transfer of pectobacterium chrysanthemi (burkholder et al. 1953) brenner et al. 1973 and brenneria paradisiaca to the genus dickeya gen. nov. as dickeya chrysanthemi comb. nov. and dickeya paradisiaca comb. nov. and delineation of four novel species, dickeya dadantii sp. nov., dickeya dianthicola sp. nov., dickeya dieffenbachiae sp. nov. and dickeya zeae sp. nov.a collection of 75 strains of pectobacterium chrysanthemi (including all biovars and pathovars) and the type strains of brenneria paradisiaca (cfbp 4178(t)) and pectobacterium cypripedii (cfbp 3613(t)) were studied by dna-dna hybridization, numerical taxonomy of 121 phenotypic characteristics, serology and 16s rrna gene-based phylogenetic analyses. from analysis of 16s rrna gene sequences, it was deduced that p. chrysanthemi strains and b. paradisiaca cfbp 4178(t) formed a clade distinct from th ...200516014461
the phytopathogen dickeya dadantii (erwinia chrysanthemi 3937) is a pathogen of the pea aphid.dickeya dadantii (erwinia chrysanthemi) is a phytopathogenic bacterium causing soft rot diseases on many crops. the sequencing of its genome identified four genes encoding homologues of the cyt family of insecticidal toxins from bacillus thuringiensis, which are not present in the close relative pectobacterium carotovorum subsp. atrosepticum. the pathogenicity of d. dadantii was tested on the pea aphid acyrthosiphon pisum, and the bacterium was shown to be highly virulent for this insect, either ...200616517643
proteomic analysis of the carbonate insoluble outer membrane fraction of the soft-rot pathogen dickeya dadantii (syn. erwinia chrysanthemi) strain 3937.we present results of the first comprehensive proteomic analysis of the outer membrane of the bacterial phytopathogen dickeya dadantii strain 3937 and its response to virulence-contributing factors such as host plant extract, acidic stress, and iron starvation. we analyzed the carbonate-insoluble membrane fractions, which are highly enriched for outer membrane proteins, using two-dimensional electrophoresis and identified the proteins by maldi-tof ms. forty unique proteins were identified, some ...200717203949
relationships of plant pathogenic enterobacteria based on partial atpd, cara, and reca as individual and concatenated nucleotide and peptide sequences.relationships of the genera in the enterobacteriaceae containing plant pathogenic species: brenneria, dickeya, enterobacter, erwinia, pantoea, pectobacterium, and samsonia, were investigated by comparison of their nucleotide and peptide sequences of atpd, cara, reca, and the concatenated sequences. erwinia spp. and pantoea spp., with pectobacterium cypripedii, formed a group distinct from other pathogenic taxa. pectobacterium, brenneria, dickeya, and samsonia formed a contiguous clade. samsonia ...200717451899
differential regulation of two oligogalacturonate outer membrane channels, kdgn and kdgm, of dickeya dadantii (erwinia chrysanthemi).the entry of oligogalacturonates into dickeya dadantii occurs through the specific channel kdgm. the genome of the bacterium encodes a second member of this family of outer membrane proteins, kdgn. we showed that this protein is also involved in the uptake of oligogalacturonates. when kdgn was reconstituted in proteoliposomes, it formed channels with a conductance of about 450 ps at a positive potential. these channels had weak anionic selectivity. the regulation of kdgn is complex, and five gen ...200717573480
dynamic regulation of gaca in type iii secretion, pectinase gene expression, pellicle formation, and pathogenicity of dickeya dadantii (erwinia chrysanthemi 3937).dickeya dadantii (erwinia chrysanthemi 3937) secretes exoenzymes, including pectin-degrading enzymes, leading to the loss of structural integrity of plant cell walls. a type iii secretion system (t3ss) is essential for full virulence of this bacterium within plant hosts. the gacs/gaca two-component signal transduction system participates in important biological roles in several gram-negative bacteria. in this study, a gaca deletion mutant (ech137) of d. dadantii was constructed to investigate th ...200818052890
the response regulator hrpy of dickeya dadantii 3937 regulates virulence genes not linked to the hrp cluster.hrpx/y is a putative two-component system (tcs) encoded within the type iii secretion system (t3ss) gene cluster of dickeya dadantii. a linear regulatory cascade initiated by hrpx/y that leads to activation of the downstream t3ss genes via hrps and hrpl was described previously. therefore, in d. dadantii, hrpx/y plays an important role in regulation of genes involved in bacteria-plant interactions and bacterial aggregation via the t3ss. hrpx/y is the only tcs shared among the plant-pathogenic en ...200818257680
a new way out: protein localization on the bacterial cell surface via tat and a novel type ii secretion system.summary: the ability to move proteins out of the cytoplasm and across membranes is a key aspect of the physiology and pathogenicity of gram-negative bacteria. in this issue of molecular microbiology, ferrandez and condemine describe a novel protein targeting system in the enteric phytopathogen, dickeya dadantii. the pectin lyase, pnlh, is exported by the tat system and is somehow targeted to the outer membrane by its uncleaved n-terminal tat signal anchor. a novel type ii secretion system, stt, ...200818643933
