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type iii chaperones & co in bacterial plant pathogens: a set of specialized bodyguards mediating effector delivery.gram-negative plant pathogenic bacteria possess a type iii secretion system (t3ss) to inject bacterial proteins, called type iii effectors (t3es), into host cells through a specialized syringe structure. t3es are virulence factors that can suppress plant immunity but they can also conversely be recognized by the plant and trigger specific resistance mechanisms. the t3ss and injected t3es play a central role in determining the outcome of a host-pathogen interaction. still little is known in plant ...201324319448
plant antimicrobial peptides.plant antimicrobial peptides (amps) are a component of barrier defense system of plants. they have been isolated from roots, seeds, flowers, stems, and leaves of a wide variety of species and have activities towards phytopathogens, as well as against bacteria pathogenic to humans. thus, plant amps are considered as promising antibiotic compounds with important biotechnological applications. plant amps are grouped into several families and share general features such as positive charge, the prese ...201324092498
plant antimicrobial peptides.plant antimicrobial peptides (amps) are a component of barrier defense system of plants. they have been isolated from roots, seeds, flowers, stems, and leaves of a wide variety of species and have activities towards phytopathogens, as well as against bacteria pathogenic to humans. thus, plant amps are considered as promising antibiotic compounds with important biotechnological applications. plant amps are grouped into several families and share general features such as positive charge, the prese ...201324092498
hrp mutant bacteria as biocontrol agents: toward a sustainable approach in the fight against plant pathogenic bacteria.sustainable agriculture necessitates development of environmentally safe methods to protect plants against pathogens. among these methods, application of biocontrol agents has been efficiently used to minimize disease development. here we review current understanding of mechanisms involved in biocontrol of the main gram-phytopathogenic bacteria-induced diseases by plant inoculation with strains mutated in hrp (hypersensitive response and pathogenicity) genes. these mutants are able to penetrate ...201323887499
pathogenicity of and plant immunity to soft rot pectobacteria.soft rot pectobacteria are broad host range enterobacterial pathogens that cause disease on a variety of plant species including the major crop potato. pectobacteria are aggressive necrotrophs that harbor a large arsenal of plant cell wall-degrading enzymes as their primary virulence determinants. these enzymes together with additional virulence factors are employed to macerate the host tissue and promote host cell death to provide nutrients for the pathogens. in contrast to (hemi)biotrophs such ...201323781227
natural genetic variation of xanthomonas campestris pv. campestris pathogenicity on arabidopsis revealed by association and reverse genetics.abstract the pathogenic bacterium xanthomonas campestris pv. campestris, the causal agent of black rot of brassicaceae, manipulates the physiology and the innate immunity of its hosts. association genetic and reverse-genetic analyses of a world panel of 45 x. campestris pv. campestris strains were used to gain understanding of the genetic basis of the bacterium's pathogenicity to arabidopsis thaliana. we found that the compositions of the minimal predicted type iii secretome varied extensively, ...201323736288
trehalases: a neglected carbon metabolism regulator?trehalases are enzymes that carry out the degradation of the non-reducing disaccharide trehalose. trehalase phylogeny unveiled three major branches comprising those from bacteria; plant and animals; and those from fungal origin. comparative analysis between several deduced trehalase structures and the crystallographic structure of bacterial trehalase indicated that these enzyme's structures are highly conserved in spite of the marked differences found at the sequence level. these results suggest ...201323656873
the xylem as battleground for plant hosts and vascular wilt pathogens.vascular wilts are among the most destructive plant diseases that occur in annual crops as well as in woody perennials. these diseases are generally caused by soil-borne bacteria, fungi, and oomycetes that infect through the roots and enter the water-conducting xylem vessels where they proliferate and obstruct the transportation of water and minerals. as a consequence, leaves wilt and die, which may lead to impairment of the whole plant and eventually to death of the plant. cultural, chemical, a ...201323630534
comparative genomics of 12 strains of erwinia amylovora identifies a pan-genome with a large conserved core.the plant pathogen erwinia amylovora can be divided into two host-specific groupings; strains infecting a broad range of hosts within the rosaceae subfamily spiraeoideae (e.g., malus, pyrus, crataegus, sorbus) and strains infecting rubus (raspberries and blackberries). comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin) of e. amylovora was used to describe the pan-genome of this major pathogen. the pan-genome contains 5751 coding ...201323409014
draft genome sequence of the antibiotic-producing epiphytic isolate pantoea ananatis brt175.pantoea is a member of the enterobacteriaceae, whose members have been shown to produce novel antibiotics. here, we report the 4.8-mb genome sequence of pantoea ananatis strain brt175, an epiphytic isolate from strawberries that produces an antibiotic that is effective against the fire blight pathogen, erwinia amylovora.201324201193
draft genome sequence of the antibiotic-producing cystic fibrosis isolate pantoea agglomerans tx10.pantoea agglomerans is an enteric bacterium that is capable of causing both plant and human disease. here, we report the genome sequence of a cystic fibrosis isolate, p. agglomerans tx10, which produces an antibiotic that is effective against staphylococcus aureus.201324179115
a brief multi-disciplinary review on antimicrobial resistance in medicine and its linkage to the global environmental microbiota.the discovery and introduction of antimicrobial agents to clinical medicine was one of the greatest medical triumphs of the 20th century that revolutionized the treatment of bacterial infections. however, the gradual emergence of populations of antimicrobial-resistant pathogenic bacteria resulting from use, misuse, and abuse of antimicrobials has today become a major global health concern. antimicrobial resistance (amr) genes have been suggested to originate from environmental bacteria, as clini ...201323675371
comparative genomic analysis of rapid evolution of an extreme-drug-resistant acinetobacter baumannii clone.the emergence of extreme-drug-resistant (edr) bacterial strains in hospital and nonhospital clinical settings is a big and growing public health threat. understanding the antibiotic resistance mechanisms at the genomic levels can facilitate the development of next-generation agents. here, comparative genomics has been employed to analyze the rapid evolution of an edr acinetobacter baumannii clone from the intensive care unit (icu) of rigshospitalet at copenhagen. two resistant a. baumannii strai ...201323538992
