Publications

ttsi regulates symbiotic genes in rhizobium species ngr234 by binding to tts boxes.	infection of legumes by rhizobium sp. ngr234 and subsequent development of nitrogen-fixing nodules are dependent on the coordinated actions of nod factors, proteins secreted by a type iii secretion system (t3ss) and modifications to surface polysaccharides. the production of these signal molecules is dependent on plant flavonoids which trigger a regulatory cascade controlled by the transcriptional activators nodd1, nodd2, syrm2 and ttsi. ttsi is known to control the genes responsible for t3ss fu ...	2008	18363648
symbiosis-promoting and deleterious effects of nopt, a novel type 3 effector of rhizobium sp. strain ngr234.	establishment of symbiosis between certain host plants and nitrogen-fixing bacteria ("rhizobia") depends on type 3 effector proteins secreted via the bacterial type 3 secretion system (t3ss). here, we report that the open reading frame y4zc of strain ngr234 encodes a novel rhizobial type 3 effector, termed nopt (for nodulation outer protein t). analysis of secreted proteins from ngr234 and t3ss mutants revealed that nopt is secreted via the t3ss. nopt possessed autoproteolytic activity when expr ...	2008	18487326
the exopolysaccharide of rhizobium sp. yas34 is not necessary for biofilm formation on arabidopsis thaliana and brassica napus roots but contributes to root colonization.	microbial exopolysaccharides (epss) play key roles in plant-microbe interactions, such as biofilm formation on plant roots and legume nodulation by rhizobia. here, we focused on the function of an eps produced by rhizobium sp. yas34 in the colonization and biofilm formation on non-legume plant roots (arabidopsis thaliana and brassica napus). using random transposon mutagenesis, we isolated an eps-deficient mutant of strain yas34 impaired in a glycosyltransferase gene (gta). wild type and mutant ...	2008	18507672
crystallization and preliminary x-ray diffraction studies of maleylacetate reductase from rhizobium sp. strain mtp-10005.	maleylacetate reductase (ec 1.3.1.32), which catalyzes the reduction of maleylacetate to 3-oxoadipate, plays an important role in the aerobic microbial catabolism of resorcinol. the enzyme has been crystallized at 293 k by the sitting-drop vapour-diffusion method supplemented with a microseeding technique, using ammonium sulfate as the precipitating agent. the crystal belonged to the monoclinic space group c2, with unit-cell parameters a = 56.85, b = 121.13, c = 94.09 a, beta = 101.48 degrees , ...	2008	18678945
y4lo of rhizobium sp. strain ngr234 is a symbiotic determinant required for symbiosome differentiation.	type 3 (t3) effector proteins, secreted by nitrogen-fixing rhizobia with a bacterial t3 secretion system, affect the nodulation of certain host legumes. the open reading frame y4lo of rhizobium sp. strain ngr234 encodes a protein with sequence similarities to t3 effectors from pathogenic bacteria (the yopj effector family). transcription studies showed that the promoter activity of y4lo depended on the transcriptional activator ttsi. recombinant y4lo protein expressed in escherichia coli did not ...	2009	19060155
delayed maturation of nodules reduces symbiotic effectiveness of the lotus japonicus-rhizobium sp. ngr234 interaction.	lotus japonicus, a model legume, develops an efficient, nitrogen-fixing symbiosis with mesorhizobium loti that promotes plant growth. lotus japonicus also forms functional nodules with rhizobium sp. ngr234 and r. etli. yet, in a plant defence-like reaction, nodules induced by r. etli quickly degenerate, thus limiting plant growth. in contrast, nodules containing ngr234 are long-lasting. it was found that ngr234 initiates nodule formation in a similar way to m. loti maff303099, but that the nodul ...	2009	19060298
use of folding modulators to improve heterologous protein production in escherichia coli.	abstract: despite the fundamental importance of e. coli in the manufacture of a wide range of biotechnological and biomedical products, extensive process and/or target optimisation is routinely required in order to achieve functional yields in excess of low mg/l levels. molecular chaperones and folding catalysts appear to present a panacea for problems of heterologous protein folding in the organism, due largely to their broad substrate range compared with, e.g., protein-specific mutagenesis app ...	2009	19173718
a novel endo-hydrogenase activity recycles hydrogen produced by nitrogen fixation.	nitrogen (n(2)) fixation also yields hydrogen (h(2)) at 1:1 stoichiometric amounts. in aerobic diazotrophic (able to grow on n(2) as sole n-source) bacteria, orthodox respiratory hupsl-encoded hydrogenase activity, associated with the cell membrane but facing the periplasm (exo-hydrogenase), has nevertheless been presumed responsible for recycling such endogenous hydrogen.	2009	19277114
cycle inhibiting factors (cifs) are a growing family of functional cyclomodulins present in invertebrate and mammal bacterial pathogens.	the cycle inhibiting factor (cif) produced by enteropathogenic and enterohemorrhagic escherichia coli was the first cyclomodulin to be identified that is injected into host cells via the type iii secretion machinery. cif provokes cytopathic effects characterized by g(1) and g(2) cell cycle arrests, accumulation of the cyclin-dependent kinase inhibitors (ckis) p21(waf1/cip1) and p27(kip1) and formation of actin stress fibres. the x-ray crystal structure of cif revealed it to be a divergent member ...	2009	19308257