novel mechanism of outer membrane targeting of proteins in gram-negative bacteria.summary: in gram-negative bacteria, all the proteins destined for the outer membrane are synthesized with a signal sequence that is cleaved, either by the signal peptidase lepb for integral outer membrane proteins or by lspa for lipoproteins, when they cross the cytoplasmic membrane. the dickeya dadantii protein pnlh does not possess a cleavable signal sequence but is anchored in the outer membrane by an n-terminal targeting signal. addition of the 41 n-terminal amino acids of pnlh is sufficient ...200818643934
evaluation of isolation methods and rna integrity for bacterial rna quantitation.rna integrity is critical for successful rna quantitation for mammalian tissues, but the level of integrity required differs among tissues. the level of integrity required for quantitation has not been determined for bacterial rna. three rna isolation methods were evaluated for their ability to produce high quality rna from dickeya dadantii, a bacterium refractory to rna isolation. bacterial lysis with trizol using standard protocols consistently gave low rna yields with this organism. higher yi ...200818674572
gene cloning, expression, and characterization of a novel phytase from dickeya paradisiaca.a novel phytase gene, appa, was isolated by degenerate polymerase chain reaction (pcr) and thermal asymmetric interlaced pcr from dickeya paradisiaca. the full-length appa comprises 1278 bp and encodes 425 amino acid residues, including a 23-residue putative n-terminal signal peptide. the deduced amino acid sequence of appa reveals the conserved motifs rhgxrxp and hd, which are typical of histidine acid phosphatases; significantly, appa shows maximum identity (49%) to a phytase from klebsiella p ...200918679591
type iii secretion system genes of dickeya dadantii 3937 are induced by plant phenolic acids.dickeya dadantii is a broad-host range phytopathogen. d. dadantii 3937 (ech3937) possesses a type iii secretion system (t3ss), a major virulence factor secretion system in many gram-negative pathogens of plants and animals. in ech3937, the t3ss is regulated by two major regulatory pathways, hrpx/hrpy-hrps-hrpl and gacs/gaca-rsmb-rsma pathways. although the plant apoplast environment, low ph, low temperature, and absence of complex nitrogen sources in media have been associated with the induction ...200818698421
pecs is a global regulator of the symptomatic phase in the phytopathogenic bacterium erwinia chrysanthemi 3937.pathogenicity of the enterobacterium erwinia chrysanthemi (dickeya dadantii), the causative agent of soft-rot disease in many plants, is a complex process involving several factors whose production is subject to temporal regulation during infection. pecs is a transcriptional regulator that controls production of various virulence factors. here, we used microarray analysis to define the pecs regulon and demonstrated that pecs notably regulates a wide range of genes that could be linked to pathoge ...200818790868
the flagellar sigma factor flia is required for dickeya dadantii virulence.the genome sequence of the enterobacteriaceae phytopathogen dickeya dadantii (formerly erwinia chrysanthemi) revealed homologs of genes required for a complete flagellar secretion system and one flagellin gene. we found that d. dadantii was able to swim and swarm but that ability to swarm was dependent upon both growth media and temperature. mutation of the d. dadantii flia gene was pleiotropic, with the alternate sigma factor required for flagella production and development of disease symptoms ...200818842093
analysis of the laci family regulators of erwinia chrysanthemi 3937, involvement in the bacterial phytopathogenicity.analysis of the regulators of the laci family was performed in order to identify those potentially involved in pathogenicity of erwinia chrysanthemi (dickeya dadantii). among the 18 members of the laci family, the function of 11 members is either known or predicted and only 7 members have, as yet, no proposed function. inactivation of these seven genes, called lfar, lfbr, lfcr, lfdr, lfer, lffr, and lfgr, demonstrated that four of them are important for plant infection. the lfar and lfcr mutants ...200818842096
host range and molecular phylogenies of the soft rot enterobacterial genera pectobacterium and dickeya.abstract pectobacterium and dickeya spp. are related broad-host-range entero-bacterial pathogens of angiosperms. a review of the literature shows that these genera each cause disease in species from at least 35% of angiosperm plant orders. the known host ranges of these pathogens partially overlap and, together, these two genera are pathogens of species from 50% of angiosperm plant orders. notably, there are no reported hosts for either genus in the eudicots clade and no reported dickeya hosts i ...200718944180
distinguishing bacterial pathogens of potato using a genome-wide microarray approach.a set of 9676 probes was designed for the most harmful bacterial pathogens of potato and tested in a microarray format. gene-specific probes could be designed for all genes of pectobacterium atrosepticum, c. 50% of the genes of streptomyces scabies and c. 30% of the genes of clavibacter michiganensis ssp. sepedonicus utilizing the whole-genome sequence information available. for streptomyces turgidiscabies, 226 probes were designed according to the sequences of a pathogenicity island containing ...200819018999
potential of bulb-associated bacteria for biocontrol of hyacinth soft rot caused by dickeya zeae.dickeya zeae is a pectinolytic bacterium responsible for soft rot disease in flower bulb crops. in this study, the possibility of controlling soft rot disease in hyacinth by using antagonistic bacteria isolated from hyacinth bulbs was explored.200919054227
