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in silico insights into the symbiotic nitrogen fixation in sinorhizobium meliloti via metabolic reconstruction.sinorhizobium meliloti is a soil bacterium, known for its capability to establish symbiotic nitrogen fixation (snf) with leguminous plants such as alfalfa. s. meliloti 1021 is the most extensively studied strain to understand the mechanism of snf and further to study the legume-microbe interaction. in order to provide insight into the metabolic characteristics underlying the snf mechanism of s. meliloti 1021, there is an increasing demand to reconstruct a metabolic network for the stage of snf i ...201222319621
attenuation of quorum sensing in the pathogen acinetobacter baumannii using non-native n-acyl homoserine lactones.many bacterial pathogens use quorum sensing (qs) to control virulence. as a result, the development of methods to intercept qs has attracted significant interest as a potential anti-infective therapy. acinetobacter baumannii has emerged as a pan-drug-resistant pathogen and displays a remarkable ability to persist in hospital settings despite desiccation and antimicrobial treatment. recent studies have shown that a. baumannii qs mutants have limited motility and fail to form mature biofilms; thes ...201222853441
rapa2 is a calcium-binding lectin composed of two highly conserved cadherin-like domains that specifically recognize rhizobium leguminosarum acidic exopolysaccharides.in silico analyses have revealed a conserved protein domain (chdl) widely present in bacteria that has significant structural similarity to eukaryotic cadherins. a chdl domain was shown to be present in rapa, a protein that is involved in autoaggregation of rhizobium cells, biofilm formation, and adhesion to plant roots as shown by us and others. structural similarity to cadherins suggested calcium-dependent oligomerization of chdl domains as a mechanistic basis for rapa action. here we show by ...201223235153
rapa2 is a calcium-binding lectin composed of two highly conserved cadherin-like domains that specifically recognize rhizobium leguminosarum acidic exopolysaccharides.in silico analyses have revealed a conserved protein domain (chdl) widely present in bacteria that has significant structural similarity to eukaryotic cadherins. a chdl domain was shown to be present in rapa, a protein that is involved in autoaggregation of rhizobium cells, biofilm formation, and adhesion to plant roots as shown by us and others. structural similarity to cadherins suggested calcium-dependent oligomerization of chdl domains as a mechanistic basis for rapa action. here we show by ...201223235153
aggregation by depletion attraction in cultures of bacteria producing exopolysaccharide.in bacteria, the production of exopolysaccharides--polysaccharides secreted by the cells into their growth medium--is integral to the formation of aggregates and biofilms. these exopolysaccharides often form part of a matrix that holds the cells together. investigating the bacterium sinorhizobium meliloti, we found that a mutant that overproduces the exopolysaccharide succinoglycan showed enhanced aggregation, resulting in phase separation of the cultures. however, the aggregates did not appear ...201222896568
minimum requirements of flagellation and motility for infection of agrobacterium sp. strain h13-3 by flagellotropic bacteriophage 7-7-1.the flagellotropic phage 7-7-1 specifically adsorbs to agrobacterium sp. strain h13-3 (formerly rhizobium lupini h13-3) flagella for efficient host infection. the agrobacterium sp. h13-3 flagellum is complex and consists of three flagellin proteins: the primary flagellin flaa, which is essential for motility, and the secondary flagellins flab and flad, which have minor functions in motility. using quantitative infectivity assays, we showed that absence of flad had no effect on phage infection, w ...201222865074
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 ...201224031880
identification and phylogenetic characterization of cobalamin biosynthetic genes of ensifer adhaerens.ensifer adhaerens csba was screened as a cobalamin producer. the draft genome sequence revealed that the strain possesses 22 cobalamin biosynthetic genes (cob genes). the cob gene arrangement on the genome of e. adhaerens csba was similar to that of other ensifer species, and most similar to that of pseudomonas denitrificans sc510. the cobn sequence phylogeny was generally congruent with that of the 16s rrna gene, and it is suggeted that e. adhaerens csba might have inherited the cob genes from ...201223257908
identification and phylogenetic characterization of cobalamin biosynthetic genes of ensifer adhaerens.ensifer adhaerens csba was screened as a cobalamin producer. the draft genome sequence revealed that the strain possesses 22 cobalamin biosynthetic genes (cob genes). the cob gene arrangement on the genome of e. adhaerens csba was similar to that of other ensifer species, and most similar to that of pseudomonas denitrificans sc510. the cobn sequence phylogeny was generally congruent with that of the 16s rrna gene, and it is suggeted that e. adhaerens csba might have inherited the cob genes from ...201223257908
delineation of the caffeine c-8 oxidation pathway in pseudomonas sp. strain cbb1 via characterization of a new trimethyluric acid monooxygenase and genes involved in trimethyluric acid metabolism.the molecular basis of the ability of bacteria to live on caffeine via the c-8 oxidation pathway is unknown. the first step of this pathway, caffeine to trimethyluric acid (tmu), has been attributed to poorly characterized caffeine oxidases and a novel quinone-dependent caffeine dehydrogenase. here, we report the detailed characterization of the second enzyme, a novel nadh-dependent trimethyluric acid monooxygenase (tmum), a flavoprotein that catalyzes the conversion of tmu to 1,3,7-trimethyl-5- ...201222609920
the abc transporters in candidatus liberibacter asiaticus.candidatus liberibacter asiaticus (ca. l. asiaticus) is a gram-negative bacterium and the pathogen of citrus greening disease (huanglongbing, hlb). as a parasitic bacterium, ca. l. asiaticus harbors abc transporters that play important roles in exchanging chemical compounds between ca. l. asiaticus and its host. here, we analyzed all the abc transporter-related proteins in ca. l. asiaticus. we identified 14 abc transporter systems and predicted their structures and substrate specificities. in-de ...201222807026
transcriptomic profiling of bacillus amyloliquefaciens fzb42 in response to maize root exudates.plant root exudates have been shown to play an important role in mediating interactions between plant growth-promoting rhizobacteria (pgpr) and their host plants. most investigations were performed on gram-negative rhizobacteria, while much less is known about gram-positive rhizobacteria. to elucidate early responses of pgpr to root exudates, we investigated changes in the transcriptome of a gram-positive pgpr to plant root exudates.201222720735