induction of viable but nonculturable escherichia coli o157:h7 by high pressure co2 and its characteristics.the viable but nonculturable (vbnc) state is a survival strategy adopted by many pathogens when exposed to harsh environmental stresses. in this study, we investigated for the first time that whether high pressure co2 (hpcd), one of the nonthermal pasteurization techniques, can induce escherichia coli o157:h7 into the vbnc state. by measuring plate counts, viable cell counts and total cell counts, e. coli o157:h7 in 0.85% nacl solution (ph 7.0) was able to enter the vbnc state by hpcd treatment ...201323626816
host exopolysaccharide quantity and composition impact erwinia amylovora bacteriophage pathogenesis.erwinia amylovora bacteriophages (phages) belonging to the myoviridae and podoviridae families demonstrated a preference for either high-exopolysaccharide-producing (hep) or low-exopolysaccharide-producing (lep) bacterial hosts when grown on artificial medium without or with sugar supplementation. myoviridae phages produced clear plaques on lep hosts and turbid plaques on hep hosts. the reverse preference was demonstrated by most podoviridae phages, where clear plaques were seen on hep hosts. ef ...201323503310
a highly-conserved single-stranded dna-binding protein in xanthomonas functions as a harpin-like protein to trigger plant immunity.harpins are produced by gram-negative phytopathogenic bacteria and typically elicit hypersensitive response (hr) in non-host plants. the characterization of harpins in xanthomonas species is largely unexplored. here we demonstrate that xanthomonas produce a highly conserved single-stranded dna-binding protein (ssb(x)) that elicits hr in tobacco as by harpin hpa1. ssb(x), like hpa1, is an acidic, glycine-rich, heat-stable protein that lacks cysteine residues. ssb(x)-triggered hr in tobacco, as by ...201323418541
characterization of the msmeg_2631 gene (mmp) encoding a multidrug and toxic compound extrusion (mate) family protein in mycobacterium smegmatis and exploration of its polyspecific nature using biolog phenotype microarray.in mycobacterium, multidrug efflux pumps can be associated with intrinsic drug resistance. comparison of putative mycobacterial transport genes revealed a single annotated open reading frame (orf) for a multidrug and toxic compound extrusion (mate) family efflux pump in all sequenced mycobacteria except mycobacterium leprae. since mate efflux pumps function as multidrug efflux pumps by conferring resistance to structurally diverse antibiotics and dna-damaging chemicals, we studied this gene (msm ...201323292779
polymyxin p is the active principle in suppressing phytopathogenic erwinia spp. by the biocontrol rhizobacterium paenibacillus polymyxa m-1.nine gene clusters dedicated to nonribosomal synthesis of secondary metabolites with possible antimicrobial action, including polymyxin and fusaricidin, were detected within the whole genome sequence of the plant growth-promoting rhizobacterium (pgpr) paenibacillus polymyxa m-1. to survey the antimicrobial compounds expressed by m-1 we analyzed the active principle suppressing phytopathogenic erwinia spp.201323773687
cyclic di-gmp modulates the disease progression of erwinia amylovora.the second messenger cyclic di-gmp (c-di-gmp) is a nearly ubiquitous intracellular signal molecule known to regulate various cellular processes, including biofilm formation, motility, and virulence. the intracellular concentration of c-di-gmp is inversely governed by diguanylate cyclase (dgc) enzymes and phosphodiesterase (pde) enzymes, which synthesize and degrade c-di-gmp, respectively. the role of c-di-gmp in the plant pathogen and causal agent of fire blight disease erwinia amylovora has not ...201323475975
xylella fastidiosa differentially accumulates mineral elements in biofilm and planktonic cells.xylella fastidiosa is a bacterial plant pathogen that infects numerous plant hosts. disease develops when the bacterium colonizes the xylem vessels and forms a biofilm. inductively coupled plasma optical emission spectroscopy was used to examine the mineral element content of this pathogen in biofilm and planktonic states. significant accumulations of copper (30-fold), manganese (6-fold), zinc (5-fold), calcium (2-fold) and potassium (2-fold) in the biofilm compared to planktonic cells were obse ...201323349991
the resveratrol tetramer (-)-hopeaphenol inhibits type iii secretion in the gram-negative pathogens yersinia pseudotuberculosis and pseudomonas aeruginosa.society faces huge challenges, as a large number of bacteria have developed resistance towards many or all of the antibiotics currently available. novel strategies that can help solve this problem are urgently needed. one such strategy is to target bacterial virulence, the ability to cause disease e.g., by inhibition of type iii secretion systems (t3sss) utilized by many clinically relevant gram-negative pathogens. many of the antibiotics used today originate from natural sources. in contrast, m ...201324324737
differential expression of cpks and cytosolic ca2+ variation in resistant and susceptible apple cultivars (malus x domestica) in response to the pathogen erwinia amylovora and mechanical wounding.plant calcium (ca2+) signals are involved in a wide array of intracellular signalling pathways following pathogen invasion. ca2+-binding sensory proteins such as ca2+-dependent protein kinases (cpks) have been predicted to mediate signalling following ca2+ influx after pathogen infection. however, to date this prediction has remained elusive.201324192013
streptomycin application has no detectable effect on bacterial community structure in apple orchard soil.streptomycin is commonly used to control fire blight disease on apple trees. although the practice has incited controversy, little is known about its nontarget effects in the environment. we investigated the impact of aerial application of streptomycin on nontarget bacterial communities in soil beneath streptomycin-treated and untreated trees in a commercial apple orchard. soil samples were collected in two consecutive years at 4 or 10 days before spraying streptomycin and 8 or 9 days after the ...201323974143
the complete genome sequence of ec1-upm, a novel n4-like bacteriophage that infects escherichia coli o78:k80.bacteriophage ec1-upm is an n4-like bacteriophage which specifically infects escherichia coli o78:k80, an avian pathogenic strain that causes colibacillosis in poultry. the complete genome sequence of bacteriophage ec1-upm was analysed and compared with other closely related n4-like phage groups to assess their genetic similarities and differences.201324134834
identification of pyrus single nucleotide polymorphisms (snps) and evaluation for genetic mapping in european pear and interspecific pyrus hybrids.we have used new generation sequencing (ngs) technologies to identify single nucleotide polymorphism (snp) markers from three european pear (pyrus communis l.) cultivars and subsequently developed a subset of 1096 pear snps into high throughput markers by combining them with the set of 7692 apple snps on the irsc apple infinium® ii 8k array. we then evaluated this apple and pear infinium® ii 9k snp array for large-scale genotyping in pear across several species, using both pear and apple snps. t ...201324155917