the plant phenolic compound p-coumaric acid represses gene expression in the dickeya dadantii type iii secretion system.the type iii secretion system (t3ss) is a major virulence factor in many gram-negative bacterial pathogens. this secretion system translocates effectors directly into the cytosol of eukaryotic host cells, where the effector proteins facilitate bacterial pathogenesis by interfering with host cell signal transduction and other cellular processes. plants defend themselves against bacterial pathogens by recognizing either the type 3 effectors or their actions and initiating a cascade of defense resp ...200919114532
pseudomonas cichorii as the causal agent of midrib rot, an emerging disease of greenhouse-grown butterhead lettuce in flanders.bacterial midrib rot of greenhouse-grown butterhead lettuce (lactuca sativa l. var. capitata) is an emerging disease in flanders (belgium) and fluorescent pseudomonads are suspected to play an important role in the disease. isolations from infected lettuces, collected from 14 commercial greenhouses in flanders, yielded 149 isolates that were characterized polyphasically, which included morphological characteristics, pigmentation, pathogenicity tests by both injection and spraying of lettuce, lop ...200919157742
role of motility and chemotaxis in the pathogenesis of dickeya dadantii 3937 (ex erwinia chrysanthemi 3937).dickeya dadantii 3937 (ex erwinia chrysanthemi), a member of the enterobacteriaceae, causes soft rot in many economically important crops. a successful pathogen has to reach the interior of the plant in order to cause disease. to study the role of motility and chemotaxis in the pathogenicity of d. dadantii 3937, genes involved in the chemotactic signal transduction system (chew, cheb, chey and chez) and in the structure of the flagellar motor (mota) were mutagenized. all the mutant strains grew ...200919202091
slya, a marr family transcriptional regulator, is essential for virulence in dickeya dadantii 3937.slya, a marr family transcriptional regulator, controls an assortment of biological functions in several animal-pathogenic bacteria. in order to elucidate the functions of slya in the phytopathogen dickeya dadantii (formerly erwinia chrysanthemi) 3937, a slya gene deletion mutant (denoted deltaslya) was constructed. the mutant exhibited increased sensitivity to sodium hypochlorite, the cationic antimicrobial peptide polymyxin b, and oxidative stress. the mutant showed reduced production of pecta ...200919542281
dickeya species relatedness and clade structure determined by comparison of reca sequences.using sequences from the reca locus, we have produced a phylogeny of 188 dickeya strains from culture collections and identified species relatedness and subspecies clade structure within the genus. of the six recognized species, dickeya paradisiaca, d. chrysanthemi and d. zeae were discriminated with long branch lengths. the clade containing the d. paradisiaca type strain included just one additional strain, isolated from banana in colombia. strains isolated from chrysanthemum and parthenium spe ...200919620370
phylogenetic evidence for extensive horizontal gene transfer of type iii secretion system genes among enterobacterial plant pathogens.this study uses sequences from four genes, which are involved in the formation of the type iii secretion apparatus, to determine the role of horizontal gene transfer in the evolution of virulence genes for the enterobacterial plant pathogens. sequences of erwinia, brenneria, pectobacterium, dickeya and pantoea were compared (a) with one another, (b) with sequences of enterobacterial animal pathogens, and (c) with sequences of plant pathogenic gamma and beta proteobacteria, to evaluate probable p ...200919643761
microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens.microarray comparative genomic hybridisation (acgh) provides an estimate of the relative abundance of genomic dna (gdna) taken from comparator and reference organisms by hybridisation to a microarray containing probes that represent sequences from the reference organism. the experimental method is used in a number of biological applications, including the detection of human chromosomal aberrations, and in comparative genomic analysis of bacterial strains, but optimisation of the analysis is desi ...200919696881
catabolism of raffinose, sucrose, and melibiose in erwinia chrysanthemi 3937.erwinia chrysanthemi (dickeya dadantii) is a plant pathogenic bacterium that has a large capacity to degrade the plant cell wall polysaccharides. the present study reports the metabolic pathways used by e. chrysanthemi to assimilate the oligosaccharides sucrose and raffinose, which are particularly abundant plant sugars. e. chrysanthemi is able to use sucrose, raffinose, or melibiose as a sole carbon source for growth. the two gene clusters scrkyabr and rafrba are necessary for their catabolism. ...200919734309
bacterial chemoattraction towards jasmonate plays a role in the entry of dickeya dadantii through wounded tissues.jasmonate is a key signalling compound in plant defence that is synthesized in wounded tissues. in this work, we have found that this molecule is also a strong chemoattractant for the phythopathogenic bacteria dickeya dadantii (ex-erwinia chysanthemi). jasmonic acid induced the expression of a subset of bacterial genes possibly involved in virulence/survival in the plant apoplast and bacterial cells pre-treated with jasmonate showed increased virulence in chicory and saintpaulia leaves. we also ...200919818025
