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conformational changes associated with the binding of zinc acetate at the putative active site of xctcmj, a cupin from xanthomonas campestris pv. campestris.in the plant pathogen xanthomonas campestris pv. campestris, the product of the tcmj gene, xctcmj, encodes a protein belonging to the rmlc family of cupins. xctcmj was crystallized in a monoclinic space group (c2) in the presence of zinc acetate and the structure was determined to 1.6 å resolution. previously, the apo structure has been reported in the absence of any bound metal ion [chin et al. (2006), proteins, 65, 1046-1050]. the most significant difference between the apo structure and the s ...201020944231
conformational changes associated with the binding of zinc acetate at the putative active site of xctcmj, a cupin from xanthomonas campestris pv. campestris.in the plant pathogen xanthomonas campestris pv. campestris, the product of the tcmj gene, xctcmj, encodes a protein belonging to the rmlc family of cupins. xctcmj was crystallized in a monoclinic space group (c2) in the presence of zinc acetate and the structure was determined to 1.6 å resolution. previously, the apo structure has been reported in the absence of any bound metal ion [chin et al. (2006), proteins, 65, 1046-1050]. the most significant difference between the apo structure and the s ...201020944231
metabolic stress-induced programmed cell death in xanthomonas.xanthomonas campestris pv. glycines (xcg), an etiological agent of the bacterial pustule disease of soybean, displayed nutritionally regulated caspase-dependent programmed cell death (pcd). experiments showed that xcg was under metabolic stress during pcd, as evident from the intracellular accumulation of nadh and atp. further, the accumulation of reactive oxygen species (ros), as confirmed by 2',7'-dichlorofluorescein diacetate labeling, electron spin resonance spectroscopy, and scopoletin assa ...201020958788
insights into the extracytoplasmic stress response of xanthomonas campestris pv. campestris: role and regulation of {sigma}e-dependent activity.xanthomonas campestris pv. campestris is an epiphytic bacterium that can become a vascular pathogen responsible for black rot disease of crucifers. to adapt gene expression in response to ever-changing habitats, phytopathogenic bacteria have evolved signal transduction regulatory pathways, such as extracytoplasmic function (ecf) σ factors. the alternative sigma factor σ(e), encoded by rpoe, is crucial for envelope stress response and plays a role in the pathogenicity of many bacterial species. h ...201020971899
insights into the extracytoplasmic stress response of xanthomonas campestris pv. campestris: role and regulation of {sigma}e-dependent activity.xanthomonas campestris pv. campestris is an epiphytic bacterium that can become a vascular pathogen responsible for black rot disease of crucifers. to adapt gene expression in response to ever-changing habitats, phytopathogenic bacteria have evolved signal transduction regulatory pathways, such as extracytoplasmic function (ecf) σ factors. the alternative sigma factor σ(e), encoded by rpoe, is crucial for envelope stress response and plays a role in the pathogenicity of many bacterial species. h ...201020971899
homologue structure of the slac1 anion channel for closing stomata in leaves.the plant slac1 anion channel controls turgor pressure in the aperture-defining guard cells of plant stomata, thereby regulating the exchange of water vapour and photosynthetic gases in response to environmental signals such as drought or high levels of carbon dioxide. here we determine the crystal structure of a bacterial homologue (haemophilus influenzae) of slac1 at 1.20 å resolution, and use structure-inspired mutagenesis to analyse the conductance properties of slac1 channels. slac1 is a sy ...201020981093
copper ions potentiate organic hydroperoxide and hydrogen peroxide toxicity through different mechanisms in xanthomonas campestris pv. campestris.copper (cu)-based biocides are important chemical controls for both fungal and bacterial diseases in crop fields. here, we showed that cu ions at a concentration of 100 μm enhanced t-butyl hydroperoxide (tbooh) and hydrogen peroxide (h(2) o(2) ) killing of xanthomonas campestris pv. campestris through different mechanisms. the addition of an antilipid peroxidation agent (α-tocopherol) and hydroxyl radical scavengers (glycerol and dimethyl sulphoxide) partially protected the bacteria from the cu- ...201021029152
expression of sweet pepper hrap gene in banana enhances resistance to xanthomonas campestris pv. musacearum.banana xanthomonas wilt (bxw), caused by the bacterium xanthomonas campestris pv. musacearum, is the most devastating disease of banana in the great lakes region of africa. the pathogen's rapid spread has threatened the livelihood of millions of africans who rely on banana fruit for food security and income. the disease is very destructive, infecting all banana varieties, including both east african highland bananas and exotic types of banana. in the absence of natural host plant resistance amon ...201021029318
effector-triggered innate immunity contributes arabidopsis resistance to xanthomonas campestris.xanthomonas campestris pv. campestris, the causal agent of black rot disease, depends on its type iii secretion system (ttss) to infect cruciferous plants, including brassica oleracea, b. napus and arabidopsis. previous studies on the arabidopsis-pseudomonas syringae model pathosystem have indicated that a major function of ttss from virulent bacteria is to suppress host defences triggered by pathogen-associated molecular patterns. similar analyses have not been made for the arabidopsis-x. campe ...201021029323
development of an efficient real-time quantitative pcr protocol for detection of xanthomonas arboricola pv. pruni in prunus species.xanthomonas arboricola pv. pruni, the causal agent of bacterial spot disease of stone fruit, is considered a quarantine organism by the european union and the european and mediterranean plant protection organization (eppo). the bacterium can undergo an epiphytic phase and/or be latent and can be transmitted by plant material, but currently, only visual inspections are used to certify plants as being x. arboricola pv. pruni free. a novel and highly sensitive real-time taqman pcr detection protoco ...201021037298
development of an efficient real-time quantitative pcr protocol for detection of xanthomonas arboricola pv. pruni in prunus species.xanthomonas arboricola pv. pruni, the causal agent of bacterial spot disease of stone fruit, is considered a quarantine organism by the european union and the european and mediterranean plant protection organization (eppo). the bacterium can undergo an epiphytic phase and/or be latent and can be transmitted by plant material, but currently, only visual inspections are used to certify plants as being x. arboricola pv. pruni free. a novel and highly sensitive real-time taqman pcr detection protoco ...201021037298
a fadd mutant of vibrio cholerae is impaired in the production of virulence factors and membrane localization of the virulence regulatory protein tcpp.in the enteric pathogen vibrio cholerae, expression of the major virulence factors is controlled by the hierarchical expression of several regulatory proteins comprising the toxr regulon. in this study, we demonstrate that disruption of the fadd gene encoding a long-chain fatty acyl coenzyme a ligase has marked effects on expression of the toxr virulence regulon, motility, and in vivo lethality of v. cholerae. in the v. cholerae fadd mutant, expression of the major virulence genes ctxab and tcpa ...201021041490