reversible acetylation regulates acetate and propionate metabolism in mycobacterium smegmatis.carbon metabolic pathways are important to the pathogenesis of mycobacterium tuberculosis, the causative agent of tuberculosis. however, extremely little is known about metabolic regulation in mycobacteria. there is growing evidence for lysine acetylation being a mechanism of regulating bacterial metabolism. lysine acetylation is a post-translational modification in which an acetyl group is covalently attached to the side chain of a lysine residue. this modification is mediated by acetyltransfer ...201323813678
acetylation of the response regulator rcsb controls transcription from a small rna promoter.nε-lysine acetylation was recently discovered on many bacterial proteins that function in diverse cellular processes. thus, many questions remain unanswered. for example, what mechanisms regulate lysine acetylation? does acetylation affect physiology? to help answer these questions, we studied the escherichia coli response regulator and transcription factor rcsb, which is reported to be acetylated in vitro. to characterize rcsb acetylation, we monitored transcription from the rpra promoter, whic ...201323852870
antibiotic resistance in salmonella typhimurium associates with crispr sequence type.salmonella enterica subspecies enterica serovar typhimurium is a leading cause of foodborne salmonellosis in the united states. the number of antibiotic resistant isolates identified in humans is steadily increasing, suggesting that the spread of antibiotic resistant strains is a major threat to public health. s. typhimurium is commonly identified in a wide range of animal hosts, food sources, and environments, but little is known about the factors mediating the spread of antibiotic resistance i ...201323796925
do honeybees shape the bacterial community composition in floral nectar?floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. nectar and honeybees were sampled from two plant species: amygdalus communis and citrus paradisi. to prevent the contact of nectar with pollinators, c. paradisi flowers were covered with net bags before blooming (covered flowers). comparative analysis of bacterial co ...201323844027
baseline survey of the anatomical microbial ecology of an important food plant: solanum lycopersicum (tomato).research to understand and control microbiological risks associated with the consumption of fresh fruits and vegetables has examined many environments in the farm to fork continuum. an important data gap however, that remains poorly studied is the baseline description of microflora that may be associated with plant anatomy either endemically or in response to environmental pressures. specific anatomical niches of plants may contribute to persistence of human pathogens in agricultural environment ...201323705801
cloning, expression, purification, crystallization and preliminary x-ray analysis of ealsc, a levansucrase from erwinia amylovora.the gram-negative bacterium erwinia amylovora is a destructive pathogen of rosaceae. during infection, e. amylovora produces the exopolysaccharide levan, which contributes to the occlusion of plant vessels, causing the wilting of shoots. levan is a fructose polymer that is synthesized by multifunctional enzymes called levansucrases. the levansucrase from e. amylovora (ealsc) was heterologously expressed as a gst-fusion protein in escherichia coli, purified and crystallized after tag removal. the ...201323695580
roles of the gac-rsm pathway in the regulation of phenazine biosynthesis in pseudomonas chlororaphis 30-84.the gacs/gaca two-component regulatory system activates the production of secondary metabolites including phenazines crucial for biological control activity in pseudomonas chlororaphis 30-84. to better understand the role of the gac system on phenazine regulation, transcriptomic analyses were conducted by comparing the wild-type strain to a gaca mutant. rna-seq analysis identified 771 genes under gaca control, including many novel genes. consistent with previous findings, phenazine biosynthetic ...201323606419
shotgun analysis of the secretome of fusarium graminearum.fusarium head blight, caused predominately by fusarium graminearum, is one of the most destructive diseases of wheat (triticum aestivum l.) worldwide. to characterize the profile of proteins secreted by f. graminearum, the extracellular proteins were collectively obtained from f. graminearum culture supernatants and evaluated using one-dimensional sds-page and liquid chromatography-tandem mass spectrometry. a total of 87 proteins have been identified, of which 63 were predicted as secretory prot ...201324426143
unexpected diversity during community succession in the apple flower microbiome.despite its importance to the host, the flower microbiome is poorly understood. we report a culture-independent, community-level assessment of apple flower microbial diversity and dynamics. we collected flowers from six apple trees at five time points, starting before flowers opened and ending at petal fall. we applied streptomycin to half of the trees when flowers opened. assessment of microbial diversity using tag pyrosequencing of 16s rrna genes revealed that the apple flower communities were ...201323443006
does changing the predicted dynamics of a phospholipase c alter activity and membrane binding?the enzymatic activity of secreted phosphatidylinositol-specific phospholipase c (pi-plc) enzymes is associated with bacterial virulence. although the pi-plc active site has no obvious lid, molecular-dynamics simulations suggest that correlated loop motions may limit access to the active site, and two pro residues, pro(245) and pro(254), are associated with these correlated motions. whereas the region containing both pro residues is quite variable among pi-plcs, it shows high conservation in vir ...201323332071
ingress of salmonella enterica typhimurium into tomato leaves through hydathodes.internal contamination of salmonella in plants is attracting increasing attention for food safety reasons. in this study, three different tomato cultivars "florida lanai", "crown jewel", "ailsa craig" and the transgenic line sp5 of "ailsa craig" were inoculated with 1 µl gfp-labeled salmonella typhimurium through guttation droplets at concentrations of 10(9) or 10(7) cfu/ml. survival of salmonella on/in tomato leaves was detected by both direct plating and enrichment methods. salmonella cells su ...201323320087
comparative genomics of incl/m-type plasmids: evolution by acquisition of resistance genes and insertion sequences. 201323114767
champacyclin, a new cyclic octapeptide from streptomyces strain c42 isolated from the baltic sea.new isolates of streptomyces champavatii were isolated from marine sediments of the gotland deep (baltic sea), from the urania basin (eastern mediterranean), and from the kiel bight (baltic sea). the isolates produced several oligopeptidic secondary metabolites, including the new octapeptide champacyclin (1a) present in all three strains. herein, we report on the isolation, structure elucidation and determination of the absolute stereochemistry of this isoleucine/leucine (ile/leu = xle) rich cyc ...201324317473