robust markers reflecting phylogeny and taxonomy of rhizobia.genomic ani (average nucleotide identity) has been found to be able to replace dna-dna hybridization in prokaryote taxonomy. the ani of each of the core genes that has a phylogeny congruent with the reference species tree of rhizobia was compared to the genomic ani. this allowed us to identify three housekeeping genes (smc00019-trua-thra) whose ani reflected the intraspecies and interspecies genomic ani among rhizobial strains, revealing an ani gap (≥2%) between the inter- and intra-species comp ...201223028691
calcium causes multimerization of the large adhesin lapf and modulates biofilm formation by pseudomonas putida.lapf is a large secreted protein involved in microcolony formation and biofilm maturation in pseudomonas putida. its c-terminal domain shows the characteristics of proteins secreted through a type i secretion system and includes a predicted calcium binding motif. we provide experimental evidence of specific binding of ca(2+) to the purified c-terminal domain of lapf (clapf). calcium promotes the formation of large aggregates, which disappear in the presence of the calcium chelator egta. immunolo ...201223042991
regulatable vectors for environmental gene expression in alphaproteobacteria.two expression vectors utilizing the inducible taurine promoter (tauap) were developed. plasmid plmb51 is a stable low-copy vector enabling expression in the environment and in planta. the higher copy number plmb509 enables bd restriction-independent cloning, expression, and purification of polyhistidine-tagged proteins.201222820336
extracytoplasmic function (ecf) sigma factor σf is involved in caulobacter crescentus response to heavy metal stress.the α-proteobacterium caulobacter crescentus inhabits low-nutrient environments and can tolerate certain levels of heavy metals in these sites. it has been reported that c. crescentus responds to exposure to various heavy metals by altering the expression of a large number of genes.201222985357
modifications of xanthomonas axonopodis pv. citri lipopolysaccharide affect the basal response and the virulence process during citrus canker.xanthomonas axonopodis pv. citri (xac) is the phytopathogen responsible for citrus canker, one of the most devastating citrus diseases in the world. a broad range of pathogens is recognized by plants through so-called pathogen-associated molecular patterns (pamps), which are highly conserved fragments of pathogenic molecules. in plant pathogenic bacteria, lipopolisaccharyde (lps) is considered a virulence factor and it is being recognized as a pamp. the study of the participation of xac lps in c ...201222792211
regulation and evolution of malonate and propionate catabolism in proteobacteria.bacteria catabolize malonate via two pathways, encoded by the mdc and mat genes. in various bacteria, transcription of these genes is controlled by the gntr family transcription factors (tfs) matr/mdcy and/or the lysr family transcription factor mdcr. propionate is metabolized via the methylcitrate pathway, comprising enzymes encoded by the prp and acn genes. prpr, the fis family sigma 54-dependent transcription factor, is known to be a transcriptional activator of the prp genes. here, we report ...201222505679
engineering microbes for plant polyketide biosynthesis.polyketides are an important group of secondary metabolites, many of which have important industrial applications in the food and pharmaceutical industries. polyketides are synthesized from one of three classes of enzymes differentiated by their biochemical features and product structure: type i, type ii or type iii polyketide synthases (pkss). plant type iii pks enzymes, which will be the main focus of this review, are relatively small homodimeric proteins that catalyze iterative decarboxylativ ...201224688680
engineering microbes for plant polyketide biosynthesis.polyketides are an important group of secondary metabolites, many of which have important industrial applications in the food and pharmaceutical industries. polyketides are synthesized from one of three classes of enzymes differentiated by their biochemical features and product structure: type i, type ii or type iii polyketide synthases (pkss). plant type iii pks enzymes, which will be the main focus of this review, are relatively small homodimeric proteins that catalyze iterative decarboxylativ ...201224688680
unique secreted-surface protein complex of lactobacillus rhamnosus, identified by phage display.proteins are the most diverse structures on bacterial surfaces; hence, they are candidates for species- and strain-specific interactions of bacteria with the host, environment, and other microorganisms. genomics has decoded thousands of bacterial surface and secreted proteins, yet the function of most cannot be predicted because of the enormous variability and a lack of experimental data that would allow deduction of function through homology. here, we used phage display to identify a pair of in ...201223233310
unique secreted-surface protein complex of lactobacillus rhamnosus, identified by phage display.proteins are the most diverse structures on bacterial surfaces; hence, they are candidates for species- and strain-specific interactions of bacteria with the host, environment, and other microorganisms. genomics has decoded thousands of bacterial surface and secreted proteins, yet the function of most cannot be predicted because of the enormous variability and a lack of experimental data that would allow deduction of function through homology. here, we used phage display to identify a pair of in ...201223233310
draft genome sequence of agrobacterium albertimagni strain aol15.agrobacterium albertimagni strain aol15 is an alphaproteobacterium isolated from arsenite-oxidizing biofilms whose draft genome contains 5.1 mb in 55 contigs with 61.2% gc content and includes a 21-gene arsenic gene island. this is the first available genome for this species and the second agrobacterium arsenic gene island.201223209236
how does pea architecture influence light sharing in virtual wheat-pea mixtures? a simulation study based on pea genotypes with contrasting architectures.light interception is a key factor driving the functioning of wheat-pea intercrops. the sharing of light is related to the canopy structure, which results from the architectural parameters of the mixed species. in the present study, we characterized six contrasting pea genotypes and identified architectural parameters whose range of variability leads to various levels of light sharing within virtual wheat-pea mixtures.201223240074
pathology-dependent effects linked to small heat shock proteins expression: an update.small heat shock proteins (small hsps) are stress-induced molecular chaperones that act as holdases towards polypeptides that have lost their folding in stress conditions or consequently of mutations in their coding sequence. a cellular protection against the deleterious effects mediated by damaged proteins is thus provided to cells. these chaperones are also highly expressed in response to protein conformational and inflammatory diseases and cancer pathologies. through specific and reversible m ...201224278676
