glycolaldehyde. a mutant of the key pathway ge ...201424463964
role of corynebacterium glutamicum spra encoding a serine protease in glxr-mediated global gene regulation.the global regulator glxr of corynebacterium glutamicum is involved in many cellular activities. considering its role, the glxr protein likely interacts with other proteins to obtain, maintain, and control its activity. to isolate proteins interacting with glxr, we used a two-hybrid system with glxr as the bait. subsequently, the partner, a subtilisin-like serine protease, was isolated from a c. glutamicum genomic library. unlike glxr, which showed constitutive expression, the expression of spra ...201424691519
bioinformatic approaches reveal metagenomic characterization of soil microbial community.as is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the earth. in recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. however, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. in the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, arctic soil ...201424691166
activation and inhibition of the receptor histidine kinase agrc occurs through opposite helical transduction motions.staphylococcus aureus virulence is regulated when secreted autoinducing peptides (aips) are recognized by a membrane-bound receptor histidine kinase (rhk), agrc. some aips are agonists of virulence gene expression, while others are antagonists. it is unclear how aip binding regulates agrc activity. here, we reconstitute an agrc family member, agrc-i, using nanometer-scale lipid bilayer discs. we show that agrc-i requires membranes rich in anionic lipids to function. the agonist, aip-i, binds agr ...201424656130
a novel chimeric avidin with increased thermal stability using dna shuffling.avidins are a family of proteins widely employed in biotechnology. we have previously shown that functional chimeric mutant proteins can be created from avidin and avidin-related protein 2 using a methodology combining random mutagenesis by recombination and selection by a tailored biopanning protocol (phage display). here, we report the crystal structure of one of the previously selected and characterized chimeric avidin forms, a/a2-1. the structure was solved at 1.8 å resolution and revealed t ...201424632863
effect of nitrate on nodule and root growth of soybean (glycine max (l.) merr.).the application of combined nitrogen, especially nitrate, to soybean plants is known to strongly inhibit nodule formation, growth and nitrogen fixation. in the present study, we measured the effects of supplying 5 mm nitrate on the growth of nodules, primary root, and lateral roots under light at 28 °c or dark at 18 °c conditions. photographs of the nodulated roots were periodically taken by a digital camera at 1-h intervals, and the size of the nodules was measured with newly developed computer ...201424633200
taxonomical and functional microbial community selection in soybean rhizosphere.this study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in amazon forest soils. we used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. our results showed a clear selection at b ...201424553468
structures of the puta peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site.proline utilization a (puta) proteins are bifunctional peripheral membrane flavoenzymes that catalyze the oxidation of l-proline to l-glutamate by the sequential activities of proline dehydrogenase and aldehyde dehydrogenase domains. located at the inner membrane of gram-negative bacteria, putas play a major role in energy metabolism by coupling the oxidation of proline imported from the environment to the reduction of membrane-associated quinones. here, we report seven crystal structures of the ...201424550478
cell growth inhibition upon deletion of four toxin-antitoxin loci from the megaplasmids of sinorhizobium meliloti.toxin and antitoxin (ta) gene pairs are addiction systems that are present in many microbial genomes. sinorhizobium meliloti is an n2-fixing bacterial symbiont of alfalfa and other leguminous plants, and its genome consists of three large replicons, a circular chromosome (3.7 mb) and the megaplasmids psyma (1.4 mb) and psymb (1.7 mb). s. meliloti carries 211 predicted type ii ta genes, each encoding a toxin or an antitoxin. we constructed defined deletion strains that collectively removed the en ...201424317400