a fadd mutant of vibrio cholerae is impaired in the production of virulence factors and membrane localization of the virulence regulatory protein tcpp.in the enteric pathogen vibrio cholerae, expression of the major virulence factors is controlled by the hierarchical expression of several regulatory proteins comprising the toxr regulon. in this study, we demonstrate that disruption of the fadd gene encoding a long-chain fatty acyl coenzyme a ligase has marked effects on expression of the toxr virulence regulon, motility, and in vivo lethality of v. cholerae. in the v. cholerae fadd mutant, expression of the major virulence genes ctxab and tcpa ...201021041490
multiple fadd acyl-coa synthetases contribute to differential fatty acid degradation and virulence in pseudomonas aeruginosa.a close interconnection between nutrient metabolism and virulence factor expression contributes to the pathophysiology of pseudomonas aeruginosa as a successful pathogen. p. aeruginosa fatty acid (fa) degradation is complicated with multiple acyl-coa synthetase homologs (fadds) expressed in vivo in lung tissue during cystic fibrosis infections. the promoters of two genetically linked p. aeruginosa fadd genes (fadd1 and fadd2) were mapped and northern blot analysis indicated they could exist on t ...201021042406
in silico prediction of human pathogenicity in the γ-proteobacteria.although the majority of bacteria are innocuous or even beneficial for their host, others are highly infectious pathogens that can cause widespread and deadly diseases. when investigating the relationships between bacteria and other living organisms, it is therefore essential to be able to separate pathogenic organisms from non-pathogenic ones. using traditional experimental methods for this purpose can be very costly and time-consuming, and also uncertain since animal models are not always good ...201021048922
tomato mapkkkε is a positive regulator of cell-death signaling networks associated with plant immunity.mitogen-activated protein (map) kinase cascades are fundamental components of the signaling pathways associated with plant immunity. despite the large number of map kinase kinase kinases (mapkkk) encoded in the plant genome, only very few of them have an assigned function. here, we identified mapkkk gene of tomato (solanum lycopersicum), simapkkkε, which is required for hypersensitive response cell death and disease resistance against gram-negative bacterial pathogens. silencing of simapkkkε com ...201021049563
epr and mössbauer spectroscopy show inequivalent hemes in tryptophan dioxygenase.tryptophan 2,3-dioxygenase (tdo) is an essential enzyme in the pathway of nad biosynthesis and important for all living organisms. tdo catalyzes oxidative cleavage of the indole ring of l-tryptophan (l-trp), converting it to n-formylkynurenine (nfk). the crystal structure of tdo shows a dimer of dimer quaternary structure of the homotetrameric protein. the four catalytic sites of the protein, one per subunit, contain a heme that catalyzes the activation and insertion of dioxygen into l-trp. beca ...201020047315
a novel pepper (capsicum annuum) receptor-like kinase functions as a negative regulator of plant cell death via accumulation of superoxide anions.plant receptor-like kinases belong to a large gene family. the capsicum annuum receptor-like kinase 1 (carlk1) gene encodes a transmembrane protein with a cytoplasmic kinase domain and an extracellular domain. the carlk1 extracellular domain (ecd)-green fluorescent protein (gfp) fusion protein was targeted to the plasma membrane, and the kinase domain of the carlk1 protein exhibited autophosphorylation activity. carlk1 transcripts were more strongly induced in treatment with xag8ra than in treat ...201020002319
the camp receptor-like protein clp is a novel c-di-gmp receptor linking cell-cell signaling to virulence gene expression in xanthomonas campestris.cyclic-di-gmp [bis-(3'-5')-cyclic diguanosine monophosphate] controls a wide range of functions in eubacteria, yet little is known about the underlying regulatory mechanisms. in the plant pathogen xanthomonas campestris, expression of a subset of virulence genes is regulated by c-di-gmp and also by the cap (catabolite activation protein)-like protein xcclp, a global regulator in the crp/fnr superfamily. here, we report structural and functional insights into the interplay between xcclp and c-di- ...201020004667
the cyclic nucleotide monophosphate domain of xanthomonas campestris global regulator clp defines a new class of cyclic di-gmp effectors.the widely conserved second messenger cyclic diguanosine monophosphate (c-di-gmp) plays a key role in quorum-sensing (qs)-dependent production of virulence factors in xanthomonas campestris pv. campestris. the detection of qs diffusible signal factor (dsf) by the sensor rpfc leads to the activation of response regulator rpfg, which activates virulence gene expression by degrading c-di-gmp. here, we show that a global regulator in the x. campestris pv. campestris qs regulatory pathway, clp, is a ...201020008070
the cyclic nucleotide monophosphate domain of xanthomonas campestris global regulator clp defines a new class of cyclic di-gmp effectors.the widely conserved second messenger cyclic diguanosine monophosphate (c-di-gmp) plays a key role in quorum-sensing (qs)-dependent production of virulence factors in xanthomonas campestris pv. campestris. the detection of qs diffusible signal factor (dsf) by the sensor rpfc leads to the activation of response regulator rpfg, which activates virulence gene expression by degrading c-di-gmp. here, we show that a global regulator in the x. campestris pv. campestris qs regulatory pathway, clp, is a ...201020008070
prhg, a transcriptional regulator responding to growth conditions, is involved in the control of the type iii secretion system regulon in ralstonia solanacearum.the ability of ralstonia solanacearum to cause disease in plants depends on its type iii secretion system (t3ss). the expression of the t3ss and its effector substrates is coordinately controlled by a regulatory cascade, at the bottom of which is hrpb. transcription of the hrpb gene is activated by a plant-responsive regulator named hrpg, which is a master regulator of a wide array of pathogenicity functions in r. solanacearum. we have identified in the genome of strain gmi1000 a close paralog o ...201020008073
prhg, a transcriptional regulator responding to growth conditions, is involved in the control of the type iii secretion system regulon in ralstonia solanacearum.the ability of ralstonia solanacearum to cause disease in plants depends on its type iii secretion system (t3ss). the expression of the t3ss and its effector substrates is coordinately controlled by a regulatory cascade, at the bottom of which is hrpb. transcription of the hrpb gene is activated by a plant-responsive regulator named hrpg, which is a master regulator of a wide array of pathogenicity functions in r. solanacearum. we have identified in the genome of strain gmi1000 a close paralog o ...201020008073
complex regulatory network encompassing the csr, c-di-gmp and motility systems of salmonella typhimurium.bacterial survival depends on the ability to switch between sessile and motile lifestyles in response to changing environmental conditions. in many species, this switch is governed by (3'-5')-cyclic-diguanosine monophosphate (c-di-gmp), a signalling molecule, which is metabolized by proteins containing ggdef and/or eal domains. salmonella typhimurium contains 20 such proteins. here, we show that the rna-binding protein csra regulates the expression of eight genes encoding ggdef, ggdef-eal and ea ...201019919539