rhizobium sp. strain ngr234 possesses a remarkable number of secretion systems.	rhizobium sp. strain ngr234 is a unique alphaproteobacterium (order rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other microsymbiont. we report here that the 3.93-mbp chromosome (cngr234) encodes most functions required for cellular growth. few essential functions are encoded on the 2.43-mbp megaplasmid (pngr234b), and none are present on the second 0.54-mbp symbiotic plasmid (pngr234a). among many striking features, the 6.9-mbp genome encodes more different secreti ...	2009	19376903
impact of (+/-)-catechin on soil microbial communities.	catechin is a highly studied but controversial allelochemical reported as a component of the root exudates of centaurea maculosa. initial reports of high and consistent exudation rates and soil concentrations have been shown to be highly inaccurate, but the chemical has been found in root exudates at and much less frequently in soil but sporadically at high concentrations. part of the problem of detection and measuring phytotoxicity in natural soils may be due to the confounding effect of soil m ...	2009	19704908
n- and c-terminal regions of the quorum-sensing activator trar cooperate in interactions with the alpha and sigma-70 components of rna polymerase.	positive control (pc) mutants defining 20 residues of the quorum-sensing activator trar were isolated that bind dna but show defects in activating transcription from class i, class ii or both types of promoters. these pc residues, located in both the n- and c-terminal regions, combine to form three patches, one on the top (ii) and two near the dna binding domain on both lateral faces of the dimer (i and iii). patches i and ii, but not patch iii, involve residues from both protomers and are essen ...	2009	19732344
enzymatic tailoring of ornithine in the biosynthesis of the rhizobium cyclic trihydroxamate siderophore vicibactin.	to acquire iron, the n(2)-fixing, symbiotic bacterium rhizobium sp. produce the cyclic trihydroxamate siderophore vicibactin, containing a 30-membered trilactone scaffold. herein we report the overproduction and purification of the six proteins vbsacgols in the bacterial host escherichia coli and the reconstitution of the biosynthesis of vicibactin from primary metabolites. the flavoprotein vbso acts as a pathway-initiating l-ornithine n(5)-hydroxylase, followed by vbsa, which transfers (r)-3-hy ...	2009	19778043
a novel signaling network essential for regulating pseudomonas aeruginosa biofilm development.	the important human pathogen pseudomonas aeruginosa has been linked to numerous biofilm-related chronic infections. here, we demonstrate that biofilm formation following the transition to the surface attached lifestyle is regulated by three previously undescribed two-component systems: bfisr (pa4196-4197) harboring an rpod-like domain, an ompr-like bfmsr (pa4101-4102), and mifsr (pa5511-5512) belonging to the family of ntrc-like transcriptional regulators. these two-component systems become sequ ...	2009	19936057
production of a blue pigment (glaukothalin) by marine rheinheimera spp.	two gamma-proteobacteria strains, that is, hp1 and hp9, which both produce a diffusible deep blue pigment, were isolated from the german wadden sea and from the øresund, denmark, respectively. both strains affiliate with the genus rheinheimera. small amounts of the pigment could be extracted from hp1 grown in a 50 l fermenter and were purified chromatographically. chemical analysis of the pigment including nmr and mass spectrometry led to a molecular formula of c(34)h(56)n(4)o(4) (m.w. 584.85) w ...	2009	20016676
genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order rhizobiales.	species belonging to the rhizobiales are intriguing and extensively researched for including both bacteria with the ability to fix nitrogen when in symbiosis with leguminous plants and pathogenic bacteria to animals and plants. similarities between the strategies adopted by pathogenic and symbiotic rhizobiales have been described, as well as high variability related to events of horizontal gene transfer. although it is well known that chromosomal rearrangements, mutations and horizontal gene tra ...	2010	20144182
phenolic acids act as signaling molecules in plant-microbe symbioses.	phenolic acids are the main polyphenols made by plants. these compounds have diverse functions and are immensely important in plant-microbe interactions/symbiosis. phenolic compounds act as signaling molecules in the initiation of legumerhizobia symbioses, establishment of arbuscular mycorrhizal symbioses and can act as agents in plant defense. flavonoids are a diverse class of polyphenolic compounds that have received considerable attention as signaling molecules involved in plant-microbe inter ...	2010	20400851
the small subunit arob of arsenite oxidase: lessons on the [2fe-2s] rieske protein superfamily.	here, we describe the characterization of the [2fe-2s] clusters of arsenite oxidases from rhizobium sp. nt-26 and ralstonia sp. 22. both reduced rieske proteins feature epr signals similar to their homologs from rieske-cyt b complexes, with g values at 2.027, 1.88, and 1.77. redox titrations in a range of ph values showed that both [2fe-2s] centers have constant e(m) values up to ph 8 at approximately +210 mv. above this ph value, the e(m) values of both centers are ph-dependent, similar to what ...	2010	20421651
symbiotic legume nodules employ both rhizobial exo- and endo-hydrogenases to recycle hydrogen produced by nitrogen fixation.	in symbiotic legume nodules, endosymbiotic rhizobia (bacteroids) fix atmospheric n(2), an atp-dependent catalytic process yielding stoichiometric ammonium and hydrogen gas (h(2)). while in most legume nodules this h(2) is quantitatively evolved, which loss drains metabolic energy, certain bacteroid strains employ uptake hydrogenase activity and thus evolve little or no h(2). rather, endogenous h(2) is efficiently respired at the expense of o(2), driving oxidative phosphorylation, recouping atp u ...	2010	20838423