the soil bacterial communities of south african fynbos riparian ecosystems invaded by australian acacia species.riparian ecosystem along rivers and streams are characterised by lateral and longitudinal ecological gradients and, as a result, harbour unique biodiversity. riparian ecosystems in the fynbos of the western cape, south africa, are characterised by seasonal dynamics, with summer droughts followed by high flows during winter. the unique hydrology and geomorphology of riparian ecosystems play an important role in shaping these ecosystems. the riparian vegetation in the western cape has, however, la ...201424475145
plant dependence on rhizobia for nitrogen influences induced plant defenses and herbivore performance.symbiotic rhizobia induce many changes in legumes that could affect aboveground interactions with herbivores. we explored how changing the intensity of bradyrhizobium japonicum, as modulated by soil nitrogen (n) levels, influenced the interaction between soybean (glycine max) and herbivores of different feeding guilds. when we employed a range of fertilizer applications to manipulate soil n, plants primarily dependent on rhizobia for n exhibited increased root nodulation and higher levels of fol ...201424451132
intracytoplasmic copper homeostasis controls cytochrome c oxidase production.copper is an essential micronutrient used as a metal cofactor by a variety of enzymes, including cytochrome c oxidase (cox). in all organisms from bacteria to humans, cellular availability and insertion of copper into target proteins are tightly controlled due to its toxicity. the major subunit of cox contains a copper atom that is required for its catalytic activity. previously, we identified ccoa (a member of major facilitator superfamily transporters) as a component required for cbb3-type cox ...201424425735
oxygen sensing strategies in mammals and bacteria.the ability to sense and adapt to changes in po2 is crucial for basic metabolism in most organisms, leading to elaborate pathways for sensing hypoxia (low po2). this review focuses on the mechanisms utilized by mammals and bacteria to sense hypoxia. while responses to acute hypoxia in mammalian tissues lead to altered vascular tension, the molecular mechanism of signal transduction is not well understood. in contrast, chronic hypoxia evokes cellular responses that lead to transcriptional changes ...201424468676
prediction of potential novel micrornas in soybean when in symbiosis.micrornas (mirnas) are small molecules, noncoding proteins that are involved in many biological processes, especially in plants; among these processes is nodulation in the legume. biological nitrogen fixation is a key process, with critical importance to the soybean crop. this study aimed to identify the potential of novel mirnas to act during the root nodulation process. we utilized a set of transcripts that were differentially expressed in soybean roots 10 days after inoculation with bradyrhiz ...201425366746
a single amino acid substitution affects the substrate specificity of the seryl-trna synthetase homologue.recently described and characterized bradyrhizobium japonicum glycine:[carrier protein] ligase 1 (bj gly:cp ligase 1), a homologue of methanogenic type seryl-trna synthetase (serrs) is an intriguing enzyme whose physiological role is not yet known. while aminoacyl-trna synthetases supply ribosome with amino acids for protein biosynthesis, this homologue transfers the activated amino acid to a specific carrier protein. despite remarkable structural similarity between the bj gly:cp ligase 1 and th ...201425272963
enzymatic preparation of optically pure (+)-2-azabicyclo[2.2.1]hept-5-en-3-one by (-)-γ-lactamase from bradyrhizobium japonicum usda 6.whole cells of bradyrhizobium japonicum usda 6 showed both (+)-γ-lactamase activity and (-)-γ-lactamase activity. insight into the genome of b. japonicum usda 6 revealed two potential γ-lactamases: a type i (+)-γ-lactamase and a (-)-γ-lactamase, making it the first strain to contain two totally different enantioselective lactamases. both recombinant enzymes could easily be used to prepare either optically pure (+)-γ-lactam ((+)-2-azabicyclo[2.2.1]hept-5-en-3-one) or optically pure (-)-γ-lactam ( ...201425240615