complex regulatory network encompassing the csr, c-di-gmp and motility systems of salmonella typhimurium.bacterial survival depends on the ability to switch between sessile and motile lifestyles in response to changing environmental conditions. in many species, this switch is governed by (3'-5')-cyclic-diguanosine monophosphate (c-di-gmp), a signalling molecule, which is metabolized by proteins containing ggdef and/or eal domains. salmonella typhimurium contains 20 such proteins. here, we show that the rna-binding protein csra regulates the expression of eight genes encoding ggdef, ggdef-eal and ea ...201019919539
gyra interacts with marr to reduce repression of the marrab operon in escherichia coli.bacterial two-hybrid studies of randomly cloned escherichia coli dna identified a physical interaction between gyra, subunit a of gyrase, and marr, a repressor of the marrab operon. gyra-his immobilized on ni-nitrilotriacetic acid (ninta) resin bound marr, while marr alone did not bind. gyra interfered with marr binding to maro, as detected by electrophoretic mobility assays. in a strain bearing the marrab operon and a maro-lacz reporter, overexpression of gyra increased lacz activity, indicatin ...201019933356
gyra interacts with marr to reduce repression of the marrab operon in escherichia coli.bacterial two-hybrid studies of randomly cloned escherichia coli dna identified a physical interaction between gyra, subunit a of gyrase, and marr, a repressor of the marrab operon. gyra-his immobilized on ni-nitrilotriacetic acid (ninta) resin bound marr, while marr alone did not bind. gyra interfered with marr binding to maro, as detected by electrophoretic mobility assays. in a strain bearing the marrab operon and a maro-lacz reporter, overexpression of gyra increased lacz activity, indicatin ...201019933356
the major catalase gene (kata) of pseudomonas aeruginosa pa14 is under both positive and negative control of the global transactivator oxyr in response to hydrogen peroxide.the adaptive response to hydrogen peroxide (h(2)o(2)) in pseudomonas aeruginosa involves the major catalase, kata, and oxyr. however, neither the molecular basis nor the relationship between the aforementioned proteins has been established. here, we demonstrate that the transcriptional activation of the kata promoter (katap) in response to h(2)o(2) was abrogated in the p. aeruginosa pa14 oxyr null mutant. promoter deletion analyses revealed that h(2)o(2)-mediated induction was dependent on a reg ...201019933365
the major catalase gene (kata) of pseudomonas aeruginosa pa14 is under both positive and negative control of the global transactivator oxyr in response to hydrogen peroxide.the adaptive response to hydrogen peroxide (h(2)o(2)) in pseudomonas aeruginosa involves the major catalase, kata, and oxyr. however, neither the molecular basis nor the relationship between the aforementioned proteins has been established. here, we demonstrate that the transcriptional activation of the kata promoter (katap) in response to h(2)o(2) was abrogated in the p. aeruginosa pa14 oxyr null mutant. promoter deletion analyses revealed that h(2)o(2)-mediated induction was dependent on a reg ...201019933365
the pepper 9-lipoxygenase gene calox1 functions in defense and cell death responses to microbial pathogens.lipoxygenases (loxs) are crucial for lipid peroxidation processes during plant defense responses to pathogen infection. a pepper (capsicum annuum) 9-lox gene, calox1, which encodes a 9-specific lipoxygenase, was isolated from pepper leaves. recombinant calox1 protein expressed in escherichia coli catalyzed the hydroperoxidation of linoleic acid, with a k(m) value of 113. 9 mum. expression of calox1 was differentially induced in pepper leaves not only during xanthomonas campestris pv vesicatoria ...201019939946
pseudomonas aeruginosa ospr is an oxidative stress sensing regulator that affects pigment production, antibiotic resistance and dissemination during infection.oxidative stress is one of the main challenges bacteria must cope with during infection. here, we identify a new oxidative stress sensing and response ospr (oxidative stress response and pigment production regulator) gene in pseudomonas aeruginosa. deletion of ospr leads to a significant induction in h(2)o(2) resistance. this effect is mediated by de-repression of pa2826, which lies immediately upstream of ospr and encodes a glutathione peroxidase. constitutive expression of ospr alters pigment ...201019943895
pseudomonas aeruginosa ospr is an oxidative stress sensing regulator that affects pigment production, antibiotic resistance and dissemination during infection.oxidative stress is one of the main challenges bacteria must cope with during infection. here, we identify a new oxidative stress sensing and response ospr (oxidative stress response and pigment production regulator) gene in pseudomonas aeruginosa. deletion of ospr leads to a significant induction in h(2)o(2) resistance. this effect is mediated by de-repression of pa2826, which lies immediately upstream of ospr and encodes a glutathione peroxidase. constitutive expression of ospr alters pigment ...201019943895
distribution of cepacian biosynthesis genes among environmental and clinical burkholderia strains and role of cepacian exopolysaccharide in resistance to stress conditions.the genus burkholderia includes strains pathogenic to animals and plants, bioremediators, or plant growth promoters. genome sequence analyses of representative burkholderia cepacia complex (bcc) and non-bcc strains for the presence of the bce-i gene cluster, directing the biosynthesis of the exopolysaccharide (eps) cepacian, further extended this previously described cluster by another 9 genes. the genes in the bce-ii cluster were named bcem to bceu and encode products putatively involved in nuc ...201019948863
distribution of cepacian biosynthesis genes among environmental and clinical burkholderia strains and role of cepacian exopolysaccharide in resistance to stress conditions.the genus burkholderia includes strains pathogenic to animals and plants, bioremediators, or plant growth promoters. genome sequence analyses of representative burkholderia cepacia complex (bcc) and non-bcc strains for the presence of the bce-i gene cluster, directing the biosynthesis of the exopolysaccharide (eps) cepacian, further extended this previously described cluster by another 9 genes. the genes in the bce-ii cluster were named bcem to bceu and encode products putatively involved in nuc ...201019948863
the bam complex subunit bame (smpa) is required for membrane integrity, stalk growth and normal levels of outer membrane {beta}-barrel proteins in caulobacter crescentus.the outer membrane of gram-negative bacteria is an essential compartment containing a specific complement of lipids and proteins that constitute a protective, selective permeability barrier. outer membrane beta-barrel proteins are assembled into the membrane by the essential hetero-oligomeric bam complex, which contains the lipoprotein bame. we have identified a homologue of bame, encoded by cc1365, which is located in the outer membrane of the stalked alpha-proteobacterium caulobacter crescentu ...201019959579