unique features of erwinia chrysanthemi (dickeya dadantii) ra3b genes involved in the blue indigoidine production.erwinia chrysanthemi (ech) ra3b produces a large amount of blue indigoidine. using tn5-induced mutagenesis, three indigoidine-deficient mutants were generated. followed by library screening, a 5.8kb fragment complemented mutants for indigoidine synthesis was cloned. this fragment contains four complete open-reading frames (orfs), pecs, pecm, idga, and idgb, and two partial orfs, argg, and idgc. these genes are nearly identical to those in strain ech3937. primer extension assays demonstrated a cl ...201019879116
the tat pathway of plant pathogen dickeya dadantii 3937 contributes to virulence and fitness.protein secretion plays a very important role in the virulence of the bacterium dickeya dadantii, the causative agent of soft rot disease, in a wide range of plant species. we studied the contribution of the twin-arginine translocation (tat) protein system to the adaptation of d. dadantii 3937 to different growth conditions and to the interaction with the plant host. first, a list of 44 putative tat substrates was obtained using bioinformatic programs taking advantage of the availability of the ...201019929966
13c labeling reveals multiple amination reactions in the biosynthesis of a novel polyketide polyamine antibiotic zeamine from dickeya zeae.the structure of zeamine, a novel polyamino-amide antibiotic metabolite of dickeya zeae has been established by nmr and detailed ms analyses; labelling studies with (13)c-labelled acetates suggest that the repeating secondary amine containing motif may be biosynthesised via a modular pks containing aminotransferase domains.201020024369
systemic colonization of potato plants by a soilborne, green fluorescent protein-tagged strain of dickeya sp. biovar 3.abstract colonization of potato plants by soilborne, green fluorescent protein (gfp)-tagged dickeya sp. ipo2254 was investigated by selective plating, epifluorescence stereo microscopy (esm), and confocal laser scanning microscopy (clsm). replicated experiments were carried out in a greenhouse using plants with an intact root system and plants from which ca. 30% of the lateral roots was removed. one day after soil inoculation, adherence of the pathogen on the roots and the internal colonization ...201020055647
the virulence of a dickeya dadantii 3937 mutant devoid of osmoregulated periplasmic glucans is restored by inactivation of the rcscd-rcsb phosphorelay.dickeya dadantii is a pectinolytic phytopathogen enterobacterium that causes soft rot disease on a wide range of plant species. the virulence of d. dadantii involves several factors, including the osmoregulated periplasmic glucans (opgs) that are general constituents of the envelope of proteobacteria. in addition to the loss of virulence, opg-negative mutants display a pleiotropic phenotype, including decreased motility and increased exopolysaccharide synthesis. a nitrosoguanidine-induced mutage ...201020418397
variation in permissiveness for broad-host-range plasmids among genetically indistinguishable isolates of dickeya sp. from a small field plot.phytopathogenic populations need genetic flexibility to adapt to continually improving plant defences. the gene pool transferred by broad-host-range plasmids provides genetic variation for the population. however, a population has to balance this benefit with the risk of acquiring deleterious foreign dna. this could be achieved by modulating the ratio of individuals with high or low permissiveness to broad-host-range plasmids. we investigated whether plasmid uptake varied among genetically indis ...201020455941
clpxp protease regulates the type iii secretion system of dickeya dadantii 3937 and is essential for the bacterial virulence.the type iii secretion system (t3ss) is considered one of the major virulence factors in many bacterial pathogens. this report demonstrates that rssb, clpxp, and rpos play a role in t3ss regulation of dickeya dadantii 3937. clpp is a serine-type protease which associates with the clpx chaperone to form a functional clp proteolytic complex for degradation of proteins. with the assistance of recognition factor rssb, clpxp degrades the rpos sigma factor. rpos positively regulates the expression of ...201020521950
comparison of specificity and sensitivity of immunochemical and molecular techniques for determination of clavibacter michiganensis subsp. michiganensis.detection of clavibacter michiganensis subsp. michiganensis (cmm), causing bacterial canker of tomato, was verified using pta-elisa and ifas with pabs of neogen europe ltd. (uk), and with published and also laboratory-generated pcr primers from the cmm tomatinase gene. the specificity of this technique was determined with 15 plant-pathogenic and 4 common, saprophytic bacteria. with ifas, crossreactions were found for pantoea dispersa, p. agglomerans and rahnella aquatilis, and with pta-elisa for ...201020526836
toward a quantitative modeling of the synthesis of the pectate lyases, essential virulence factors in dickeya dadantii.a dynamic mathematical model has been developed and validated to describe the synthesis of pectate lyases (pels), the major virulence factors in dickeya dadantii. this work focuses on the simultaneous modeling of the metabolic degradation of pectin by pel enzymes and the genetic regulation of pel genes by 2-keto-3-deoxygluconate (kdg), a catabolite product of pectin that inactivates kdgr, one of the main repressors of pel genes. this modeling scheme takes into account the fact that the system is ...201020581112