identification of novel antimicrobial resistance genes from microbiota on retail spinach.drug resistance genes and their mobile genetic elements are frequently identified from environmental saprophytic organisms. it is widely accepted that the use of antibiotics in animal husbandry selects for drug resistant microorganisms, which are then spread from the farm environment to humans through the consumption of contaminated food products. we wished to identify novel drug resistance genes from microbial communities on retail food products. here, we chose to study the microbial communitie ...201324289541
pa506, a conjugative plasmid of the plant epiphyte pseudomonas fluorescens a506.conjugative plasmids are known to facilitate the acquisition and dispersal of genes contributing to the fitness of pseudomonas spp. here, we report the characterization of pa506, the 57-kb conjugative plasmid of pseudomonas fluorescens a506, a plant epiphyte used in the united states for the biological control of fire blight disease of pear and apple. twenty-nine of the 67 open reading frames (orfs) of pa506 have putative functions in conjugation, including a type iv secretion system related to ...201323811504
the type iii secreted effector dspe is required early in solanum tuberosum leaf infection by pectobacterium carotovorum to cause cell death, and requires wx(3-6)d/e motifs.pectobacterium species are enterobacterial plant-pathogens that cause soft rot disease in diverse plant species. unlike hemi-biotrophic plant pathogenic bacteria, the type iii secretion system (t3ss) of pectobacterium carotovorum subsp. carotovorum (p. carotovorum) appears to secrete only one effector protein, dspe. previously, we found that the t3ss regulator hrpl and the effector dspe are required for p. carotovorum pathogenesis on leaves. here, we identified genes up-regulated by hrpl, visual ...201323755246
pseudomonas fluorescens sbw25 produces furanomycin, a non-proteinogenic amino acid with selective antimicrobial properties.pseudomonas fluorescens sbw25 has been extensively studied because of its plant growth promoting properties and potential as a biocontrol agent. the genome of sbw25 has been sequenced, and among sequenced strains of pseudomonads, sbw25 appears to be most closely related to p. fluorescens wh6. in the authors' laboratories, wh6 was previously shown to produce and secrete 4-formylaminooxyvinylglycine (fvg), a non-proteinogenic amino acid with selective herbicidal and antimicrobial activity. althoug ...201323688329
small rna-mediated regulation of host-pathogen interactions.the rise in antimicrobial drug resistance, alongside the failure of conventional research to discover new antibiotics, will inevitably lead to a public health crisis that can drastically curtail our ability to combat infectious disease. thus, there is a great global health need for development of antimicrobial countermeasures that target novel cell molecules or processes. rna represents a largely unexploited category of potential targets for antimicrobial design. for decades, control of cellular ...201323958954
global small rna chaperone hfq and regulatory small rnas are important virulence regulators in erwinia amylovora.hfq is a global small rna (srna) chaperone that interacts with hfq-regulated srnas and functions in the posttranscriptional regulation of gene expression. in this work, we identified hfq to be a virulence regulator in the gram-negative fire blight pathogen erwinia amylovora. deletion of hfq in e. amylovora ea1189 significantly reduced bacterial virulence in both immature pear fruits and apple shoots. analysis of virulence determinants in strain ea1189δhfq showed that hfq exerts pleiotropic regul ...201323378513
restricted streptomycin use in apple orchards did not adversely alter the soil bacteria communities.streptomycin has been authorized for restricted use in the prevention of the fire blight disease of pome fruit orchards in the eu and switzerland. this study addresses the important topic of the influence of the use of streptomycin in agriculture on the total bacteria community within the soil ecosystem. soil samples were taken from soils under apple trees, prior to streptomycin application and 2 weeks post streptomycin application or water application (untreated control). high throughput 16s rr ...201324550889
restricted streptomycin use in apple orchards did not adversely alter the soil bacteria communities.streptomycin has been authorized for restricted use in the prevention of the fire blight disease of pome fruit orchards in the eu and switzerland. this study addresses the important topic of the influence of the use of streptomycin in agriculture on the total bacteria community within the soil ecosystem. soil samples were taken from soils under apple trees, prior to streptomycin application and 2 weeks post streptomycin application or water application (untreated control). high throughput 16s rr ...201324550889
metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in shanghai, china.activated sludge of wastewater treatment plants carries a diverse microflora. however, up to 80-90 % of microorganisms in activated sludge cannot be cultured by current laboratory techniques, leaving an enzyme reservoir largely unexplored. in this study, we investigated carboxypeptidase diversity in activated sludge of a wastewater treatment plant in shanghai, china, by a culture-independent metagenomic approach. three sets of consensus degenerate hybrid oligonucleotide primers (codehops) target ...201324860282
metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in shanghai, china.activated sludge of wastewater treatment plants carries a diverse microflora. however, up to 80-90 % of microorganisms in activated sludge cannot be cultured by current laboratory techniques, leaving an enzyme reservoir largely unexplored. in this study, we investigated carboxypeptidase diversity in activated sludge of a wastewater treatment plant in shanghai, china, by a culture-independent metagenomic approach. three sets of consensus degenerate hybrid oligonucleotide primers (codehops) target ...201324860282
molecular cloning, expression of mind gene from lactobacillus acidophilus vtcc-b-871 and analyses to identify lactobacillus rhamnosus pn04 from vietnam hottuynia cordata thunb.the mind gene encoding an inhibitor cell division mind homolog from lactobacillus acidophilus vtcc-b-871 was cloned. we showed that there were 97 % homology between mind genes of l. acidophilus vtcc-b-871 and lactobacillus rhamnosus gg and lactobacillus rhamnosus lc705. based on the analysis of the dna sequence data from the l. rhamnosus genome project and sequenced mind gene of l. acidophilus vtcc-b-871, a pair of primers was designed to identified the different mind genes from l. acidophilus a ...201324426140
luxs in bacteria isolated from 25- to 40-million-year-old amber.interspecies bacterial communication is mediated by autoinducer-2, whose synthesis depends on luxs. due to the apparent universality of luxs (present in more than 40 bacterial species), it may have an ancient origin; however, no direct evidence is currently available. we amplified luxs in bacteria isolated from 25- to 40-million-year-old amber. the phylogenies and molecular clocks of luxs and the 16s rrna gene from ancient and extant bacteria were determined as well. luminescence assays using vi ...201324102660
