Publications

uncovering the transmembrane metal binding site of the novel bacterial major facilitator superfamily-type copper importer ccoa.	uptake and trafficking of metals and their delivery to their respective metalloproteins are important processes. cells need precise control of each step to avoid exposure to excessive metal concentrations and their harmful consequences. copper (cu) is a required micronutrient used as a cofactor in proteins. however, in large amounts, it can induce oxidative damage; hence, cu homeostasis is indispensable for cell survival. biogenesis of respiratory heme-cu oxygen (hco) reductases includes inserti ...	2016	26787831
the effect of root exudate 7,4'-dihydroxyflavone and naringenin on soil bacterial community structure.	our goal was to investigate how root exudate flavonoids influence the soil bacterial community structure and to identify members of the community that change their relative abundance in response to flavonoid exudation. using a model system that approximates flavonoid exudation of medicago sativa roots, we treated a soil with 7,4'-dihydroxyflavone and naringenin in two separate experiments using three different rates: medium (equivalent to the exudation rate of 7,4'-dihydroxyflavone from m. sativ ...	2016	26752410
the role of flavonoids in nodulation host-range specificity: an update.	flavonoids are crucial signaling molecules in the symbiosis between legumes and their nitrogen-fixing symbionts, the rhizobia. the primary function of flavonoids in the interaction is to induce transcription of the genes for biosynthesis of the rhizobial signaling molecules called nod factors, which are perceived by the plant to allow symbiotic infection of the root. many legumes produce specific flavonoids that only induce nod factor production in homologous rhizobia, and therefore act as impor ...	2016	27529286
reactive oxygen species and nitric oxide control early steps of the legume - rhizobium symbiotic interaction.	the symbiotic interaction between legumes and nitrogen-fixing rhizobium bacteria leads to the formation of a new organ, the nodule. early steps of the interaction are characterized by the production of bacterial nod factors, the reorientation of root-hair tip growth, the formation of an infection thread (it) in the root hair, and the induction of cell division in inner cortical cells of the root, leading to a nodule primordium formation. reactive oxygen species (ros) and nitric oxide (no) have b ...	2016	27092165
proclat, a new bioinformatics tool for in silico protein reclassification: case study of drab, a protein coded from the dratgb operon in azospirillum brasilense.	azopirillum brasilense is a plant-growth promoting nitrogen-fixing bacteria that is used as bio-fertilizer in agriculture. since nitrogen fixation has a high-energy demand, the reduction of n2 to nh4(+) by nitrogenase occurs only under limiting conditions of nh4(+) and o2. moreover, the synthesis and activity of nitrogenase is highly regulated to prevent energy waste. in a. brasilense nitrogenase activity is regulated by the products of drag and drat. the product of the drab gene, located downst ...	2016	28105917
nitrous oxide reduction kinetics distinguish bacteria harboring clade i nosz from those harboring clade ii nosz.	bacteria capable of reduction of nitrous oxide (n2o) to n2 separate into clade i and clade ii organisms on the basis of nos operon structures and nosz sequence features. to explore the possible ecological consequences of distinct nos clusters, the growth of bacterial isolates with either clade i (pseudomonas stutzeri strain dcp-ps1, shewanella loihica strain pv-4) or clade ii (dechloromonas aromatica strain rcb, anaeromyxobacter dehalogenans strain 2cp-c) nosz with n2o was examined. growth curve ...	2016	27084012
molecular evidence for sediment nitrogen fixation in a temperate new england estuary.	primary production in coastal waters is generally nitrogen (n) limited with denitrification outpacing nitrogen fixation (n2-fixation). however, recent work suggests that we have potentially underestimated the importance of heterotrophic sediment n2-fixation in marine ecosystems. we used clone libraries to examine transcript diversity of nifh (a gene associated with n2-fixation) in sediments at three sites in a temperate new england estuary (waquoit bay, massachusetts, usa) and compared our resul ...	2016	26977375
multidrug efflux pumps at the crossroad between antibiotic resistance and bacterial virulence.	multidrug efflux pumps can be involved in bacterial resistance to antibiotics at different levels. some efflux pumps are constitutively expressed at low levels and contribute to intrinsic resistance. in addition, their overexpression may allow higher levels of resistance. this overexpression can be transient, in the presence of an effector (phenotypic resistance), or constitutive when mutants in the regulatory elements of the expression of efflux pumps are selected (acquired resistance). efflux ...	2016	27708632