expression of a synthesized gene encoding cationic peptide cecropin b in transgenic tomato plants protects against bacterial diseases.the cationic lytic peptide cecropin b (cb), isolated from the giant silk moth (hyalophora cecropia), has been shown to effectively eliminate gram-negative and some gram-positive bacteria. in this study, the effects of chemically synthesized cb on plant pathogens were investigated. the s(50)s (the peptide concentrations causing 50% survival of a pathogenic bacterium) of cb against two major pathogens of the tomato, ralstonia solanacearum and xanthomonas campestris pv. vesicatoria, were 529.6 micr ...201019966019
expression of a synthesized gene encoding cationic peptide cecropin b in transgenic tomato plants protects against bacterial diseases.the cationic lytic peptide cecropin b (cb), isolated from the giant silk moth (hyalophora cecropia), has been shown to effectively eliminate gram-negative and some gram-positive bacteria. in this study, the effects of chemically synthesized cb on plant pathogens were investigated. the s(50)s (the peptide concentrations causing 50% survival of a pathogenic bacterium) of cb against two major pathogens of the tomato, ralstonia solanacearum and xanthomonas campestris pv. vesicatoria, were 529.6 micr ...201019966019
the zur regulon of corynebacterium glutamicum atcc 13032.zinc is considered as an essential element for all living organisms, but it can be toxic at large concentrations. bacteria therefore tightly regulate zinc metabolism. the cg2502 protein of corynebacterium glutamicum was a candidate to control zinc metabolism in this species, since it was classified as metalloregulator of the zinc uptake regulator (zur) subgroup of the ferric uptake regulator (fur) family of dna-binding transcription regulators.201020055984
functional analysis of a tomato salicylic acid methyl transferase and its role in synthesis of the flavor volatile methyl salicylate.methyl salicylate (mesa) is a volatile plant secondary metabolite that is an important contributor to taste and scent of many fruits and flowers. it is synthesized from salicylic acid (sa), a phytohormone that contributes to plant pathogen defense. mesa is synthesized by members of a family of o-methyltransferases. in order to elaborate the mechanism of mesa synthesis in tomato, we screened a set of o-methyltransferases for activity against multiple substrates. an enzyme that specifically cataly ...201020070566
transcriptional regulation and molecular characterization of the mana gene encoding the biofilm dispersing enzyme mannan endo-1,4-beta-mannosidase in xanthomonas campestris.exopolysaccharide and several extracellular enzymes of xanthomonas campestris pv. campestris (xcc), the causative agent of black rot in crucifers, are important virulence determinants. it is known that clp (camp receptor protein-like protein) and rpff (an enoyl-coa hydratase homologue required for the synthesis of diffusible signal factor, dsf) regulate the production of these determinants. addition of dsf or xcc extracellular protein containing partially purified mannanase (ec 3.2.1.78, encoded ...201020073482
the proteolytic system of lactic acid bacteria revisited: a genomic comparison.lactic acid bacteria (lab) are a group of gram-positive, lactic acid producing firmicutes. they have been extensively used in food fermentations, including the production of various dairy products. the proteolytic system of lab converts proteins to peptides and then to amino acids, which is essential for bacterial growth and also contributes significantly to flavor compounds as end-products. recent developments in high-throughput genome sequencing and comparative genomics hybridization arrays pr ...201020078865
amyloid fibers provide structural integrity to bacillus subtilis biofilms.bacillus subtilis forms biofilms whose constituent cells are held together by an extracellular matrix. previous studies have shown that the protein tasa and an exopolysaccharide are the main components of the matrix. given the importance of tasa in biofilm formation, we characterized the physicochemical properties of this protein. we report that purified tasa forms fibers of variable length and 10-15 nm in width. biochemical analyses, in combination with the use of specific dyes and microscopic ...201020080671
identification and regulation of the n-acetylglucosamine utilization pathway of the plant pathogenic bacterium xanthomonas campestris pv. campestris.xanthomonas campestris pv. campestris, the causal agent of black rot disease of brassicas, is known for its ability to catabolize a wide range of plant compounds. this ability is correlated with the presence of specific carbohydrate utilization loci containing tonb-dependent transporters (cut loci) devoted to scavenging specific carbohydrates. in this study, we demonstrate that there is an x. campestris pv. campestris cut system involved in the import and catabolism of n-acetylglucosamine (glcna ...201020081036
response regulator, vemr, positively regulates the virulence and adaptation of xanthomonas campestris pv. campestris.xanthomonas campestris pv. campestris (xcc) is the causal agent of black rot disease in cruciferous plants. the synthesis of known virulence factors in this organism, such as extracellular enzymes and biofilm, is strictly regulated in response to environmental stimuli. two-component signal transduction systems sense environmental signals and alter bacterial behavior by regulating gene expression. here, we identified a response regulator, vemr, that regulates xcc pathogenesis. the vemr gene encod ...201020082640
[identification of a gene involved in the expression of the pathogenicity-related gene xc3814 in xanthomonas campestris].xanthomonas campestris pv. campestris (xcc) is the causal agent of the black rot disease of cruciferous plants. our previous work had demonstrated that xc3814 is required for full virulence and extracellular polysaccharide production. in this work, the reporter plasmid pl3814sac was constructed by fusing the promoter region of xc3814 to the coding region of the gene sacb, and introduced into xcc wild-type strain 8004. the resulted strain 8004/pl3814sac was mutagenized randomly by the transposon ...201020085890
molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent d-cycloserine produced by streptomyces lavendulae.in the present study, we successfully cloned a 21-kb dna fragment containing a d-cycloserine (dcs) biosynthetic gene cluster from a dcs-producing streptomyces lavendulae strain, atcc 11924. the putative gene cluster consists of 10 open reading frames (orfs), designated dcsa to dcsj. this cluster includes two orfs encoding d-alanyl-d-alanine ligase (dcsi) and a putative membrane protein (dcsj) as the self-resistance determinants of the producer organism, indicated by our previous work. when the 1 ...201020086163
critical biophysical properties in the pseudomonas aeruginosa efflux gene regulator mexr are targeted by mutations conferring multidrug resistance.the self-assembling mexa-mexb-oprm efflux pump system, encoded by the mexo operon, contributes to facile resistance of pseudomonas aeruginosa by actively extruding multiple antimicrobials. mexr negatively regulates the mexo operon, comprising two adjacent mexr binding sites, and is as such highly targeted by mutations that confer multidrug resistance (mdr). to understand how mdr mutations impair mexr function, we studied mexr-wt as well as a selected set of mdr single mutants distant from the pr ...201020095047