insilico model for prediction of lateral gene transfer in rhodopseudomonas paulistris.study of evolutionary phenomenon is of great interest to biologists in discovering the secrets of life. the presence of reticulation events due to lateral gene transfer (lgt) among species poses new challenges for such evolutionary studies. in this paper an attempt has been made to develop an insilico model to predict lgt in the rhodopseudomonas paulistris. neighbour joining method is employed to generate phylogenetic tree of 26 sequences of alphaproteobacteria and one sequence of cyanobacteria ...201425108459
increased expression of fe-chelatase leads to increased metabolic flux into heme and confers protection against photodynamically induced oxidative stress.fe-chelatase (fech, ec 4.99.1.1) inserts fe(2+) into protoporphyrin ix (proto ix) to form heme, which influences the flux through the tetrapyrrole biosynthetic pathway as well as fundamental cellular processes. in transgenic rice (oryza sativa), the ectopic expression of bradyrhizobium japonicum fech protein in cytosol results in a substantial increase of fech activity compared to wild-type (wt) rice and an increasing level of heme. interestingly, the transgenic rice plants showed resistance to ...201425037078
the nitrate-sensing nasst system regulates nitrous oxide reductase and periplasmic nitrate reductase in bradyrhizobium japonicum.the soybean endosymbiont bradyrhizobium japonicum is able to scavenge the greenhouse gas n2o through the n2o reductase (nos). in previous research, n2o emission from soybean rhizosphere was mitigated by b. japonicum nos(++) strains (mutants with increased nos activity). here, we report the mechanism underlying the nos(++) phenotype. comparative analysis of nos(++) mutant genomes showed that mutation of bll4572 resulted in nos(++) phenotype. bll4572 encodes nass, the nitrate (no3(-))-sensor of th ...201424947409
[influence of bradyrhizobium japonicum ykm b-6035 inoculation on the microstructure of soybean rhizosphere cenosis and photosynthetic apparatus].development of bradyrhizobium japonicum ykm b-6035 bacterial cells in suspension culture, aseptic soil and rhizosphere of soybean plants inoculated by nodulate bacteria were investigated. the increase of bacteria number on the surface of main root and rhizosphere was determined in nodulated soybean plants. photosynthetic apparatus of inoculated plants increased due to morphological characteristics: the leaf blade area and width of mezophyll palisade and spongy layers. morphological changes in th ...201424800509
genomic analysis of cyclic-di-gmp-related genes in rhizobial type strains and functional analysis in rhizobium etli.rhizobia are soil bacteria that can fix nitrogen in symbiosis with leguminous plants or exist free living in the rhizosphere. crucial to their complex lifestyle is the ability to sense and respond to diverse environmental stimuli, requiring elaborate signaling pathways. in the majority of bacteria, the nucleotide-based second messenger cyclic diguanosine monophosphate (c-di-gmp) is involved in signal transduction. surprisingly, little is known about the importance of c-di-gmp signaling in rhizob ...201424728599
soybean ureases, but not that of bradyrhizobium japonicum, are involved in the process of soybean root nodulation.ureases are abundant in plants, bacteria, and in the soil, but their role in signaling between soybean and soil microorganisms has not been investigated. the bacterium bradyrhizobium japonicum forms nitrogen-fixing nodules on soybean roots. here, we evaluated the role(s) of ureases in the process of soybean nodulation. chemotaxis assays demonstrated that soybean and jack bean ureases were more chemotactic toward bacterial cells than the corresponding plant lectins. the eu1-a,eu4 soybean, deficie ...201424716625
genetic diversity patterns and functional traits of bradyrhizobium strains associated with pterocarpus officinalis jacq. in caribbean islands and amazonian forest (french guiana).pterocarpus officinalis jacq. is a legume tree native to the caribbean islands and south america growing as a dominant species in swamp forests. to analyze (i) the genetic diversity and (ii) the symbiotic properties of its associated nitrogen-fixing soil bacteria, root nodules were collected from p. officinalis distributed in 16 forest sites of the caribbean islands and french guiana. the sequencing of the 16s-23s ribosomal rna intergenic spacer region (its) showed that all bacteria belonged to ...201424595907