nod factor effects on root hair-specific transcriptome of medicago truncatula: focus on plasma membrane transport systems and reactive oxygen species networks.	root hairs are involved in water and nutrient uptake, and thereby in plant autotrophy. in legumes, they also play a crucial role in establishment of rhizobial symbiosis. to obtain a holistic view of medicago truncatula genes expressed in root hairs and of their regulation during the first hours of the engagement in rhizobial symbiotic interaction, a high throughput rna sequencing on isolated root hairs from roots challenged or not with lipochitooligosaccharides nod factors (nf) for 4 or 20 h was ...	2016	27375649
vascular sap proteomics: providing insight into long-distance signaling during stress.	the plant vascular system, composed of the xylem and phloem, is important for the transport of water, mineral nutrients, and photosynthate throughout the plant body. the vasculature is also the primary means by which developmental and stress signals move from one organ to another. due to practical and technological limitations, proteomics analysis of xylem and phloem sap has been understudied in comparison to accessible sample types such as leaves and roots. however, recent advances in sample co ...	2016	27242852
decipher the molecular response of plant single cell types to environmental stresses.	the analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single ...	2016	27088086
site-directed mutagenesis from arg195 to his of a microalgal putatively chloroplastidial glycerol-3-phosphate acyltransferase causes an increase in phospholipid levels in yeast.	to analyze the contribution of glycerol-3-phosphate acyltransferase (gpat) to the first acylation of glycerol-3-phosphate (g-3-p), the present study focused on a functional analysis of the gpat gene from lobosphaera incisa (designated as ligpat). a full-length cdna of ligpat consisting of a 1,305-bp orf, a 1,652-bp 5'-utr, and a 354-bp 3'-utr, was cloned. the orf encoded a 434-amino acid peptide, of which 63 residues at the n-terminus defined a chloroplast transit peptide. multiple sequence alig ...	2016	27014309
genome-wide transcription start site mapping of bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation.	differential rna-sequencing (drna-seq) is indispensable for determination of primary transcriptomes. however, using drna-seq data to map transcriptional start sites (tsss) and promoters genome-wide is a bioinformatics challenge. we performed drna-seq of bradyrhizobium japonicum usda 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map tsss and promoters.	2016	27107716
development of a microemulsion formulation for antimicrobial seca inhibitors.	in our previous study, we have identified five antimicrobial small molecules via structure based design, which inhibit seca of candidatus liberibacter asiaticus (las). seca is a critical protein translocase atpase subunit and is involved in pre-protein translocation across and integration into the cellular membrane in bacteria. in this study, eleven compounds were identified using similarity search method based on the five lead seca inhibitors identified previously. the identified seca inhibitor ...	2016	26963811
hydrogen overproducing nitrogenases obtained by random mutagenesis and high-throughput screening.	when produced biologically, especially by photosynthetic organisms, hydrogen gas (h2) is arguably the cleanest fuel available. an important limitation to the discovery or synthesis of better h2-producing enzymes is the absence of methods for the high-throughput screening of h2 production in biological systems. here, we re-engineered the natural h2 sensing system of rhodobacter capsulatus to direct the emission of lacz-dependent fluorescence in response to nitrogenase-produced h2. a lacz gene was ...	2016	27910898
function of the borrelia burgdorferi ftsh homolog is essential for viability both in vitro and in vivo and independent of hflk/c.	in many bacteria, the ftsh protease and its modulators, hflk and hflc, form a large protein complex that contributes to both membrane protein quality control and regulation of the cellular response to environmental stress. both activities are crucial to the lyme disease pathogen borrelia burgdorferi, which depends on membrane functions, such as motility, protein transport, and cell signaling, to respond to rapid changes in its environment. using an inducible system, we demonstrate that ftsh prod ...	2016	27094329
cyclic di-gmp regulates multiple cellular functions in the symbiotic alphaproteobacterium sinorhizobium meliloti.	sinorhizobium meliloti undergoes major lifestyle changes between planktonic states, biofilm formation, and symbiosis with leguminous plant hosts. in many bacteria, the second messenger 3',5'-cyclic di-gmp (c-di-gmp, or cdg) promotes a sessile lifestyle by regulating a plethora of processes involved in biofilm formation, including motility and biosynthesis of exopolysaccharides (eps). here, we systematically investigated the role of cdg in s. meliloti rm2011 encoding 22 proteins putatively associ ...	2016	26574513