genetic analysis of two phosphodiesterases reveals cyclic diguanylate regulation of virulence factors in dickeya dadantii.cyclic diguanylate (c-di-gmp) is a second messenger implicated in the regulation of various cellular properties in several bacterial species. however, its function in phytopathogenic bacteria is not yet understood. in this study we investigated a panel of ggdef/eal domain proteins which have the potential to regulate c-di-gmp levels in the phytopathogen dickeya dadantii 3937. two proteins, ecpb (contains ggdef and eal domains) and ecpc (contains an eal domain) were shown to regulate multiple cel ...201020584146
cyt toxin expression reveals an inverse regulation of insect and plant virulence factors of dickeya dadantii.the plant pathogenic bacteria dickeya dadantii is also a pathogen of the pea aphid acyrthosiphon pisum. the genome of the bacteria contains four cyt genes, encoding homologues of bacillus thuringiensis cyt toxins, which are involved in its pathogenicity to insects. we show here that these genes are transcribed as an operon, and we determined the conditions necessary for their expression. their expression is induced at high temperature and at an osmolarity equivalent to that found in the plant ph ...201020649641
regulatory mechanisms of exoribonuclease pnpase and regulatory small rna on t3ss of dickeya dadantii.the type iii secretion system (t3ss) is an essential virulence factor for many bacterial pathogens. polynucleotide phosphorylase (pnpase) is one of the major exoribonucleases in bacteria and plays important roles in mrna degradation, trna processing, and small rna (srna) turnover. in this study, we showed that pnpase downregulates the transcription of t3ss structural and effector genes of the phytopathogenic bacterium dickeya dadantii. this negative regulation of t3ss by pnpase occurs by repress ...201020831411
downward vascular translocation of a green fluorescent protein-tagged strain of dickeya sp. (biovar 3) from stem and leaf inoculation sites on potato.translocation of a green fluorescent protein (gfp)-tagged dickeya sp. from stems or from leaves to underground parts of potato plants was studied in greenhouse experiments. thirty days after stem inoculation, 90% of plants expressed symptoms at the stem base and 95% of plants showed browning of internal stem tissue. the gfp-tagged dickeya sp. was detected by dilution plating in extracts of the stem interiors (100%), stem bases (90%), roots (80%), stolons (55%), and progeny tubers (24%). in roots ...201020932162
genome-wide identification of hrpl-regulated genes in the necrotrophic phytopathogen dickeya dadantii 3937.background: dickeya dadantii is a necrotrophic pathogen causing disease in many plants. previous studies have demonstrated that the type iii secretion system (t3ss) of d. dadantii is required for full virulence. hrpl is an alternative sigma factor that binds to the hrp box promoter sequence of t3ss genes to up-regulate their expression. methodology/principal findings: to explore the inventory of hrpl-regulated genes of d. dadantii 3937 (3937), transcriptome profiles of wild-type 3937 and a hrpl ...201020976052
specificity of monoclonal antibodies to strains of dickeya sp. that cause bacterial heart rot of pineapple.during a severe outbreak of bacterial heart rot that occurred in pineapple plantations on oahu, hawaii, in 2003 and years following, 43 bacterial strains were isolated from diseased plants or irrigation water and identified as erwinia chrysanthemi (now dickeya sp.) by phenotypic, molecular, and pathogenicity assays. rep-pcr fingerprint patterns grouped strains from pineapple plants and irrigation water into five genotypes (a-e) that differed from representatives of other dickeya species, pectoba ...201021050038
systematic targeted mutagenesis of the marr/slya family members of dickeya dadantii 3937 reveals a role for mfbr in the modulation of virulence gene expression in response to acidic ph.pathogenicity of dickeya dadantii is a process involving several factors, such as plant cell wall-degrading enzymes and adaptation systems to adverse conditions encountered in the apoplast. regulators of the marr family control a variety of biological processes, including adaptation to hostile environments and virulence. analysis of the members of this family in d. dadantii led to the identification of a new regulator, mfbr, which controls virulence. mfbr represses its own expression but activat ...201021062374
commensal effect of pectate lyases secreted from dickeya dadantii on proliferation of escherichia coli o157:h7 edl933 on lettuce leaves.the outbreaks caused by enterohemorrhagic escherichia coli o157:h7 on leafy greens have raised serious and immediate food safety concerns. it has been suggested that several phytopathogens aid in the persistence and proliferation of the human enteropathogens in the phyllosphere. in this work, we examined the influence of virulence mechanisms of dickeya dadantii 3937, a broad-host-range phytopathogen, on the proliferation of the human pathogen e. coli o157:h7 edl933 (edl933) on postharvest lettuc ...201021075884