polymorphic mutation frequencies of clinical and environmental stenotrophomonas maltophilia populations.mutation frequencies were studied in 174 stenotrophomonas maltophilia isolates from clinical and nonclinical environments by detecting spontaneous rifampin-resistant mutants in otherwise-susceptible populations. the distribution of mutation frequencies followed a pattern similar to that found for other bacterial species, with a modal value of 1 x 10(-8). nevertheless, the proportion of isolates showing mutation frequencies below the modal value (hypomutators) was significantly higher for s. malt ...201020097818
antibacterial activity of artemisia nilagirica leaf extracts against clinical and phytopathogenic bacteria.the six organic solvent extracts of artemisia nilagirica were screened for the potential antimicrobial activity against phytopathogens and clinically important standard reference bacterial strains.201020109237
requirement of the galu gene for polysaccharide production by and pathogenicity and growth in planta of xanthomonas citri subsp. citri.xanthomonas citri subsp. citri is the causal agent of citrus canker, which has a significant impact on citrus production. in this study, we characterized the galu gene of x. citri subsp. citri. two galu mutants (f6 and d12) were identified in an x. citri subsp. citri ez-tn5 <r6kgammaori/kan-2> tnp transposon library. rescue cloning, sequence analysis, and southern blot analysis indicated that both of these mutants had a single copy of the ez-tn5 transposon inserted in galu in the chromosome. fur ...201020118360
transcriptional response of burkholderia cenocepacia j2315 sessile cells to treatments with high doses of hydrogen peroxide and sodium hypochlorite.burkholderia cepacia complex bacteria are opportunistic pathogens, which can cause severe respiratory tract infections in patients with cystic fibrosis (cf). as treatment of infected cf patients is problematic, multiple preventive measures are taken to reduce the infection risk. besides a stringent segregation policy to prevent patient-to-patient transmission, clinicians also advise patients to clean and disinfect their respiratory equipment on a regular basis. however, problems regarding the ef ...201020137066
structural basis for catalysis by the mono- and dimetalated forms of the dape-encoded n-succinyl-l,l-diaminopimelic acid desuccinylase.biosynthesis of lysine and meso-diaminopimelic acid in bacteria provides essential components for protein synthesis and construction of the bacterial peptidoglycan cell wall. the dape operon enzymes synthesize both meso-diaminopimelic acid and lysine and, therefore, represent potential targets for novel antibacterials. the dape-encoded n-succinyl-l,l-diaminopimelic acid desuccinylase functions in a late step of the pathway and converts n-succinyl-l,l-diaminopimelic acid to l,l-diaminopimelic aci ...201020138056
analyses of the regulatory mechanism and physiological roles of pseudomonas aeruginosa ohrr, a transcription regulator and a sensor of organic hydroperoxides.ohrr encodes an organic hydroperoxide sensor and a transcriptional repressor that regulates organic hydroperoxide-inducible expression of a thiol peroxidase gene, ohr, and itself. ohrr binds directly to the operators and represses transcription of these genes. exposure to an organic hydroperoxide leads to oxidation of ohrr and to subsequent structural changes that result in the loss of the repressor's ability to bind to the operators that allow expression of the target genes. differential induct ...201020139188
biofilm dispersal: mechanisms, clinical implications, and potential therapeutic uses.like all sessile organisms, surface-attached communities of bacteria known as biofilms must release and disperse cells into the environment to colonize new sites. for many pathogenic bacteria, biofilm dispersal plays an important role in the transmission of bacteria from environmental reservoirs to human hosts, in horizontal and vertical cross-host transmission, and in the exacerbation and spread of infection within a host. the molecular mechanisms of bacterial biofilm dispersal are only beginni ...201020139339
frequency and diversity of small cryptic plasmids in the genus rahnella.rahnella is a widely distributed genus belonging to the enterobacteriaceae and frequently present on vegetables. although rahnella has interesting agro-economical and industrial properties and several strains possess antibiotic resistances and toxin genes which might spread within microbial communities, little is known about plasmids of this genus. thus, we isolated a number of rahnella strains and investigated their complements of small plasmids.201020170524
phylogenomics reveals a diverse rickettsiales type iv secretion system.with an obligate intracellular lifestyle, alphaproteobacteria of the order rickettsiales have inextricably coevolved with their various eukaryotic hosts, resulting in small, reductive genomes and strict dependency on host resources. unsurprisingly, large portions of rickettsiales genomes encode proteins involved in transport and secretion. one particular transporter that has garnered recent attention from researchers is the type iv secretion system (t4ss). homologous to the well-studied archetyp ...201020176788
virulence and immunomodulatory roles of bacterial outer membrane vesicles.outer membrane (om) vesicles are ubiquitously produced by gram-negative bacteria during all stages of bacterial growth. om vesicles are naturally secreted by both pathogenic and nonpathogenic bacteria. strong experimental evidence exists to categorize om vesicle production as a type of gram-negative bacterial virulence factor. a growing body of data demonstrates an association of active virulence factors and toxins with vesicles, suggesting that they play a role in pathogenesis. one of the most ...201020197500
a dominant-negative needle mutant blocks type iii secretion of early but not late substrates in yersinia.yersinia pseudotuberculosis uses a type iii secretion system (t3ss) to deliver effectors into host cells. a key component of the t3ss is the needle, which is a hollow tube on the bacterial surface through which effectors are secreted, composed of the yscf protein. to study needle assembly, we performed a screen for dominant-negative yscf alleles that prevented effector secretion in the presence of wild-type (wt) yscf. one allele, yscf-l54v, prevents wt yscf secretion and needle assembly, althoug ...201020199604
structural characterization of the catalytic calcium-binding site in diisopropyl fluorophosphatase (dfpase)--comparison with related beta-propeller enzymes.the calcium-dependent phosphotriesterase diisopropyl fluorophosphatase (dfpase) from the squid loligo vulgaris efficiently hydrolyzes a wide range of organophosphorus nerve agents. the two calcium ions within dfpase play essential roles for its function. the lower affinity calcium ion located at the bottom of the active site participates in the reaction mechanism, while the high affinity calcium in the center of the protein maintains structural integrity of the enzyme. the activity and structure ...201020206152
twisting of the dna-binding surface by a beta-strand-bearing proline modulates dna gyrase activity.dna gyrase is the only topoisomerase capable of introducing (-) supercoils into relaxed dna. the c-terminal domain of the gyrase a subunit (gyra-ctd) and the presence of a gyrase-specific 'gyra-box' motif within this domain are essential for this unique (-) supercoiling activity by allowing gyrase to wrap dna around itself. here we report the crystal structure of xanthomonas campestris gyra-ctd and provide the first view of a canonical gyra-box motif. this structure resembles the gyra-box-disord ...201020215433