emerging themes in seca2-mediated protein export.the conserved general secretion (sec) pathway carries out most protein export in bacteria and is powered by the essential atpase seca. interestingly, mycobacteria and some gram-positive bacteria possess two seca proteins: seca1 and seca2. in these species, seca1 is responsible for exporting most proteins, whereas seca2 exports only a subset of substrates and is implicated in virulence. however, despite the impressive body of knowledge about the canonical seca1, less is known concerning seca2 fun ...201223000954
metallation and mismetallation of iron and manganese proteins in vitro and in vivo: the class i ribonucleotide reductases as a case study.how cells ensure correct metallation of a given protein and whether a degree of promiscuity in metal binding has evolved are largely unanswered questions. in a classic case, iron- and manganese-dependent superoxide dismutases (sods) catalyze the disproportionation of superoxide using highly similar protein scaffolds and nearly identical active sites. however, most of these enzymes are active with only one metal, although both metals can bind in vitro and in vivo. iron(ii) and manganese(ii) bind ...201222991063
role of rhizobium endoglucanase celc2 in cellulose biosynthesis and biofilm formation on plant roots and abiotic surfaces.the synthesis of cellulose is among the most important but poorly understood biochemical processes, especially in bacteria, due to its complexity and high degree of regulation. in this study, we analyzed both the production of cellulose by all known members of the rhizobiaceae and the diversity of rhizobium celabc operon predicted to be involved in cellulose biosynthesis. we also investigated the involvement in cellulose production and biofilm formation of celc gene encoding an endoglucanase (ce ...201222970813
simple and efficient methods to generate split roots and grafted plants useful for long-distance signaling studies in medicago truncatula and other small plants. 201222971438
the nsrr regulon in nitrosative stress resistance of salmonella enterica serovar typhimurium.nitric oxide (no·) is an important mediator of innate immunity. the facultative intracellular pathogen salmonella has evolved mechanisms to detoxify and evade the antimicrobial actions of host-derived no· produced during infection. expression of the no·-detoxifying flavohaemoglobin hmp is controlled by the no·-sensing transcriptional repressor nsrr and is required for salmonella virulence. in this study we show that nsrr responds to very low no· concentrations, suggesting that it plays a primary ...201222831173
unconventional initiator trnas sustain escherichia coli.of all trnas, initiator trna is unique in its ability to start protein synthesis by directly binding the ribosomal p-site. this ability is believed to derive from the almost universal presence of three consecutive g-c base (3g-c) pairs in the anticodon stem of initiator trna. consistent with the hypothesis, a plasmid-borne initiator trna with one, two, or all 3g-c pairs mutated displays negligible initiation activity when tested in a wt escherichia coli cell. given this, the occurrence of unconv ...201222829667
the metadata coverage index (mci): a standardized metric for quantifying database metadata richness.variability in the extent of the descriptions of data ('metadata') held in public repositories forces users to assess the quality of records individually, which rapidly becomes impractical. the scoring of records on the richness of their description provides a simple, objective proxy measure for quality that enables filtering that supports downstream analysis. pivotally, such descriptions should spur on improvements. here, we introduce such a measure - the 'metadata coverage index' (mci): the pe ...201223409217
identification of olivetolic acid cyclase from cannabis sativa reveals a unique catalytic route to plant polyketides.δ(9)-tetrahydrocannabinol (thc) and other cannabinoids are responsible for the psychoactive and medicinal properties of cannabis sativa l. (marijuana). the first intermediate in the cannabinoid biosynthetic pathway is proposed to be olivetolic acid (oa), an alkylresorcinolic acid that forms the polyketide nucleus of the cannabinoids. oa has been postulated to be synthesized by a type iii polyketide synthase (pks) enzyme, but so far type iii pkss from cannabis have been shown to produce catalytic ...201222802619
arabinogalactan proteins in root and pollen-tube cells: distribution and functional aspects.arabinogalactan proteins (agps) are complex proteoglycans of the cell wall found in the entire plant kingdom and in almost all plant organs. agps encompass a large group of heavily glycosylated cell-wall proteins which share common features, including the presence of glycan chains especially enriched in arabinose and galactose and a protein backbone particularly rich in hydroxyproline residues. however, agps also exhibit strong heterogeneities among their members in various plant species. agp ub ...201222786747
viperin: a radical response to viral infection.one of the first lines of defense of the host immune response to infection is upregulation of interferons, which play a vital role in triggering the early nonspecific antiviral state of the host. interferons prompt the generation of numerous downstream products, known as interferon-stimulated genes (isgs). one such isg found to be either directly induced by type i, ii, and iii interferons or indirectly through viral infection is the 'virus inhibitory protein, endoplasmic reticulum-associated, in ...201225254077
effect of arabinogalactan proteins from the root caps of pea and brassica napus on aphanomyces euteiches zoospore chemotaxis and germination.root tips of many plant species release a number of border, or border-like, cells that are thought to play a major role in the protection of root meristem. however, little is currently known on the structure and function of the cell wall components of such root cells. here, we investigate the sugar composition of the cell wall of the root cap in two species: pea (pisum sativum), which makes border cells, and brassica napus, which makes border-like cells. we find that the cell walls are highly en ...201222645070
evolution of burkholderia pseudomallei in recurrent melioidosis.burkholderia pseudomallei, the etiologic agent of human melioidosis, is capable of causing severe acute infection with overwhelming septicemia leading to death. a high rate of recurrent disease occurs in adult patients, most often due to recrudescence of the initial infecting strain. pathogen persistence and evolution during such relapsing infections are not well understood. bacterial cells present in the primary inoculum and in late infections may differ greatly, as has been observed in chronic ...201222615773