a widespread family of polymorphic contact-dependent toxin delivery systems in bacteria.bacteria have developed mechanisms to communicate and compete with one another in diverse environments. a new form of intercellular communication, contact-dependent growth inhibition (cdi), was discovered recently in escherichia coli. cdi is mediated by the cdib/cdia two-partner secretion (tps) system. cdib facilitates secretion of the cdia 'exoprotein' onto the cell surface. an additional small immunity protein (cdii) protects cdi(+) cells from autoinhibition. the mechanisms by which cdi blocks ...201021085179
identification of two feruloyl esterases in dickeya dadantii 3937 and induction of the major feruloyl esterase and of pectate lyases by ferulic acid.the plant-pathogenic bacterium dickeya dadantii (formerly erwinia chrysanthemi) produces a large array of plant cell wall-degrading enzymes. using an in situ detection test, we showed that it produces two feruloyl esterases, faed and faet. these enzymes cleave the ester link between ferulate and the pectic or xylan chains. faed and faet belong to the carbohydrate esterase family ce10, and they are the first two feruloyl esterases to be identified in this family. cleavage of synthetic substrates ...201021169494
genome sequence of the plant-pathogenic bacterium dickeya dadantii 3937.dickeya dadantii is a plant-pathogenic enterobacterium responsible for the soft rot disease of many plants of economic importance. we present here the sequence of strain 3937, a strain widely used as a model system for research on the molecular biology and pathogenicity of this group of bacteria.201121217001
origin and examination of a leafhopper facultative endosymbiont.eukaryotes engage in intimate interactions with microbes that range in age and type of association. although many conspicuous examples of ancient insect associates are studied (e.g., buchnera aphidicola), fewer examples of younger associations are known. here, we further characterize a recently evolved bacterial endosymbiont of the leafhopper euscelidius variegatus (hemiptera, cicadellidae), called bev. we found that bev, continuously maintained in e. variegatus hosts at uc berkeley since 1984, ...201121336565
characterization of an obligate intracellular bacterium in the midgut epithelium of the bulrush bug chilacis typhae (heteroptera, lygaeidae, artheneinae).many members of the suborder heteroptera have symbiotic bacteria, which are usually found extracellularly in specific sacs or tubular outgrowths of the midgut or intracellularly in mycetomes. in this study, we describe the second molecular characterization of a symbiotic bacterium in a monophagous, seed-sucking stink bug of the family lygaeidae (sensu stricto). chilacis typhae possesses at the end of the first section of the midgut a structure which is composed of circularly arranged, strongly e ...201121378044
rice root-associated bacteria: insights into community structures across 10 this study, the effects of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. thus, total bacteria, alpha- and betaproteobacteria, pseudomonas and actinobacteria were studied using pcr, followed by denaturing gradient gel electrophoresis (pcr-dgge). rice genotype determined, to a large extent, the composition of the different bacterial communities across cultivars. several cultivars belongin ...201121426364
tmrna regulates synthesis of the arfa ribosome rescue factor.translation of mrna lacking an in-frame stop codon leads to ribosome arrest at the 3' end of the transcript. in bacteria, the tmrna quality control system recycles these stalled ribosomes and tags the incomplete nascent chains for degradation. although ubiquitous in eubacteria, the ssra gene encoding tmrna is not essential for the viability of escherichia coli and other model bacterial species. arfa (yhdl) is a mediator of tmrna-independent ribosome rescue that is essential for the viability of ...201121435036
classification of plant associated bacteria using rif, a computationally derived dna marker.a dna marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of xanthomonas, a genus that contains many important phytopathogens. this dna marker comprises a portion of the dnaa replication initiation factor (rif). unlike the rrna genes, dnaa is a single copy gene in the vast majority of sequenced bacterial genomes, and amplification of rif requires genus-specific primers. in silico analysis revealed that rif has equal or ...201121533033
analysis of the plant bos1 mutant highlights necrosis as an efficient defence mechanism during d. dadantii/arabidospis thaliana interaction.dickeya dadantii is a broad host range phytopathogenic bacterium provoking soft rot disease on many plants including arabidopsis. we showed that, after d. dadantii infection, the expression of the arabidopsis bos1 gene was specifically induced by the production of the bacterial pelb/c pectinases able to degrade pectin. this prompted us to analyze the interaction between the bos1 mutant and d. dadantii. the phenotype of the infected bos1 mutant is complex. indeed, maceration symptoms occurred mor ...201121533045
chrysobactin siderophores produced by dickeya chrysanthemi ec16.the plant pathogen dickeya chrysanthemi ec16 (formerly known as petrobacterium chrysanthemi ec16 and erwinia chrysanthemi ec16) was found to produce a new triscatecholamide siderophore, cyclic trichrysobactin, the related catecholamide compounds, linear trichrysobactin and dichrysobactin, and the previously reported monomeric siderophore unit, chrysobactin. chrysobactin is comprised of l-serine, d-lysine, and 2,3-dihydroxybenzoic acid (dhba). trichrysobactin is a cyclic trimer of chrysobactin jo ...201121545171