the novel regulatory ncrna, nfis, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifk mrna in pseudomonas stutzeri a1501.	unlike most pseudomonas, the root-associated bacterium pseudomonas stutzeri a1501 fixes nitrogen after the horizontal acquisition of a nitrogen-fixing (nif) island. a genome-wide search for small noncoding rnas (ncrnas) in p. stutzeri a1501 identified the novel p. stutzeri-specific ncrna nfis in the core genome, whose synthesis was significantly induced under nitrogen fixation or sorbitol stress conditions. the expression of nfis was rna chaperone hfq-dependent and activated by the sigma factor ...	2016	27407147
conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone.	protein-protein interactions are fundamental for the proper functioning of the cell. as a result, protein interaction surfaces are subject to strong evolutionary constraints. recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. so far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compi ...	2016	27965389
plant root-microbe communication in shaping root microbiomes.	a growing body of research is highlighting the impacts root-associated microbial communities can have on plant health and development. these impacts can include changes in yield quantity and quality, timing of key developmental stages and tolerance of biotic and abiotic stresses. with such a range of effects it is clear that understanding the factors that contribute to a plant-beneficial root microbiome may prove advantageous. increasing demands for food by a growing human population increases t ...	2016	26729479
establishing a role for bacterial cellulose in environmental interactions: lessons learned from diverse biofilm-producing proteobacteria.	bacterial cellulose (bc) serves as a molecular glue to facilitate intra- and inter-domain interactions in nature. biosynthesis of bc-containing biofilms occurs in a variety of proteobacteria that inhabit diverse ecological niches. the enzymatic and regulatory systems responsible for the polymerization, exportation, and regulation of bc are equally as diverse. though the magnitude and environmental consequences of bc production are species-specific, the common role of bc-containing biofilms is to ...	2015	26635751
maize growth promotion by inoculation with azospirillum brasilense and metabolites of rhizobium tropici enriched on lipo-chitooligosaccharides (lcos).	there is an increasing interest in the development and use of inoculants carrying plant growth-promoting bacteria (pgpb) in crops of agronomic interest. the great majority of the inoculants commercialized worldwide contain rhizobia for legume crops, but the use of pgpb as azospirillum spp. for non-legume is expanding, as well as of inoculants combining microorganisms and microbial metabolites. in this study we evaluated the effects of inoculants containing azospirillum brasilense with or without ...	2015	26567001
characterization of flavin-containing opine dehydrogenase from bacteria.	opines, in particular nopaline and octopine, are specific compounds found in crown gall tumor tissues induced by infections with agrobacterium species, and are synthesized by well-studied nad(p)h-dependent dehydrogenases (synthases), which catalyze the reductive condensation of α-ketoglutarate or pyruvate with l-arginine. the corresponding genes are transferred into plant cells via a tumor-inducing (ti) plasmid. in addition to the reverse oxidative reaction(s), the genes noxb-noxa and ooxb-ooxa ...	2015	26382958
rhizosphere ecology of lumichrome and riboflavin, two bacterial signal molecules eliciting developmental changes in plants.	lumichrome and riboflavin are novel molecules from rhizobial exudates that stimulate plant growth. reported studies have revealed major developmental changes elicited by lumichrome at very low nanomolar concentrations (5 nm) in plants, which include early initiation of trifoliate leaves, expansion of unifoliate and trifoliate leaves, increased stem elongation and leaf area, and consequently greater biomass accumulation in monocots and dicots. but higher lumichrome concentration (50 nm) depressed ...	2015	26442016
effect of point mutations on herbaspirillum seropedicae nifa activity.	nifa is the transcriptional activator of the nif genes in proteobacteria. it is usually regulated by nitrogen and oxygen, allowing biological nitrogen fixation to occur under appropriate conditions. nifa proteins have a typical three-domain structure, including a regulatory n-terminal gaf domain, which is involved in control by fixed nitrogen and not strictly required for activity, a catalytic aaa+ central domain, which catalyzes open complex formation, and a c-terminal domain involved in dna-bi ...	2015	26176311
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