luxs in bacteria isolated from 25- to 40-million-year-old amber.interspecies bacterial communication is mediated by autoinducer-2, whose synthesis depends on luxs. due to the apparent universality of luxs (present in more than 40 bacterial species), it may have an ancient origin; however, no direct evidence is currently available. we amplified luxs in bacteria isolated from 25- to 40-million-year-old amber. the phylogenies and molecular clocks of luxs and the 16s rrna gene from ancient and extant bacteria were determined as well. luminescence assays using vi ...201324102660
the antimicrobial compound xantholysin defines a new group of pseudomonas cyclic lipopeptides.the rhizosphere isolate pseudomonas putida bw11m1 produces a mixture of cyclic lipopeptide congeners, designated xantholysins. properties of the major compound xantholysin a, shared with several other pseudomonas lipopeptides, include antifungal activity and toxicity to gram-positive bacteria, a supportive role in biofilm formation, and facilitation of surface colonization through swarming. atypical is the lipopeptide's capacity to inhibit some gram-negative bacteria, including several xanthomon ...201323690965
exploring the risks of phage application in the environment.interest in using bacteriophages to control the growth and spread of bacterial pathogens is being revived in the wake of widespread antibiotic resistance. however, little is known about the ecological effects that high concentrations of phages in the environment might have on natural microbial communities. we review the current evidence suggesting phage-mediated environmental perturbation, with a focus on agricultural examples, and describe the potential implications for human health and agricul ...201324348468
pathogenfinder--distinguishing friend from foe using bacterial whole genome sequence data.although the majority of bacteria are harmless or even beneficial to their host, others are highly virulent and can cause serious diseases, and even death. due to the constantly decreasing cost of high-throughput sequencing there are now many completely sequenced genomes available from both human pathogenic and innocuous strains. the data can be used to identify gene families that correlate with pathogenicity and to develop tools to predict the pathogenicity of newly sequenced strains, investiga ...201324204795
combining quantitative genetic footprinting and trait enrichment analysis to identify fitness determinants of a bacterial pathogen.strains of extraintestinal pathogenic escherichia c oli (expec) exhibit an array of virulence strategies and are a major cause of urinary tract infections, sepsis and meningitis. efforts to understand expec pathogenesis are challenged by the high degree of genetic and phenotypic variation that exists among isolates. determining which virulence traits are widespread and which are strain-specific will greatly benefit the design of more effective therapies. towards this goal, we utilized a quantita ...201323990803
tripping on acid: trans-kingdom perspectives on biological acids in immunity and pathogenesis. 201323874196
antimicrobial resistance in the food chain: a review.antimicrobial resistant zoonotic pathogens present on food constitute a direct risk to public health. antimicrobial resistance genes in commensal or pathogenic strains form an indirect risk to public health, as they increase the gene pool from which pathogenic bacteria can pick up resistance traits. food can be contaminated with antimicrobial resistant bacteria and/or antimicrobial resistance genes in several ways. a first way is the presence of antibiotic resistant bacteria on food selected by ...201323812024
thermo-regulation of genes mediating motility and plant interactions in pseudomonas syringae.pseudomonas syringae is an important phyllosphere colonist that utilizes flagellum-mediated motility both as a means to explore leaf surfaces, as well as to invade into leaf interiors, where it survives as a pathogen. we found that multiple forms of flagellum-mediated motility are thermo-suppressed, including swarming and swimming motility. suppression of swarming motility occurs between 28° and 30 °c, which coincides with the optimal growth temperature of p. syringae. both flic (encoding flagel ...201323527276
resistance-nodulation-division multidrug efflux pumps in gram-negative bacteria: role in virulence.resistance-nodulation-division (rnd) efflux pumps are one of the most important determinants of multidrug resistance (mdr) in gram-negative bacteria. with an ever increasing number of gram-negative clinical isolates exhibiting mdr phenotypes as a result of the activity of rnd pumps, it is clear that the design of novel effective clinical strategies against such pathogens must be grounded in a better understanding of these pumps, including their physiological roles. to this end, recent evidence s ...201327029297
rnd multidrug efflux pumps: what are they good for?multidrug efflux pumps are chromosomally encoded genetic elements capable of mediating resistance to toxic compounds in several life forms. in bacteria, these elements are involved in intrinsic and acquired resistance to antibiotics. unlike other well-known horizontally acquired antibiotic resistance determinants, genes encoding for multidrug efflux pumps belong to the core of bacterial genomes and thus have evolved over millions of years. the selective pressure stemming from the use of antibiot ...201323386844
a sequential statistical approach towards an optimized production of a broad spectrum bacteriocin substance from a soil bacterium bacillus sp. yas 1 strain.bacteriocins, ribosomally synthesized antimicrobial peptides, display potential applications in agriculture, medicine, and industry. the present study highlights integral statistical optimization and partial characterization of a bacteriocin substance from a soil bacterium taxonomically affiliated as bacillus sp. yas 1 after biochemical and molecular identifications. a sequential statistical approach (plackett-burman and box-behnken) was employed to optimize bacteriocin (bac yas 1) production. u ...201425614886
siderophore-mediated iron acquisition influences motility and is required for full virulence of the xylem-dwelling bacterial phytopathogen pantoea stewartii subsp. stewartii.iron is a key micronutrient for microbial growth but is often present in low concentrations or in biologically unavailable forms. many microorganisms overcome this challenge by producing siderophores, which are ferric-iron chelating compounds that enable the solubilization and acquisition of iron in a bioactive form. pantoea stewartii subsp. stewartii, the causal agent of stewart's wilt of sweet corn, produces a siderophore under iron-limiting conditions. the proteins involved in the biosynthesi ...201425326304
siderophore-mediated iron acquisition influences motility and is required for full virulence of the xylem-dwelling bacterial phytopathogen pantoea stewartii subsp. stewartii.iron is a key micronutrient for microbial growth but is often present in low concentrations or in biologically unavailable forms. many microorganisms overcome this challenge by producing siderophores, which are ferric-iron chelating compounds that enable the solubilization and acquisition of iron in a bioactive form. pantoea stewartii subsp. stewartii, the causal agent of stewart's wilt of sweet corn, produces a siderophore under iron-limiting conditions. the proteins involved in the biosynthesi ...201425326304