regulation of inflammatory gene expression in pbmcs by immunostimulatory botanicals.	many hundreds of botanicals are used in complementary and alternative medicine for therapeutic use as antimicrobials and immune stimulators. while there exists many centuries of anecdotal evidence and few clinical studies on the activity and efficacy of these botanicals, limited scientific evidence exists on the ability of these botanicals to modulate the immune and inflammatory responses. using botanogenomics (or herbogenomics), this study provides novel insight into inflammatory genes which ar ...	2010	20838436
molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases.	cytosolic glutathione transferases (cgst) are a large group of ubiquitous enzymes involved in detoxification and are well known for their undesired side effects during chemotherapy. in this work we have performed thorough phylogenetic analyses to understand the various aspects of the evolution and functional diversification of cgsts. furthermore, we assessed plausible correlations between gene duplication and substrate specificity of gene paralogs in humans and selected species, notably in mamma ...	2010	20843339
the nodulation of alfalfa by the acid-tolerant rhizobium sp. strain lpu83 does not require sulfated forms of lipochitooligosaccharide nodulation signals.	the induction of root nodules by the majority of rhizobia has a strict requirement for the secretion of symbiosis-specific lipochitooligosaccharides (nodulation factors [nfs]). the nature of the chemical substitution on the nfs depends on the particular rhizobium and contributes to the host specificity imparted by the nfs. we present here a description of the genetic organization of the nod gene cluster and the characterization of the chemical structure of the nfs associated with the broad-host- ...	2010	20971905
temporal transcriptomic response during arsenic stress in herminiimonas arsenicoxydans.	arsenic is present in numerous ecosystems and microorganisms have developed various mechanisms to live in such hostile environments. herminiimonas arsenicoxydans, a bacterium isolated from arsenic contaminated sludge, has acquired remarkable capabilities to cope with arsenic. in particular our previous studies have suggested the existence of a temporal induction of arsenite oxidase, a key enzyme in arsenic metabolism, in the presence of as(iii).	2010	21167028
cyclic gmp controls rhodospirillum centenum cyst development.	adenylyl cyclases are widely distributed across all kingdoms whereas guanylyl cyclases are generally thought to be restricted to eukaryotes. here we report that the α-proteobacterium rhodospirillum centenum secretes cgmp when developing cysts and that a guanylyl cyclase deletion strain fails to synthesize cgmp and is defective in cyst formation. the r. centenum cyclase was purified and shown to effectively synthesize cgmp from gtp in vitro, demonstrating that it is a functional guanylyl cyclase. ...	2011	21214648
a highly conserved protein of unknown function in sinorhizobium meliloti affects srna regulation similar to hfq.	the smc01113/ybey protein, belonging to the upf0054 family, is highly conserved in nearly every bacterium. however, the function of these proteins still remains elusive. our results show that smc01113/ybey proteins share structural similarities with the mid domain of the argonaute (ago) proteins, and might similarly bind to a small-rna (srna) seed, making a special interaction with the phosphate on the 5'-side of the seed, suggesting they may form a component of the bacterial srna pathway. indee ...	2011	21325267
role of baca in lipopolysaccharide synthesis, peptide transport, and nodulation by rhizobium sp. strain ngr234.	baca of sinorhizobium meliloti plays an essential role in the establishment of nitrogen-fixing symbioses with medicago plants, where it is involved in peptide import and in the addition of very-long-chain fatty acids (vlcfa) to lipid a of lipopolysaccharide (lps). we investigated the role of baca in rhizobium species strain ngr234 by mutating the baca gene. in the ngr234 baca mutant, peptide import was impaired, but no effect on vlcfa addition was observed. more importantly, the symbiotic abilit ...	2011	21357487
the homogentisate and homoprotocatechuate central pathways are involved in 3- and 4-hydroxyphenylacetate degradation by burkholderia xenovorans lb400.	genome characterization of the model pcb-degrading bacterium burkholderia xenovorans lb400 revealed the presence of eleven central pathways for aromatic compounds degradation, among them, the homogentisate and the homoprotocatechuate pathways. however, the functionality of these central pathways in strain lb400 has not been assessed and related peripheral pathways has not been described.	2011	21423751
housekeeping genes essential for pantothenate biosynthesis are plasmid-encoded in rhizobium etli and rhizobium leguminosarum.	a traditional concept in bacterial genetics states that housekeeping genes, those involved in basic metabolic functions needed for maintenance of the cell, are encoded in the chromosome, whereas genes required for dealing with challenging environmental conditions are located in plasmids. exceptions to this rule have emerged from genomic sequence data of bacteria with multipartite genomes. the genome sequence of r. etli cfn42 predicts the presence of panc and panb genes clustered together on the ...	2011	21463532