the polar and lateral flagella from plesiomonas shigelloides are glycosylated with legionaminic acid.	plesiomonas shigelloides is the unique member of the enterobacteriaceae family able to produce polar flagella when grow in liquid medium and lateral flagella when grown in solid or semisolid media. in this study on p. shigelloides 302-73 strain, we found two different gene clusters, one exclusively for the lateral flagella biosynthesis and the other one containing the biosynthetic polar flagella genes with additional putative glycosylation genes. p. shigelloides is the first enterobacteriaceae w ...	2015	26167161
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
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
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
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
pseudomonas induces salinity tolerance in cotton (gossypium hirsutum) and resistance to fusarium root rot through the modulation of indole-3-acetic acid.	abiotic stresses cause changes in the balance of phytohormones in plants and result in inhibited root growth and an increase in the susceptibility of plants to root rot disease. the aim of this work was to ascertain whether microbial indole-3-acetic acid (iaa) plays a role in the regulation of root growth and microbially mediated control of root rot of cotton caused by fusarium solani. seed germination and seedling growth were improved by both nacl and mg2so4 (100 mm) solutions when treated with ...	2015	26587006
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
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
the contribution of co-reference resolution to supervised relation detection between bacteria and biotopes entities.	the acquisition of knowledge about relations between bacteria and their locations (habitats and geographical locations) in short texts about bacteria, as defined in the bionlp-st 2013 bacteria biotope task, depends on the detection of co-reference links between mentions of entities of each of these three types. to our knowledge, no participant in this task has investigated this aspect of the situation. the present work specifically addresses issues raised by this situation: (i) how to detect the ...	2015	26201352
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
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
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
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
perspective for aquaponic systems: "omic" technologies for microbial community analysis.	aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. in this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. the nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. in this particular field, the microbial research, the "omic" technologies will allow a broader scope of studies about a cu ...	2015	26509157
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
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
signal transduction in light-oxygen-voltage receptors lacking the adduct-forming cysteine residue.	light-oxygen-voltage (lov) receptors sense blue light through the photochemical generation of a covalent adduct between a flavin-nucleotide chromophore and a strictly conserved cysteine residue. here we show that, after cysteine removal, the circadian-clock lov-protein vivid still undergoes light-induced dimerization and signalling because of flavin photoreduction to the neutral semiquinone (nsq). similarly, photoreduction of the engineered lov histidine kinase yf1 to the nsq modulates activity ...	2015	26648256
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
rj4, a gene controlling nodulation specificity in soybeans, encodes a thaumatin-like protein but not the one previously reported.	rj4 is a dominant gene in soybeans (glycine max) that restricts nodulation by many strains of bradyrhizobium elkanii. the soybean-b. elkanii symbiosis has a low nitrogen-fixation efficiency, but b. elkanii strains are highly competitive for nodulation; thus, cultivars harboring an rj4 allele are considered favorable. cloning the rj4 gene is the first step in understanding the molecular basis of rj4-mediated nodulation restriction and facilitates the development of molecular tools for genetic imp ...	2015	26582727
rj4, a gene controlling nodulation specificity in soybeans, encodes a thaumatin-like protein but not the one previously reported.	rj4 is a dominant gene in soybeans (glycine max) that restricts nodulation by many strains of bradyrhizobium elkanii. the soybean-b. elkanii symbiosis has a low nitrogen-fixation efficiency, but b. elkanii strains are highly competitive for nodulation; thus, cultivars harboring an rj4 allele are considered favorable. cloning the rj4 gene is the first step in understanding the molecular basis of rj4-mediated nodulation restriction and facilitates the development of molecular tools for genetic imp ...	2015	26582727