the languages spoken in the water body (or the biological role of cyanobacterial toxins).although intensification of toxic cyanobacterial blooms over the last decade is a matter of growing concern due to bloom impact on water quality, the biological role of most of the toxins produced is not known. in this critical review we focus primarily on the biological role of two toxins, microcystins and cylindrospermopsin, in inter- and intra-species communication and in nutrient acquisition. we examine the experimental evidence supporting some of the dogmas in the field and raise several op ...201222529842
interrogation of global active site occupancy of a fungal iterative polyketide synthase reveals strategies for maintaining biosynthetic fidelity.nonreducing iterative polyketide synthases (nr-pkss) are responsible for assembling the core of fungal aromatic natural products with diverse biological properties. despite recent advances in the field, many mechanistic details of polyketide assembly by these megasynthases remain unknown. to expand our understanding of substrate loading, polyketide elongation, cyclization, and product release, active site occupancy and product output were explored by fourier transform mass spectrometry using the ...201222452347
identification and characterization of γ-aminobutyric acid uptake system gabpcg (ncgl0464) in corynebacterium glutamicum.corynebacterium glutamicum is widely used for industrial production of various amino acids and vitamins, and there is growing interest in engineering this bacterium for more commercial bioproducts such as γ-aminobutyric acid (gaba). in this study, a c. glutamicum gaba-specific transporter (gabp(cg)) encoded by ncgl0464 was identified and characterized. gabp(cg) plays a major role in gaba uptake and is essential to c. glutamicum growing on gaba. gaba uptake by gabp(cg) was weakly competed by l-as ...201222307305
icmf family protein tssm exhibits atpase activity and energizes type vi secretion.the type vi secretion system (t6ss) with diversified functions is widely distributed in pathogenic proteobacteria. the icmf (intracellular multiplication protein f) family protein tssm is a conserved t6ss inner membrane protein. despite the conservation of its walker a nucleotide-binding motif, the ntpase activity of tssm and its role in t6ss remain obscure. in this study, we characterized tssm in the plant pathogen agrobacterium tumefaciens and provided the first biochemical evidence for tssm e ...201222393043
neisseria conserved protein dmp19 is a dna mimic protein that prevents dna binding to a hypothetical nitrogen-response transcription factor.dna mimic proteins occupy the dna binding sites of dna-binding proteins, and prevent these sites from being accessed by dna. we show here that the neisseria conserved hypothetical protein dmp19 acts as a dna mimic. the crystal structure of dmp19 shows a dsdna-like negative charge distribution on the surface, suggesting that this protein should be added to the short list of known dna mimic proteins. the crystal structure of another related protein, nhtf (neisseria hypothetical transcription facto ...201222373915
contribution of a genomic accessory region encoding a putative cellobiose phosphotransferase system to virulence of streptococcus pneumoniae.streptococcus pneumoniae (the pneumococcus) is a formidable human pathogen, responsible for massive global morbidity and mortality. the ability to utilize carbohydrates in a variety of host niches appears to be integral to pneumococcal pathogenesis. in this study we investigated a genomic island, which includes a rok family protein, a putative cellobiose phosphotransferase system (pts) and a putative sulfatase. this accessory region is widespread in the pneumococcus in strains of various serotyp ...201222363821
synthetic biological approaches to natural product biosynthesis.small molecules produced in nature possess exquisite chemical diversity and continue to be an inspiration for the development of new therapeutic agents. in their host organisms, natural products are assembled and modified using dedicated biosynthetic pathways. by rationally reprogramming and manipulating these pathways, unnatural metabolites containing enhanced structural features that were otherwise inaccessible can be obtained. additionally, new chemical entities can be synthesized by developi ...201222221832
characterization of nitric oxide-inducing lipid a derived from mesorhizobium loti lipopolysaccharide.mesorhizobium loti is a member of the rhizobia and forms nitrogen-fixing symbioses with several lotus species. recently, it was reported that m. loti bacterial cells and their lipopolysaccharide (lps) preparations transiently induced nitric oxide (no) production in the roots of l. japonicus. we subsequently found that polysaccharides and the lipid a moiety were responsible for this no induction. in this study, we elucidated the chemical structure of m. loti lipid a and characterized its no-induc ...201223059724
sequence, structure and functional diversity of pd-(d/e)xk phosphodiesterase superfamily.proteins belonging to pd-(d/e)xk phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, dna repair and trna-intron splicing. their malfunction in humans triggers severe diseases, such as fanconi anemia and xeroderma pigmentosum. to date there have been several attempts to identify and classify new pd-(d/e)kk phosphodiesterases using remote homology detection methods. such efforts are complicated, because the superfamily exhibit ...201222638584
keys to eukaryality: planctomycetes and ancestral evolution of cellular complexity.planctomycetes are known to display compartmentalization via internal membranes, thus resembling eukaryotes. significantly, the planctomycete gemmata obscuriglobus has not only a nuclear region surrounded by a double-membrane, but is also capable of protein uptake via endocytosis. in order to clearly analyze implications for homology of their characters with eukaryotes, a correct understanding of planctomycete structure is an essential starting point. here we outline the major features of such s ...201222586422
intruders below the radar: molecular pathogenesis of bartonella spp.summary: bartonella spp. are facultative intracellular pathogens that employ a unique stealth infection strategy comprising immune evasion and modulation, intimate interaction with nucleated cells, and intraerythrocytic persistence. infections with bartonella are ubiquitous among mammals, and many species can infect humans either as their natural host or incidentally as zoonotic pathogens. upon inoculation into a naive host, the bartonellae first colonize a primary niche that is widely accepted ...201222232371
mercury-resistant rhizobial bacteria isolated from nodules of leguminous plants growing in high hg-contaminated soils.a survey of symbiotic bacteria from legumes grown in high mercury-contaminated soils (almadén, spain) was performed to produce a collection of rhizobia which could be well adapted to the environmental conditions of this region and be used for restoration practices. nineteen hg-tolerant rhizobia were isolated from nodules of 11 legume species (of the genera medicago, trifolium, vicia, lupinus, phaseolus, and retama) and characterized. based on their growth on hg-supplemented media, the isolates w ...201222246528
comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, gujarat, india.soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to co2 dynamics in soil. in this study, we used culture dependent and independent methods to assess the community structure and diversity of chemolithoautotrophs in agricultural and coastal barren saline soils (low and high salinity). we studied the composition and distribution of chemolithoautotrophs by means of functional marker gene cbbl encoding large subunit of ribulo ...201222834535
phylogenomics of prokaryotic ribosomal proteins.archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. we developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 arch ...201222615861
greenhouse studies of thiamethoxam effects on pea leaf weevil, sitona lineatus.the pea leaf weevil, sitona lineatus l. (coleoptera: curculionidae), has recently emerged as an important pest of field peas in the canadian prairies. systemic seed-coated insecticides may provide a tool for the integrated pest management of this pest. therefore, several controlled assays were performed in order to determine effects of a recently registered neonicotinoid, (thiamethoxam) on s. lineatus damage to foliage, weevil mortality, fertility, egg viability, larval mortality, and root nodul ...201223461362
evaluation of the effects of erythritol on gene expression in brucella abortus.bacteria of the genus brucella have the unusual capability to catabolize erythritol and this property has been associated with their virulence mainly because of the presence of erythritol in bovine foetal tissues and because the attenuated s19 vaccine strain is the only brucella strain unable to oxydize erythritol. in this work we have analyzed the transcriptional changes produced in brucella by erythritol by means of two high throughput approaches: rna hybridization against a microarray contain ...201223272076
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 ...201223270491
quorum sensing: a nobel target for antibacterial agents. 201223826557
structural changes in medicago truncatula root nodules caused by short-term aluminum stress.aluminum in the form of al(3+) is one of the most toxic heavy metal pollutants in nature and its effects are primarily root-related. roots of medicago truncatula exposed to 50 μm of alcl3 for 2 h and 24 h were examined by light and electron microscopy. changes in the appearance of the host cells, infection threads and bacteroidal tissue occurred during the first 2 h of al stress. microscopic observations showed that aluminum: (1) induced thickening of plant cell and infection threads (its) walls ...201223482822
Substitutions in the BamA ß-Barrel Domain Overcome the Conditional Lethal Phenotype of a {Delta}bamB {Delta}bamE Strain of Escherichia coli.BamA interacts with the BamBCDE lipoproteins, and together they constitute the essential ß-barrel assembly machine (BAM) of Escherichia coli. The simultaneous absence of BamB and BamE confers a conditional lethal phenotype and a severe ß-barrel outer membrane protein (OMP) biogenesis defect. Without BamB and BamE, wild-type BamA levels are significantly reduced, and the folding of the BamA ß-barrel, as assessed by the heat-modifiability assay, is drastically compromised. Single-amino-acid substi ...201222037403
wide variation in antibiotic resistance proteins identified by functional metagenomic screening of a soil dna library.most genes for antibiotic resistance present in soil microbes remain unexplored because most environmental microbes cannot be cultured. only recently has the identification of these genes become feasible through the use of culture-independent methods. we screened a soil metagenomic dna library in an escherichia coli host for genes that can confer resistance to kanamycin, gentamicin, rifampin, trimethoprim, chloramphenicol, or tetracycline. the screen revealed 41 genes that encode novel protein v ...201222247132
specific metal recognition in nickel trafficking.nickel is an essential metal for a number of bacterial species that have developed systems for acquiring, delivering, and incorporating the metal into target enzymes and controlling the levels of nickel in cells to prevent toxic effects. as with other transition metals, these trafficking systems must be able to distinguish between the desired metal and other transition metal ions with similar physical and chemical properties. because there are few enzymes (targets) that require nickel for activi ...201222970729
the main aeromonas pathogenic factors.the members of the aeromonas genus are ubiquitous, water-borne bacteria. they have been isolated from marine waters, rivers, lakes, swamps, sediments, chlorine water, water distribution systems, drinking water and residual waters; different types of food, such as meat, fish, seafood, vegetables, and processed foods. aeromonas strains are predominantly pathogenic to poikilothermic animals, and the mesophilic strains are emerging as important pathogens in humans, causing a variety of extraintestin ...201223724321
the role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription.bacterial enhancer binding proteins (bebps) are transcriptional activators that assemble as hexameric rings in their active forms and utilize atp hydrolysis to remodel the conformation of rna polymerase containing the alternative sigma factor σ(54). we present a comprehensive and detailed summary of recent advances in our understanding of how these specialized molecular machines function. the review is structured by introducing each of the three domains in turn: the central catalytic domain, the ...201222933558
bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control.under a shortage of oxygen, bacterial growth can be faced mainly by two atp-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. this bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells ...201222098259
signature tagged mutagenesis in the functional genetic analysis of gastrointestinal pathogens.signature tagged mutagenesis is a genetic approach that was developed to identify novel bacterial virulence factors. it is a negative selection method in which unique identification tags allow analysis of pools of mutants in mixed populations. the approach is particularly well suited to functional genetic analysis of the gastrointestinal phase of infection in foodborne pathogens and has the capacity to guide the development of novel vaccines and therapeutics. in this review we outline the techni ...201222555467
prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. the existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. ...201223185476
revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen pectobacterium wasabiae scc3193.soft rot disease is economically one of the most devastating bacterial diseases affecting plants worldwide. in this study, we present novel insights into the phylogeny and virulence of the soft rot model pectobacterium sp. scc3193, which was isolated from a diseased potato stem in finland in the early 1980s. genomic approaches, including proteome and genome comparisons of all sequenced soft rot bacteria, revealed that scc3193, previously included in the species pectobacterium carotovorum, can no ...201223133391
microbial diversity of vermicompost bacteria that exhibit useful agricultural traits and waste management potential.vermicomposting is a non-thermophilic, boioxidative process that involves earthworms and associated microbes. this biological organic waste decomposition process yields the biofertilizer namely the vermicompost. vermicompost is a finely divided, peat like material with high porosity, good aeration, drainage, water holding capacity, microbial activity, excellent nutrient status and buffering capacity thereby resulting the required physiochemical characters congenial for soil fertility and plant g ...201223961356
genome sequence of azospirillum brasilense cbg497 and comparative analyses of azospirillum core and accessory genomes provide insight into niche adaptation.bacteria of the genus azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. the genomes of several azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. in this study, an additional genome of an a. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of mexico, strain cbg497, was obtained. compa ...201224705077
reactive oxygen species-inducible ecf σ factors of bradyrhizobium japonicum.extracytoplasmic function (ecf) σ factors control the transcription of genes involved in different cellular functions, such as stress responses, metal homeostasis, virulence-related traits, and cell envelope structure. the genome of bradyrhizobium japonicum, the nitrogen-fixing soybean endosymbiont, encodes 17 putative ecf σ factors belonging to nine different ecf σ factor families. the genes for two of them, ecfq (bll1028) and ecff (blr3038), are highly induced in response to the reactive oxyge ...201222916258
simple absolute quantification method correcting for quantitative pcr efficiency variations for microbial community samples.real-time quantitative pcr (qpcr) is a widely used technique in microbial community analysis, allowing the quantification of the number of target genes in a community sample. currently, the standard-curve (sc) method of absolute quantification is widely employed for these kinds of analysis. however, the sc method assumes that the amplification efficiency (e) is the same for both the standard and the sample target template. we analyzed 19 bacterial strains and nine environmental samples in qpcr a ...201222492459
respiratory membrane endo-hydrogenase activity in the microaerophile azorhizobium caulinodans is bidirectional.the microaerophilic bacterium azorhizobium caulinodans, when fixing n(2) both in pure cultures held at 20 µm dissolved o(2) tension and as endosymbiont of sesbania rostrata legume nodules, employs a novel, respiratory-membrane endo-hydrogenase to oxidize and recycle endogenous h(2) produced by soluble mo-dinitrogenase activity at the expense of o(2).201222662125
whole genome analysis of leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.the whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (leptospira licerasiae strains var010 and mmd0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including l. licerasiae) that are likely to be pa ...201223145189
characterization of the genome, proteome, and structure of yersiniophage ϕr1-37.the bacteriophage vb_yecm-ϕr1-37 (ϕr1-37) is a lytic yersiniophage that can propagate naturally in different yersinia species carrying the correct lipopolysaccharide receptor. this large-tailed phage has deoxyuridine (du) instead of thymidine in its dna. in this study, we determined the genomic sequence of phage ϕr1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. t ...201222973030
a positive correlation between bacterial autoaggregation and biofilm formation in native sinorhizobium meliloti isolates from argentina.sinorhizobium meliloti is a symbiotic nitrogen-fixing bacterium that elicits nodule formation on roots of alfalfa plants. s. meliloti produces two exopolysaccharides (epss), termed eps i and eps ii, that are both able to promote symbiosis. eps i and eps ii are secreted in two major fractions that reflect differing degrees of subunit polymerization, designated high- and low-molecular-weight fractions. we reported previously that epss are crucial for autoaggregation and biofilm formation in s. mel ...201222492433
metagenomic analysis of streptomyces lividans reveals host-dependent functional expression.most functional metagenomic studies have been limited by the poor expression of many genes derived from metagenomic dna in escherichia coli, which has been the predominant surrogate host to date. to expand the range of expressed genes, we developed tools for construction and functional screening of metagenomic libraries in streptomyces lividans. we expanded on previously published protocols by constructing a system that enables retrieval and characterization of the metagenomic dna from biologica ...201222427497
mucosal immunization with live attenuated francisella novicida u112δiglb protects against pulmonary f. tularensis schu s4 in the fischer 344 rat model.the need for an efficacious vaccine against francisella tularensis is a consequence of its low infectious dose and high mortality rate if left untreated. this study sought to characterize a live attenuated subspecies novicida-based vaccine strain (u112δiglb) in an established second rodent model of pulmonary tularemia, namely the fischer 344 rat using two distinct routes of vaccination (intratracheal [i.t.] and oral). attenuation was verified by comparing replication of u112δiglb with wild type ...201223118885
plasticity of rhizosphere hydraulic properties as a key for efficient utilization of scarce resources.it is known that the soil near roots, the so-called rhizosphere, has physical and chemical properties different from those of the bulk soil. rhizosphere properties are the result of several processes: root and soil shrinking/swelling during drying/wetting cycles, soil compaction by root growth, mucilage exuded by root caps, interaction of mucilage with soil particles, mucilage shrinking/swelling and mucilage biodegradation. these processes may lead to variable rhizosphere properties, i.e. the pr ...201223235697
plasticity of rhizosphere hydraulic properties as a key for efficient utilization of scarce resources.it is known that the soil near roots, the so-called rhizosphere, has physical and chemical properties different from those of the bulk soil. rhizosphere properties are the result of several processes: root and soil shrinking/swelling during drying/wetting cycles, soil compaction by root growth, mucilage exuded by root caps, interaction of mucilage with soil particles, mucilage shrinking/swelling and mucilage biodegradation. these processes may lead to variable rhizosphere properties, i.e. the pr ...201223235697