the human gut mobile metagenome: a metazoan perspective.	using the culture independent traca system in conjunction with a comparative metagenomic approach, we have recently explored the pool of plasmids associated with the human gut mobile metagenome. this revealed that some plasmids or plasmid families are present in the gut microbiomes of geographically isolated human hosts with a broad global distribution (america, japan and europe), and are potentially unique to the human gut microbiome. functions encoded by the most widely distributed plasmid (pt ...	2010	21468227
isolation of xylose isomerases by sequence- and function-based screening from a soil metagenome library.	abstract: background: xylose isomerase (xi) catalyses the isomerization of xylose to xylulose in bacteria and some fungi. currently, only a limited number of xi genes have been functionally expressed in saccharomyces cerevisiae, the microorganism of choice for lignocellulosic ethanol production. the objective of the present study was to search for novel xi genes in the vastly diverse microbial habitat present in soil. as the exploitation of microbial diversity is impaired by the ability to culti ...	2011	21545702
the complete genome sequence of 'candidatus liberibacter solanacearum', the bacterium associated with potato zebra chip disease.	zebra chip (zc) is an emerging plant disease that causes aboveground decline of potato shoots and generally results in unusable tubers. this disease has led to multi-million dollar losses for growers in the central and western united states over the past decade and impacts the livelihood of potato farmers in mexico and new zealand. zc is associated with 'candidatus liberibacter solanacearum', a fastidious alpha-proteobacterium that is transmitted by a phloem-feeding psyllid vector, bactericera c ...	2011	21552483
exploring the symbiotic pangenome of the nitrogen-fixing bacterium sinorhizobium meliloti.	abstract: background: sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. an extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. ak83 and bl225c are two nodule-isolated strains with diverse symbiotic phenotypes; bl225c is more efficient in promoting growth of the medicago sativa plants than strain ak83. in order to investigate the genetic ...	2011	21569405
multiple loci are involved in quorum quenching of autoinducer i molecules in the nitrogen-fixing symbiont (sino-) rhizobium sp. ngr234.	rhizobium sp. ngr234 is a unique α-proteobacterium (order - rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other micro-symbiont. since we have previously described the complete genome sequence of ngr234, we now report on a genome wide functional analysis of the genes and enzymes involved in autoinducer i hydrolysis in this microbe. altogether we identified five cosmid clones that repeatedly gave a positive result in our function-based approach for the detection of aut ...	2011	21642401
functional analysis of the type 3 effector nopl from rhizobium sp. ngr234: symbiotic effects, phosphorylation and interference with mapk signaling.	pathogenic bacteria use type 3 secretion systems to deliver virulence factors (type 3 effector proteins) directly into eukaryotic host cells. similarly, type 3 effectors of certain nitrogen-fixing rhizobial strains affect nodule formation in the symbiosis with host legumes. nodulation outer protein l (nopl) of rhizobium sp. strain ngr234 is a rhizobium-specific type 3 effector. nodulation tests and microscopic analysis showed that distinct necrotic areas were rapidly formed in ineffective nodule ...	2011	21775427
Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia.	Methanotrophs play a key role in the global carbon cycle, in which they affect methane emissions and help to sustain diverse microbial communities through the conversion of methane to organic compounds. To investigate the microbial interactions that cause positive effects on methanotrophs, cocultures were constructed using Methylovulum miyakonense HT12 and each of nine nonmethanotrophic bacteria, which were isolated from a methane-utilizing microbial consortium culture established from forest so ...	2011	21984248
Identification and Characterization of the Rhizobium sp. Strain GIN611 Glycoside Oxidoreductase Resulting in the Deglycosylation of Ginsenosides.	Using enrichment culture, Rhizobium sp. strain GIN611 was isolated as having activity for deglycosylation of a ginsenoside, compound K (CK). The purified heterodimeric protein complex from Rhizobium sp. GIN611 consisted of two subunits with molecular masses of 63.5 kDa and 17.5 kDa. In the genome, the coding sequence for the small subunit was located right after the sequence for the large subunit, with one nucleotide overlapping. The large subunit showed CK oxidation activity, and the deglycosyl ...	2012	22020506
Could petroleum biodegradation be a joint achievement of aerobic and anaerobic microrganisms in deep sea reservoirs?	ABSTRACT: Several studies suggest that petroleum biodegradation can be achieved by either aerobic or anaerobic microorganisms, depending on oxygen input or other electron acceptors and appropriate nutrients. Evidence from in vitro experiments with samples of petroleum formation water and oils from Pampo Field indicate that petroleum biodegradation is more likely to be a joint achievement of both aerobic and anaerobic bacterial consortia, refining our previous observations of aerobic degradation. ...	2011	22196374