phosphorylation-dependent regulation of g-protein cycle during nodule formation in soybean.	signaling pathways mediated by heterotrimeric g-protein complexes comprising gα, gβ, and gγ subunits and their regulatory rgs (regulator of g-protein signaling) protein are conserved in all eukaryotes. we have shown that the specific gβ and gγ proteins of a soybean (glycine max) heterotrimeric g-protein complex are involved in regulation of nodulation. we now demonstrate the role of nod factor receptor 1 (nfr1)-mediated phosphorylation in regulation of the g-protein cycle during nodulation in so ...	2015	26498905
a jaz protein in astragalus sinicus interacts with a leghemoglobin through the tify domain and is involved in nodule development and nitrogen fixation.	leghemoglobins (lbs) play an important role in legumes-rhizobia symbiosis. lbs bind o2 and protect nitrogenase activity from damage by o2 in nodules, therefore, they are regarded as a marker of active nitrogen fixation in nodules. additionally, lbs are involved in the nitric oxide (no) signaling pathway, acting as a no scavenger during nodule development and nitrogen fixation. however, regulators responsible for lb expression and modulation of lb activity have not been characterized. in our prev ...	2015	26460857
a novel sucrose-regulatory mads-box transcription factor gmnmhc5 promotes root development and nodulation in soybean (glycine max [l.] merr.).	the mads-box protein family includes many transcription factors that have a conserved dna-binding mads-box domain. the proteins in this family were originally recognized to play prominent roles in floral development. recent findings, especially with regard to the regulatory roles of the agl17 subfamily in root development, have greatly broadened their known functions. in this study, a gene from soybean (glycine max [l.] merr.), gmnmhc5, was cloned from the zigongdongdou cultivar and identified a ...	2015	26404246
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
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
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
transcriptome profiling of the endophyte burkholderia phytofirmans psjn indicates sensing of the plant environment and drought stress.	it is widely accepted that bacterial endophytes actively colonize plants, interact with their host, and frequently show beneficial effects on plant growth and health. however, the mechanisms of plant-endophyte communication and bacterial adaption to the plant environment are still poorly understood. here, whole-transcriptome sequencing of b. phytofirmans psjn colonizing potato (solanum tuberosum l.) plants was used to analyze in planta gene activity and the response of strain psjn to plant stres ...	2015	26350963
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
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
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
identification and characterization of a novel gentisate 1,2-dioxygenase gene from a halophilic martelella strain.	halophilic martelella strain ad-3, isolated from highly saline petroleum-contaminated soil, can efficiently degrade polycyclic aromatic hydrocarbons (pahs), such as phenanthrene and anthracene, in 3-5% salinity. gentisic acid is a key intermediate in the microbial degradation of pah compounds. however, there is little information on pah degradation by moderately halophilic bacteria. in this study, a 1,077-bp long gene encoding gentisate 1,2-dioxygenase (gdo) from a halophilic martelella strain a ...	2015	26394696
secretion systems and signal exchange between nitrogen-fixing rhizobia and legumes.	the formation of symbiotic nitrogen-fixing nodules on the roots and/or stem of leguminous plants involves a complex signal exchange between both partners. since many microorganisms are present in the soil, legumes and rhizobia must recognize and initiate communication with each other to establish symbioses. this results in the formation of nodules. rhizobia within nodules exchange fixed nitrogen for carbon from the legume. symbiotic relationships can become non-beneficial if one partner ceases t ...	2015	26191069
the 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
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
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
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
transcriptomic profiling of methylococcus capsulatus (bath) during growth with two different methane monooxygenases.	methylococcus capsulatus (bath) is a methanotroph that possesses both a membrane-embedded (pmmo) and a soluble methane monooxygenase (smmo). the expression of these two mmo's is tightly controlled by the availability of copper in the growth medium, but the underlying mechanisms and the number of genes involved in this switch in methane oxidation is not yet fully elucidated. microarray analyses were used to assess the transcriptome in cells producing either pmmo or smmo. a total of 137 genes were ...	2015	26687591