inactivation of the lpcc gene alters surface-related properties and symbiotic capability of bradyrhizobium japonicum.we investigated the role of the bradyrhizobium japonicum lpcc gene, encoding a mannosyl transferase, involved in the lipopolysaccharide (lps) biosynthesis. the inactivation of the lpcc gene considerably altered the lps structure and the cell surface properties. lps analysis showed that the lpcc mutant js715 had an abnormal lps structure deficient in o-antigen. the cell surface hydrophobicity increased approximately threefold in js715 compared to the wild type. the increased cell surface hydropho ...201424521100
gibberellin oxidase activities in bradyrhizobium japonicum bacteroids.bradyrhizobium japonicum bacteroids isolated from root nodules of soybean (glycine max.) plants converted the gibberellin (ga) precursor [(14)c1]ga12 into several products identified by combined gas chromatography-mass spectrometry as [(14)c1]ga24, [(14)c1]ga9, [(14)c1]ga15, ga9 17-nor-16-one and unidentified products. the oxidation of ga12, catalyzed by the ga 20-oxidase, was present in symbiotic bacteroids from plants around flowering, but not in bacteroids from plants at either an early veget ...201424378220
homology modeling and docking studies of bjgl, a novel (+) gamma-lactamase from bradyrhizobium japonicum.(+) gamma-lactamases are enantioselective hydrolysis enzymes that can be used to produce optically pure (-) gamma-lactam, an important pharmaceutical intermediate for the anti-aids drug abacavir. in this study, homology modeling and molecular dynamic simulation studies of a 3d homology model of bjgl, a novel (+) gamma-lactamase from bradyrhizobium japonicum, were constructed and refined. the specific substrate (+) gamma-lactam and its enantiomer (-) gamma-lactam which can not be hydrolyzed was d ...201424215997
a new pgpr co-inoculated with bradyrhizobium japonicum enhances soybean nodulation.a new pgpr (plant growth promoting rhizobacteria) strain was isolated from soybean seeds and the bacterial mechanisms related to plant growth promotion were evaluated and characterized. isolates were genotypically compared and identified by amplification of partial sequences of 16s dnar as bacillus amyloliquefaciens strain ll2012. isolates were grown until exponential growth phase to evaluate the atmospheric nitrogen fixation, enzymatic activities, phosphate solubilization, siderophores and phyt ...201424280513
cytisus villosus from northeastern algeria is nodulated by genetically diverse bradyrhizobium strains.fifty-one rhizobial strains isolated from root nodules of cytisus villosus growing in northeastern algeria were characterized by genomic and phenotypic analyses. isolates were grouped into sixteen different patterns by pcr-rapd. the phylogenetic status of one representative isolate from each pattern was examined by multilocus sequence analyses of four housekeeping genes (16s rrna, glnii, reca, and atpd) and one symbiotic gene (nodc). analysis of 16s rrna gene sequences showed that all the isolat ...201424756908
changes in bacterial co2 fixation with depth in agricultural soils.soils were incubated continuously in an atmosphere of (14)co2 and the distribution of labeled c into soil organic carbon ((14)c-soc) was determined at 0-1, 1-5, and 5-17 cm down the profile. significant amounts of (14)c-soc were measured in paddy soils with a mean of 1,180.6 ± 105.2 mg kg(-1) at 0-1 cm and 135.3 ± 47.1 mg kg(-1) at 1-5 cm. this accounted for 5.9 ± 0.7% and 0.7 ± 0.2%, respectively, of the total soil organic carbon at these depths. in the upland soils, the mean (14)c-soc concentr ...201423989975
average oxidation state of carbon in proteins.the formal oxidation state of carbon atoms in organic molecules depends on the covalent structure. in proteins, the average oxidation state of carbon (z(c)) can be calculated as an elemental ratio from the chemical formula. to investigate oxidation-reduction (redox) patterns, groups of proteins from different subcellular locations and phylogenetic groups were selected for comparison. extracellular proteins of yeast have a relatively high oxidation state of carbon, corresponding with oxidizing co ...201425165594