new aba-hypersensitive arabidopsis mutants are affected in loci mediating responses to water deficit and dickeya dadantii infection.on water deficit, abscisic acid (aba) induces stomata closure to reduce water loss by transpiration. to identify arabidopsis thaliana mutants which transpire less on drought, infrared thermal imaging of leaf temperature has been used to screen for suppressors of an aba-deficient mutant (aba3-1) cold-leaf phenotype. three novel mutants, called hot aba-deficiency suppressor (has), have been identified with hot-leaf phenotypes in the absence of the aba3 mutation. the defective genes imparted no app ...201121633512
lpxc and yafs are the most suitable internal controls to normalize real time rt-qpcr expression in the phytopathogenic bacteria dickeya dadantii.quantitative rt-pcr is the method of choice for studying, with both sensitivity and accuracy, the expression of genes. a reliable normalization of the data, using several reference genes, is critical for an accurate quantification of gene expression. here, we propose a set of reference genes, of the phytopathogenic bacteria dickeya dadantii and pectobacterium atrosepticum, which are stable in a wide range of growth conditions.201121637857
pantoea stewartii subsp. stewartii: lessons learned from a xylem-dwelling pathogen of sweet corn.pantoea stewartii subsp. stewartii is a gram-negative enteric bacterium that primarily infects sweet corn. studies of this bacterium have provided useful insight into how xylem-dwelling bacteria establish themselves and incite disease in their hosts. pantoea stewartii subsp. stewartii is a remarkable bacterial system for laboratory studies because of its relative ease of propagation and genetic manipulation, and the fact that it appears to employ a minimal number of pathogenicity mechanisms. in ...201121726365
structural basis for acyl acceptor specificity in the achromobactin biosynthetic enzyme acsd.siderophores are known virulence factors, and their biosynthesis is a target for new antibacterial agents. a non-ribosomal peptide synthetase-independent siderophore biosynthetic pathway in dickeya dadantii is responsible for production of the siderophore achromobactin. the d. dadantii achromobactin biosynthesis protein d (acsd) enzyme has been shown to enantioselectively esterify citric acid with l-serine in the first committed step of achromobactin biosynthesis. the reaction occurs in two step ...201121835184
toxin on a stick: modular cdi toxin delivery systems play roles in bacterial growth inhibition (cdi) is the first contact-dependent competition system identified in bacteria. cdi is mediated by the cdia/cdib two-partner secretion system, and the bama outer membrane protein serves as the cdi receptor on target cells. a small immunity protein, cdii, is required to protect inhibitor cells from their own cdi system. recent results from our group show that cdi systems are present in a number of important gram-negative plant and animal pathogens. the c-termin ...201121705856
identification of functional toxin/immunity genes linked to contact-dependent growth inhibition (cdi) and rearrangement hotspot (rhs) systems.bacterial contact-dependent growth inhibition (cdi) is mediated by the cdia/cdib family of two-partner secretion proteins. each cdia protein exhibits a distinct growth inhibition activity, which resides in the polymorphic c-terminal region (cdia-ct). cdi(+) cells also express unique cdii immunity proteins that specifically block the activity of cognate cdia-ct, thereby protecting the cell from autoinhibition. here we show that many cdi systems contain multiple cdia gene fragments that encode cdi ...201121829394
the dickeya dadantii biofilm matrix consists of cellulose nanofibers and is an emergent property dependent upon the type iii secretion system and the cellulose synthesis operon.dickeya dadantii is a plant pathogenic bacterium that produces cellulose-containing biofilms, called pellicles, at the air-liquid interface of liquid cultures. d. dadantii pellicle formation appears to be an emergent property dependent upon at least three gene clusters, including cellulose synthesis, type iii secretion system (t3ss), and flagellar genes. the d. dadantii cellulose synthesis operon is homologous to that of gluconacetobacter xylinus, which is used for industrial cellulose productio ...201121719543
Role of the Dickeya dadantii Dps protein.During infection, the phytopathogenic enterobacterium Dickeya dadantii has to cope with iron-limiting conditions and the production of reactive oxygen species by plant cells. A tight control of the bacterial intracellular iron content is necessary for full virulence of D. dadantii: previous studies have shown that the ferritin FtnA and the bacterioferrtin Bfr, devoted to iron storage, contribute differentially to the virulence of this species. In this work, we investigated the role of the Dps mi ...201122203404
cell individuality: the bistable gene expression of the type iii secretion system in dickeya dadantii 3937.dickeya dadantii 3937 is a gram-negative phytopathogenic bacterium that expresses genes encoding a type iii secretion system (t3ss) in a bistable pattern when cultured in a homogeneous minimal media. in this work, we further characterized the bistable gene expression of t3ss at the single-cell level. we demonstrated that bistable expression of the hrpl-regulon genes, such as hrpa and hrpn, is controlled by the same regulatory mechanism. we also showed that the expression level of the t3ss master ...201222150074