transcriptomic profiling of methylococcus capsulatus (bath) during growth with two different methane monooxygenases.	methylococcus capsulatus (bath) is a methanotroph that possesses both a membrane-embedded (pmmo) and a soluble methane monooxygenase (smmo). the expression of these two mmo's is tightly controlled by the availability of copper in the growth medium, but the underlying mechanisms and the number of genes involved in this switch in methane oxidation is not yet fully elucidated. microarray analyses were used to assess the transcriptome in cells producing either pmmo or smmo. a total of 137 genes were ...	2015	26687591
defining the metabolic functions and roles in virulence of the rpon1 and rpon2 genes in ralstonia solanacearum gmi1000.	the alternative sigma factor rpon is a unique regulator found among bacteria. it controls numerous processes that range from basic metabolism to more complex functions such as motility and nitrogen fixation. our current understanding of rpon function is largely derived from studies on prototypical bacteria such as escherichia coli. bacillus subtilis and pseudomonas putida. although the extent and necessity of rpon-dependent functions differ radically between these model organisms, each bacterium ...	2015	26659655
bacteriocins from the rhizosphere microbiome - from an agriculture perspective.	bacteria produce and excrete a versatile and dynamic suit of compounds to defend against microbial competitors and mediate local population dynamics. these include a wide range of broad-spectrum non-ribosomally synthesized antibiotics, lytic enzymes, metabolic by-products, proteinaceous exotoxins, and ribosomally produced antimicrobial peptides (bacteriocins). most bacteria produce at least one bacteriocin. bacteriocins are of interest in the food industry as natural preservatives and in the pro ...	2015	26579159
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
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
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
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 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
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
comparative genomics of pseudomonas fluorescens subclade iii strains from human lungs.	while the taxonomy and genomics of environmental strains from the p. fluorescens species-complex has been reported, little is known about p. fluorescens strains from clinical samples. in this report, we provide the first genomic analysis of p. fluorescens strains in which human vs. environmental isolates are compared.	2015	26644001
comparative metagenomics reveals impact of contaminants on groundwater microbiomes.	to understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (fw301) and contaminated groundwater (fw106) samples from the oak ridge integrated field research center (or-ifrc) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. proteobacteria (e.g., burkholderia, pseudomonas) are the most abundant lineages in the pristine community, though a significant proporti ...	2015	26583008
identification of bradyrhizobium elkanii genes involved in incompatibility with soybean plants carrying the rj4 allele.	symbioses between leguminous plants and soil bacteria known as rhizobia are of great importance to agricultural production and nitrogen cycling. while these mutualistic symbioses can involve a wide range of rhizobia, some legumes exhibit incompatibility with specific strains, resulting in ineffective nodulation. the formation of nodules in soybean plants (glycine max) is controlled by several host genes, which are referred to as rj genes. the soybean cultivar barc2 carries the rj4 gene, which re ...	2015	26187957
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
lipopolysaccharide o-chain core region required for cellular cohesion and compaction of in vitro and root biofilms developed by rhizobium leguminosarum.	the formation of biofilms is an important survival strategy allowing rhizobia to live on soil particles and plant roots. within the microcolonies of the biofilm developed by rhizobium leguminosarum, rhizobial cells interact tightly through lateral and polar connections, forming organized and compact cell aggregates. these microcolonies are embedded in a biofilm matrix, whose main component is the acidic exopolysaccharide (eps). our work shows that the o-chain core region of the r. leguminosarum ...	2015	25416773
cbbr, the master regulator for microbial carbon dioxide fixation.	biological carbon dioxide fixation is an essential and crucial process catalyzed by both prokaryotic and eukaryotic organisms to allow ubiquitous atmospheric co2 to be reduced to usable forms of organic carbon. this process, especially the calvin-bassham-benson (cbb) pathway of co2 fixation, provides the bulk of organic carbon found on earth. the enzyme ribulose 1,5-bisphosphate (rubp) carboxylase/oxygenase (rubisco) performs the key and rate-limiting step whereby co2 is reduced and incorporated ...	2015	26324454