motif depletion in bacteriophages infecting hosts with crispr systems.crispr is a microbial immune system likely to be involved in host-parasite coevolution. it functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. the system also requires protospacer associated motifs (pams), short motifs close to the target sequence that are required for interference in crispr types i and ii. here, we investigate whether pams are depleted in phage genomes due to selection pressure to escap ...201425103210
mechanisms of post-transcriptional gene regulation in bacterial biofilms.biofilms are characterized by a dense multicellular community of microorganisms that can be formed by the attachment of bacteria to an inert surface and to each other. the development of biofilm involves the initial attachment of planktonic bacteria to a surface, followed by replication, cell-to-cell adhesion to form microcolonies, maturation, and detachment. mature biofilms are embedded in a self-produced extracellular polymeric matrix composed primarily of bacterial-derived exopolysaccharides, ...201424724055
the arable ecosystem as battleground for emergence of new human pathogens.disease incidences related to escherichia coli and salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the "classical" routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of enterobacteriace ...201424688484
crisprs: molecular signatures used for pathogen subtyping.rapid and accurate strain identification is paramount in the battle against microbial outbreaks, and several subtyping approaches have been developed. one such method uses clustered regular interspaced short palindromic repeats (crisprs), dna repeat elements that are present in approximately half of all bacteria. though their signature function is as an adaptive immune system against invading dna such as bacteriophages and plasmids, crisprs also provide an excellent framework for pathogen tracki ...201424162568
paidb v2.0: exploration and analysis of pathogenicity and resistance islands.pathogenicity is a complex multifactorial process confounded by the concerted activity of genetic regions associated with virulence and/or resistance determinants. pathogenicity islands (pais) and resistance islands (reis) are key to the evolution of pathogens and appear to play complimentary roles in the process of bacterial infection. while pais promote disease development, reis give a fitness advantage to the host against multiple antimicrobial agents. the pathogenicity island database (paidb ...201425336619
paidb v2.0: exploration and analysis of pathogenicity and resistance islands.pathogenicity is a complex multifactorial process confounded by the concerted activity of genetic regions associated with virulence and/or resistance determinants. pathogenicity islands (pais) and resistance islands (reis) are key to the evolution of pathogens and appear to play complimentary roles in the process of bacterial infection. while pais promote disease development, reis give a fitness advantage to the host against multiple antimicrobial agents. the pathogenicity island database (paidb ...201425336619
a brief review: the z-curve theory and its application in genome analysis.in theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. in the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. the z-curve theory is a geometrical approach to genome analysis. the z-curve is a three-dimensional curve that represents a given dna sequence in the sense that each can be uniquely reconst ...201424822026
the role of bacterial protein tyrosine phosphatases in the regulation of the biosynthesis of secreted polysaccharides.tyrosine phosphorylation and associated protein tyrosine phosphatases are gaining prominence as critical mechanisms in the regulation of fundamental processes in a wide variety of bacteria. in particular, these phosphatases have been associated with the control of the biosynthesis of capsular polysaccharides and extracellular polysaccharides, critically important virulence factors for bacteria.201424295407
the role of crispr-cas systems in virulence of pathogenic bacteria.clustered regularly interspaced short palindromic repeats (crispr) and crispr-associated (cas) genes are present in many bacterial and archaeal genomes. since the discovery of the typical crispr loci in the 1980s, well before their physiological role was revealed, their variable sequences have been used as a complementary typing tool in diagnostic, epidemiologic, and evolutionary analyses of prokaryotic strains. the discovery that crispr spacers are often identical to sequence fragments of mobil ...201424600041
disruption of gene pqqa or pqqb reduces plant growth promotion activity and biocontrol of crown gall disease by rahnella aquatilis hx2.rahnella aquatilis strain hx2 has the ability to promote maize growth and suppress sunflower crown gall disease caused by agrobacterium vitis, a. tumefaciens, and a. rhizogenes. pyrroloquinoline quinone (pqq), a cofactor of aldose and alcohol dehydrogenases, is required for the synthesis of an antibacterial substance, gluconic acid, by hx2. mutants of hx2 unable to produce pqq were obtained by in-frame deletion of either the pqqa or pqqb gene. in this study, we report the independent functions o ...201425502691
draft genome sequence of burkholderia pyrrocinia lyc2, a biological control strain that can suppress multiple plant microbial pathogens.burkholderia pyrrocinia strain lyc2 was isolated from the tobacco rhizosphere in china. this bacterium exhibits a remarkable capacity to inhibit the growth of multiple pathogens and shows strong suppression of cotton seedling damping-off. here, we present the draft genome sequence of burkholderia pyrrocinia strain lyc2.201425278535
endophytic fungi: a reservoir of antibacterials.multidrug drug resistant bacteria are becoming increasingly problematic particularly in the under developed countries of the world. the most important microorganisms that have seen a geometric rise in numbers are methicillin resistant staphylococcus aureus, vancomycin resistant enterococcus faecium, penicillin resistant streptococcus pneumonia and multiple drug resistant tubercule bacteria to name a just few. new drug scaffolds are essential to tackle this every increasing problem. these scaffol ...201425620957
endophytic fungi: a reservoir of antibacterials.multidrug drug resistant bacteria are becoming increasingly problematic particularly in the under developed countries of the world. the most important microorganisms that have seen a geometric rise in numbers are methicillin resistant staphylococcus aureus, vancomycin resistant enterococcus faecium, penicillin resistant streptococcus pneumonia and multiple drug resistant tubercule bacteria to name a just few. new drug scaffolds are essential to tackle this every increasing problem. these scaffol ...201425620957
cytosine chemoreceptor mcpc in pseudomonas putida f1 also detects nicotinic acid.soil bacteria are generally capable of growth on a wide range of organic chemicals, and pseudomonads are particularly adept at utilizing aromatic compounds. pseudomonads are motile bacteria that are capable of sensing a wide range of chemicals, using both energy taxis and chemotaxis. whilst the identification of specific chemicals detected by the ≥26 chemoreceptors encoded in pseudomonas genomes is ongoing, the functions of only a limited number of pseudomonas chemoreceptors have been revealed t ...201425294107