identification and characterization of rhodopseudomonas palustris tie-1 hopanoid biosynthesis mutants.	hopanes preserved in both modern and ancient sediments are recognized as the molecular fossils of bacteriohopanepolyols, pentacyclic hopanoid lipids. based on the phylogenetic distribution of hopanoid production by extant bacteria, hopanes have been used as indicators of specific bacterial groups and/or their metabolisms. however, our ability to interpret them ultimately depends on understanding the physiological roles of hopanoids in modern bacteria. toward this end, we set out to identify gene ...	2012	22221333
new beta rhizobial strains able to efficiently nodulate parapiptadenia rigida (benth.) brenan.	among the leguminous trees natives to uruguay parapiptadenia rigida (angico), a mimosoideae legume, is one of the most promising species for agroforestry. like many other legumes, it is able to establish symbiotic associations with rhizobia and belongs to the group known as "nitrogen fixing trees", which are major components of agroforestry systems. information about rhizobial symbionts for this genus is scarce, and thus the aim of this work was to identify and characterize rhizobia associated w ...	2012	22226956
characterization of outer membrane vesicles from brucella melitensis and protection induced in mice.	the outer membrane vesicles (omvs) from smooth b. melitensis 16 m and a derived rough mutant, vtrm1 strain, were purified and characterized with respect to protein content and induction of immune responses in mice. proteomic analysis showed 29 proteins present in omvs from b. melitensis 16 m; some of them are well-known brucella immunogens such as sod, groes, omp31, omp25, omp19, bp26, and omp16. omvs from a rough vtrm1 induced significantly higher expression of il-12, tnfα, and ifnγ genes in bo ...	2011	22242036
characterization of outer membrane vesicles from brucella melitensis and protection induced in mice.	the outer membrane vesicles (omvs) from smooth b. melitensis 16 m and a derived rough mutant, vtrm1 strain, were purified and characterized with respect to protein content and induction of immune responses in mice. proteomic analysis showed 29 proteins present in omvs from b. melitensis 16 m; some of them are well-known brucella immunogens such as sod, groes, omp31, omp25, omp19, bp26, and omp16. omvs from a rough vtrm1 induced significantly higher expression of il-12, tnfα, and ifnγ genes in bo ...	2011	22242036
biological control of chickpea collar rot by co-inoculation of antagonistic bacteria and compatible rhizobia.	two hundred and seven bacteria were isolated from composts and macrofauna and screened for plant growth promoting and antagonistic traits. seven of the 207 isolates showed antagonistic activity against sclerotium rolfsii in plate culture. inhibition of s. rolfsii by the bacterial isolates ranged between 61 and 84%. two of the seven isolates were bacillus sp. and rest belonged to pseudomonas sp. two isolates, pseudomonas sp. cdb 35 and pseudomonas sp. bwb 21 was compatible with chickpea rhizobium ...	2011	22282609
distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone.	pyrroloquinoline quinone (pqq) is a small, redox active molecule that serves as a cofactor for several bacterial dehydrogenases, introducing pathways for carbon utilization that confer a growth advantage. early studies had implicated a ribosomally translated peptide as the substrate for pqq production. this study presents a sequence- and structure-based analysis of the components of the pqq operon. we find the necessary components for pqq production are present in 126 prokaryotes, most of which ...	2012	22324760
computer-based annotation of putative arac/xyls-family transcription factors of known structure but unknown function.	currently, about 20 crystal structures per day are released and deposited in the protein data bank. a significant fraction of these structures is produced by research groups associated with the structural genomics consortium. the biological function of many of these proteins is generally unknown or not validated by experiment. therefore, a growing need for functional prediction of protein structures has emerged. here we present an integrated bioinformatics method that combines sequence-based rel ...	2012	22505803
isolation and characterization of nodule-associated exiguobacterium sp. from the root nodules of fenugreek (trigonella foenum-graecum) and their possible role in plant growth promotion.	one of the ways to increase the competitive survivability of rhizobial biofertilizers and thus achieve better plant growth under such conditions is by modifying the rhizospheric environment or community by addition of nonrhizobial nodule-associated bacteria (nab) that cause better nodulation and plant growth when coinoculated with rhizobia. a study was performed to investigate the most commonly associated nodule-associated bacteria and the rhizospheric microorganisms associated with the fenugree ...	2012	22518149
formation of se (0) nanoparticles by duganella sp. and agrobacterium sp. isolated from se-laden soil of north-east punjab, india.	selenium (se) is an essential trace element, but is toxic at high concentrations. depending upon the geological background, the land use or on anthropogenic pollution, different amounts of se may be present in soil. its toxicity is related to the oxyanions selenate and selenite as they are water soluble and bioavailable. microorganisms play an important role in se transformations in soil and its cycling in the environment by transforming water-soluble oxyanions into water insoluble, non-toxic el ...	2012	22607265