Proposal to reclassify Brenneria quercina (Hildebrand & Schroth 1967) Hauben et al. 1999 into a novel genus, Lonsdalea gen. nov., as Lonsdalea quercina comb. nov., descriptions of Lonsdalea quercina subsp. quercina comb. nov., Lonsdalea quercina subsp. iberica subsp. nov. and Lonsdalea quercina subsp. britannica subsp. nov., emendation of the description of the genus Brenneria, reclassification of Dickeya dieffenbachiae as Dickeya dadantii subsp. dieffenbachiae comb. nov., and emendation of the description of Dickeya dadantii.Bacterial isolates from oak in Spain and Britain, showing symptoms of bark canker and Acute Oak Decline (AOD) respectively, were examined by a polyphasic approach. Both 16S rRNA gene sequencing and multilocus sequence analysis (MLSA), based on partial sequences of gyrB, rpoB, infB and atpD, revealed that the isolates were separated into two genetic groups according to their origin. Their closest phylogenetic relative was B. quercina, the causal agent of drippy nut disease of oak, which clustered ...201121890733
genome-wide analysis of the response of dickeya dadantii 3937 to plant antimicrobial peptides.antimicrobial peptides constitute an important factor in the defense of plants against pathogens, and bacterial resistance to these peptides have previously been shown as an important virulence factor in dickeya dadantii, the causal agent of soft-rot disease of vegetables. in order to understand the bacterial response to antimicrobial peptides, a transcriptional microarray analysis was performed upon treatment with sub-lethal concentration of thionins, a widespread plant peptide. 36 genes were f ...201122204647
pecs is an important player in the regulatory network governing the coordinated expression of virulence genes during the interaction between dickeya dadantii 3937 and plants.successful infection of a pathogen relies on the coordinated expression of numerous virulence factor-encoding genes. in plant-bacteria interactions, this control is very often achieved through the integration of several regulatory circuits controlling cell-cell communication or sensing environmental conditions. dickeya dadantii (formerly erwinia chrysanthemi), the causal agent of soft rot on many crops and ornamentals, provokes maceration of infected plants mainly by producing and secreting a ba ...201121906221
multiple origins of endosymbiosis within the enterobacteriaceae (gamma-proteobacteria): convergence of complex phylogenetic approaches.abstract: background: the bacterial family enterobacteriaceae gave rise to a variety of symbiotic forms, from the loosely associated commensals, often designated as secondary (s) symbionts, to obligate mutualists, called primary (p) symbionts. determination of the evolutionary processes behind this phenomenon has long been hampered by the unreliability of phylogenetic reconstructions within this group of bacteria. the main reasons have been the absence of sufficient data, the highly derived nat ...201122201529
a novel multidomain polyketide synthase is essential for zeamine production and the virulence of dickeya zeae.dickeya zeae is the causal agent of the rice foot rot disease, but its mechanism of infection remains largely unknown. in this study, we identified and characterized a novel gene designated as zmsa. the gene encodes a large protein of 2,346 amino acids in length, which consists of multidomains arranged in the order of n-terminus, β-ketoacyl synthase, acyl transferase, acyl carrier protein, β-ketoacyl reductase, dehydratase. this multidomain structure and sequence alignment analysis suggest that ...201121899437
massive production of butanediol during plant infection by phytopathogenic bacteria of the genera dickeya and pectobacterium.plant pathogenic bacteria of the genera dickeya and pectobacterium are broad-host-range necrotrophs which cause soft-rot diseases in important crops. a metabolomic analysis, based on (13)c-nmr spectroscopy, was used to characterize the plant-bacteria interaction. metabolic profiles revealed a decline in plant sugars and amino acids during infection and the concomitant appearance of a compound identified as 2,3-butanediol. butanediol is the major metabolite found in macerated tissues of various h ...201122032684
the nucleoid-associated proteins h-ns and fis modulate the dna supercoiling response of the pel genes, the major virulence factors in the plant pathogen bacterium dickeya dadantii.dickeya dadantii is a pathogen infecting a wide range of plant species. soft rot, the visible symptom, is mainly due to the production of pectate lyases (pels) that can destroy the plant cell walls. previously we found that the pel gene expression is modulated by h-ns and fis, two nucleoid-associated proteins (naps) modulating the dna topology. here, we show that relaxation of the dna in growing d. dadantii cells decreases the expression of pel genes. deletion of fis aggravates, whereas that of ...201222275524
slya regulates t3ss genes in parallel with the t3ss master regulator hrpl in dickeya dadantii 3937.the hrp (hypersensitive response and pathogenicity) genes of dickeya dadantii 3937 encode a type iii secretion system (t3ss) which is essential for its full virulence. previous studies of the t3ss regulation in d. dadantii 3937 revealed that the expression of the hrp genes is regulated by a master regulator hrpl through the hrpx-hrpy-hrps-hrpl and gacs-gaca-rsmb-rsma pathways. in this work, we identified a novel regulator of the slya/marr family, slya, which regulates hrp genes of the hrpl regul ...201222267675
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