the plant pathogen xanthomonas campestris pv. campestris exploits n-acetylglucosamine during infection.n-acetylglucosamine (glcnac), the main component of chitin and a major constituent of bacterial peptidoglycan, is present only in trace amounts in plants, in contrast to the huge amount of various sugars that compose the polysaccharides of the plant cell wall. thus, glcnac has not previously been considered a substrate exploited by phytopathogenic bacteria during plant infection. xanthomonas campestris pv. campestris, the causal agent of black rot disease of brassica plants, expresses a carbohyd ...201425205095
connecting lignin-degradation pathway with pre-treatment inhibitor sensitivity of cupriavidus necator.to produce lignocellulosic biofuels economically, the complete release of monomers from the plant cell wall components, cellulose, hemicellulose, and lignin, through pre-treatment and hydrolysis (both enzymatic and chemical), and the efficient utilization of these monomers as carbon sources, is crucial. in addition, the identification and development of robust microbial biofuel production strains that can tolerate the toxic compounds generated during pre-treatment and hydrolysis is also essentia ...201424904560
cyclic lipodepsipeptides produced by pseudomonas spp. naturally present in raw milk induce inhibitory effects on microbiological inhibitor assays for antibiotic residue screening.two pseudomonas strains, identified as closely related to pseudomonas tolaasii, were isolated from milk of a farm with frequent false-positive delvotest results for screening putative antibiotic residues in raw milk executed as part of the regulatory quality programme. growth at 5 to 7°c of these isolates in milk resulted in high lipolysis and the production of bacterial inhibitors. the two main bacterial inhibitors have a molecular weight of 1168.7 and 1140.7 da respectively, are heat-tolerant ...201424853676
transposon mutagenesis of the plant-associated bacillus amyloliquefaciens ssp. plantarum fzb42 revealed that the nfra and rbam17410 genes are involved in plant-microbe-interactions.bacillus amyloliquefaciens ssp. plantarum fzb42 represents the prototype of gram-positive plant growth promoting and biocontrol bacteria. in this study, we applied transposon mutagenesis to generate a transposon library, which was screened for genes involved in multicellular behavior and biofilm formation on roots as a prerequisite of plant growth promoting activity. transposon insertion sites were determined by rescue-cloning followed by dna sequencing. as in b. subtilis, the global transcripti ...201424847778
identification of a pantoea biosynthetic cluster that directs the synthesis of an antimicrobial natural product.fire blight is a destructive disease of apple and pear caused by the enteric bacterial pathogen, erwinia amylovora. e. amylovora initiates infection by colonizing the stigmata of apple and pear trees, and entering the plants through natural openings. epiphytic populations of the related enteric bacterium, pantoea, reduce the incidence of disease through competition and antibiotic production. in this study, we identify an antibiotic from pantoea ananatis brt175, which is effective against e. amyl ...201424796857
conventional and real-time pcrs for detection of erwinia piriflorinigrans allow its distinction from the fire blight pathogen, erwinia amylovora.erwinia piriflorinigrans is a new pathogenic species of the bacterial genus erwinia that has been described recently in spain. accurate detection and identification of e. piriflorinigrans are challenging because its symptoms on pear blossoms are similar to those caused by erwinia amylovora, the causal agent of fire blight. moreover, these two species share phenotypic and molecular characteristics. two specific and sensitive conventional and real-time pcr protocols were developed to identify and ...201424509928
identification of bacteriophages for biocontrol of the kiwifruit canker phytopathogen pseudomonas syringae pv. actinidiae.pseudomonas syringae pv. actinidiae is a reemerging pathogen which causes bacterial canker of kiwifruit (actinidia sp.). since 2008, a global outbreak of p. syringae pv. actinidiae has occurred, and in 2010 this pathogen was detected in new zealand. the economic impact and the development of resistance in p. syringae pv. actinidiae and other pathovars against antibiotics and copper sprays have led to a search for alternative management strategies. we isolated 275 phages, 258 of which were active ...201424487530
comparative genomics of type vi secretion systems in strains of pantoea ananatis from different environments.the type vi secretion system (t6ss) has been identified in several different bacteria, including the plant pathogenpantoea ananatis. previous in silico analyses described three different t6ss loci present in the pathogenic strain of p. ananatis lmg 20103. this initial investigation has been extended to include an additional seven sequenced strains of p. ananatis together with 39 strains from different ecological niches. comparative and phylogenetic analyses were used to investigate the distribut ...201424571088
bacilysin from bacillus amyloliquefaciens fzb42 has specific bactericidal activity against harmful algal bloom species.harmful algal blooms, caused by massive and exceptional overgrowth of microalgae and cyanobacteria, are a serious environmental problem worldwide : in the present study, we looked for bacillus strains with sufficiently strong anticyanobacterial activity to be used as biocontrol agents. among 24 strains, bacillus amyloliquefaciens fzb42 showed the strongest bactericidal activity against microcystis aeruginosa, with a kill rate of 98.78%. the synthesis of the anticyanobacterial substance did not d ...201425261512
cloning, purification, crystallization and 1.57 å resolution x-ray data analysis of amsi, the tyrosine phosphatase controlling amylovoran biosynthesis in the plant pathogen erwinia amylovora.the gram-negative bacterium erwinia amylovora is a destructive pathogen of plants belonging to the rosaceae family. amongst its pathogenicity factors, e. amylovora produces the exopolysaccharide amylovoran, which contributes to the occlusion of plant vessels, causing wilting of shoots and eventually resulting in plant death. amylovoran biosynthesis requires the presence of 12 genes (from amsa to amsl) clustered in the ams region of the e. amylovora genome. they mostly encode glycosyl transferase ...201425484228
identification of virulence associated loci in the emerging broad host range plant pathogen pseudomonas fuscovaginae.pseudomonas fuscovaginae (pfv) is an emerging plant pathogen of rice and also of other gramineae plants. it causes sheath brown rot disease in rice with symptoms that are characterized by brown lesions on the flag leaf sheath, grain discoloration and sterility. it was first isolated as a high altitude pathogen in japan and has since been reported in several countries throughout the world. pfv is a broad host range pathogen and very little is known about its virulence mechanisms.201425394860