genomic basis of broad host range and environmental adaptability of rhizobium tropici ciat 899 and rhizobium sp. prf 81 which are used in inoculants for common bean (phaseolus vulgaris l.).	rhizobium tropici ciat 899 and rhizobium sp. prf 81 are α-proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. these strains are broadly used in commercial inoculants for application to common bean (phaseolus vulgaris) in south america and africa. both strains display intrinsic resistance to several abiotic stressful conditions such as low soil ph and high temperatures, which are common in tropical environments, and to several antimicrobials, including pesticides ...	2012	23270491
structure prediction, molecular dynamics simulation and docking studies of d-specific dehalogenase from rhizobium sp. rc1.	currently, there is no three-dimensional structure of d-specific dehalogenase (dehd) in the protein database. we modeled dehd using ab initio technique, performed molecular dynamics (md) simulation and docking of d-2-chloropropionate (d-2cp), d-2-bromopropionate (d-2bp), monochloroacetate (mca), monobromoacetate (mba), 2,2-dichloropropionate (2,2-dcp), d,l-2,3-dichloropropionate (d,l-2,3-dcp), and 3-chloropropionate (3-cp) into the dehd active site. the sequences of dehd and d-2-haloacid dehalog ...	2012	23443090
prediction of cross-recognition of peptide-hla a2 by melan-a-specific cytotoxic t lymphocytes using three-dimensional quantitative structure-activity relationships.	the cross-recognition of peptides by cytotoxic t lymphocytes is a key element in immunology and in particular in peptide based immunotherapy. here we develop three-dimensional (3d) quantitative structure-activity relationships (qsars) to predict cross-recognition by melan-a-specific cytotoxic t lymphocytes of peptides bound to hla a*0201 (hereafter referred to as hla a2). first, we predict the structure of a set of self- and pathogen-derived peptides bound to hla a2 using a previously developed ...	2013	23874382
chitinolytic microorganisms and their possible application in environmental protection.	this paper provides a review of the latest research findings on the applications of microbial chitinases to biological control. microorganisms producing these enzymes can inhibit the growth of many fungal diseases that pose a serious threat to global crop production. currently, efforts are being made to discover producers of chitinolytic enzymes. the potential exists that natural biofungicides will replace chemical fungicides or will be used to supplement currently used fungicides, which would r ...	2013	23989799
chitinolytic microorganisms and their possible application in environmental protection.	this paper provides a review of the latest research findings on the applications of microbial chitinases to biological control. microorganisms producing these enzymes can inhibit the growth of many fungal diseases that pose a serious threat to global crop production. currently, efforts are being made to discover producers of chitinolytic enzymes. the potential exists that natural biofungicides will replace chemical fungicides or will be used to supplement currently used fungicides, which would r ...	2013	23989799
characterization of epiphytic bacterial communities from grapes, leaves, bark and soil of grapevine plants grown, and their relations.	despite its importance in plant health and crop quality, the diversity of epiphytic bacteria on grape berries and other plant parts, like leaves and bark, remains poorly described, as does the role of telluric bacteria in plant colonization. in this study, we compare the bacterial community size and structure in vineyard soils, as well as on grapevine bark, leaves and berries. analyses of culturable bacteria revealed differences in the size and structure of the populations in each ecosystem. the ...	2013	24023666
genetic diversity of rhizobia isolates from amazon soils using cowpea (vigna unguiculata) as trap plant.	the aim of this work was to characterize rhizobia isolated from the root nodules of cowpea (vigna unguiculata) plants cultivated in amazon soils samples by means of ardra (amplified rdna restriction analysis) and sequencing analysis, to know their phylogenetic relationships. the 16s rrna gene of rhizobia was amplified by pcr (polymerase chain reaction) using universal primers y1 and y3. the amplification products were analyzed by the restriction enzymes hinfi, mspi and ddei and also sequenced wi ...	2012	24031880
cyanobase and rhizobase: databases of manually curated annotations for cyanobacterial and rhizobial genomes.	to understand newly sequenced genomes of closely related species, comprehensively curated reference genome databases are becoming increasingly important. we have extended cyanobase (http://genome.microbedb.jp/cyanobase), a genome database for cyanobacteria, and newly developed rhizobase (http://genome.microbedb.jp/rhizobase), a genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants. both databases focus on the representation and reusability of reference genome a ...	2013	24275496
cyanobase and rhizobase: databases of manually curated annotations for cyanobacterial and rhizobial genomes.	to understand newly sequenced genomes of closely related species, comprehensively curated reference genome databases are becoming increasingly important. we have extended cyanobase (http://genome.microbedb.jp/cyanobase), a genome database for cyanobacteria, and newly developed rhizobase (http://genome.microbedb.jp/rhizobase), a genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants. both databases focus on the representation and reusability of reference genome a ...	2013	24275496
annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms.	the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ...	2011	24710297
evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.	to assess the potential of different types of sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences.	2014	24930142
alfalfa snakin-1 prevents fungal colonization and probably coevolved with rhizobia.	the production of antimicrobial peptides is a common defense strategy of living cells against a wide range of pathogens. plant snakin peptides inhibit bacterial and fungal growth at extremely low concentrations. however, little is known of their molecular and ecological characteristics, including origin, evolutionary equivalence, specific functions and activity against beneficial microbes. the aim of this study was to identify and characterize snakin-1 from alfalfa (mssn1).	2014	25227589
evidence for methionine-sulfoxide-reductase gene transfer from alphaproteobacteria to the transcriptionally active (macro)nucleus of the ciliate, euplotes raikovi.	deleterious phenomena of protein oxidation affect every aerobic organism and methionine residues are their elective targets. the reduction of methionine sulfoxides back to methionines is catalyzed by methionine-sulfoxide reductases (msrs), enzymes which are particularly active in microorganisms because of their unique nature of individual cells directly exposed to environmental oxidation.	2014	25420622
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
a bioinformatic survey of distribution, conservation, and probable functions of luxr solo regulators in bacteria.	luxr solo transcriptional regulators contain both an autoinducer binding domain (abd; n-terminal) and a dna binding helix-turn-helix domain (hth; c-terminal), but are not associated with a cognate n-acyl homoserine lactone (ahl) synthase coding gene in the same genome. although a few luxr solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. in this study we have carried out a systematic survey of distri ...	2015	25759807
rhizobium leguminosarum bv. viciae 3841 adapts to 2,4-dichlorophenoxyacetic acid with "auxin-like" morphological changes, cell envelope remodeling and upregulation of central metabolic pathways.	there is a growing need to characterize the effects of environmental stressors at the molecular level on model organisms with the ever increasing number and variety of anthropogenic chemical pollutants. the herbicide 2,4-dichlorophenoxyacetic acid (2,4-d), as one of the most widely applied pesticides in the world, is one such example. this herbicide is known to have non-targeted undesirable effects on humans, animals and soil microbes, but specific molecular targets at sublethal levels are unkno ...	2015	25919284
plant-microbe cross-talk in the rhizosphere: insight and biotechnological potential.	rhizosphere, the interface between soil and plant roots, is a chemically complex environment which supports the development and growth of diverse microbial communities. the composition of the rhizosphere microbiome is dynamic and controlled by multiple biotic and abiotic factors that include environmental parameters, physiochemical properties of the soil, biological activities of the plants and chemical signals from the plants and bacteria which inhabit the soil adherent to root-system. recent a ...	2015	25926899
enzymological characterization of atm, the first laccase from agrobacterium sp. s5-1, with the ability to enhance in vitro digestibility of maize straw.	laccase is an enzyme that catalyzes oxidation of phenolic compounds, diamines and aromatic amines. in this study, a novel laccase-like gene (atm) in a ligninolyitic isolate agrobacterium sp. s5-1 from soil humus was identified and heterologously expressed in escherichia coli. atm exhibited its maximal activity at ph 4.5 and at 50°c. this enzyme was tolerant to high temperature, a broad range of ph, heavy metal ions (co3+, mn2+, cu2+ and ni2+, 20 mm) and all tested organic solvents. furthermore, ...	2015	26010258
does plant immunity play a critical role during initiation of the legume-rhizobium symbiosis?	plants are exposed to many different microbes in their habitats. these microbes may be benign or pathogenic, but in some cases they are beneficial for the host. the rhizosphere provides an especially rich palette for colonization by beneficial (associative and symbiotic) microorganisms, which raises the question as to how roots can distinguish such 'friends' from possible 'foes' (i.e., pathogens). plants possess an innate immune system that can recognize pathogens, through an arsenal of protein ...	2015	26082790
biosynthetic machinery involved in aberrant glycosylation: promising targets for developing of drugs against cancer.	cancer cells depend on altered metabolism and nutrient uptake to generate and keep the malignant phenotype. the hexosamine biosynthetic pathway is a branch of glucose metabolism that produces udp-glcnac and its derivatives, udp-galnac and cmp-neu5ac and donor substrates used in the production of glycoproteins and glycolipids. growing evidence demonstrates that alteration of the pool of activated substrates might lead to different glycosylation and cell signaling. it is already well established t ...	2015	26161361
dryland soil chemical properties and crop yields affected by long-term tillage and cropping sequence.	information on the effect of long-term management on soil nutrients and chemical properties is scanty. we examined the 30-year effect of tillage frequency and cropping sequence combination on dryland soil olsen-p, k, ca, mg, na, so4-s, and zn concentrations, ph, electrical conductivity (ec), and cation exchange capacity (cec) at the 0-120 cm depth and annualized crop yield in the northern great plains, usa. treatments were no-till continuous spring wheat (triticum aestivum l.) (ntcw), spring til ...	2015	26171303