a novel family of plasmid-transferred anti-sense ncrnas.the genome of xanthomonas campestris pv. vesicatoria encodes a constitutively expressed small rna, which we designate ptarna1, "plasmid transferred anti-sense rna". it exhibits all hallmarks of a novel rna antitoxin that proliferates by frequent horizontal transfer. it shows an erratic phylogenetic distribution with occurrences on chromosomes in a few individual strains distributed across both beta- and gamma-proteobacteria. moreover, a homologous gene located on plasmid pmatvim-7 of pseudomonas ...201020220307
stenotrophomonas panacihumi sp. nov., isolated from soil of a ginseng field.the study isolated a gram-negative, rod-shaped, non-motile bacterium from the soil of a ginseng field in daejeon, south korea and characterized it to determine its taxonomic position. phylogenetic analysis, based on the 16s rrna gene sequence, revealed that strain mk06(t) belongs to the family xanthomonadacea, and showed the highest degree of sequence similarity to stenotrophomonas rhizophila e-p10(t) (98.6%), xanthomonas campestris lmg 568t (98.0%), stenotrophomonas maltophilia atcc 1d3637(t) ( ...201020221726
salmonella typhimurium infection increases p53 acetylation in intestinal epithelial cells.the ability of salmonella typhimurium to enter intestinal epithelial cells constitutes a crucial step in pathogenesis. salmonella invasion of the intestinal epithelium requires bacterial type three secretion system. type three secretion system is a transport device that injects virulence proteins, called effectors, to paralyze or reprogram the eukaryotic cells. avirulence factor for salmonella (avra) is a salmonella effector that inhibits the host's inflammatory responses. the mechanism by which ...201020224008
cell-cell signal-dependent dynamic interactions between hd-gyp and ggdef domain proteins mediate virulence in xanthomonas campestris.rpfg is a paradigm for a class of widespread bacterial two-component regulators with a chey-like receiver domain attached to a histidine-aspartic acid-glycine-tyrosine-proline (hd-gyp) cyclic di-gmp phosphodiesterase domain. in the plant pathogen xanthomonas campestris pv. campestris (xcc), a two-component system comprising rpfg and the complex sensor kinase rpfc is implicated in sensing and responding to the diffusible signaling factor (dsf), which is essential for cell-cell signaling. rpff is ...201020231439
mutation in the pssm gene encoding ketal pyruvate transferase leads to disruption of rhizobium leguminosarum bv. viciae-pisum sativum symbiosis.to study the question whether acidic exopolysaccharide (eps) modification, e.g. pyruvylation, plays any role in the development of rhizobium leguminosarum/pisum sativum symbiosis.201020233262
mutations of ferric uptake regulator (fur) impair iron homeostasis, growth, oxidative stress survival, and virulence of xanthomonas campestris pv. campestris.iron is essential in numerous cellular functions. intracellular iron homeostasis must be maintained for cell survival and protection against iron's toxic effects. here, we characterize the roles of xanthomonas campestris pv. campestris (xcc) fur, which encodes an iron sensor and a transcriptional regulator that acts in iron homeostasis, oxidative stress, and virulence. herein, we isolated spontaneous xcc fur mutants that had high intracellular iron concentrations due to constitutively high sider ...201020237769
n-acetylglutamate synthase: structure, function and defects.n-acetylglutamate (nag) is a unique enzyme cofactor, essential for liver ureagenesis in mammals while it is the first committed substrate for de novo arginine biosynthesis in microorganisms and plants. the enzyme that produces nag from glutamate and coa, nag synthase (nags), is allosterically inhibited by arginine in microorganisms and plants and activated in mammals. this transition of the allosteric effect occurred when tetrapods moved from sea to land. the first mammalian nags gene (from mous ...201020303810
the actinomycin biosynthetic gene cluster of streptomyces chrysomallus: a genetic hall of mirrors for synthesis of a molecule with mirror symmetry.a gene cluster was identified which contains genes involved in the biosynthesis of actinomycin encompassing 50 kb of contiguous dna on the chromosome of streptomyces chrysomallus. it contains 28 genes with biosynthetic functions and is bordered on both sides by is elements. unprecedentedly, the cluster consists of two large inverted repeats of 11 and 13 genes, respectively, with four nonribosomal peptide synthetase genes in the middle. nine genes in each repeat have counterparts in the other, in ...201020304989
crystal structure of human senescence marker protein 30: insights linking structural, enzymatic, and physiological functions .human senescence marker protein 30 (smp30), which functions enzymatically as a lactonase, hydrolyzes various carbohydrate lactones. the penultimate step in vitamin-c biosynthesis is catalyzed by this enzyme in nonprimate mammals. it has also been implicated as an organophosphate hydrolase, with the ability to hydrolyze diisopropyl phosphofluoridate and other nerve agents. smp30 was originally identified as an aging marker protein, whose expression decreased androgen independently in aging cells. ...201020329768
structural and biochemical characterization of peroxiredoxin qbeta from xylella fastidiosa: catalytic mechanism and high reactivity.the phytopathogenic bacterium xylella fastidiosa is the etiological agent of various plant diseases. to survive under oxidative stress imposed by the host, microorganisms express antioxidant proteins, including cysteine-based peroxidases named peroxiredoxins. this work is a comprehensive analysis of the catalysis performed by prxq from x. fastidiosa (xfprxq) that belongs to a peroxiredoxin class still poorly characterized and previously considered as moderately reactive toward hydroperoxides. co ...201020335172
involvement of abscisic acid in the coordinated regulation of a stress-inducible hexose transporter (vvht5) and a cell wall invertase in grapevine in response to biotrophic fungal infection.biotrophic fungal and oomycete pathogens alter carbohydrate metabolism in infected host tissues. symptoms such as elevated soluble carbohydrate concentrations and increased invertase activity suggest that a pathogen-induced carbohydrate sink is established. to identify pathogen-induced regulators of carbohydrate sink strength, quantitative real-time polymerase chain reaction was used to measure transcript levels of invertase and hexose transporter genes in biotrophic pathogen-infected grapevine ...201020348211
probing the ternary complexes of indoleamine and tryptophan 2,3-dioxygenases by cryoreduction epr and endor spectroscopy.we have applied cryoreduction/epr/endor techniques to characterize the active-site structure of the ferrous-oxy complexes of human (hido) and shewanella oneidensis (sido) indoleamine 2,3-dioxygenases, xanthomonas campestris (xctdo) tryptophan 2,3-dioxygenase, and the h55s variant of xctdo in the absence and in the presence of the substrate l-trp and a substrate analogue, l-me-trp. the results reveal the presence of multiple conformations of the binary ferrous-oxy species of the idos. in more pop ...201020353179