polysac3db: an annotated data base of 3 dimensional structures of polysaccharides.polysaccharides are ubiquitously present in the living world. their structural versatility makes them important and interesting components in numerous biological and technological processes ranging from structural stabilization to a variety of immunologically important molecular recognition events. the knowledge of polysaccharide three-dimensional (3d) structure is important in studying carbohydrate-mediated host-pathogen interactions, interactions with other bio-macromolecules, drug design and ...201223151233
rhizobium promotes non-legumes growth and quality in several production steps: towards a biofertilization of edible raw vegetables healthy for humans.the biofertilization of crops with plant-growth-promoting microorganisms is currently considered as a healthy alternative to chemical fertilization. however, only microorganisms safe for humans can be used as biofertilizers, particularly in vegetables that are raw consumed, in order to avoid sanitary problems derived from the presence of pathogenic bacteria in the final products. in the present work we showed that rhizobium strains colonize the roots of tomato and pepper plants promoting their g ...201222675441
stereochemical insignificance discovered in acinetobacter baumannii quorum sensing.stereochemistry is a key aspect of molecular recognition for biological systems. as such, receptors and enzymes are often highly stereospecific, only recognizing one stereoisomer of a ligand. recently, the quorum sensing signaling molecules used by the nosocomial opportunistic pathogen, acinetobacter baumannii, were identified, and the primary signaling molecule isolated from this species was n-(3-hydroxydodecanoyl)-l-homoserine lactone. a plethora of bacterial species have been demonstrated to ...201222629354
detection, characterization, and biological effect of quorum-sensing signaling molecules in peanut-nodulating bradyrhizobia.bacteria of the genus bradyrhizobium are able to establish a symbiotic relationship with peanut (arachis hypogaea) root cells and to fix atmospheric nitrogen by converting it to nitrogenous compounds. quorum sensing (qs) is a cell-cell communication mechanism employed by a variety of bacterial species to coordinate behavior at a community level through regulation of gene expression. the qs process depends on bacterial production of various signaling molecules, among which the n-acylhomoserine la ...201222736981
characterization of the flavonoid-responsive regulator frra and its binding sites.previous microarray analyses revealed that in bradyrhizobium japonicum, about 100 genes are induced by genistein, an isoflavonoid secreted by soybean. this includes the three genes frec, frea, and freb (systematic designations bll4319, bll4320, and bll4321), which are likely to form a genistein-, daidzein-, and coumestrol-inducible operon and to encode a multidrug efflux system. upstream of frecab and in the opposite orientation, frra (systematic designation blr4322), which has similarity to tet ...201222389485
dual role of hupf in the biosynthesis of [nife] hydrogenase in rhizobium leguminosarum.[nife] hydrogenases are enzymes that catalyze the oxidation of hydrogen into protons and electrons, to use h₂ as energy source, or the production of hydrogen through proton reduction, as an escape valve for the excess of reduction equivalents in anaerobic metabolism. biosynthesis of [nife] hydrogenases is a complex process that occurs in the cytoplasm, where a number of auxiliary proteins are required to synthesize and insert the metal cofactors into the enzyme structural units. the endosymbioti ...201223136881
bacterial iron-sulfur regulatory proteins as biological sensor-switches.in recent years, bacterial iron-sulfur cluster proteins that function as regulators of gene transcription have emerged as a major new group. in all cases, the cluster acts as a sensor of the environment and enables the organism to adapt to the prevailing conditions. this can range from mounting a response to oxidative or nitrosative stress to switching between anaerobic and aerobic respiratory pathways. the sensitivity of these ancient cofactors to small molecule reactive oxygen and nitrogen spe ...201222239203
the gtar protein negatively regulates transcription of the gtari operon and modulates gene transfer agent (rcgta) expression in rhodobacter capsulatus.the gtai gene of rhodobacter capsulatus encodes an n-acyl-homoserine lactone (acyl-hsl) synthase. immediately 5' of the gtai gene is orf rcc00328 that encodes a potential acyl-hsl receptor protein. a combination of genetic and biochemical approaches showed that rcc00328 (renamed gtar) modulates the production of a genetic exchange element called the gene transfer agent (rcgta), and regulates the transcription of gtai. although gtai mutants exhibited decreased levels of rcgta production, mutagene ...201222211723
mining the sinorhizobium meliloti transportome to develop fret biosensors for sugars, dicarboxylates and cyclic polyols.förster resonance energy transfer (fret) biosensors are powerful tools to detect biologically important ligands in real time. currently fret bisosensors are available for twenty-two compounds distributed in eight classes of chemicals (two pentoses, two hexoses, two disaccharides, four amino acids, one nucleobase, two nucleotides, six ions and three phytoestrogens). to expand the number of available fret biosensors we used the induction profile of the sinorhizobium meliloti transportome to system ...201223028462
molecular characterization of nad+-dependent dna ligase from wolbachia endosymbiont of lymphatic filarial parasite brugia malayi.the lymphatic filarial parasite, brugia malayi contains wolbachia endobacteria that are essential for development, viability and fertility of the parasite. therefore, wolbachial proteins have been currently seen as the potential antifilarial drug targets. nad(+)-dependent dna ligase is characterized as a promising drug target in several organisms due to its crucial, indispensable role in dna replication, recombination and dna repair. we report here the cloning, expression and purification of nad ...201222815933
lon protease of azorhizobium caulinodans ors571 is required for suppression of reb gene expression.bacterial lon proteases play important roles in a variety of biological processes in addition to housekeeping functions. in this study, we focused on the lon protease of azorhizobium caulinodans, which can fix nitrogen both during free-living growth and in stem nodules of the legume sesbania rostrata. the nitrogen fixation activity of an a. caulinodans lon mutant in the free-living state was not significantly different from that of the wild-type strain. however, the stem nodules formed by the lo ...201222752172