nitrogen-fixing rhizobial strains isolated from common bean seeds: phylogeny, physiology, and genome analysis.rhizobial bacteria are commonly found in soil but also establish symbiotic relationships with legumes, inhabiting the root nodules, where they fix nitrogen. endophytic rhizobia have also been reported in the roots and stems of legumes and other plants. we isolated several rhizobial strains from the nodules of noninoculated bean plants and looked for their provenance in the interiors of the seeds. nine isolates were obtained, covering most known bean symbiont species, which belong to the rhizobiu ...201425002426
riboregulation in plant-associated α-proteobacteria.the symbiotic α-rhizobia sinorhizobium meliloti, bradyrhizobium japonicum, rhizobium etli and the related plant pathogen agrobacterium tumefaciens are important model organisms for studying plant-microbe interactions. these metabolically versatile soil bacteria are characterized by complex lifestyles and large genomes. here we summarize the recent knowledge on their small non-coding rnas (srnas) including conservation, function, and interaction of the srnas with the rna chaperone hfq. in each of ...201425003187
the complete genome of burkholderia phenoliruptrix strain br3459a, a symbiont of mimosa flocculosa: highlighting the coexistence of symbiotic and pathogenic genes.burkholderia species play an important ecological role related to xenobiosis, the promotion of plant growth, the biocontrol of agricultural diseases, and symbiotic and non-symbiotic biological nitrogen fixation. here, we highlight our study as providing the first complete genome of a symbiotic strain of b. phenoliruptrix, br3459a (=cla1), which was originally isolated in brazil from nodules of mimosa flocculosa and is effective in fixing nitrogen in association with this leguminous species.201424972629
phenotypic characterization of astragalus glycyphyllos symbionts and their phylogeny based on the 16s rdna sequences and rflp of 16s rrna gene.in this study, the nitrogen fixing astragalus glycyphyllos symbionts were characterized by phenotypic properties, restriction fragment length polymorphism (rflp), and sequences of 16s rdna. the generation time of a. glycyphyllos rhizobia in yeast extract mannitol medium was in the range 4-6 h. the studied isolates exhibited a low resistance to antibiotics, a moderate tolerance to nacl, assimilated di- and trisaccharides, and produced acid in medium containing mannitol as a sole carbon source. in ...201424710996
the growth of steroidobacter agariperforans sp. nov., a novel agar-degrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to rhizobiales.an agar-degrading bacterium was isolated from soil collected in a vegetable cropping field. the growth of this isolate was enhanced by supplying culture supernatants of bacteria belonging to the order rhizobiales. phylogenetic analysis based on 16s rrna gene sequences indicated the novel bacterium, strain ka5-b(t), belonged to the genus steroidobacter in gammaproteobacteria, but differed from its closest relative, steroidobacter denitrificans fs(t), at the species level with 96.5% similarity. st ...201424621511
a proteomic approach of bradyrhizobium/aeschynomene root and stem symbioses reveals the importance of the fixa locus for symbiosis.rhizobia are soil bacteria that are able to form symbiosis with plant hosts of the legume family. these associations result in the formation of organs, called nodules in which bacteria fix atmospheric nitrogen to the benefit of the plant. most of our knowledge on the metabolism and the physiology of the bacteria during symbiosis derives from studying roots nodules of terrestrial plants. here we used a proteomics approach to investigate the bacterial physiology of photosynthetic bradyrhizobium sp ...201424590127
detecting nitrous oxide reductase (nosz) genes in soil metagenomes: method development and implications for the nitrogen cycle.microbial activities in soils, such as (incomplete) denitrification, represent major sources of nitrous oxide (n2o), a potent greenhouse gas. the key enzyme for mitigating n2o emissions is nosz, which catalyzes n2o reduction to n2. we recently described "atypical" functional nosz proteins encoded by both denitrifiers and nondenitrifiers, which were missed in previous environmental surveys (r. a. sanford et al., proc. natl. acad. sci. u. s. a. 109:19709-19714, 2012, doi:10.1073/pnas.1211238109). ...201424895307