a unique uracil-dna binding protein of the uracil dna glycosylase superfamily.	uracil dna glycosylases (udgs) are an important group of dna repair enzymes, which pioneer the base excision repair pathway by recognizing and excising uracil from dna. based on two short conserved sequences (motifs a and b), udgs have been classified into six families. here we report a novel udg, udgx, from mycobacterium smegmatis and other organisms. udgx specifically recognizes uracil in dna, forms a tight complex stable to sodium dodecyl sulphate, 2-mercaptoethanol, urea and heat treatment, ...	2015	26304551
cautions about the reliability of pairwise gene correlations based on expression data.	rapid growth in the availability of genome-wide transcript abundance levels through gene expression microarrays and rnaseq promises to provide deep biological insights into the complex, genome-wide transcriptional behavior of single-celled organisms. however, this promise has not yet been fully realized.	2015	26167162
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
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
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
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
σ54-dependent regulome in desulfovibrio vulgaris hildenborough.	the σ(54) subunit controls a unique class of promoters in bacteria. such promoters, without exception, require enhancer binding proteins (ebps) for transcription initiation. desulfovibrio vulgaris hildenborough, a model bacterium for sulfate reduction studies, has a high number of ebps, more than most sequenced bacteria. the cellular processes regulated by many of these ebps remain unknown.	2015	26555820
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
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
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
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
new insights into the biological role of the osmoregulated periplasmic glucans in pathogenic and symbiotic bacteria.	this review emphasizes the biological roles of the osmoregulated periplasmic glucans (opgs). osmoregulated periplasmic glucans occur in almost all α-, β- and γ-proteobacteria. this polymer of glucose is required for full virulence. the roles of the opgs are complex and vary depending on the species. here, we outline the four major roles of the opgs through four different pathogenic and one symbiotic bacterial models (dickeya dadantii, salmonella enterica, pseudomonas aeruginosa, brucella abortus ...	2015	26265506
adhesins involved in attachment to abiotic surfaces by gram-negative bacteria.	during the first step of biofilm formation, initial attachment is dictated by physicochemical and electrostatic interactions between the surface and the bacterial envelope. depending on the nature of these interactions, attachment can be transient or permanent. to achieve irreversible attachment, bacterial cells have developed a series of surface adhesins promoting specific or nonspecific adhesion under various environmental conditions. this article reviews the recent advances in our understandi ...	2015	26350310
biochemistry and genetics of acc deaminase: a weapon to "stress ethylene" produced in plants.	1-aminocyclopropane-1-carboxylate deaminase (accd), a pyridoxal phosphate-dependent enzyme, is widespread in diverse bacterial and fungal species. owing to accd activity, certain plant associated bacteria help plant to grow under biotic and abiotic stresses by decreasing the level of "stress ethylene" which is inhibitory to plant growth. accd breaks down acc, an immediate precursor of ethylene, to ammonia and α-ketobutyrate, which can be further metabolized by bacteria for their growth. acc deam ...	2015	26441873
general stress signaling in the alphaproteobacteria.	the alphaproteobacteria uniquely integrate features of two-component signal transduction and alternative σ factor regulation to control transcription of genes that ensure growth and survival across a range of stress conditions. research over the past decade has led to the discovery of the key molecular players of this general stress response (gsr) system, including the sigma factor σ(ecfg), its anti-σ factor nepr, and the anti-anti-σ factor phyr. the central molecular event of gsr activation ent ...	2015	26442844
structured and dynamic disordered domains regulate the activity of a multifunctional anti-σ factor.	the anti-σ factor nepr plays a central role in regulation of the general stress response (gsr) in alphaproteobacteria. this small protein has two known interaction partners: its cognate extracytoplasmic function (ecf) σ factor and the anti-anti-σ factor, phyr. stress-dependent phosphorylation of phyr initiates a protein partner switch that promotes phospho-phyr binding to nepr, which frees ecf σ to activate transcription of genes required for cell survival under adverse or fluctuating conditions ...	2015	26220965
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
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
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
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