the first step of the dioxygenation reaction carried out by tryptophan dioxygenase and indoleamine 2,3-dioxygenase as revealed by quantum mechanical/molecular mechanical studies.tryptophan dioxygenase (tdo) and indoleamine 2,3-dioxygenase (ido) are two heme-containing enzymes which catalyze the conversion of l: -tryptophan to n-formylkynurenine (nfk). in mammals, tdo is mostly expressed in liver and is involved in controlling homeostatic serum tryptophan concentrations, whereas ido is ubiquitous and is involved in modulating immune responses. previous studies suggested that the first step of the dioxygenase reaction involves the deprotonation of the indoleamine group of ...201020361220
the genes coding for the conversion of carbazole to catechol are flanked by is6100 elements in sphingomonas sp. strain xldn2-5.carbazole is a recalcitrant compound with a dioxin-like structure and possesses mutagenic and toxic activities. bacteria respond to a xenobiotic by recruiting exogenous genes to establish a pathway to degrade the xenobiotic, which is necessary for their adaptation and survival. usually, this process is mediated by mobile genetic elements such as plasmids, transposons, and insertion sequences.201020368802
allele-specific virulence attenuation of the pseudomonas syringae hopz1a type iii effector via the arabidopsis zar1 resistance protein.plant resistance (r) proteins provide a robust surveillance system to defend against potential pathogens. despite their importance in plant innate immunity, relatively few of the approximately 170 r proteins in arabidopsis have well-characterized resistance specificity. in order to identify the r protein responsible for recognition of the pseudomonas syringae type iii secreted effector (t3se) hopz1a, we assembled an arabidopsis r gene t-dna insertion collection (artic) from publicly available ar ...201020368970
membrane topology of conserved components of the type iii secretion system from the plant pathogen xanthomonas campestris pv. vesicatoria.type iii secretion (t3s) systems play key roles in the assembly of flagella and the translocation of bacterial effector proteins into eukaryotic host cells. eleven proteins which are conserved among gram-negative plant and animal pathogenic bacteria have been proposed to build up the basal structure of the t3s system, which spans both inner and outer bacterial membranes. we studied six conserved proteins, termed hrc, predicted to reside in the inner membrane of the plant pathogen xanthomonas cam ...201020378646
role of the feob protein and siderophore in promoting virulence of xanthomonas oryzae pv. oryzae on rice.xanthomonas oryzae pv. oryzae causes bacterial blight, a serious disease of rice. our analysis revealed that the x. oryzae pv. oryzae genome encodes genes responsible for iron uptake through feob (homolog of the major bacterial ferrous iron transporter) and a siderophore. a mutation in the x. oryzae pv. oryzae feob gene causes severe virulence deficiency, growth deficiency in iron-limiting medium, and constitutive production of a siderophore. we identified an iron regulated xss gene cluster, in ...201020382771
phylogenetic and multivariate analyses to determine the effects of different tillage and residue management practices on soil bacterial communities.bacterial communities are important not only in the cycling of organic compounds but also in maintaining ecosystems. specific bacterial groups can be affected as a result of changes in environmental conditions caused by human activities, such as agricultural practices. the aim of this study was to analyze the effects of different forms of tillage and residue management on soil bacterial communities by using phylogenetic and multivariate analyses. treatments involving zero tillage (zt) and conven ...201020382808
comprehensive investigation of marine actinobacteria associated with the sponge halichondria panicea.representatives of actinobacteria were isolated from the marine sponge halichondria panicea collected from the baltic sea (germany). for the first time, a comprehensive investigation was performed with regard to phylogenetic strain identification, secondary metabolite profiling, bioactivity determination, and genetic exploration of biosynthetic genes, especially concerning the relationships of the abundance of biosynthesis gene fragments to the number and diversity of produced secondary metaboli ...201020382810
novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of xanthomonas fuscans subsp. aurantifolii.citrus canker is a disease that has severe economic impact on the citrus industry worldwide. there are three types of canker, called a, b, and c. the three types have different phenotypes and affect different citrus species. the causative agent for type a is xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. xanthomonas fuscans subsp. aurantifolii strain b causes canker b and xanthomonas fuscans subsp. aurantifolii strain c causes canker c.201020388224
identification of genes differentially expressed in cauliflower associated with resistance to xanthomonas campestris pv. campestris.black rot, caused by xanthomonas campestris pv. campestris (pammel) dowson (xcc), is one of the most damaging diseases of cauliflower and other crucifers. in order to investigate the molecular resistance mechanisms and to find the genes related to black rot resistance in cauliflower, a suppression subtractive hybridization (ssh) cdna library was constructed using resistant line c712 and its susceptible near-isogenic line c731 as tester and driver, respectively. a total of 280 clones were obtaine ...201120397055
expression of xanthomonas campestris pv. vesicatoria type iii effectors in yeast affects cell growth and viability.the gram-negative bacterium xanthomonas campestris pv. vesicatoria is the causal agent of spot disease in tomato and pepper. x. campestris pv. vesicatoria pathogenicity depends on a type iii secretion system delivering effector proteins into the host cells. we hypothesized that some x. campestris pv. vesicatoria effectors target conserved eukaryotic cellular processes and examined phenotypes induced by their expression in yeast. out of 21 effectors tested, 14 inhibited yeast growth in normal or ...201121062109
determinants of eukaryal cell killing by the bacterial ribotoxin prrc.trna damage inflicted by the escherichia coli anticodon nuclease prrc (ecoprrc) underlies an antiviral response to phage t4 infection. prrc homologs are present in many bacterial proteomes, though their biological activities are uncharted. prrcs consist of two domains: an n-terminal ntpase module related to the abc family and a distinctive c-terminal ribonuclease module. in this article, we report that the expression of ecoprrc in budding yeast is fungicidal, signifying that prrc is toxic in a e ...201120855293
determinants of eukaryal cell killing by the bacterial ribotoxin prrc.trna damage inflicted by the escherichia coli anticodon nuclease prrc (ecoprrc) underlies an antiviral response to phage t4 infection. prrc homologs are present in many bacterial proteomes, though their biological activities are uncharted. prrcs consist of two domains: an n-terminal ntpase module related to the abc family and a distinctive c-terminal ribonuclease module. in this article, we report that the expression of ecoprrc in budding yeast is fungicidal, signifying that prrc is toxic in a e ...201120855293
endofungal bacterium controls its host by an hrp type iii secretion system.burkholderia rhizoxinica and rhizopus microsporus form a unique symbiosis in which intracellular bacteria produce the virulence factor of the phytopathogenic fungus. notably, the host strictly requires endobacteria to sporulate. in this study, we show that the endofungal bacteria possess a type iii secretion system (t3ss), which has a crucial role in the maintenance of the alliance. mutants defective in type iii secretion show reduced intracellular survival and fail to elicit sporulation of the ...201120720578