identification of 9α-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid in steroid degradation by comamonas testosteroni ta441 and its conversion to the corresponding 6-en-5-oyl coenzyme a (coa) involving open reading frame 28 (orf28)- and orf30-encoded acyl-coa dehydrogenases.comamonas testosteroni ta441 degrades steroids via aromatization and meta-cleavage of the a ring, followed by hydrolysis, and produces 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid as an intermediate compound. herein, we identify a new intermediate compound, 9α-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid. open reading frame 28 (orf28)- and orf30-encoded acyl coenzyme a (acyl-coa) dehydrogenase was shown to convert the coa ester of 9α-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandros ...201425092028
molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis.the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ...201425492513
molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis.the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ...201425492513
magnesium-dependent processes are targets of bacterial manganese toxicity.a bradyrhizobium japonicum mutant defective in the gene encoding the high-affinity mn(2+) transporter mnth has a severe growth phenotype under manganese limitation. here, we isolated suppressor mutants of an mnth strain that grew under manganese limitation, and activities of high-affinity mn(2+) transport and mn(2+) -dependent enzymes were partially rescued. the suppressor strains harbour gain-of-function mutations in the gene encoding the mg(2+) channel mgte. the mgte variants likely allow mn(2 ...201424975873
a putative bifunctional histidine kinase/phosphatase of the hwe family exerts positive and negative control on the sinorhizobium meliloti general stress response.the ecfg-type sigma factor rpoe2 is the regulator of the general stress response in sinorhizobium meliloti. rpoe2 activity is negatively regulated by two nepr-type anti-sigma factors (rsia1/a2), themselves under the control of two anti-anti-sigma factors (rsib1/b2) belonging to the phyr family of response regulators. the current model of rpoe2 activation suggests that in response to stress, rsib1/b2 are activated by phosphorylation of an aspartate residue in their receiver domain. once activated ...201424794560
the global response regulator regr controls expression of denitrification genes in bradyrhizobium japonicum.bradyrhizobium japonicum regsr regulatory proteins belong to the family of two-component regulatory systems, and orthologs are present in many proteobacteria where they globally control gene expression mostly in a redox-responsive manner. in this work, we have performed a transcriptional profiling of wild-type and regr mutant cells grown under anoxic denitrifying conditions. the comparative analyses of wild-type and regr strains revealed that almost 620 genes induced in the wild type under denit ...201424949739
differential control of bradyrhizobium japonicum iron stimulon genes through variable affinity of the iron response regulator (irr) for target gene promoters and selective loss of activator function.bradyrhizobium japonicum irr is a conditionally stable transcriptional activator and repressor that accumulates in cells under iron-limited, manganese-replete conditions, but degrades in a haem-dependent manner under high iron conditions, manganese limitation or upon exposure to h2 o2 . here, we identified irr-regulated genes that were relatively unresponsive to factors that promote irr degradation. the promoters of those genes bound irr with at least 200-fold greater affinity than promoters of ...201424646221
rna-seq and microarrays analyses reveal global differential transcriptomes of mesorhizobium huakuii 7653r between bacteroids and free-living cells.mesorhizobium huakuii 7653r occurs either in nitrogen-fixing symbiosis with its host plant, astragalus sinicus, or free-living in the soil. the m. huakuii 7653r genome has recently been sequenced. to better understand the complex biochemical and developmental changes that occur in 7653r during bacteroid development, rna-seq and microarrays were used to investigate the differential transcriptomes of 7653r bacteroids and free-living cells. the two approaches identified several thousand differentia ...201424695521
secondary bacterial flagellar system improves bacterial spreading by increasing the directional persistence of swimming.as numerous bacterial species, shewanella putrefaciens cn-32 possesses a complete secondary flagellar system. a significant subpopulation of cn-32 cells induces expression of the secondary system under planktonic conditions, resulting in formation of one, sometimes two, filaments at lateral positions in addition to the primary polar flagellum. mutant analysis revealed that the single chemotaxis system primarily or even exclusively addresses the main polar flagellar system. cells with secondary f ...201425049414