defining sequence space and reaction products within the cyanuric acid hydrolase (atzd)/barbiturase protein family.cyanuric acid hydrolases (atzd) and barbiturases are homologous, found almost exclusively in bacteria, and comprise a rare protein family with no discernible linkage to other protein families or an x-ray structural class. there has been confusion in the literature and in genome projects regarding the reaction products, the assignment of individual sequences as either cyanuric acid hydrolases or barbiturases, and spurious connection of this family to another protein family. the present study has ...201222730121
expression of phenazine biosynthetic genes during the arbuscular mycorrhizal symbiosis of glomus intraradices.to explore the molecular mechanisms that prevail during the establishment of the arbuscular mycorrhiza symbiosis involving the genus glomus, we transcriptionally analysed spores of glomus intraradices be3 during early hyphal growth. among 458 transcripts initially identified as being expressed at presymbiotic stages, 20% of sequences had homology to previously characterized eukaryotic genes, 30% were homologous to fungal coding sequences, and 9% showed homology to previously characterized bacter ...201224031884
comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations.the rhizobium-legume symbiosis has been widely studied as the model of mutualistic evolution and the essential component of sustainable agriculture. extensive genetic and recent genomic studies have led to the hypothesis that many distinct strategies, regardless of rhizobial phylogeny, contributed to the varied rhizobium-legume symbiosis. we sequenced 26 genomes of sinorhizobium and bradyrhizobium nodulating soybean to test this hypothesis. the bradyrhizobium core genome is disproportionally enr ...201222586130
nontarget effects of foliar fungicide application on the rhizosphere: diversity of nifh gene and nodulation in chickpea field.this study explores nontarget effects of fungicide application on field-grown chickpea.201222335393
nad(p)+-malic enzyme mutants of sinorhizobium sp. strain ngr234, but not azorhizobium caulinodans ors571, maintain symbiotic n2 fixation capabilities.c(4)-dicarboxylic acids appear to be metabolized via the tricarboxylic acid (tca) cycle in n(2)-fixing bacteria (bacteroids) within legume nodules. in sinorhizobium meliloti bacteroids from alfalfa, nad(+)-malic enzyme (dme) is required for n(2) fixation, and this activity is thought to be required for the anaplerotic synthesis of pyruvate. in contrast, in the pea symbiont rhizobium leguminosarum, pyruvate synthesis occurs via either dme or a pathway catalyzed by phosphoenolpyruvate carboxykinas ...201222307295
thiol synthetases of legumes: immunogold localization and differential gene regulation by phytohormones.in plants and other organisms, glutathione (gsh) biosynthesis is catalysed sequentially by γ-glutamylcysteine synthetase (γecs) and glutathione synthetase (gshs). in legumes, homoglutathione (hgsh) can replace gsh and is synthesized by γecs and a specific homoglutathione synthetase (hgshs). the subcellular localization of the enzymes was examined by electron microscopy in several legumes and gene expression was analysed in lotus japonicus plants treated for 1-48 h with 50 μm of hormones. immunog ...201222442424
the genetics of symbiotic nitrogen fixation: comparative genomics of 14 rhizobia strains by resolution of protein clusters.the symbiotic relationship between legumes and nitrogen fixing bacteria is critical for agriculture, as it may have profound impacts on lowering costs for farmers, on land sustainability, on soil quality, and on mitigation of greenhouse gas emissions. however, despite the importance of the symbioses to the global nitrogen cycling balance, very few rhizobial genomes have been sequenced so far, although there are some ongoing efforts in sequencing elite strains. in this study, the genomes of fourt ...201224704847
quantitative proteomic analysis of the hfq-regulon in sinorhizobium meliloti 2011.riboregulation stands for rna-based control of gene expression. in bacteria, small non-coding rnas (srnas) are a major class of riboregulatory elements, most of which act at the post-transcriptional level by base-pairing target mrna genes. the rna chaperone hfq facilitates antisense interactions between target mrnas and regulatory srnas, thus influencing mrna stability and/or translation rate. in the α-proteobacterium sinorhizobium meliloti strain 2011, the identification and detection of multip ...201223119037
comparative genomics of early-diverging brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.brucella species are gram-negative bacteria that infect mammals. recently, two unusual strains (brucella inopinata bo1(t) and b. inopinata-like bo2) have been isolated from human patients, and their similarity to some atypical brucellae isolated from australian native rodent species was noted. here we present a phylogenomic analysis of the draft genome sequences of bo1(t) and bo2 and of the australian rodent strains 83-13 and nf2653 that shows that they form two groups well separated from the ot ...201222930339
role of the irr protein in the regulation of iron metabolism in rhodobacter sphaeroides.in rhizobia the irr protein is an important regulator for iron-dependent gene expression. we studied the role of the irr homolog rsp_3179 in the photosynthetic alpha-proteobacterium rhodobacter sphaeroides. while irr had little effect on growth under iron-limiting or non-limiting conditions its deletion resulted in increased resistance to hydrogen peroxide and singlet oxygen. this correlates with an elevated expression of kate for catalase in the irr mutant compared to the wild type under non-st ...201222879920
genome, integration, and transduction of a novel temperate phage of helicobacter pylori.helicobacter pylori is a common human pathogen that has been identified to be carcinogenic. this study isolated the temperate bacteriophage 1961p from the lysate of a clinical strain of h. pylori isolated in taiwan. the bacteriophage has an icosahedral head and a short tail, typical of the podoviridae family. its double-stranded dna genome is 26,836 bp long and has 33 open reading frames. only 9 of the predicted proteins have homologs of known functions, while the remaining 24 are only similar t ...201222696647
sinorhizobium meliloti exor is the target of periplasmic proteolysis.sinorhizobium meliloti exor regulates the production of succinoglycan and flagella through the exos/chvi two-component regulatory system. exor has been proposed to inhibit the exos sensor through direct interaction in the periplasm. to understand how exor suppression of exos is relieved, which is required for the expression of exos/chvi-regulated symbiosis genes, we characterized wild-type exor and exor95 mutant proteins. in addition to the previously identified precursor and mature forms of exo ...201222636773
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