review of methods to probe single cell metabolism and bioenergetics.single cell investigations have enabled unexpected discoveries, such as the existence of biological noise and phenotypic switching in infection, metabolism and treatment. herein, we review methods that enable such single cell investigations specific to metabolism and bioenergetics. firstly, we discuss how to isolate and immobilize individuals from a cell suspension, including both permanent and reversible approaches. we also highlight specific advances in microbiology for its implications in met ...201425448400
review of methods to probe single cell metabolism and bioenergetics.single cell investigations have enabled unexpected discoveries, such as the existence of biological noise and phenotypic switching in infection, metabolism and treatment. herein, we review methods that enable such single cell investigations specific to metabolism and bioenergetics. firstly, we discuss how to isolate and immobilize individuals from a cell suspension, including both permanent and reversible approaches. we also highlight specific advances in microbiology for its implications in met ...201425448400
genomic characterisation of the effector complement of the potato cyst nematode globodera pallida.the potato cyst nematode globodera pallida has biotrophic interactions with its host. the nematode induces a feeding structure - the syncytium - which it keeps alive for the duration of the life cycle and on which it depends for all nutrients required to develop to the adult stage. interactions of g. pallida with the host are mediated by effectors, which are produced in two sets of gland cells. these effectors suppress host defences, facilitate migration and induce the formation of the syncytium ...201425342461
detection of the virulent form of avr3a from phytophthora infestans following artificial evolution of potato resistance gene r3a.engineering resistance genes to gain effector recognition is emerging as an important step in attaining broad, durable resistance. we engineered potato resistance gene r3a to gain recognition of the virulent avr3aem effector form of phytophthora infestans. random mutagenesis, gene shuffling and site-directed mutagenesis of r3a were conducted to produce r3a* variants with gain of recognition towards avr3aem. programmed cell death following gain of recognition was enhanced in iterative rounds of a ...201425340613
comparative genomics defines the core genome of the growing n4-like phage genus and identifies n4-like roseophage specific genes.two bacteriophages, rpp1 and rlp1, infecting members of the marine roseobacter clade were isolated from seawater. their linear genomes are 74.7 and 74.6 kb and encode 91 and 92 coding dna sequences, respectively. around 30% of these are homologous to genes found in enterobacter phage n4. comparative genomics of these two new roseobacter phages and 23 other sequenced n4-like phages (three infecting members of the roseobacter lineage and 20 infecting other gammaproteobacteria) revealed that n4-lik ...201425346726
transmission and retention of salmonella enterica by phytophagous hemipteran insects.several pest insects of human and livestock habitations are known as vectors of salmonella enterica; however, the role of plant-feeding insects as vectors of s. enterica to agricultural crops remains unexamined. using a hemipteran insect pest-lettuce system, we investigated the potential for transmission and retention of s. enterica. specifically, macrosteles quadrilineatus and myzus persicae insects were fed s. enterica-inoculated lettuce leaf discs or artificial liquid diets confined in parafi ...201424973069
arac/xyls family stress response regulators rob, soxs, plia, and opia in the fire blight pathogen erwinia amylovora.transcriptional regulators of the arac/xyls family have been associated with multidrug resistance, organic solvent tolerance, oxidative stress, and virulence in clinically relevant enterobacteria. in the present study, we identified four homologous arac/xyls regulators, rob, soxs, plia, and opia, from the fire blight pathogen erwinia amylovora ea1189. previous studies have shown that the regulators mara, rob, and soxs from escherichia coli mediate multiple-antibiotic resistance, primarily by upr ...201424936054
expression, purification, crystallization and preliminary x-ray analysis of glucose-1-phosphate uridylyltransferase (galu) from erwinia amylovora.glucose-1-phosphate uridylyltransferase from erwinia amylovora cfpb1430 was expressed as a his-tag fusion protein in escherichia coli. after tag removal, the purified protein was crystallized from 100 mm tris ph 8.5, 2 m ammonium sulfate, 5% ethylene glycol. diffraction data sets were collected to a maximum resolution of 2.46 å using synchrotron radiation. the crystals belonged to the hexagonal space group p62, with unit-cell parameters a = 80.67, b = 80.67, c = 169.18. the structure was solved ...201425195902
characterization and regulation of the resistance-nodulation-cell division-type multidrug efflux pumps mdtabc and mdtuvw from the fire blight pathogen erwinia amylovora.the gram-negative bacterium erwinia amylovora is the causal agent of the devastating disease fire blight in rosaceous plants such as apple, pear, quince, raspberry, and cotoneaster. in order to survive and multiply in a host, microbes must be able to circumvent the toxic effects of antimicrobial plant compounds, such as flavonoids and tannins. e. amylovora uses multidrug efflux transporters that recognize and actively export toxic compounds out of the cells. here, two heterotrimeric resistance-n ...201425012600
diversity of o-antigen repeat unit structures can account for the substantial sequence variation of wzx translocases.the most common system for synthesis of cell surface polysaccharides is the wzx/wzy-dependent pathway, which involves synthesis, on the cytoplasmic face of the cell membrane, of repeat units, which are then translocated to the periplasmic face by a wzx translocase and then polymerized by wzy to generate the polysaccharide. one such polysaccharide is o antigen, which is incorporated into lipopolysaccharide (lps). the o antigen is extremely variable, with over 186 forms in escherichia coli. wzx pr ...201424532778
mapping in an apple (malus x domestica) f1 segregating population based on physical clustering of differentially expressed genes.apple tree breeding is slow and difficult due to long generation times, self-incompatibility, and complex genetics. the identification of molecular markers linked to traits of interest is a way to expedite the breeding process. in the present study, we aimed to identify genes whose steady-state transcript abundance was associated with inheritance of specific traits segregating in an apple (malus × domestica) rootstock f1 breeding population, including resistance to powdery mildew (podosphaera le ...201424708064
whole-genome sequencing of erwinia amylovora strains from mexico detects single nucleotide polymorphisms in rpsl conferring streptomycin resistance and in the avrrpt2 effector altering host interactions.we report draft genome sequences of three mexican erwinia amylovora strains. a novel plasmid, pea78, was identified. comparative genomics revealed an rpsl chromosomal mutation conferring high-level streptomycin resistance in two strains. in the effector gene avrrpt2, a single nucleotide polymorphism was detected that overcomes fire blight disease resistance in malus × robusta 5.201424459281
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