endofungal bacterium controls its host by an hrp type iii secretion system.burkholderia rhizoxinica and rhizopus microsporus form a unique symbiosis in which intracellular bacteria produce the virulence factor of the phytopathogenic fungus. notably, the host strictly requires endobacteria to sporulate. in this study, we show that the endofungal bacteria possess a type iii secretion system (t3ss), which has a crucial role in the maintenance of the alliance. mutants defective in type iii secretion show reduced intracellular survival and fail to elicit sporulation of the ...201120720578
thiol-based redox switches and gene regulation.cysteine is notable among the universal, proteinogenic amino acids for its facile redox chemistry. cysteine thiolates are readily modified by reactive oxygen species (ros), reactive electrophilic species (res), and reactive nitrogen species (rns). although thiol switches are commonly triggered by disulfide bond formation, they can also be controlled by s-thiolation, s-alkylation, or modification by rns. thiol-based switches are common in both prokaryotic and eukaryotic organisms and activate fun ...201120626317
the hypersensitive induced reaction and leucine-rich repeat proteins regulate plant cell death associated with disease and plant immunity.pathogen-induced programmed cell death (pcd) is intimately linked with disease resistance and susceptibility. however, the molecular components regulating pcd, including hypersensitive and susceptible cell death, are largely unknown in plants. in this study, we show that pathogen-induced capsicum annuum hypersensitive induced reaction 1 (cahir1) and leucine-rich repeat 1 (calrr1) function as distinct plant pcd regulators in pepper plants during xanthomonas campestris pv. vesicatoria infection. c ...201120635864
involvement of type iv pili in pathogenicity of plant pathogenic bacteria.type iv pili (t4p) are hair-like appendages found on the surface of a wide range of bacteria belonging to the β-, γ-, and δ-proteobacteria, cyanobacteria and firmicutes. they constitute an efficient device for a particular type of bacterial surface motility, named twitching, and are involved in several other bacterial activities and functions, including surface adherence, colonization, biofilm formation, genetic material uptake and virulence. tens of genes are involved in t4p synthesis and regul ...201124710288
antibiotics as signal molecules. 201121786783
across bacterial phyla, distantly-related genomes with similar genomic gc content have similar patterns of amino acid usage.the gc content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic gc content are observed within many bacterial phyla, including both gram negative and gram positive phyla. thus, divergent genomic gc content has evolved repeatedly in widely separated bacterial taxa. since genomic gc content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic gc content within eight different phyla or classes of bacteria. w ...201121423704
distribution of genes encoding nucleoid-associated protein homologs in plasmids.bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ...201121350637
insights into cross-kingdom plant pathogenic bacteria.plant and human pathogens have evolved disease factors to successfully exploit their respective hosts. phytopathogens utilize specific determinants that help to breach reinforced cell walls and manipulate plant physiology to facilitate the disease process, while human pathogens use determinants for exploiting mammalian physiology and overcoming highly developed adaptive immune responses. emerging research, however, has highlighted the ability of seemingly dedicated human pathogens to cause plant ...201124710301
evolutionary pressures on simple sequence repeats in prokaryotic coding regions.simple sequence repeats (ssrs) are indel mutational hotspots in genomes. in prokaryotes, ssr loci can cause phase variation, a microbial survival strategy that relies on stochastic, reversible on-off switching of gene activity. by analyzing multiple strains of 42 fully sequenced prokaryotic species, we measure the relative variability and density distribution of ssrs in coding regions. we demonstrate that repeat type strongly influences indel mutation rates, and that the most mutable types are m ...201122123746
evolutionary pressures on simple sequence repeats in prokaryotic coding regions.simple sequence repeats (ssrs) are indel mutational hotspots in genomes. in prokaryotes, ssr loci can cause phase variation, a microbial survival strategy that relies on stochastic, reversible on-off switching of gene activity. by analyzing multiple strains of 42 fully sequenced prokaryotic species, we measure the relative variability and density distribution of ssrs in coding regions. we demonstrate that repeat type strongly influences indel mutation rates, and that the most mutable types are m ...201122123746
xenobiotic efflux in bacteria and fungi: a genomics update. 201121692371
the great screen anomaly--a new frontier in product discovery through functional metagenomics.functional metagenomics, the study of the collective genome of a microbial community by expressing it in a foreign host, is an emerging field in biotechnology. over the past years, the possibility of novel product discovery through metagenomics has developed rapidly. thus, metagenomics has been heralded as a promising mining strategy of resources for the biotechnological and pharmaceutical industry. however, in spite of innovative work in the field of functional genomics in recent years, yields ...201122189864
the great screen anomaly--a new frontier in product discovery through functional metagenomics.functional metagenomics, the study of the collective genome of a microbial community by expressing it in a foreign host, is an emerging field in biotechnology. over the past years, the possibility of novel product discovery through metagenomics has developed rapidly. thus, metagenomics has been heralded as a promising mining strategy of resources for the biotechnological and pharmaceutical industry. however, in spite of innovative work in the field of functional genomics in recent years, yields ...201122189864
insights into auxin signaling in plant-pathogen interactions.the phytohormone auxin has been known to be a regulator of plant growth and development ever since its discovery. recent studies on plant-pathogen interactions identify auxin as a key character in pathogenesis and plant defense. like plants, diverse pathogens possess the capacity to synthesize indole-3-acetic acid (iaa), the major form of auxin in plants. the emerging knowledge on auxin-signaling components, auxin metabolic processes, and indole-derived phytoalexins in plant responses to pathoge ...201122639609
the role of ubiquitylation in immune defence and pathogen evasion.ubiquitylation is a widely used post-translational protein modification that regulates many biological processes, including immune responses. the role of ubiquitin in immune regulation was originally uncovered through studies of antigen presentation and the nuclear factor-κb family of transcription factors, which orchestrate host defence against microorganisms. recent studies have revealed crucial roles of ubiquitylation in many aspects of the immune system, including innate and adaptive immunit ...201122158412
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