cytochrome c biogenesis system i: an intricate process catalyzed by a maturase supercomplex?cytochromes c are ubiquitous heme proteins that are found in most living organisms and are essential for various energy production pathways as well as other cellular processes. their biosynthesis relies on a complex post-translational process, called cytochrome c biogenesis, responsible for the formation of stereo-specific thioether bonds between the vinyl groups of heme b (protoporphyrin ix-fe) and the thiol groups of apocytochromes c heme-binding site (c1xxc2h) cysteine residues. in some organ ...201424631867
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 ...201425566225
enzymatic characterization and in vivo function of five terminal oxidases in pseudomonas aeruginosa.the ubiquitous opportunistic pathogen pseudomonas aeruginosa has five aerobic terminal oxidases: bo(3)-type quinol oxidase (cyo), cyanide-insensitive oxidase (cio), aa3-type cytochrome c oxidase (aa3), and two cbb(3)-type cytochrome c oxidases (cbb(3)-1and cbb(3)-2). these terminal oxidases are differentially regulated under various growth conditions and are thought to contribute to the survival of this microorganism in a wide variety of environmental niches. here, we constructed multiple mutant ...201425182500
the genome of the intracellular bacterium of the coastal bivalve, solemya velum: a blueprint for thriving in and out of symbiosis.symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. these associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of ch ...201425342549
metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. 201424758379
radical s-adenosylmethionine enzymes. 201424476342
molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen ix.tetrapyrroles such as heme and chlorophyll are essential for biological processes, including oxygenation, respiration, and photosynthesis. in the tetrapyrrole biosynthesis pathway, protoporphyrinogen ix oxidase (protox) catalyzes the formation of protoporphyrin ix, the last common intermediate for the biosynthesis of heme and chlorophyll. three nonhomologous isofunctional enzymes, hemg, hemj, and hemy, for protox have been identified. to reveal the distribution and evolution of the three protox ...201425108393
evolutionary insights about bacterial glxrs from whole genome analyses: is glurs2 a chimera?evolutionary histories of glutamyl-trna synthetase (glurs) and glutaminyl-trna synthetase (glnrs) in bacteria are convoluted. after the divergence of eubacteria and eukarya, bacterial glurs glutamylated both trnagln and trnaglu until glnrs appeared by horizontal gene transfer (hgt) from eukaryotes or a duplicate copy of glurs (glurs2) that only glutamylates trnagln appeared. the current understanding is based on limited sequence data and not always compatible with available experimental results. ...201424521160
fha interaction with phosphothreonine of tssl activates type vi secretion in agrobacterium tumefaciens.the type vi secretion system (t6ss) is a widespread protein secretion system found in many gram-negative bacteria. t6sss are highly regulated by various regulatory systems at multiple levels, including post-translational regulation via threonine (thr) phosphorylation. the ser/thr protein kinase ppka is responsible for this thr phosphorylation regulation, and the forkhead-associated (fha) domain-containing fha-family protein is the sole t6ss phosphorylation substrate identified to date. here we d ...201424626341
release of nonstop ribosomes is essential.bacterial ribosomes frequently translate to the 3' end of an mrna without terminating at a stop codon. almost all bacteria use the transfer-messenger rna (tmrna)-based trans-translation pathway to release these "nonstop" ribosomes and maintain protein synthesis capacity. trans-translation is essential in some species, but in others, such as caulobacter crescentus, trans-translation can be inactivated. to determine why trans-translation is dispensable in c. crescentus, a tn-seq screen was used to ...201425389176
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