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
a fragrant neighborhood: volatile mediated bacterial interactions in soil.	there is increasing evidence that volatile organic compounds (vocs) play essential roles in communication and competition between soil microorganisms. here we assessed volatile-mediated interactions of a synthetic microbial community in a model system that mimics the natural conditions in the heterogeneous soil environment along the rhizosphere. phylogenetic different soil bacterial isolates (burkholderia sp., dyella sp., janthinobacterium sp., pseudomonas sp., and paenibacillus sp.) were inocul ...	2015	26579111
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
insights into the stereospecificity of the d-specific dehalogenase from rhizobium sp. rc1 toward d- and l-2-chloropropionate.	halogenated compounds are recalcitrant environmental pollutants prevalent in agricultural fields, waste waters and industrial by-products, but they can be degraded by dehalogenase-containing microbes. notably, 2-haloalkanoic acid dehalogenases are employed to resolve optically active chloropropionates, as exemplified by the d-specific dehalogenase from rhizobium sp. rci (dehd), which acts on d-2-chloropropionate but not on its l-enantiomer. the catalytic residues of this dehalogenase responsible ...	2014	26740767
recent developments in using advanced sequencing technologies for the genomic studies of lignin and cellulose degrading microorganisms.	lignin is a complex polyphenyl aromatic compound which exists in tight associations with cellulose and hemicellulose to form plant primary and secondary cell wall. lignocellulose is an abundant renewable biomaterial present on the earth. it has gained much attention in the scientific community in recent years because of its potential applications in bio-based industries. microbial degradation of lignocellulose polymers was well studied in wood decaying fungi. based on the plant materials they de ...	2016	26884714
an improved method for high quality metagenomics dna extraction from human and environmental samples.	to explore the natural microbial community of any ecosystems by high-resolution molecular approaches including next generation sequencing, it is extremely important to develop a sensitive and reproducible dna extraction method that facilitate isolation of microbial dna of sufficient purity and quantity from culturable and uncultured microbial species living in that environment. proper lysis of heterogeneous community microbial cells without damaging their genomes is a major challenge. in this st ...	2016	27240745
drought stress responses in soybean roots and nodules.	drought is considered to be a major threat to soybean production worldwide and yet our current understanding of the effects of drought on soybean productively is largely based on studies on above-ground traits. although the roots and root nodules are important sensors of drought, the responses of these crucial organs and their drought tolerance features remain poorly characterized. the symbiotic interaction between soybean and rhizobia facilitates atmospheric nitrogen fixation, a process that pr ...	2016	27462339
modification of bacterial effector proteins inside eukaryotic host cells.	pathogenic bacteria manipulate their hosts by delivering a number of virulence proteins -called effectors- directly into the plant or animal cells. recent findings have shown that such effectors can suffer covalent modifications inside the eukaryotic cells. here, we summarize the recent reports where effector modifications by the eukaryotic machinery have been described. we restrict our focus on proteins secreted by the type iii or type iv systems, excluding other bacterial toxins. we describe t ...	2016	27489796
nitrogen fixation and molecular oxygen: comparative genomic reconstruction of transcription regulation in alphaproteobacteria.	biological nitrogen fixation plays a crucial role in the nitrogen cycle. an ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of bacteria and archaea. the transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the class alphaproteobacteria. this regulatory network includes the activator of nitrogen fixation nifa, working in tandem with the alternative sigma-factor rpon as well as oxygen-respons ...	2016	27617010
the comparatively proteomic analysis in response to cold stress in cassava plantlets.	cassava (manihot esculenta crantz) is a tropical root crop and sensitive to low temperature. however, it is poorly to know how cassava can modify its metabolism and growth to adapt to cold stress. an investigation aimed at a better understanding of cold-tolerant mechanism of cassava plantlets was carried out with the approaches of physiology and proteomics in the present study. the principal component analysis of seven physiological characteristics showed that electrolyte leakage (el), chlorophy ...	2016	27881899
agrobacterium tumefaciens estc, encoding an enzyme containing esterase activity, is regulated by estr, a regulator in the marr family.	analysis of the a. tumefaciens genome revealed estc, which encodes an esterase located next to its transcriptional regulator estr, a regulator of esterase in the marr family. inactivation of estc results in a small increase in the resistance to organic hydroperoxides, whereas a high level of expression of estc from an expression vector leads to a reduction in the resistance to organic hydroperoxides and menadione. the estc gene is transcribed divergently from its regulator, estr. expression anal ...	2016	28036400